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Repository: kingaa/pomp
Branch: master
Commit: 1a9b0ad44e06
Files: 513
Total size: 2.1 MB
Directory structure:
gitextract_mv8sofvg/
├── .Rbuildignore
├── .Rprofile
├── .github/
│ ├── ISSUE_TEMPLATE/
│ │ ├── bug_report.md
│ │ └── feature_request.md
│ └── workflows/
│ ├── binary-build.yml
│ ├── r-cmd-check.yml
│ └── test-coverage.yml
├── .gitignore
├── BUILD.md
├── CRAN.md
├── DESCRIPTION
├── Doxyfile
├── LICENSE.md
├── Makefile
├── NAMESPACE
├── R/
│ ├── abc.R
│ ├── accumulators.R
│ ├── as_data_frame.R
│ ├── as_pomp.R
│ ├── bake.R
│ ├── basic_components.R
│ ├── basic_probes.R
│ ├── betabinom.R
│ ├── blowflies.R
│ ├── bsflu.R
│ ├── bsmc2.R
│ ├── bsplines.R
│ ├── builder.R
│ ├── childhood.R
│ ├── coef.R
│ ├── conc.R
│ ├── concat.R
│ ├── cond_logLik.R
│ ├── continue.R
│ ├── covariate_table.R
│ ├── covmat.R
│ ├── csnippet.R
│ ├── dacca.R
│ ├── design.R
│ ├── dinit_spec.R
│ ├── dmeasure_spec.R
│ ├── dprocess_spec.R
│ ├── ebola.R
│ ├── eff_sample_size.R
│ ├── elementary_algorithms.R
│ ├── emeasure_spec.R
│ ├── estimation_algorithms.R
│ ├── eulermultinom.R
│ ├── extract.R
│ ├── filter_mean.R
│ ├── filter_traj.R
│ ├── flow.R
│ ├── forecast.R
│ ├── gompertz.R
│ ├── kalman.R
│ ├── kf.R
│ ├── listie.R
│ ├── load.R
│ ├── loglik.R
│ ├── logmeanexp.R
│ ├── lookup.R
│ ├── mcap.R
│ ├── melt.R
│ ├── mif2.R
│ ├── nlf.R
│ ├── objfun.R
│ ├── obs.R
│ ├── ou2.R
│ ├── package.R
│ ├── parameter_trans.R
│ ├── parmat.R
│ ├── parus.R
│ ├── pfilter.R
│ ├── plot.R
│ ├── pmcmc.R
│ ├── pomp.R
│ ├── pomp_class.R
│ ├── pomp_examp.R
│ ├── pomp_fun.R
│ ├── pred_mean.R
│ ├── pred_var.R
│ ├── print.R
│ ├── prior_spec.R
│ ├── probe.R
│ ├── probe_match.R
│ ├── profile_design.R
│ ├── proposals.R
│ ├── pstop.R
│ ├── resample.R
│ ├── ricker.R
│ ├── rinit_spec.R
│ ├── rmeasure_spec.R
│ ├── rprocess_spec.R
│ ├── runif_design.R
│ ├── rw2.R
│ ├── safecall.R
│ ├── sannbox.R
│ ├── saved_states.R
│ ├── show.R
│ ├── simulate.R
│ ├── sir.R
│ ├── skeleton_spec.R
│ ├── slice_design.R
│ ├── sobol_design.R
│ ├── spect.R
│ ├── spect_match.R
│ ├── spy.R
│ ├── states.R
│ ├── summary.R
│ ├── templates.R
│ ├── time.R
│ ├── timezero.R
│ ├── traces.R
│ ├── traj_match.R
│ ├── trajectory.R
│ ├── transformations.R
│ ├── undefined.R
│ ├── userdata.R
│ ├── verhulst.R
│ ├── vmeasure_spec.R
│ ├── window.R
│ ├── workhorses.R
│ ├── wpfilter.R
│ └── wquant.R
├── README.md
├── TODO.md
├── codecov.yml
├── data/
│ ├── LondonYorke.rda
│ ├── blowflies.csv
│ ├── bsflu.rda
│ ├── ebolaWA2014.rda
│ ├── ewcitmeas.rda
│ ├── ewmeas.rda
│ └── parus.csv
├── examples/
│ ├── accumulators.R
│ ├── bake.R
│ ├── bsflu.R
│ ├── concat.R
│ ├── dacca.R
│ ├── design.R
│ ├── dmeasure_spec.R
│ ├── ebola.R
│ ├── eulermultinom.R
│ ├── kf.R
│ ├── logmeanexp.R
│ ├── nlf.R
│ ├── ou2.R
│ ├── parus.R
│ ├── pfilter.R
│ ├── pmcmc.R
│ ├── prior_spec.R
│ ├── probe_match.R
│ ├── ricker-bifdiag.R
│ ├── ricker.R
│ ├── rinit_spec.R
│ ├── rmeasure_spec.R
│ ├── rw2.R
│ ├── sir.R
│ ├── skeleton_spec.R
│ ├── spect_match.R
│ ├── spy.R
│ ├── traj_match.R
│ ├── trajectory.R
│ ├── userdata.R
│ └── verhulst.R
├── inst/
│ ├── CITATION
│ ├── GPL
│ ├── NEWS
│ ├── NEWS.Rd
│ ├── doc/
│ │ ├── Makefile
│ │ ├── index.html
│ │ └── index.md
│ └── include/
│ ├── pomp.h
│ └── pomp_defines.h
├── man/
│ ├── abc.Rd
│ ├── accumvars.Rd
│ ├── as_data_frame.Rd
│ ├── as_pomp.Rd
│ ├── bake.Rd
│ ├── basic_components.Rd
│ ├── basic_probes.Rd
│ ├── betabinom.Rd
│ ├── blowflies.Rd
│ ├── bsflu.Rd
│ ├── bsmc2.Rd
│ ├── bsplines.Rd
│ ├── childhood.Rd
│ ├── coef.Rd
│ ├── conc.Rd
│ ├── concat.Rd
│ ├── cond_logLik.Rd
│ ├── continue.Rd
│ ├── covariate_table.Rd
│ ├── covmat.Rd
│ ├── csnippet.Rd
│ ├── dacca.Rd
│ ├── design.Rd
│ ├── dinit.Rd
│ ├── dinit_spec.Rd
│ ├── dmeasure.Rd
│ ├── dmeasure_spec.Rd
│ ├── dprior.Rd
│ ├── dprocess.Rd
│ ├── dprocess_spec.Rd
│ ├── ebola.Rd
│ ├── eff_sample_size.Rd
│ ├── elementary_algorithms.Rd
│ ├── emeasure.Rd
│ ├── emeasure_spec.Rd
│ ├── estimation_algorithms.Rd
│ ├── eulermultinom.Rd
│ ├── filter_mean.Rd
│ ├── filter_traj.Rd
│ ├── flow.Rd
│ ├── forecast.Rd
│ ├── gompertz.Rd
│ ├── hitch.Rd
│ ├── kalman.Rd
│ ├── kf.Rd
│ ├── listie.Rd
│ ├── load.Rd
│ ├── loglik.Rd
│ ├── logmeanexp.Rd
│ ├── lookup.Rd
│ ├── macros/
│ │ └── citations.Rd
│ ├── mcap.Rd
│ ├── melt.Rd
│ ├── mif2.Rd
│ ├── nlf.Rd
│ ├── objfun.Rd
│ ├── obs.Rd
│ ├── ou2.Rd
│ ├── pStop.Rd
│ ├── parameter_trans.Rd
│ ├── parmat.Rd
│ ├── partrans.Rd
│ ├── parus.Rd
│ ├── pfilter.Rd
│ ├── plot.Rd
│ ├── pmcmc.Rd
│ ├── pomp-package.Rd
│ ├── pomp.Rd
│ ├── pomp_class.Rd
│ ├── pomp_examp.Rd
│ ├── pomp_fun.Rd
│ ├── pred_mean.Rd
│ ├── pred_var.Rd
│ ├── print.Rd
│ ├── prior_spec.Rd
│ ├── probe.Rd
│ ├── probe_match.Rd
│ ├── proposals.Rd
│ ├── resample.Rd
│ ├── ricker.Rd
│ ├── rinit.Rd
│ ├── rinit_spec.Rd
│ ├── rmeasure.Rd
│ ├── rmeasure_spec.Rd
│ ├── roxygen/
│ │ └── meta.R
│ ├── rprior.Rd
│ ├── rprocess.Rd
│ ├── rprocess_spec.Rd
│ ├── rw2.Rd
│ ├── rw_sd.Rd
│ ├── sannbox.Rd
│ ├── saved_states.Rd
│ ├── show.Rd
│ ├── simulate.Rd
│ ├── sir.Rd
│ ├── skeleton.Rd
│ ├── skeleton_spec.Rd
│ ├── spect.Rd
│ ├── spect_match.Rd
│ ├── spy.Rd
│ ├── states.Rd
│ ├── summary.Rd
│ ├── time.Rd
│ ├── timezero.Rd
│ ├── traces.Rd
│ ├── traj_match.Rd
│ ├── trajectory.Rd
│ ├── transformations.Rd
│ ├── undefined.Rd
│ ├── userdata.Rd
│ ├── verhulst.Rd
│ ├── vmeasure.Rd
│ ├── vmeasure_spec.Rd
│ ├── window.Rd
│ ├── workhorses.Rd
│ ├── wpfilter.Rd
│ └── wquant.Rd
├── revdep/
│ ├── .gitignore
│ ├── Makefile
│ └── timings.tab
├── rules.mk
├── src/
│ ├── Makevars
│ ├── backports.h
│ ├── bspline.c
│ ├── decls.h
│ ├── dinit.c
│ ├── distributions.c
│ ├── dmeasure.c
│ ├── dprior.c
│ ├── dprocess.c
│ ├── emeasure.c
│ ├── euler.c
│ ├── gompertz.c
│ ├── init.c
│ ├── internal.h
│ ├── logmeanexp.c
│ ├── lookup_table.c
│ ├── mif2.c
│ ├── ou2.c
│ ├── partrans.c
│ ├── pfilter.c
│ ├── pomp.h
│ ├── pomp_defines.h
│ ├── pomp_fun.c
│ ├── pomp_mat.h
│ ├── probe.c
│ ├── probe_acf.c
│ ├── probe_marginal.c
│ ├── probe_nlar.c
│ ├── resample.c
│ ├── rinit.c
│ ├── rmeasure.c
│ ├── rprior.c
│ ├── rprocess.c
│ ├── simulate.c
│ ├── skeleton.c
│ ├── soboldata.h
│ ├── sobolseq.c
│ ├── ssa.c
│ ├── synth_lik.c
│ ├── trajectory.c
│ ├── transformations.c
│ ├── userdata.c
│ ├── vmeasure.c
│ └── wpfilter.c
├── tests/
│ ├── Makefile
│ ├── R_v_C.R
│ ├── R_v_C.Rout
│ ├── abc.R
│ ├── abc.Rout.save
│ ├── baddm.R
│ ├── baddm.Rout.save
│ ├── bake.R
│ ├── bake.Rout.save
│ ├── basic_probes.R
│ ├── basic_probes.Rout.save
│ ├── betabinom.R
│ ├── betabinom.Rout.save
│ ├── blowflies.R
│ ├── blowflies.Rout.save
│ ├── bsmc2.R
│ ├── bsmc2.Rout.save
│ ├── bsplines1.R
│ ├── bsplines1.Rout.save
│ ├── bsplines2.R
│ ├── bsplines2.Rout.save
│ ├── concat.R
│ ├── concat.Rout.save
│ ├── covmat.R
│ ├── covmat.Rout.save
│ ├── csnippet.R
│ ├── csnippet.Rout.save
│ ├── dacca.R
│ ├── dacca.Rout.save
│ ├── dinit.R
│ ├── dinit.Rout.save
│ ├── dp.R
│ ├── dp.Rout.save
│ ├── dprocess.R
│ ├── dprocess.Rout.save
│ ├── ebola.R
│ ├── ebola.Rout.save
│ ├── emeasure.R
│ ├── emeasure.Rout.save
│ ├── eulermultinom.R
│ ├── eulermultinom.Rout.save
│ ├── flow.R
│ ├── flow.Rout.save
│ ├── gillespie.R
│ ├── gillespie.Rout.save
│ ├── gompertz.R
│ ├── gompertz.Rout.save
│ ├── helpers.R
│ ├── helpers.Rout.save
│ ├── hitch.R
│ ├── hitch.Rout.save
│ ├── issue109.R
│ ├── issue109.Rout.save
│ ├── issue222.R
│ ├── issue222.Rout.save
│ ├── issue56.R
│ ├── issue56.Rout.save
│ ├── kalman.R
│ ├── kalman.Rout.save
│ ├── kalman2.R
│ ├── kalman2.Rout.save
│ ├── link.R
│ ├── link.Rout.save
│ ├── load.R
│ ├── load.Rout.save
│ ├── logmeanexp.R
│ ├── logmeanexp.Rout.save
│ ├── lookup.R
│ ├── lookup.Rout.save
│ ├── map.R
│ ├── map.Rout.save
│ ├── mcap.R
│ ├── mcap.Rout.save
│ ├── measure.R
│ ├── measure.Rout.save
│ ├── mif2.R
│ ├── mif2.Rout.save
│ ├── mif2_index.R
│ ├── mif2_index.Rout.save
│ ├── mif2_kf.R
│ ├── mif2_kf.Rout.save
│ ├── nlf.R
│ ├── nlf.Rout.save
│ ├── nullcases.R
│ ├── nullcases.Rout.save
│ ├── ou2.R
│ ├── ou2.Rout.save
│ ├── parmat.R
│ ├── parmat.Rout.save
│ ├── partrans.R
│ ├── partrans.Rout.save
│ ├── pfilter.R
│ ├── pfilter.Rout.save
│ ├── pfilter2.R
│ ├── pfilter2.Rout.save
│ ├── pmcmc.R
│ ├── pmcmc.Rout.save
│ ├── pomp.R
│ ├── pomp.Rout.save
│ ├── pomp_fun.R
│ ├── pomp_fun.Rout.save
│ ├── pomp_methods.R
│ ├── pomp_methods.Rout.save
│ ├── prior.R
│ ├── prior.Rout.save
│ ├── probe.R
│ ├── probe.Rout.save
│ ├── probe_match.R
│ ├── probe_match.Rout.save
│ ├── process.R
│ ├── process.Rout.save
│ ├── profile_design.R
│ ├── profile_design.Rout.save
│ ├── proposals.R
│ ├── proposals.Rout.save
│ ├── resample.R
│ ├── resample.Rout.save
│ ├── rgammawn.R
│ ├── rgammawn.Rout.save
│ ├── ricker.R
│ ├── ricker.Rout.save
│ ├── rinit.R
│ ├── rinit.Rout.save
│ ├── runif_design.R
│ ├── runif_design.Rout.save
│ ├── rw2.R
│ ├── rw2.Rout.save
│ ├── sannbox.R
│ ├── sannbox.Rout.save
│ ├── save.R
│ ├── save.Rout.save
│ ├── simulate.R
│ ├── simulate.Rout.save
│ ├── simulate_data_frame.R
│ ├── simulate_data_frame.Rout.save
│ ├── sir.R
│ ├── sir.Rout.save
│ ├── sir2.R
│ ├── sir2.Rout.save
│ ├── skeleton.R
│ ├── skeleton.Rout.save
│ ├── slice_design.R
│ ├── slice_design.Rout.save
│ ├── sobol.R
│ ├── sobol.Rout.save
│ ├── spect.R
│ ├── spect.Rout.save
│ ├── spect_match.R
│ ├── spect_match.Rout.save
│ ├── spy.R
│ ├── spy.Rout
│ ├── steps.R
│ ├── steps.Rout.save
│ ├── synlik.R
│ ├── synlik.Rout.save
│ ├── traj_match.R
│ ├── traj_match.Rout.save
│ ├── trajectory.R
│ ├── trajectory.Rout.save
│ ├── transformations.R
│ ├── transformations.Rout.save
│ ├── undefined.R
│ ├── undefined.Rout.save
│ ├── userdata.R
│ ├── userdata.Rout.save
│ ├── verhulst.R
│ ├── verhulst.Rout.save
│ ├── vmeasure.R
│ ├── vmeasure.Rout.save
│ ├── wpfilter.R
│ ├── wpfilter.Rout.save
│ ├── wquant.R
│ └── wquant.Rout.save
└── tools/
└── check.env
================================================
FILE CONTENTS
================================================
================================================
FILE: .Rbuildignore
================================================
^check
^examples
^lib
^libs
^library
^rchk
^repo
^revdep
^scripts
^tools
^wiki
^www
^yaml
^Makefile
^TAGS
^rules.mk
^tests/Makefile
^tests/(.+?)\.png$
^tests/(.+?)\.pdf$
^tests/(.+?)\.Rout$
^inst/doc/Makefile
^inst/doc/(.+?).md
^inst/doc/(.+?).Rmd
^man/roxygen
^Doxyfile
LICENSE\.md$
README\.(.?)$
CRAN\.md$
TODO\.md$
BUILD\.md$
^rchk\.out$
^\.gitignore$
^\.github
^\.travis\.yml$
^codecov\.yml$
^.*\.Rproj$
^\.Rproj\.user$
\.Rprofile
\.Rhistory
\.NEWS
\.dist
\.instdocs
\.install
\.roxy
\.source
\.testsource
\.includes
\.headers
\.tests
^(.+?)\.pdf
^(.+?)\.tar\.gz
^(.+?)\.tgz
^(.+?)\.zip
covr.html
covr.rds
================================================
FILE: .Rprofile
================================================
options(
help_type="html",
repos=c(
CRAN="https://cloud.r-project.org/",
kingaa="https://kingaa.github.io"
),
useFancyQuotes=FALSE,
Ncpus=12
)
================================================
FILE: .github/ISSUE_TEMPLATE/bug_report.md
================================================
---
name: Bug report
about: Create a report to help us improve **pomp**
title: ''
labels: ''
assignees: ''
---
**Describe the bug**
A clear and concise description of what the bug is.
**To Reproduce**
1. **R** code that produces the problem.
2. Transcript of the R session that gave the errors.
3. Any graphics that show the problematic results.
**Expected behavior**
A clear and concise description of what you expected to happen.
**Session information**
Output of the command
```
source("https://kingaa.github.io/scripts/diagnostics.R")
```
================================================
FILE: .github/ISSUE_TEMPLATE/feature_request.md
================================================
---
name: Feature request
about: Suggest an idea for this project
title: ''
labels: ''
assignees: ''
---
**Is your feature request related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
**Describe the solution you'd like**
A clear and concise description of what you want to happen.
**Describe alternatives you've considered**
A clear and concise description of any alternative solutions or features you've considered.
**Additional context**
Add any other context or screenshots about the feature request here.
================================================
FILE: .github/workflows/binary-build.yml
================================================
# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
tags:
- '*.*.*.*'
workflow_dispatch:
name: binary-build
env:
release_name: ${{ vars.repo_name }}_${{ github.ref_name }}
jobs:
source_build:
runs-on: ubuntu-latest
name: Build source tarball
strategy:
fail-fast: false
steps:
- uses: actions/checkout@v6
- uses: r-lib/actions/setup-r@v2
with:
r-version: latest
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: |
any::pkgbuild
- name: Build source tarball
run: |
R CMD build --force --no-manual --resave-data --compact-vignettes=both --md5 .
mkdir -p ${{ github.workspace }}/artifacts
cp ${{ env.release_name }}.tar.gz ${{ github.workspace }}/artifacts
- uses: actions/upload-artifact@v7
with:
name: source_tarball
path: ${{ github.workspace }}/artifacts/${{ env.release_name }}.tar.gz
binary_build:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
strategy:
fail-fast: false
matrix:
config:
- {os: macOS-latest, r: 'release', ext: "tgz"}
- {os: windows-latest, r: 'release', ext: "zip"}
steps:
- uses: actions/checkout@v4
- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: |
any::pkgbuild
- name: Build binary
run: pkgbuild::build(binary=TRUE,manual=TRUE)
shell: Rscript {0}
- name: Copy tarball
run: |
mkdir -p ${{ github.workspace }}/artifacts
cp ../${{ env.release_name }}.${{ matrix.config.ext }} ${{ github.workspace }}/artifacts
- uses: actions/upload-artifact@v4
with:
name: ${{ matrix.config.os }}-${{ matrix.config.r }}
path: ${{ github.workspace }}/artifacts/${{ env.release_name }}.${{ matrix.config.ext }}
# Workflow derived from https://github.com/marketplace/actions/create-release
create_release:
needs: [ source_build, binary_build ]
runs-on: ubuntu-latest
permissions:
contents: write
steps:
- uses: actions/checkout@v4
- uses: actions/download-artifact@v4
with:
path: artifacts
- uses: ncipollo/release-action@v1
with:
draft: true
artifacts: "artifacts/*/*"
================================================
FILE: .github/workflows/r-cmd-check.yml
================================================
# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
schedule:
- cron: '13 11 * * 0'
push:
branches:
- '*'
paths:
- DESCRIPTION
- NAMESPACE
- R/**
- src/**
- tests/**
- man/**
- data/**
pull_request:
paths:
- DESCRIPTION
- NAMESPACE
- R/**
- src/**
- tests/**
- man/**
- data/**
workflow_dispatch:
name: R-CMD-check
jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
strategy:
fail-fast: false
matrix:
config:
- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
- {os: ubuntu-latest, r: 'release'}
- {os: ubuntu-22.04, r: '4.1.0'}
- {os: macOS-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes
steps:
- uses: actions/checkout@v6
- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true
extra-repositories: |
https://kingaa.github.io/
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: |
any::rcmdcheck
any::tidyr
any::ggplot2
any::dplyr
any::knitr
any::subplex
any::nloptr
- uses: r-lib/actions/check-r-package@v2
- uses: actions/upload-artifact@v7
with:
name: ${{ matrix.config.os }}-${{ matrix.config.r }}-results
path: check/${{ vars.repo_name }}.Rcheck/00check.log
================================================
FILE: .github/workflows/test-coverage.yml
================================================
# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
workflow_dispatch:
push:
branches: [master]
paths:
- DESCRIPTION
- NAMESPACE
- R/**
- src/**
- tests/**
- man/**
- data/**
pull_request:
branches: [master]
paths:
- DESCRIPTION
- NAMESPACE
- R/**
- src/**
- tests/**
- man/**
- data/**
name: test-coverage
jobs:
test-coverage:
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v6
- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: covr
- name: Test coverage
run: covr::codecov()
shell: Rscript {0}
================================================
FILE: .gitignore
================================================
\.NEWS
\.dist
\.instdocs
\.install
\.roxy
\.source
\.testsource
\.includes
\.headers
\.tests
\.Rhistory
\.Rproj.user
rchk\.out
*.tar.gz
*.tgz
*.zip
*.o
*.so
*.gcda
*.gcno
*.pdf
*.sif
check
lib
library
rchk
wiki
tmp
covr.html
covr.rds
.DS_Store
================================================
FILE: BUILD.md
================================================
----------------
# Instructions for building, checking, and installing
## Makefile usage
A `Makefile` is provided. Most of the rules are defined in the `rules.mk` file.
The following key variables are defined in the `Makefile`.
- `REPODIR`: the name of the directory in which a local copy of the Git repo used for publishing source and documentation is located.
- `INCLUDES`: names of header files that will be copied to `inst/includes`
- `HEADERS`: names of header files that must be rebuilt whenever source code changes.
The key targets are:
- `roxy`: runs `devtools::document()` to build the help pages (in `man/`), the package `NAMESPACE`, and the collation order in `DESCRIPTION`.
- `dist`: builds the package source tarball.
- `install`: installs the package locally for testing.
- `tests`: runs `make` in the `tests/` directory, causing tests to be updated as needed.
- `clean`: cleans the directory of files created during builds and tests.
- `fresh`: resets the directory for a fresh rebuild.
- `htmlhelp`: builds the package manual in HTML and PDF formats.
This command also causes `doxygen` to be run, which produces HTML documentation of the C/C++ source code.
These documentation files are installed into the `REPODIR/manuals` directory.
- `www`: installs the package and runs `make` in the `www` directory.
This causes vignettes to be updated, among other things.
- `NEWS`: builds the plain-text package NEWS file.
- `instdocs`: runs `make` in the `inst/docs` directory.
- `check`: runs `devtools::check()`.
- `qcheck`: like `check`, but tests in `tests/` are not run.
- `qqcheck`: like `qcheck`, but checks for code-documentation mismatch and examples are not run.
- `xcheck`: runs `devtools::check(cran=TRUE)`, i.e., the additional checks for CRAN suitability are also run.
- `ycheck`: runs `xcheck` but tests and examples that are ordinarily not run (because expensive) are run.
- `vcheck`: runs `check` and then tests for memory leaks using `valgrind`.
One must examine the output (printed to the console and also stored in a file, the name of which ends in `-Ex.Rout`.
- `revdeps`: causes checks of reverse-dependent packages to run.
The outputs are stored under the `revdep` directory.
- `rchk`: runs Kalibera's `rchk` utility.
This uses `docker` to download and run a Docker container.
The stdout for this is stored in `rchk.out`.
- `session`: installs the package locally and then runs an **R** session for interactive testing.
This session is controlled by the `RSESSION` environment variable.
By default, this runs an `emacs -f R` session.
- `rsession`: like `session`, but a naked **R** session is started: `RSESSION=R`.
- `debug`: like `rsession`, but the **R** session is started under a debugger.
By default, the `gdb` debugger is used: `RSESSION=R -d gdb`.
- `publish`: causes source and binary tarballs to be installed in the REPODIR respository.
- `covr`: runs `covr::package_coverage()` to evaluate unit-test coverage.
Results are stored in `covr.rds`.
- `vcovr`: like `covr`, but results are displayed in a browser.
----------------
## Github Actions
Several Github Actions are defined in `.github/workflows`:
- `r-cmd-check`: runs checks on various platforms.
- `test-coverage`: runs `covr::codecov` to upload unit-test coverage information to [codecov.io](https://codecov.io).
- `binary-build`: causes binary tarballs to be built for OS X and Windows platforms.
These must be updated manually from time to time as the Actions on which they depend change.
----------------
================================================
FILE: CRAN.md
================================================
-------------------------
# Preparing a CRAN submission
## Checks
- check [CRAN test results](https://cran.r-project.org/web/checks/check_results_pomp.html)
- check [package issues page](https://github.com/kingaa/pomp/issues)
- examine `R-CMD-CHECK` logs on Github Actions
- examine tests coverage on [codecov.com](https://codecov.io/gh/kingaa/pomp).
- copy old CRAN branch to new one and update timestamp:
```
git branch v4.6 v4.5
git rebase master v4.6
git commit --amend --date=now --no-edit
git push github v4.6
```
- rebase: `git rebase master v4.6`
- consolidate `NEWS.md`
- `make NEWS`
- verify that `.Rbuildignore` contains
- `tests`
- `README\.md$`
- `TODO\.md$`
- `CRAN\.md$`
- `^\.gitignore$`
- `^\.travis\.yml$`
- `^codecov\.yml$`
- perform extra checks:
- `make xcheck`
- `make ycheck`
- `make rchk`
- `make vcheck` and examine `valgrind` output in `pomp-Ex.Rout` for evidence of memory leaks.
- `make revdeps`
## Submitting
- Use the [webform](https://xmpalantir.wu.ac.at/cransubmit/) for submission.
- **Example submission note text:**
The package has been checked under R-4.1.0, R-release, and R-devel on linux, osx, and windows.
I have checked for memory leaks using 'valgrind'.
There are two new NOTEs generated, concerning S3 generic/method consistency.
These are false positives, since the functions in question `filter.mean` and `filter.traj` are themselves S4 generics.
I have checked that the S3 method dispatch system works properly.
In any case, these functions have been deprecated as of this version in favor of functions named `filter_mean` and `filter_traj`, so this false positive will go away when these functions are removed in a future release.
I have verified that this release does not break the reverse dependencies listed on CRAN, with the exception of **spatPomp**.
I am one of the developers of that package and we have prepared a CRAN release of this package that corrects this problem.
We will submit this as soon as this version of **pomp** is published to CRAN.
## Announcement
- Prepare an announcement for the blog: `www/_posts/`
- Update manual pages:
- `make publish`
- Then push changes to `kingaa.github.io`
- Make `X.X.0.0` release for Github site.
-------------------------
================================================
FILE: DESCRIPTION
================================================
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
Version: 6.4.0.0
Date: 2025-11-25
Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa@umich.edu",comment=c(ORCID="0000-0001-6159-3207")),
person(given=c("Edward","L."),family="Ionides",role="aut",comment=c(ORCID="0000-0002-4190-0174")) ,
person(given="Carles",family="Bretó",role="aut",comment=c(ORCID="0000-0003-4695-4902")),
person(given=c("Stephen","P."),family="Ellner",role="ctb",comment=c(ORCID="0000-0002-8351-9734")),
person(given=c("Matthew","J."),family="Ferrari",role="ctb",comment=c(ORCID="0000-0001-5251-8168")),
person(given="Sebastian",family="Funk",role="ctb",comment=c(ORCID="0000-0002-2842-3406")),
person(given=c("Steven","G."),family="Johnson",role="ctb"),
person(given=c("Bruce","E."),family="Kendall",role="ctb",comment=c(ORCID="0000-0003-1782-8106")),
person(given=c("Michael"),family="Lavine",role="ctb"),
person(given="Dao",family="Nguyen",role="ctb",comment=c(ORCID="0000-0003-2215-613X")),
person(given=c("Eamon","B."),family="O'Dea",role="ctb",comment=c(ORCID="0000-0003-4748-683X")),
person(given=c("Daniel","C."),family="Reuman",role="ctb"),
person(given=c("Helen"),family="Wearing",role="ctb",comment=c(ORCID="0000-0002-9837-9797")),
person(given=c("Simon","N."),family="Wood",role="ctb",comment=c(ORCID="0000-0002-2034-7453"))
)
URL: https://kingaa.github.io/pomp/
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Depends: R(>= 4.1.0)
Imports: methods, stats, graphics, digest, mvtnorm, deSolve, coda, data.table
Suggests: ggplot2, knitr, dplyr, tidyr, subplex, nloptr
SystemRequirements: For Windows users, Rtools (see https://cran.r-project.org/bin/windows/Rtools/).
License: GPL-3
LazyData: true
BugReports: https://github.com/kingaa/pomp/issues/
Encoding: UTF-8
Roxygen: list(roclets = c("collate", "namespace", "rd"))
RoxygenNote: 7.3.3
Collate:
'package.R'
'pstop.R'
'undefined.R'
'csnippet.R'
'pomp_fun.R'
'parameter_trans.R'
'covariate_table.R'
'skeleton_spec.R'
'rprocess_spec.R'
'safecall.R'
'pomp_class.R'
'load.R'
'workhorses.R'
'continue.R'
'summary.R'
'prior_spec.R'
'dmeasure_spec.R'
'dprocess_spec.R'
'rmeasure_spec.R'
'rinit_spec.R'
'dinit_spec.R'
'templates.R'
'builder.R'
'pomp.R'
'probe.R'
'abc.R'
'accumulators.R'
'melt.R'
'kalman.R'
'pfilter.R'
'wpfilter.R'
'proposals.R'
'pmcmc.R'
'mif2.R'
'listie.R'
'simulate.R'
'spect.R'
'plot.R'
'bsmc2.R'
'as_data_frame.R'
'as_pomp.R'
'bake.R'
'basic_components.R'
'basic_probes.R'
'betabinom.R'
'blowflies.R'
'bsflu.R'
'bsplines.R'
'childhood.R'
'coef.R'
'conc.R'
'concat.R'
'cond_logLik.R'
'covmat.R'
'dacca.R'
'design.R'
'ebola.R'
'eff_sample_size.R'
'elementary_algorithms.R'
'emeasure_spec.R'
'estimation_algorithms.R'
'eulermultinom.R'
'extract.R'
'filter_mean.R'
'filter_traj.R'
'flow.R'
'forecast.R'
'gompertz.R'
'kf.R'
'probe_match.R'
'spect_match.R'
'nlf.R'
'trajectory.R'
'traj_match.R'
'objfun.R'
'loglik.R'
'logmeanexp.R'
'lookup.R'
'mcap.R'
'obs.R'
'ou2.R'
'parmat.R'
'parus.R'
'pomp_examp.R'
'pred_mean.R'
'pred_var.R'
'show.R'
'print.R'
'profile_design.R'
'resample.R'
'ricker.R'
'runif_design.R'
'rw2.R'
'sannbox.R'
'saved_states.R'
'sir.R'
'slice_design.R'
'sobol_design.R'
'spy.R'
'states.R'
'time.R'
'timezero.R'
'traces.R'
'transformations.R'
'userdata.R'
'verhulst.R'
'vmeasure_spec.R'
'window.R'
'wquant.R'
================================================
FILE: Doxyfile
================================================
# Doxyfile 1.9.1
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# doxygen (www.doxygen.org) for a project.
#
# All text after a double hash (##) is considered a comment and is placed in
# front of the TAG it is preceding.
#
# All text after a single hash (#) is considered a comment and will be ignored.
# The format is:
# TAG = value [value, ...]
# For lists, items can also be appended using:
# TAG += value [value, ...]
# Values that contain spaces should be placed between quotes (\" \").
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
# This tag specifies the encoding used for all characters in the configuration
# file that follow. The default is UTF-8 which is also the encoding used for all
# text before the first occurrence of this tag. Doxygen uses libiconv (or the
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DOXYFILE_ENCODING = UTF-8
# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
# double-quotes, unless you are using Doxywizard) that should identify the
# project for which the documentation is generated. This name is used in the
# title of most generated pages and in a few other places.
# The default value is: My Project.
PROJECT_NAME = pomp
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
# control system is used.
PROJECT_NUMBER =
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PROJECT_LOGO =
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# into which the generated documentation will be written. If a relative path is
# entered, it will be relative to the location where doxygen was started. If
# left blank the current directory will be used.
OUTPUT_DIRECTORY = ../www/manuals/pomp/source
# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
# directories (in 2 levels) under the output directory of each output format and
# will distribute the generated files over these directories. Enabling this
# option can be useful when feeding doxygen a huge amount of source files, where
# putting all generated files in the same directory would otherwise causes
# performance problems for the file system.
# The default value is: NO.
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OPTIMIZE_OUTPUT_VHDL = NO
# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice
# sources only. Doxygen will then generate output that is more tailored for that
# language. For instance, namespaces will be presented as modules, types will be
# separated into more groups, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_SLICE = NO
# Doxygen selects the parser to use depending on the extension of the files it
# parses. With this tag you can assign which parser to use for a given
# extension. Doxygen has a built-in mapping, but you can override or extend it
# using this tag. The format is ext=language, where ext is a file extension, and
# language is one of the parsers supported by doxygen: IDL, Java, JavaScript,
# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice, VHDL,
# Fortran (fixed format Fortran: FortranFixed, free formatted Fortran:
# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser
# tries to guess whether the code is fixed or free formatted code, this is the
# default for Fortran type files). For instance to make doxygen treat .inc files
# as Fortran files (default is PHP), and .f files as C (default is Fortran),
# use: inc=Fortran f=C.
#
# Note: For files without extension you can use no_extension as a placeholder.
#
# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
# the files are not read by doxygen. When specifying no_extension you should add
# * to the FILE_PATTERNS.
#
# Note see also the list of default file extension mappings.
EXTENSION_MAPPING =
# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
# according to the Markdown format, which allows for more readable
# documentation. See https://daringfireball.net/projects/markdown/ for details.
# The output of markdown processing is further processed by doxygen, so you can
# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
# case of backward compatibilities issues.
# The default value is: YES.
MARKDOWN_SUPPORT = YES
# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
# to that level are automatically included in the table of contents, even if
# they do not have an id attribute.
# Note: This feature currently applies only to Markdown headings.
# Minimum value: 0, maximum value: 99, default value: 5.
# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
TOC_INCLUDE_HEADINGS = 5
# When enabled doxygen tries to link words that correspond to documented
# classes, or namespaces to their corresponding documentation. Such a link can
# be prevented in individual cases by putting a % sign in front of the word or
# globally by setting AUTOLINK_SUPPORT to NO.
# The default value is: YES.
AUTOLINK_SUPPORT = YES
# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
# to include (a tag file for) the STL sources as input, then you should set this
# tag to YES in order to let doxygen match functions declarations and
# definitions whose arguments contain STL classes (e.g. func(std::string);
# versus func(std::string) {}). This also make the inheritance and collaboration
# diagrams that involve STL classes more complete and accurate.
# The default value is: NO.
BUILTIN_STL_SUPPORT = NO
# If you use Microsoft's C++/CLI language, you should set this option to YES to
# enable parsing support.
# The default value is: NO.
CPP_CLI_SUPPORT = NO
# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen
# will parse them like normal C++ but will assume all classes use public instead
# of private inheritance when no explicit protection keyword is present.
# The default value is: NO.
SIP_SUPPORT = NO
# For Microsoft's IDL there are propget and propput attributes to indicate
# getter and setter methods for a property. Setting this option to YES will make
# doxygen to replace the get and set methods by a property in the documentation.
# This will only work if the methods are indeed getting or setting a simple
# type. If this is not the case, or you want to show the methods anyway, you
# should set this option to NO.
# The default value is: YES.
IDL_PROPERTY_SUPPORT = YES
# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
# tag is set to YES then doxygen will reuse the documentation of the first
# member in the group (if any) for the other members of the group. By default
# all members of a group must be documented explicitly.
# The default value is: NO.
DISTRIBUTE_GROUP_DOC = NO
# If one adds a struct or class to a group and this option is enabled, then also
# any nested class or struct is added to the same group. By default this option
# is disabled and one has to add nested compounds explicitly via \ingroup.
# The default value is: NO.
GROUP_NESTED_COMPOUNDS = NO
# Set the SUBGROUPING tag to YES to allow class member groups of the same type
# (for instance a group of public functions) to be put as a subgroup of that
# type (e.g. under the Public Functions section). Set it to NO to prevent
# subgrouping. Alternatively, this can be done per class using the
# \nosubgrouping command.
# The default value is: YES.
SUBGROUPING = YES
# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
# are shown inside the group in which they are included (e.g. using \ingroup)
# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
# and RTF).
#
# Note that this feature does not work in combination with
# SEPARATE_MEMBER_PAGES.
# The default value is: NO.
INLINE_GROUPED_CLASSES = NO
# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
# with only public data fields or simple typedef fields will be shown inline in
# the documentation of the scope in which they are defined (i.e. file,
# namespace, or group documentation), provided this scope is documented. If set
# to NO, structs, classes, and unions are shown on a separate page (for HTML and
# Man pages) or section (for LaTeX and RTF).
# The default value is: NO.
INLINE_SIMPLE_STRUCTS = NO
# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
# enum is documented as struct, union, or enum with the name of the typedef. So
# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
# with name TypeT. When disabled the typedef will appear as a member of a file,
# namespace, or class. And the struct will be named TypeS. This can typically be
# useful for C code in case the coding convention dictates that all compound
# types are typedef'ed and only the typedef is referenced, never the tag name.
# The default value is: NO.
TYPEDEF_HIDES_STRUCT = NO
# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
# cache is used to resolve symbols given their name and scope. Since this can be
# an expensive process and often the same symbol appears multiple times in the
# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
# doxygen will become slower. If the cache is too large, memory is wasted. The
# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
# symbols. At the end of a run doxygen will report the cache usage and suggest
# the optimal cache size from a speed point of view.
# Minimum value: 0, maximum value: 9, default value: 0.
LOOKUP_CACHE_SIZE = 0
# The NUM_PROC_THREADS specifies the number threads doxygen is allowed to use
# during processing. When set to 0 doxygen will based this on the number of
# cores available in the system. You can set it explicitly to a value larger
# than 0 to get more control over the balance between CPU load and processing
# speed. At this moment only the input processing can be done using multiple
# threads. Since this is still an experimental feature the default is set to 1,
# which efficively disables parallel processing. Please report any issues you
# encounter. Generating dot graphs in parallel is controlled by the
# DOT_NUM_THREADS setting.
# Minimum value: 0, maximum value: 32, default value: 1.
NUM_PROC_THREADS = 1
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
# documentation are documented, even if no documentation was available. Private
# class members and static file members will be hidden unless the
# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
# Note: This will also disable the warnings about undocumented members that are
# normally produced when WARNINGS is set to YES.
# The default value is: NO.
EXTRACT_ALL = YES
# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
# be included in the documentation.
# The default value is: NO.
EXTRACT_PRIVATE = YES
# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual
# methods of a class will be included in the documentation.
# The default value is: NO.
EXTRACT_PRIV_VIRTUAL = NO
# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
# scope will be included in the documentation.
# The default value is: NO.
EXTRACT_PACKAGE = NO
# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
# included in the documentation.
# The default value is: NO.
EXTRACT_STATIC = YES
# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
# locally in source files will be included in the documentation. If set to NO,
# only classes defined in header files are included. Does not have any effect
# for Java sources.
# The default value is: YES.
EXTRACT_LOCAL_CLASSES = YES
# This flag is only useful for Objective-C code. If set to YES, local methods,
# which are defined in the implementation section but not in the interface are
# included in the documentation. If set to NO, only methods in the interface are
# included.
# The default value is: NO.
EXTRACT_LOCAL_METHODS = NO
# If this flag is set to YES, the members of anonymous namespaces will be
# extracted and appear in the documentation as a namespace called
# 'anonymous_namespace{file}', where file will be replaced with the base name of
# the file that contains the anonymous namespace. By default anonymous namespace
# are hidden.
# The default value is: NO.
EXTRACT_ANON_NSPACES = NO
# If this flag is set to YES, the name of an unnamed parameter in a declaration
# will be determined by the corresponding definition. By default unnamed
# parameters remain unnamed in the output.
# The default value is: YES.
RESOLVE_UNNAMED_PARAMS = YES
# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
# undocumented members inside documented classes or files. If set to NO these
# members will be included in the various overviews, but no documentation
# section is generated. This option has no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_MEMBERS = NO
# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
# undocumented classes that are normally visible in the class hierarchy. If set
# to NO, these classes will be included in the various overviews. This option
# has no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_CLASSES = NO
# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
# declarations. If set to NO, these declarations will be included in the
# documentation.
# The default value is: NO.
HIDE_FRIEND_COMPOUNDS = NO
# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
# documentation blocks found inside the body of a function. If set to NO, these
# blocks will be appended to the function's detailed documentation block.
# The default value is: NO.
HIDE_IN_BODY_DOCS = NO
# The INTERNAL_DOCS tag determines if documentation that is typed after a
# \internal command is included. If the tag is set to NO then the documentation
# will be excluded. Set it to YES to include the internal documentation.
# The default value is: NO.
INTERNAL_DOCS = NO
# With the correct setting of option CASE_SENSE_NAMES doxygen will better be
# able to match the capabilities of the underlying filesystem. In case the
# filesystem is case sensitive (i.e. it supports files in the same directory
# whose names only differ in casing), the option must be set to YES to properly
# deal with such files in case they appear in the input. For filesystems that
# are not case sensitive the option should be be set to NO to properly deal with
# output files written for symbols that only differ in casing, such as for two
# classes, one named CLASS and the other named Class, and to also support
# references to files without having to specify the exact matching casing. On
# Windows (including Cygwin) and MacOS, users should typically set this option
# to NO, whereas on Linux or other Unix flavors it should typically be set to
# YES.
# The default value is: system dependent.
CASE_SENSE_NAMES = NO
# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
# their full class and namespace scopes in the documentation. If set to YES, the
# scope will be hidden.
# The default value is: NO.
HIDE_SCOPE_NAMES = NO
# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
# append additional text to a page's title, such as Class Reference. If set to
# YES the compound reference will be hidden.
# The default value is: NO.
HIDE_COMPOUND_REFERENCE= NO
# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
# the files that are included by a file in the documentation of that file.
# The default value is: YES.
SHOW_INCLUDE_FILES = YES
# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
# grouped member an include statement to the documentation, telling the reader
# which file to include in order to use the member.
# The default value is: NO.
SHOW_GROUPED_MEMB_INC = NO
# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
# files with double quotes in the documentation rather than with sharp brackets.
# The default value is: NO.
FORCE_LOCAL_INCLUDES = NO
# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
# documentation for inline members.
# The default value is: YES.
INLINE_INFO = YES
# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
# (detailed) documentation of file and class members alphabetically by member
# name. If set to NO, the members will appear in declaration order.
# The default value is: YES.
SORT_MEMBER_DOCS = YES
# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
# descriptions of file, namespace and class members alphabetically by member
# name. If set to NO, the members will appear in declaration order. Note that
# this will also influence the order of the classes in the class list.
# The default value is: NO.
SORT_BRIEF_DOCS = NO
# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
# (brief and detailed) documentation of class members so that constructors and
# destructors are listed first. If set to NO the constructors will appear in the
# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
# member documentation.
# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
# detailed member documentation.
# The default value is: NO.
SORT_MEMBERS_CTORS_1ST = NO
# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
# of group names into alphabetical order. If set to NO the group names will
# appear in their defined order.
# The default value is: NO.
SORT_GROUP_NAMES = NO
# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
# fully-qualified names, including namespaces. If set to NO, the class list will
# be sorted only by class name, not including the namespace part.
# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
# Note: This option applies only to the class list, not to the alphabetical
# list.
# The default value is: NO.
SORT_BY_SCOPE_NAME = NO
# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
# type resolution of all parameters of a function it will reject a match between
# the prototype and the implementation of a member function even if there is
# only one candidate or it is obvious which candidate to choose by doing a
# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
# accept a match between prototype and implementation in such cases.
# The default value is: NO.
STRICT_PROTO_MATCHING = NO
# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
# list. This list is created by putting \todo commands in the documentation.
# The default value is: YES.
GENERATE_TODOLIST = YES
# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
# list. This list is created by putting \test commands in the documentation.
# The default value is: YES.
GENERATE_TESTLIST = YES
# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
# list. This list is created by putting \bug commands in the documentation.
# The default value is: YES.
GENERATE_BUGLIST = YES
# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
# the deprecated list. This list is created by putting \deprecated commands in
# the documentation.
# The default value is: YES.
GENERATE_DEPRECATEDLIST= YES
# The ENABLED_SECTIONS tag can be used to enable conditional documentation
# sections, marked by \if <section_label> ... \endif and \cond <section_label>
# ... \endcond blocks.
ENABLED_SECTIONS =
# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
# initial value of a variable or macro / define can have for it to appear in the
# documentation. If the initializer consists of more lines than specified here
# it will be hidden. Use a value of 0 to hide initializers completely. The
# appearance of the value of individual variables and macros / defines can be
# controlled using \showinitializer or \hideinitializer command in the
# documentation regardless of this setting.
# Minimum value: 0, maximum value: 10000, default value: 30.
MAX_INITIALIZER_LINES = 30
# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
# the bottom of the documentation of classes and structs. If set to YES, the
# list will mention the files that were used to generate the documentation.
# The default value is: YES.
SHOW_USED_FILES = YES
# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
# will remove the Files entry from the Quick Index and from the Folder Tree View
# (if specified).
# The default value is: YES.
SHOW_FILES = YES
# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
# page. This will remove the Namespaces entry from the Quick Index and from the
# Folder Tree View (if specified).
# The default value is: YES.
SHOW_NAMESPACES = YES
# The FILE_VERSION_FILTER tag can be used to specify a program or script that
# doxygen should invoke to get the current version for each file (typically from
# the version control system). Doxygen will invoke the program by executing (via
# popen()) the command command input-file, where command is the value of the
# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
# by doxygen. Whatever the program writes to standard output is used as the file
# version. For an example see the documentation.
FILE_VERSION_FILTER =
# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
# by doxygen. The layout file controls the global structure of the generated
# output files in an output format independent way. To create the layout file
# that represents doxygen's defaults, run doxygen with the -l option. You can
# optionally specify a file name after the option, if omitted DoxygenLayout.xml
# will be used as the name of the layout file.
#
# Note that if you run doxygen from a directory containing a file called
# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
# tag is left empty.
LAYOUT_FILE =
# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
# the reference definitions. This must be a list of .bib files. The .bib
# extension is automatically appended if omitted. This requires the bibtex tool
# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info.
# For LaTeX the style of the bibliography can be controlled using
# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
# search path. See also \cite for info how to create references.
CITE_BIB_FILES =
#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
#---------------------------------------------------------------------------
# The QUIET tag can be used to turn on/off the messages that are generated to
# standard output by doxygen. If QUIET is set to YES this implies that the
# messages are off.
# The default value is: NO.
QUIET = NO
# The WARNINGS tag can be used to turn on/off the warning messages that are
# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
# this implies that the warnings are on.
#
# Tip: Turn warnings on while writing the documentation.
# The default value is: YES.
WARNINGS = YES
# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
# will automatically be disabled.
# The default value is: YES.
WARN_IF_UNDOCUMENTED = YES
# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
# potential errors in the documentation, such as not documenting some parameters
# in a documented function, or documenting parameters that don't exist or using
# markup commands wrongly.
# The default value is: YES.
WARN_IF_DOC_ERROR = YES
# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
# are documented, but have no documentation for their parameters or return
# value. If set to NO, doxygen will only warn about wrong or incomplete
# parameter documentation, but not about the absence of documentation. If
# EXTRACT_ALL is set to YES then this flag will automatically be disabled.
# The default value is: NO.
WARN_NO_PARAMDOC = NO
# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
# a warning is encountered. If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS
# then doxygen will continue running as if WARN_AS_ERROR tag is set to NO, but
# at the end of the doxygen process doxygen will return with a non-zero status.
# Possible values are: NO, YES and FAIL_ON_WARNINGS.
# The default value is: NO.
WARN_AS_ERROR = NO
# The WARN_FORMAT tag determines the format of the warning messages that doxygen
# can produce. The string should contain the $file, $line, and $text tags, which
# will be replaced by the file and line number from which the warning originated
# and the warning text. Optionally the format may contain $version, which will
# be replaced by the version of the file (if it could be obtained via
# FILE_VERSION_FILTER)
# The default value is: $file:$line: $text.
WARN_FORMAT = "$file:$line: $text"
# The WARN_LOGFILE tag can be used to specify a file to which warning and error
# messages should be written. If left blank the output is written to standard
# error (stderr).
WARN_LOGFILE =
#---------------------------------------------------------------------------
# Configuration options related to the input files
#---------------------------------------------------------------------------
# The INPUT tag is used to specify the files and/or directories that contain
# documented source files. You may enter file names like myfile.cpp or
# directories like /usr/src/myproject. Separate the files or directories with
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.
INPUT = ./src
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
# documentation (see:
# https://www.gnu.org/software/libiconv/) for the list of possible encodings.
# The default value is: UTF-8.
INPUT_ENCODING = UTF-8
# If the value of the INPUT tag contains directories, you can use the
# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
# *.h) to filter out the source-files in the directories.
#
# Note that for custom extensions or not directly supported extensions you also
# need to set EXTENSION_MAPPING for the extension otherwise the files are not
# read by doxygen.
#
# Note the list of default checked file patterns might differ from the list of
# default file extension mappings.
#
# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
# *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C comment),
# *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd, *.vhdl,
# *.ucf, *.qsf and *.ice.
FILE_PATTERNS = *.c \
*.cc \
*.cxx \
*.cpp \
*.c++ \
*.java \
*.ii \
*.ixx \
*.ipp \
*.i++ \
*.inl \
*.idl \
*.ddl \
*.odl \
*.h \
*.hh \
*.hxx \
*.hpp \
*.h++ \
*.cs \
*.d \
*.php \
*.php4 \
*.php5 \
*.phtml \
*.inc \
*.m \
*.markdown \
*.md \
*.mm \
*.dox \
*.doc \
*.txt \
*.py \
*.pyw \
*.f90 \
*.f95 \
*.f03 \
*.f08 \
*.f \
*.for \
*.tcl \
*.vhd \
*.vhdl \
*.ucf \
*.qsf \
*.ice
# The RECURSIVE tag can be used to specify whether or not subdirectories should
# be searched for input files as well.
# The default value is: NO.
RECURSIVE = NO
# The EXCLUDE tag can be used to specify files and/or directories that should be
# excluded from the INPUT source files. This way you can easily exclude a
# subdirectory from a directory tree whose root is specified with the INPUT tag.
#
# Note that relative paths are relative to the directory from which doxygen is
# run.
EXCLUDE =
# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
# directories that are symbolic links (a Unix file system feature) are excluded
# from the input.
# The default value is: NO.
EXCLUDE_SYMLINKS = NO
# If the value of the INPUT tag contains directories, you can use the
# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
# certain files from those directories.
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories for example use the pattern */test/*
EXCLUDE_PATTERNS =
# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
# (namespaces, classes, functions, etc.) that should be excluded from the
# output. The symbol name can be a fully qualified name, a word, or if the
# wildcard * is used, a substring. Examples: ANamespace, AClass,
# AClass::ANamespace, ANamespace::*Test
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories use the pattern */test/*
EXCLUDE_SYMBOLS =
# The EXAMPLE_PATH tag can be used to specify one or more files or directories
# that contain example code fragments that are included (see the \include
# command).
EXAMPLE_PATH =
# If the value of the EXAMPLE_PATH tag contains directories, you can use the
# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
# *.h) to filter out the source-files in the directories. If left blank all
# files are included.
EXAMPLE_PATTERNS = *
# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
# searched for input files to be used with the \include or \dontinclude commands
# irrespective of the value of the RECURSIVE tag.
# The default value is: NO.
EXAMPLE_RECURSIVE = NO
# The IMAGE_PATH tag can be used to specify one or more files or directories
# that contain images that are to be included in the documentation (see the
# \image command).
IMAGE_PATH =
# The INPUT_FILTER tag can be used to specify a program that doxygen should
# invoke to filter for each input file. Doxygen will invoke the filter program
# by executing (via popen()) the command:
#
# <filter> <input-file>
#
# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
# name of an input file. Doxygen will then use the output that the filter
# program writes to standard output. If FILTER_PATTERNS is specified, this tag
# will be ignored.
#
# Note that the filter must not add or remove lines; it is applied before the
# code is scanned, but not when the output code is generated. If lines are added
# or removed, the anchors will not be placed correctly.
#
# Note that for custom extensions or not directly supported extensions you also
# need to set EXTENSION_MAPPING for the extension otherwise the files are not
# properly processed by doxygen.
INPUT_FILTER =
# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
# basis. Doxygen will compare the file name with each pattern and apply the
# filter if there is a match. The filters are a list of the form: pattern=filter
# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
# patterns match the file name, INPUT_FILTER is applied.
#
# Note that for custom extensions or not directly supported extensions you also
# need to set EXTENSION_MAPPING for the extension otherwise the files are not
# properly processed by doxygen.
FILTER_PATTERNS =
# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
# INPUT_FILTER) will also be used to filter the input files that are used for
# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
# The default value is: NO.
FILTER_SOURCE_FILES = NO
# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
# it is also possible to disable source filtering for a specific pattern using
# *.ext= (so without naming a filter).
# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
FILTER_SOURCE_PATTERNS =
# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
# is part of the input, its contents will be placed on the main page
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.
USE_MDFILE_AS_MAINPAGE =
#---------------------------------------------------------------------------
# Configuration options related to source browsing
#---------------------------------------------------------------------------
# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
# generated. Documented entities will be cross-referenced with these sources.
#
# Note: To get rid of all source code in the generated output, make sure that
# also VERBATIM_HEADERS is set to NO.
# The default value is: NO.
SOURCE_BROWSER = YES
# Setting the INLINE_SOURCES tag to YES will include the body of functions,
# classes and enums directly into the documentation.
# The default value is: NO.
INLINE_SOURCES = YES
# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
# special comment blocks from generated source code fragments. Normal C, C++ and
# Fortran comments will always remain visible.
# The default value is: YES.
STRIP_CODE_COMMENTS = YES
# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
# entity all documented functions referencing it will be listed.
# The default value is: NO.
REFERENCED_BY_RELATION = NO
# If the REFERENCES_RELATION tag is set to YES then for each documented function
# all documented entities called/used by that function will be listed.
# The default value is: NO.
REFERENCES_RELATION = NO
# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
# to YES then the hyperlinks from functions in REFERENCES_RELATION and
# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
# link to the documentation.
# The default value is: YES.
REFERENCES_LINK_SOURCE = YES
# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
# source code will show a tooltip with additional information such as prototype,
# brief description and links to the definition and documentation. Since this
# will make the HTML file larger and loading of large files a bit slower, you
# can opt to disable this feature.
# The default value is: YES.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
SOURCE_TOOLTIPS = YES
# If the USE_HTAGS tag is set to YES then the references to source code will
# point to the HTML generated by the htags(1) tool instead of doxygen built-in
# source browser. The htags tool is part of GNU's global source tagging system
# (see https://www.gnu.org/software/global/global.html). You will need version
# 4.8.6 or higher.
#
# To use it do the following:
# - Install the latest version of global
# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file
# - Make sure the INPUT points to the root of the source tree
# - Run doxygen as normal
#
# Doxygen will invoke htags (and that will in turn invoke gtags), so these
# tools must be available from the command line (i.e. in the search path).
#
# The result: instead of the source browser generated by doxygen, the links to
# source code will now point to the output of htags.
# The default value is: NO.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
USE_HTAGS = NO
# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
# verbatim copy of the header file for each class for which an include is
# specified. Set to NO to disable this.
# See also: Section \class.
# The default value is: YES.
VERBATIM_HEADERS = YES
# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
# clang parser (see:
# http://clang.llvm.org/) for more accurate parsing at the cost of reduced
# performance. This can be particularly helpful with template rich C++ code for
# which doxygen's built-in parser lacks the necessary type information.
# Note: The availability of this option depends on whether or not doxygen was
# generated with the -Duse_libclang=ON option for CMake.
# The default value is: NO.
CLANG_ASSISTED_PARSING = NO
# If clang assisted parsing is enabled and the CLANG_ADD_INC_PATHS tag is set to
# YES then doxygen will add the directory of each input to the include path.
# The default value is: YES.
CLANG_ADD_INC_PATHS = YES
# If clang assisted parsing is enabled you can provide the compiler with command
# line options that you would normally use when invoking the compiler. Note that
# the include paths will already be set by doxygen for the files and directories
# specified with INPUT and INCLUDE_PATH.
# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
CLANG_OPTIONS =
# If clang assisted parsing is enabled you can provide the clang parser with the
# path to the directory containing a file called compile_commands.json. This
# file is the compilation database (see:
# http://clang.llvm.org/docs/HowToSetupToolingForLLVM.html) containing the
# options used when the source files were built. This is equivalent to
# specifying the -p option to a clang tool, such as clang-check. These options
# will then be passed to the parser. Any options specified with CLANG_OPTIONS
# will be added as well.
# Note: The availability of this option depends on whether or not doxygen was
# generated with the -Duse_libclang=ON option for CMake.
CLANG_DATABASE_PATH =
#---------------------------------------------------------------------------
# Configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
# compounds will be generated. Enable this if the project contains a lot of
# classes, structs, unions or interfaces.
# The default value is: YES.
ALPHABETICAL_INDEX = YES
# In case all classes in a project start with a common prefix, all classes will
# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
# can be used to specify a prefix (or a list of prefixes) that should be ignored
# while generating the index headers.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
IGNORE_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the HTML output
#---------------------------------------------------------------------------
# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
# The default value is: YES.
GENERATE_HTML = YES
# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_OUTPUT = html
# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
# generated HTML page (for example: .htm, .php, .asp).
# The default value is: .html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FILE_EXTENSION = .html
# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
# each generated HTML page. If the tag is left blank doxygen will generate a
# standard header.
#
# To get valid HTML the header file that includes any scripts and style sheets
# that doxygen needs, which is dependent on the configuration options used (e.g.
# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
# default header using
# doxygen -w html new_header.html new_footer.html new_stylesheet.css
# YourConfigFile
# and then modify the file new_header.html. See also section "Doxygen usage"
# for information on how to generate the default header that doxygen normally
# uses.
# Note: The header is subject to change so you typically have to regenerate the
# default header when upgrading to a newer version of doxygen. For a description
# of the possible markers and block names see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_HEADER =
# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
# generated HTML page. If the tag is left blank doxygen will generate a standard
# footer. See HTML_HEADER for more information on how to generate a default
# footer and what special commands can be used inside the footer. See also
# section "Doxygen usage" for information on how to generate the default footer
# that doxygen normally uses.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FOOTER =
# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
# sheet that is used by each HTML page. It can be used to fine-tune the look of
# the HTML output. If left blank doxygen will generate a default style sheet.
# See also section "Doxygen usage" for information on how to generate the style
# sheet that doxygen normally uses.
# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
# it is more robust and this tag (HTML_STYLESHEET) will in the future become
# obsolete.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_STYLESHEET =
# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
# cascading style sheets that are included after the standard style sheets
# created by doxygen. Using this option one can overrule certain style aspects.
# This is preferred over using HTML_STYLESHEET since it does not replace the
# standard style sheet and is therefore more robust against future updates.
# Doxygen will copy the style sheet files to the output directory.
# Note: The order of the extra style sheet files is of importance (e.g. the last
# style sheet in the list overrules the setting of the previous ones in the
# list). For an example see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_STYLESHEET =
# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the HTML output directory. Note
# that these files will be copied to the base HTML output directory. Use the
# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
# files will be copied as-is; there are no commands or markers available.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_FILES =
# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
# will adjust the colors in the style sheet and background images according to
# this color. Hue is specified as an angle on a colorwheel, see
# https://en.wikipedia.org/wiki/Hue for more information. For instance the value
# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
# purple, and 360 is red again.
# Minimum value: 0, maximum value: 359, default value: 220.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_HUE = 222
# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
# in the HTML output. For a value of 0 the output will use grayscales only. A
# value of 255 will produce the most vivid colors.
# Minimum value: 0, maximum value: 255, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_SAT = 182
# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
# luminance component of the colors in the HTML output. Values below 100
# gradually make the output lighter, whereas values above 100 make the output
# darker. The value divided by 100 is the actual gamma applied, so 80 represents
# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
# change the gamma.
# Minimum value: 40, maximum value: 240, default value: 80.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_GAMMA = 183
# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
# page will contain the date and time when the page was generated. Setting this
# to YES can help to show when doxygen was last run and thus if the
# documentation is up to date.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_TIMESTAMP = NO
# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
# documentation will contain a main index with vertical navigation menus that
# are dynamically created via JavaScript. If disabled, the navigation index will
# consists of multiple levels of tabs that are statically embedded in every HTML
# page. Disable this option to support browsers that do not have JavaScript,
# like the Qt help browser.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_DYNAMIC_MENUS = YES
# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
# documentation will contain sections that can be hidden and shown after the
# page has loaded.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_DYNAMIC_SECTIONS = NO
# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
# shown in the various tree structured indices initially; the user can expand
# and collapse entries dynamically later on. Doxygen will expand the tree to
# such a level that at most the specified number of entries are visible (unless
# a fully collapsed tree already exceeds this amount). So setting the number of
# entries 1 will produce a full collapsed tree by default. 0 is a special value
# representing an infinite number of entries and will result in a full expanded
# tree by default.
# Minimum value: 0, maximum value: 9999, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_INDEX_NUM_ENTRIES = 100
# If the GENERATE_DOCSET tag is set to YES, additional index files will be
# generated that can be used as input for Apple's Xcode 3 integrated development
# environment (see:
# https://developer.apple.com/xcode/), introduced with OSX 10.5 (Leopard). To
# create a documentation set, doxygen will generate a Makefile in the HTML
# output directory. Running make will produce the docset in that directory and
# running make install will install the docset in
# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy
# genXcode/_index.html for more information.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_DOCSET = NO
# This tag determines the name of the docset feed. A documentation feed provides
# an umbrella under which multiple documentation sets from a single provider
# (such as a company or product suite) can be grouped.
# The default value is: Doxygen generated docs.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_FEEDNAME = "Doxygen generated docs"
# This tag specifies a string that should uniquely identify the documentation
# set bundle. This should be a reverse domain-name style string, e.g.
# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_BUNDLE_ID = org.doxygen.Project
# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
# the documentation publisher. This should be a reverse domain-name style
# string, e.g. com.mycompany.MyDocSet.documentation.
# The default value is: org.doxygen.Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_ID = org.doxygen.Publisher
# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
# The default value is: Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_NAME = Publisher
# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
# (see:
# https://www.microsoft.com/en-us/download/details.aspx?id=21138) on Windows.
#
# The HTML Help Workshop contains a compiler that can convert all HTML output
# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
# files are now used as the Windows 98 help format, and will replace the old
# Windows help format (.hlp) on all Windows platforms in the future. Compressed
# HTML files also contain an index, a table of contents, and you can search for
# words in the documentation. The HTML workshop also contains a viewer for
# compressed HTML files.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_HTMLHELP = NO
# The CHM_FILE tag can be used to specify the file name of the resulting .chm
# file. You can add a path in front of the file if the result should not be
# written to the html output directory.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_FILE =
# The HHC_LOCATION tag can be used to specify the location (absolute path
# including file name) of the HTML help compiler (hhc.exe). If non-empty,
# doxygen will try to run the HTML help compiler on the generated index.hhp.
# The file has to be specified with full path.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
HHC_LOCATION =
# The GENERATE_CHI flag controls if a separate .chi index file is generated
# (YES) or that it should be included in the main .chm file (NO).
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
GENERATE_CHI = NO
# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
# and project file content.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_INDEX_ENCODING =
# The BINARY_TOC flag controls whether a binary table of contents is generated
# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
# enables the Previous and Next buttons.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
BINARY_TOC = NO
# The TOC_EXPAND flag can be set to YES to add extra items for group members to
# the table of contents of the HTML help documentation and to the tree view.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
TOC_EXPAND = NO
# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
# (.qch) of the generated HTML documentation.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_QHP = NO
# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
# the file name of the resulting .qch file. The path specified is relative to
# the HTML output folder.
# This tag requires that the tag GENERATE_QHP is set to YES.
QCH_FILE =
# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
# Project output. For more information please see Qt Help Project / Namespace
# (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace).
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_NAMESPACE = org.doxygen.Project
# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
# Help Project output. For more information please see Qt Help Project / Virtual
# Folders (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual-folders).
# The default value is: doc.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_VIRTUAL_FOLDER = doc
# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
# filter to add. For more information please see Qt Help Project / Custom
# Filters (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_NAME =
# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
# custom filter to add. For more information please see Qt Help Project / Custom
# Filters (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_ATTRS =
# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
# project's filter section matches. Qt Help Project / Filter Attributes (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_SECT_FILTER_ATTRS =
# The QHG_LOCATION tag can be used to specify the location (absolute path
# including file name) of Qt's qhelpgenerator. If non-empty doxygen will try to
# run qhelpgenerator on the generated .qhp file.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHG_LOCATION =
# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
# generated, together with the HTML files, they form an Eclipse help plugin. To
# install this plugin and make it available under the help contents menu in
# Eclipse, the contents of the directory containing the HTML and XML files needs
# to be copied into the plugins directory of eclipse. The name of the directory
# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
# After copying Eclipse needs to be restarted before the help appears.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_ECLIPSEHELP = NO
# A unique identifier for the Eclipse help plugin. When installing the plugin
# the directory name containing the HTML and XML files should also have this
# name. Each documentation set should have its own identifier.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
ECLIPSE_DOC_ID = org.doxygen.Project
# If you want full control over the layout of the generated HTML pages it might
# be necessary to disable the index and replace it with your own. The
# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
# of each HTML page. A value of NO enables the index and the value YES disables
# it. Since the tabs in the index contain the same information as the navigation
# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
DISABLE_INDEX = NO
# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
# structure should be generated to display hierarchical information. If the tag
# value is set to YES, a side panel will be generated containing a tree-like
# index structure (just like the one that is generated for HTML Help). For this
# to work a browser that supports JavaScript, DHTML, CSS and frames is required
# (i.e. any modern browser). Windows users are probably better off using the
# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
# further fine-tune the look of the index. As an example, the default style
# sheet generated by doxygen has an example that shows how to put an image at
# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
# the same information as the tab index, you could consider setting
# DISABLE_INDEX to YES when enabling this option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_TREEVIEW = YES
# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
# doxygen will group on one line in the generated HTML documentation.
#
# Note that a value of 0 will completely suppress the enum values from appearing
# in the overview section.
# Minimum value: 0, maximum value: 20, default value: 4.
# This tag requires that the tag GENERATE_HTML is set to YES.
ENUM_VALUES_PER_LINE = 4
# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
# to set the initial width (in pixels) of the frame in which the tree is shown.
# Minimum value: 0, maximum value: 1500, default value: 250.
# This tag requires that the tag GENERATE_HTML is set to YES.
TREEVIEW_WIDTH = 250
# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
# external symbols imported via tag files in a separate window.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
EXT_LINKS_IN_WINDOW = NO
# If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg
# tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see
# https://inkscape.org) to generate formulas as SVG images instead of PNGs for
# the HTML output. These images will generally look nicer at scaled resolutions.
# Possible values are: png (the default) and svg (looks nicer but requires the
# pdf2svg or inkscape tool).
# The default value is: png.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FORMULA_FORMAT = png
# Use this tag to change the font size of LaTeX formulas included as images in
# the HTML documentation. When you change the font size after a successful
# doxygen run you need to manually remove any form_*.png images from the HTML
# output directory to force them to be regenerated.
# Minimum value: 8, maximum value: 50, default value: 10.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_FONTSIZE = 10
# Use the FORMULA_TRANSPARENT tag to determine whether or not the images
# generated for formulas are transparent PNGs. Transparent PNGs are not
# supported properly for IE 6.0, but are supported on all modern browsers.
#
# Note that when changing this option you need to delete any form_*.png files in
# the HTML output directory before the changes have effect.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_TRANSPARENT = YES
# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands
# to create new LaTeX commands to be used in formulas as building blocks. See
# the section "Including formulas" for details.
FORMULA_MACROFILE =
# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
# https://www.mathjax.org) which uses client side JavaScript for the rendering
# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
# installed or if you want to formulas look prettier in the HTML output. When
# enabled you may also need to install MathJax separately and configure the path
# to it using the MATHJAX_RELPATH option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
USE_MATHJAX = NO
# When MathJax is enabled you can set the default output format to be used for
# the MathJax output. See the MathJax site (see:
# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details.
# Possible values are: HTML-CSS (which is slower, but has the best
# compatibility), NativeMML (i.e. MathML) and SVG.
# The default value is: HTML-CSS.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_FORMAT = HTML-CSS
# When MathJax is enabled you need to specify the location relative to the HTML
# output directory using the MATHJAX_RELPATH option. The destination directory
# should contain the MathJax.js script. For instance, if the mathjax directory
# is located at the same level as the HTML output directory, then
# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
# Content Delivery Network so you can quickly see the result without installing
# MathJax. However, it is strongly recommended to install a local copy of
# MathJax from https://www.mathjax.org before deployment.
# The default value is: https://cdn.jsdelivr.net/npm/mathjax@2.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_RELPATH = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/
# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
# extension names that should be enabled during MathJax rendering. For example
# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_EXTENSIONS =
# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
# of code that will be used on startup of the MathJax code. See the MathJax site
# (see:
# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details. For an
# example see the documentation.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_CODEFILE =
# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
# the HTML output. The underlying search engine uses javascript and DHTML and
# should work on any modern browser. Note that when using HTML help
# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
# there is already a search function so this one should typically be disabled.
# For large projects the javascript based search engine can be slow, then
# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
# search using the keyboard; to jump to the search box use <access key> + S
# (what the <access key> is depends on the OS and browser, but it is typically
# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
# key> to jump into the search results window, the results can be navigated
# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
# the search. The filter options can be selected when the cursor is inside the
# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
# to select a filter and <Enter> or <escape> to activate or cancel the filter
# option.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
SEARCHENGINE = YES
# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
# implemented using a web server instead of a web client using JavaScript. There
# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
# setting. When disabled, doxygen will generate a PHP script for searching and
# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
# and searching needs to be provided by external tools. See the section
# "External Indexing and Searching" for details.
# The default value is: NO.
# This tag requires that the tag SEARCHENGINE is set to YES.
SERVER_BASED_SEARCH = NO
# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
# script for searching. Instead the search results are written to an XML file
# which needs to be processed by an external indexer. Doxygen will invoke an
# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
# search results.
#
# Doxygen ships with an example indexer (doxyindexer) and search engine
# (doxysearch.cgi) which are based on the open source search engine library
# Xapian (see:
# https://xapian.org/).
#
# See the section "External Indexing and Searching" for details.
# The default value is: NO.
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTERNAL_SEARCH = NO
# The SEARCHENGINE_URL should point to a search engine hosted by a web server
# which will return the search results when EXTERNAL_SEARCH is enabled.
#
# Doxygen ships with an example indexer (doxyindexer) and search engine
# (doxysearch.cgi) which are based on the open source search engine library
# Xapian (see:
# https://xapian.org/). See the section "External Indexing and Searching" for
# details.
# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHENGINE_URL =
# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
# search data is written to a file for indexing by an external tool. With the
# SEARCHDATA_FILE tag the name of this file can be specified.
# The default file is: searchdata.xml.
# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHDATA_FILE = searchdata.xml
# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
# projects and redirect the results back to the right project.
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTERNAL_SEARCH_ID =
# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
# projects other than the one defined by this configuration file, but that are
# all added to the same external search index. Each project needs to have a
# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
# to a relative location where the documentation can be found. The format is:
# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTRA_SEARCH_MAPPINGS =
#---------------------------------------------------------------------------
# Configuration options related to the LaTeX output
#---------------------------------------------------------------------------
# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
# The default value is: YES.
GENERATE_LATEX = NO
# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: latex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_OUTPUT = latex
# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
# invoked.
#
# Note that when not enabling USE_PDFLATEX the default is latex when enabling
# USE_PDFLATEX the default is pdflatex and when in the later case latex is
# chosen this is overwritten by pdflatex. For specific output languages the
# default can have been set differently, this depends on the implementation of
# the output language.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_CMD_NAME =
# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
# index for LaTeX.
# Note: This tag is used in the Makefile / make.bat.
# See also: LATEX_MAKEINDEX_CMD for the part in the generated output file
# (.tex).
# The default file is: makeindex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
MAKEINDEX_CMD_NAME = makeindex
# The LATEX_MAKEINDEX_CMD tag can be used to specify the command name to
# generate index for LaTeX. In case there is no backslash (\) as first character
# it will be automatically added in the LaTeX code.
# Note: This tag is used in the generated output file (.tex).
# See also: MAKEINDEX_CMD_NAME for the part in the Makefile / make.bat.
# The default value is: makeindex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_MAKEINDEX_CMD = makeindex
# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
# documents. This may be useful for small projects and may help to save some
# trees in general.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
COMPACT_LATEX = NO
# The PAPER_TYPE tag can be used to set the paper type that is used by the
# printer.
# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
# 14 inches) and executive (7.25 x 10.5 inches).
# The default value is: a4.
# This tag requires that the tag GENERATE_LATEX is set to YES.
PAPER_TYPE = a4
# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
# that should be included in the LaTeX output. The package can be specified just
# by its name or with the correct syntax as to be used with the LaTeX
# \usepackage command. To get the times font for instance you can specify :
# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
# To use the option intlimits with the amsmath package you can specify:
# EXTRA_PACKAGES=[intlimits]{amsmath}
# If left blank no extra packages will be included.
# This tag requires that the tag GENERATE_LATEX is set to YES.
EXTRA_PACKAGES =
# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
# generated LaTeX document. The header should contain everything until the first
# chapter. If it is left blank doxygen will generate a standard header. See
# section "Doxygen usage" for information on how to let doxygen write the
# default header to a separate file.
#
# Note: Only use a user-defined header if you know what you are doing! The
# following commands have a special meaning inside the header: $title,
# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
# string, for the replacement values of the other commands the user is referred
# to HTML_HEADER.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HEADER =
# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
# generated LaTeX document. The footer should contain everything after the last
# chapter. If it is left blank doxygen will generate a standard footer. See
# LATEX_HEADER for more information on how to generate a default footer and what
# special commands can be used inside the footer.
#
# Note: Only use a user-defined footer if you know what you are doing!
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_FOOTER =
# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
# LaTeX style sheets that are included after the standard style sheets created
# by doxygen. Using this option one can overrule certain style aspects. Doxygen
# will copy the style sheet files to the output directory.
# Note: The order of the extra style sheet files is of importance (e.g. the last
# style sheet in the list overrules the setting of the previous ones in the
# list).
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_EXTRA_STYLESHEET =
# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the LATEX_OUTPUT output
# directory. Note that the files will be copied as-is; there are no commands or
# markers available.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_EXTRA_FILES =
# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
# contain links (just like the HTML output) instead of page references. This
# makes the output suitable for online browsing using a PDF viewer.
# The default value is: YES.
# This tag requires that the tag GENERATE_LATEX is set to YES.
PDF_HYPERLINKS = YES
# If the USE_PDFLATEX tag is set to YES, doxygen will use the engine as
# specified with LATEX_CMD_NAME to generate the PDF file directly from the LaTeX
# files. Set this option to YES, to get a higher quality PDF documentation.
#
# See also section LATEX_CMD_NAME for selecting the engine.
# The default value is: YES.
# This tag requires that the tag GENERATE_LATEX is set to YES.
USE_PDFLATEX = YES
# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
# command to the generated LaTeX files. This will instruct LaTeX to keep running
# if errors occur, instead of asking the user for help. This option is also used
# when generating formulas in HTML.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BATCHMODE = NO
# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
# index chapters (such as File Index, Compound Index, etc.) in the output.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HIDE_INDICES = NO
# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
# code with syntax highlighting in the LaTeX output.
#
# Note that which sources are shown also depends on other settings such as
# SOURCE_BROWSER.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_SOURCE_CODE = NO
# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
# bibliography, e.g. plainnat, or ieeetr. See
# https://en.wikipedia.org/wiki/BibTeX and \cite for more info.
# The default value is: plain.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BIB_STYLE = plain
# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
# page will contain the date and time when the page was generated. Setting this
# to NO can help when comparing the output of multiple runs.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_TIMESTAMP = NO
# The LATEX_EMOJI_DIRECTORY tag is used to specify the (relative or absolute)
# path from which the emoji images will be read. If a relative path is entered,
# it will be relative to the LATEX_OUTPUT directory. If left blank the
# LATEX_OUTPUT directory will be used.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_EMOJI_DIRECTORY =
#---------------------------------------------------------------------------
# Configuration options related to the RTF output
#---------------------------------------------------------------------------
# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
# RTF output is optimized for Word 97 and may not look too pretty with other RTF
# readers/editors.
# The default value is: NO.
GENERATE_RTF = NO
# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: rtf.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_OUTPUT = rtf
# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
# documents. This may be useful for small projects and may help to save some
# trees in general.
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.
COMPACT_RTF = NO
# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
# contain hyperlink fields. The RTF file will contain links (just like the HTML
# output) instead of page references. This makes the output suitable for online
# browsing using Word or some other Word compatible readers that support those
# fields.
#
# Note: WordPad (write) and others do not support links.
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_HYPERLINKS = NO
# Load stylesheet definitions from file. Syntax is similar to doxygen's
# configuration file, i.e. a series of assignments. You only have to provide
# replacements, missing definitions are set to their default value.
#
# See also section "Doxygen usage" for information on how to generate the
# default style sheet that doxygen normally uses.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_STYLESHEET_FILE =
# Set optional variables used in the generation of an RTF document. Syntax is
# similar to doxygen's configuration file. A template extensions file can be
# generated using doxygen -e rtf extensionFile.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_EXTENSIONS_FILE =
# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
# with syntax highlighting in the RTF output.
#
# Note that which sources are shown also depends on other settings such as
# SOURCE_BROWSER.
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_SOURCE_CODE = NO
#---------------------------------------------------------------------------
# Configuration options related to the man page output
#---------------------------------------------------------------------------
# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
# classes and files.
# The default value is: NO.
GENERATE_MAN = NO
# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it. A directory man3 will be created inside the directory specified by
# MAN_OUTPUT.
# The default directory is: man.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_OUTPUT = man
# The MAN_EXTENSION tag determines the extension that is added to the generated
# man pages. In case the manual section does not start with a number, the number
# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
# optional.
# The default value is: .3.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_EXTENSION = .3
# The MAN_SUBDIR tag determines the name of the directory created within
# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
# MAN_EXTENSION with the initial . removed.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_SUBDIR =
# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
# will generate one additional man file for each entity documented in the real
# man page(s). These additional files only source the real man page, but without
# them the man command would be unable to find the correct page.
# The default value is: NO.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_LINKS = NO
#---------------------------------------------------------------------------
# Configuration options related to the XML output
#---------------------------------------------------------------------------
# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
# captures the structure of the code including all documentation.
# The default value is: NO.
GENERATE_XML = NO
# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: xml.
# This tag requires that the tag GENERATE_XML is set to YES.
XML_OUTPUT = xml
# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
# listings (including syntax highlighting and cross-referencing information) to
# the XML output. Note that enabling this will significantly increase the size
# of the XML output.
# The default value is: YES.
# This tag requires that the tag GENERATE_XML is set to YES.
XML_PROGRAMLISTING = YES
# If the XML_NS_MEMB_FILE_SCOPE tag is set to YES, doxygen will include
# namespace members in file scope as well, matching the HTML output.
# The default value is: NO.
# This tag requires that the tag GENERATE_XML is set to YES.
XML_NS_MEMB_FILE_SCOPE = NO
#---------------------------------------------------------------------------
# Configuration options related to the DOCBOOK output
#---------------------------------------------------------------------------
# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
# that can be used to generate PDF.
# The default value is: NO.
GENERATE_DOCBOOK = NO
# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
# front of it.
# The default directory is: docbook.
# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
DOCBOOK_OUTPUT = docbook
# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
# program listings (including syntax highlighting and cross-referencing
# information) to the DOCBOOK output. Note that enabling this will significantly
# increase the size of the DOCBOOK output.
# The default value is: NO.
# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
DOCBOOK_PROGRAMLISTING = NO
#---------------------------------------------------------------------------
# Configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
# AutoGen Definitions (see http://autogen.sourceforge.net/) file that captures
# the structure of the code including all documentation. Note that this feature
# is still experimental and incomplete at the moment.
# The default value is: NO.
GENERATE_AUTOGEN_DEF = NO
#---------------------------------------------------------------------------
# Configuration options related to the Perl module output
#---------------------------------------------------------------------------
# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
# file that captures the structure of the code including all documentation.
#
# Note that this feature is still experimental and incomplete at the moment.
# The default value is: NO.
GENERATE_PERLMOD = NO
# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
# output from the Perl module output.
# The default value is: NO.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_LATEX = NO
# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
# formatted so it can be parsed by a human reader. This is useful if you want to
# understand what is going on. On the other hand, if this tag is set to NO, the
# size of the Perl module output will be much smaller and Perl will parse it
# just the same.
# The default value is: YES.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_PRETTY = YES
# The names of the make variables in the generated doxyrules.make file are
# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
# so different doxyrules.make files included by the same Makefile don't
# overwrite each other's variables.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_MAKEVAR_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
# C-preprocessor directives found in the sources and include files.
# The default value is: YES.
ENABLE_PREPROCESSING = YES
# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
# in the source code. If set to NO, only conditional compilation will be
# performed. Macro expansion can be done in a controlled way by setting
# EXPAND_ONLY_PREDEF to YES.
# The default value is: NO.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
MACRO_EXPANSION = NO
# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
# the macro expansion is limited to the macros specified with the PREDEFINED and
# EXPAND_AS_DEFINED tags.
# The default value is: NO.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_ONLY_PREDEF = NO
# If the SEARCH_INCLUDES tag is set to YES, the include files in the
# INCLUDE_PATH will be searched if a #include is found.
# The default value is: YES.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SEARCH_INCLUDES = YES
# The INCLUDE_PATH tag can be used to specify one or more directories that
# contain include files that are not input files but should be processed by the
# preprocessor.
# This tag requires that the tag SEARCH_INCLUDES is set to YES.
INCLUDE_PATH =
# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
# patterns (like *.h and *.hpp) to filter out the header-files in the
# directories. If left blank, the patterns specified with FILE_PATTERNS will be
# used.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
INCLUDE_FILE_PATTERNS =
# The PREDEFINED tag can be used to specify one or more macro names that are
# defined before the preprocessor is started (similar to the -D option of e.g.
# gcc). The argument of the tag is a list of macros of the form: name or
# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
# is assumed. To prevent a macro definition from being undefined via #undef or
# recursively expanded use the := operator instead of the = operator.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
PREDEFINED =
# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
# tag can be used to specify a list of macro names that should be expanded. The
# macro definition that is found in the sources will be used. Use the PREDEFINED
# tag if you want to use a different macro definition that overrules the
# definition found in the source code.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_AS_DEFINED =
# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
# remove all references to function-like macros that are alone on a line, have
# an all uppercase name, and do not end with a semicolon. Such function macros
# are typically used for boiler-plate code, and will confuse the parser if not
# removed.
# The default value is: YES.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
# Configuration options related to external references
#---------------------------------------------------------------------------
# The TAGFILES tag can be used to specify one or more tag files. For each tag
# file the location of the external documentation should be added. The format of
# a tag file without this location is as follows:
# TAGFILES = file1 file2 ...
# Adding location for the tag files is done as follows:
# TAGFILES = file1=loc1 "file2 = loc2" ...
# where loc1 and loc2 can be relative or absolute paths or URLs. See the
# section "Linking to external documentation" for more information about the use
# of tag files.
# Note: Each tag file must have a unique name (where the name does NOT include
# the path). If a tag file is not located in the directory in which doxygen is
# run, you must also specify the path to the tagfile here.
TAGFILES =
# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
# tag file that is based on the input files it reads. See section "Linking to
# external documentation" for more information about the usage of tag files.
GENERATE_TAGFILE =
# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
# the class index. If set to NO, only the inherited external classes will be
# listed.
# The default value is: NO.
ALLEXTERNALS = NO
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#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
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# The default value is: YES.
CLASS_DIAGRAMS = YES
# You can include diagrams made with dia in doxygen documentation. Doxygen will
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# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
# Bell Labs. The other options in this section have no effect if this option is
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# This tag requires that the tag HAVE_DOT is set to YES.
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# So in most cases it will be better to enable caller graphs for selected
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# accomplished by means of the command \hidecallergraph.
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# This tag requires that the tag HAVE_DOT is set to YES.
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# dependency relations are determined by the #include relations between the
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# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
DIRECTORY_GRAPH = YES
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# Note that this requires a modern browser other than Internet Explorer. Tested
# and working are Firefox, Chrome, Safari, and Opera.
# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
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INTERACTIVE_SVG = NO
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# found. If left blank, it is assumed the dot tool can be found in the path.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_PATH =
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# contain msc files that are included in the documentation (see the \mscfile
# command).
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# contain dia files that are included in the documentation (see the \diafile
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# larger than this value, doxygen will truncate the graph, which is visualized
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DOT_CLEANUP = YES
================================================
FILE: LICENSE.md
================================================
### GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc.
<http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.
### Preamble
The GNU General Public License is a free, copyleft license for
software and other kinds of works.
The licenses for most software and other practical works are designed
to take away your freedom to share and change the works. By contrast,
the GNU General Public License is intended to guarantee your freedom
to share and change all versions of a program--to make sure it remains
free software for all its users. We, the Free Software Foundation, use
the GNU General Public License for most of our software; it applies
also to any other work released this way by its authors. You can apply
it to your programs, too.
When we speak of free software, we are referring to freedom, not
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To protect your rights, we need to prevent others from denying you
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Developers that use the GNU GPL protect your rights with two steps:
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The precise terms and conditions for copying, distribution and
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### TERMS AND CONDITIONS
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if neither you nor any third party retains the ability to install
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been installed in ROM).
The requirement to provide Installation Information does not include a
requirement to continue to provide support service, warranty, or
updates for a work that has been modified or installed by the
recipient, or for the User Product in which it has been modified or
installed. Access to a network may be denied when the modification
itself materially and adversely affects the operation of the network
or violates the rules and protocols for communication across the
network.
Corresponding Source conveyed, and Installation Information provided,
in accord with this section must be in a format that is publicly
documented (and with an implementation available to the public in
source code form), and must require no special password or key for
unpacking, reading or copying.
#### 7. Additional Terms.
"Additional permissions" are terms that supplement the terms of this
License by making exceptions from one or more of its conditions.
Additional permissions that are applicable to the entire Program shall
be treated as though they were included in this License, to the extent
that they are valid under applicable law. If additional permissions
apply only to part of the Program, that part may be used separately
under those permissions, but the entire Program remains governed by
this License without regard to the additional permissions.
When you convey a copy of a covered work, you may at your option
remove any additional permissions from that copy, or from any part of
it. (Additional permissions may be written to require their own
removal in certain cases when you modify the work.) You may place
additional permissions on material, added by you to a covered work,
for which you have or can give appropriate copyright permission.
Notwithstanding any other provision of this License, for material you
add to a covered work, you may (if authorized by the copyright holders
of that material) supplement the terms of this License with terms:
- a) Disclaiming warranty or limiting liability differently from the
terms of sections 15 and 16 of this License; or
- b) Requiring preservation of specified reasonable legal notices or
author attributions in that material or in the Appropriate Legal
Notices displayed by works containing it; or
- c) Prohibiting misrepresentation of the origin of that material,
or requiring that modified versions of such material be marked in
reasonable ways as different from the original version; or
- d) Limiting the use for publicity purposes of names of licensors
or authors of the material; or
- e) Declining to grant rights under trademark law for use of some
trade names, trademarks, or service marks; or
- f) Requiring indemnification of licensors and authors of that
material by anyone who conveys the material (or modified versions
of it) with contractual assumptions of liability to the recipient,
for any liability that these contractual assumptions directly
impose on those licensors and authors.
All other non-permissive additional terms are considered "further
restrictions" within the meaning of section 10. If the Program as you
received it, or any part of it, contains a notice stating that it is
governed by this License along with a term that is a further
restriction, you may remove that term. If a license document contains
a further restriction but permits relicensing or conveying under this
License, you may add to a covered work material governed by the terms
of that license document, provided that the further restriction does
not survive such relicensing or conveying.
If you add terms to a covered work in accord with this section, you
must place, in the relevant source files, a statement of the
additional terms that apply to those files, or a notice indicating
where to find the applicable terms.
Additional terms, permissive or non-permissive, may be stated in the
form of a separately written license, or stated as exceptions; the
above requirements apply either way.
#### 8. Termination.
You may not propagate or modify a covered work except as expressly
provided under this License. Any attempt otherwise to propagate or
modify it is void, and will automatically terminate your rights under
this License (including any patent licenses granted under the third
paragraph of section 11).
However, if you cease all violation of this License, then your license
from a particular copyright holder is reinstated (a) provisionally,
unless and until the copyright holder explicitly and finally
terminates your license, and (b) permanently, if the copyright holder
fails to notify you of the violation by some reasonable means prior to
60 days after the cessation.
Moreover, your license from a particular copyright holder is
reinstated permanently if the copyright holder notifies you of the
violation by some reasonable means, this is the first time you have
received notice of violation of this License (for any work) from that
copyright holder, and you cure the violation prior to 30 days after
your receipt of the notice.
Termination of your rights under this section does not terminate the
licenses of parties who have received copies or rights from you under
this License. If your rights have been terminated and not permanently
reinstated, you do not qualify to receive new licenses for the same
material under section 10.
#### 9. Acceptance Not Required for Having Copies.
You are not required to accept this License in order to receive or run
a copy of the Program. Ancillary propagation of a covered work
occurring solely as a consequence of using peer-to-peer transmission
to receive a copy likewise does not require acceptance. However,
nothing other than this License grants you permission to propagate or
modify any covered work. These actions infringe copyright if you do
not accept this License. Therefore, by modifying or propagating a
covered work, you indicate your acceptance of this License to do so.
#### 10. Automatic Licensing of Downstream Recipients.
Each time you convey a covered work, the recipient automatically
receives a license from the original licensors, to run, modify and
propagate that work, subject to this License. You are not responsible
for enforcing compliance by third parties with this License.
An "entity transaction" is a transaction transferring control of an
organization, or substantially all assets of one, or subdividing an
organization, or merging organizations. If propagation of a covered
work results from an entity transaction, each party to that
transaction who receives a copy of the work also receives whatever
licenses to the work the party's predecessor in interest had or could
give under the previous paragraph, plus a right to possession of the
Corresponding Source of the work from the predecessor in interest, if
the predecessor has it or can get it with reasonable efforts.
You may not impose any further restrictions on the exercise of the
rights granted or affirmed under this License. For example, you may
not impose a license fee, royalty, or other charge for exercise of
rights granted under this License, and you may not initiate litigation
(including a cross-claim or counterclaim in a lawsuit) alleging that
any patent claim is infringed by making, using, selling, offering for
sale, or importing the Program or any portion of it.
#### 11. Patents.
A "contributor" is a copyright holder who authorizes use under this
License of the Program or a work on which the Program is based. The
work thus licensed is called the contributor's "contributor version".
A contributor's "essential patent claims" are all patent claims owned
or controlled by the contributor, whether already acquired or
hereafter acquired, that would be infringed by some manner, permitted
by this License, of making, using, or selling its contributor version,
but do not include claims that would be infringed only as a
consequence of further modification of the contributor version. For
purposes of this definition, "control" includes the right to grant
patent sublicenses in a manner consistent with the requirements of
this License.
Each contributor grants you a non-exclusive, worldwide, royalty-free
patent license under the contributor's essential patent claims, to
make, use, sell, offer for sale, import and otherwise run, modify and
propagate the contents of its contributor version.
In the following three paragraphs, a "patent license" is any express
agreement or commitment, however denominated, not to enforce a patent
(such as an express permission to practice a patent or covenant not to
sue for patent infringement). To "grant" such a patent license to a
party means to make such an agreement or commitment not to enforce a
patent against the party.
If you convey a covered work, knowingly relying on a patent license,
and the Corresponding Source of the work is not available for anyone
to copy, free of charge and under the terms of this License, through a
publicly available network server or other readily accessible means,
then you must either (1) cause the Corresponding Source to be so
available, or (2) arrange to deprive yourself of the benefit of the
patent license for this particular work, or (3) arrange, in a manner
consistent with the requirements of this License, to extend the patent
license to downstream recipients. "Knowingly relying" means you have
actual knowledge that, but for the patent license, your conveying the
covered work in a country, or your recipient's use of the covered work
in a country, would infringe one or more identifiable patents in that
country that you have reason to believe are valid.
If, pursuant to or in connection with a single transaction or
arrangement, you convey, or propagate by procuring conveyance of, a
covered work, and grant a patent license to some of the parties
receiving the covered work authorizing them to use, propagate, modify
or convey a specific copy of the covered work, then the patent license
you grant is automatically extended to all recipients of the covered
work and works based on it.
A patent license is "discriminatory" if it does not include within the
scope of its coverage, prohibits the exercise of, or is conditioned on
the non-exercise of one or more of the rights that are specifically
granted under this License. You may not convey a covered work if you
are a party to an arrangement with a third party that is in the
business of distributing software, under which you make payment to the
third party based on the extent of your activity of conveying the
work, and under which the third party grants, to any of the parties
who would receive the covered work from you, a discriminatory patent
license (a) in connection with copies of the covered work conveyed by
you (or copies made from those copies), or (b) primarily for and in
connection with specific products or compilations that contain the
covered work, unless you entered into that arrangement, or that patent
license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting
any implied license or other defenses to infringement that may
otherwise be available to you under applicable patent law.
#### 12. No Surrender of Others' Freedom.
If conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot convey a
covered work so as to satisfy simultaneously your obligations under
this License and any other pertinent obligations, then as a
consequence you may not convey it at all. For example, if you agree to
terms that obligate you to collect a royalty for further conveying
from those to whom you convey the Program, the only way you could
satisfy both those terms and this License would be to refrain entirely
from conveying the Program.
#### 13. Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
combined work, and to convey the resulting work. The terms of this
License will continue to apply to the part which is the covered work,
but the special requirements of the GNU Affero General Public License,
section 13, concerning interaction through a network will apply to the
combination as such.
#### 14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions
of the GNU General Public License from time to time. Such new versions
will be similar in spirit to the present version, but may differ in
detail to address new problems or concerns.
Each version is given a distinguishing version number. If the Program
specifies that a certain numbered version of the GNU General Public
License "or any later version" applies to it, you have the option of
following the terms and conditions either of that numbered version or
of any later version published by the Free Software Foundation. If the
Program does not specify a version number of the GNU General Public
License, you may choose any version ever published by the Free
Software Foundation.
If the Program specifies that a proxy can decide which future versions
of the GNU General Public License can be used, that proxy's public
statement of acceptance of a version permanently authorizes you to
choose that version for the Program.
Later license versions may give you additional or different
permissions. However, no additional obligations are imposed on any
author or copyright holder as a result of your choosing to follow a
later version.
#### 15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT
WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE
DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR
CORRECTION.
#### 16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR
CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES
ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT
NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR
LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM
TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER
PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
#### 17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
### How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these
terms.
To do so, attach the following notices to the program. It is safest to
attach them to the start of each source file to most effectively state
the exclusion of warranty; and each file should have at least the
"copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper
mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
<program> Copyright (C) <year> <name of author>
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands \`show w' and \`show c' should show the
appropriate parts of the General Public License. Of course, your
program's commands might be different; for a GUI interface, you would
use an "about box".
You should also get your employer (if you work as a programmer) or
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. For more information on this, and how to apply and follow
the GNU GPL, see <http://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your
program into proprietary programs. If your program is a subroutine
library, you may consider it more useful to permit linking proprietary
applications with the library. If this is what you want to do, use the
GNU Lesser General Public License instead of this License. But first,
please read <http://www.gnu.org/philosophy/why-not-lgpl.html>.
================================================
FILE: Makefile
================================================
REPODIR = repo
INCLUDES = inst/include/pomp.h inst/include/pomp_defines.h
HEADERS = src/decls.h
SESSION_PKGS = datasets,utils,grDevices,graphics,stats,methods,tidyverse,pomp
include rules.mk
src/decls.h: $(CSOURCE)
file=`mktemp tmpXXXXXXX.h` && \
cproto -f2 -I $(R_HOME)/include -e $(CSOURCE) > $$file && \
mv $$file $@
================================================
FILE: NAMESPACE
================================================
# Generated by roxygen2: do not edit by hand
S3method(as.character,Csnippet)
S3method(as.data.frame,abcList)
S3method(as.data.frame,bsmcd_pomp)
S3method(as.data.frame,kalmand_pomp)
S3method(as.data.frame,mif2List)
S3method(as.data.frame,pfilterList)
S3method(as.data.frame,pfilterd_pomp)
S3method(as.data.frame,pmcmcList)
S3method(as.data.frame,pomp)
S3method(as.data.frame,pompList)
S3method(as.data.frame,probed_pomp)
S3method(as.data.frame,wpfilterd_pomp)
S3method(c,Pomp)
export(Csnippet)
export(append_data)
export(as_pomp)
export(bake)
export(blowflies1)
export(blowflies2)
export(bspline_basis)
export(concat)
export(continue)
export(dacca)
export(dbetabinom)
export(deulermultinom)
export(discrete_time)
export(ebolaModel)
export(eeulermultinom)
export(euler)
export(expit)
export(freeze)
export(gillespie)
export(gillespie_hl)
export(gompertz)
export(hitch)
export(inv_log_barycentric)
export(kalmanFilter)
export(logLik)
export(log_barycentric)
export(logit)
export(logmeanexp)
export(lookup)
export(map)
export(mcap)
export(mvn_diag_rw)
export(mvn_rw)
export(mvn_rw_adaptive)
export(onestep)
export(ou2)
export(parameter_trans)
export(periodic_bspline_basis)
export(pomp)
export(probe_acf)
export(probe_ccf)
export(probe_marginal)
export(probe_mean)
export(probe_median)
export(probe_nlar)
export(probe_period)
export(probe_quantile)
export(probe_sd)
export(probe_var)
export(profile_design)
export(rbetabinom)
export(repair_lookup_table)
export(reulermultinom)
export(rgammawn)
export(ricker)
export(runif_design)
export(rw2)
export(rw_sd)
export(sannbox)
export(sir)
export(sir2)
export(slice_design)
export(sobol_design)
export(stew)
export(systematic_resample)
export(vectorfield)
export(verhulst)
export(wquant)
exportClasses(pomp)
exportMethods("[")
exportMethods("coef<-")
exportMethods("solibs<-")
exportMethods("time<-")
exportMethods("timezero<-")
exportMethods(abc)
exportMethods(bsmc2)
exportMethods(coef)
exportMethods(cond_logLik)
exportMethods(continue)
exportMethods(covariate_table)
exportMethods(covmat)
exportMethods(dinit)
exportMethods(dmeasure)
exportMethods(dprior)
exportMethods(dprocess)
exportMethods(eakf)
exportMethods(eff_sample_size)
exportMethods(emeasure)
exportMethods(enkf)
exportMethods(filter_mean)
exportMethods(filter_traj)
exportMethods(flow)
exportMethods(forecast)
exportMethods(logLik)
exportMethods(melt)
exportMethods(mif2)
exportMethods(nlf_objfun)
exportMethods(obs)
exportMethods(parameter_trans)
exportMethods(parmat)
exportMethods(partrans)
exportMethods(pfilter)
exportMethods(plot)
exportMethods(pmcmc)
exportMethods(pompLoad)
exportMethods(pompUnload)
exportMethods(pred_mean)
exportMethods(pred_var)
exportMethods(print)
exportMethods(probe)
exportMethods(probe_objfun)
exportMethods(rinit)
exportMethods(rmeasure)
exportMethods(rprior)
exportMethods(rprocess)
exportMethods(saved_states)
exportMethods(show)
exportMethods(simulate)
exportMethods(skeleton)
exportMethods(spect)
exportMethods(spect_objfun)
exportMethods(spy)
exportMethods(states)
exportMethods(summary)
exportMethods(time)
exportMethods(timezero)
exportMethods(traces)
exportMethods(traj_objfun)
exportMethods(trajectory)
exportMethods(vmeasure)
exportMethods(window)
exportMethods(wpfilter)
import(methods)
importFrom(coda,mcmc)
importFrom(coda,mcmc.list)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(data.table,rbindlist)
importFrom(deSolve,diagnostics)
importFrom(deSolve,ode)
importFrom(digest,digest)
importFrom(grDevices,dev.interactive)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,box)
importFrom(graphics,hist)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,matplot)
importFrom(graphics,mtext)
importFrom(graphics,pairs)
importFrom(graphics,par)
importFrom(graphics,plot.default)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,rect)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(mvtnorm,dmvnorm)
importFrom(mvtnorm,rmvnorm)
importFrom(stats,.lm.fit)
importFrom(stats,approx)
importFrom(stats,coef)
importFrom(stats,cor)
importFrom(stats,cov)
importFrom(stats,density)
importFrom(stats,dnorm)
importFrom(stats,kernel)
importFrom(stats,lm)
importFrom(stats,loess)
importFrom(stats,logLik)
importFrom(stats,median)
importFrom(stats,optim)
importFrom(stats,pbeta)
importFrom(stats,predict)
importFrom(stats,qchisq)
importFrom(stats,quantile)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,simulate)
importFrom(stats,smooth.spline)
importFrom(stats,spec.pgram)
importFrom(stats,time)
importFrom(stats,var)
importFrom(stats,vcov)
importFrom(stats,window)
importFrom(utils,read.csv2)
useDynLib(pomp, .registration = TRUE, .fixes="P_")
================================================
FILE: R/abc.R
================================================
##' Approximate Bayesian computation
##'
##' The approximate Bayesian computation (ABC) algorithm for estimating the parameters of a partially-observed Markov process.
##'
##' @name abc
##' @rdname abc
##' @aliases abc,missing-method abc,ANY-method
##' @docType methods
##' @include pomp_class.R probe.R continue.R workhorses.R
##' @importFrom stats runif
##' @author Edward L. Ionides, Aaron A. King
##' @family summary statistic-based methods
##' @family estimation methods
##' @family MCMC methods
##' @family Bayesian methods
##' @concept approximate Bayesian computation
##' @inheritParams probe
##' @inheritParams pmcmc
##' @inheritParams pomp
##' @param Nabc the number of ABC iterations to perform.
##' @param scale named numeric vector of scales.
##' @param epsilon ABC tolerance.
##'
##' @inheritSection pomp Note for Windows users
##'
##' @section Running ABC:
##'
##' \code{abc} returns an object of class \sQuote{abcd_pomp}.
##' One or more \sQuote{abcd_pomp} objects can be joined to form an \sQuote{abcList} object.
##'
##' @section Re-running ABC iterations:
##'
##' To re-run a sequence of ABC iterations, one can use the \code{abc} method on a \sQuote{abcd_pomp} object.
##' By default, the same parameters used for the original ABC run are re-used (except for \code{verbose}, the default of which is shown above).
##' If one does specify additional arguments, these will override the defaults.
##'
##' @section Continuing ABC iterations:
##'
##' One can continue a series of ABC iterations from where one left off using the \code{continue} method.
##' A call to \code{abc} to perform \code{Nabc=m} iterations followed by a call to \code{continue} to perform \code{Nabc=n} iterations will produce precisely the same effect as a single call to \code{abc} to perform \code{Nabc=m+n} iterations.
##' By default, all the algorithmic parameters are the same as used in the original call to \code{abc}.
##' Additional arguments will override the defaults.
##'
##' @section Methods:
##' The following can be applied to the output of an \code{abc} operation:
##' \describe{
##' \item{\code{abc}}{repeats the calculation, beginning with the last state}
##' \item{\code{\link{continue}}}{continues the \code{abc} calculation}
##' \item{\code{plot}}{produces a series of diagnostic plots}
##' \item{\code{\link{traces}}}{produces an \code{\link[coda]{mcmc}} object, to which the various \pkg{coda} convergence diagnostics can be applied}
##' }
##'
##' @references
##'
##' \Marin2012
##'
##' \Toni2010
##'
##' \Toni2009
##'
NULL
setClass(
"abcd_pomp",
contains="pomp",
slots=c(
pars = "character",
Nabc = "integer",
accepts = "integer",
probes="list",
scale = "numeric",
epsilon = "numeric",
proposal = "function",
traces = "matrix"
),
prototype=prototype(
pars = character(0),
Nabc = 0L,
accepts = 0L,
probes = list(),
scale = numeric(0),
epsilon = 1.0,
proposal = function (...) pStop(who="abc","proposal not specified."),
traces=array(dim=c(0,0))
)
)
setGeneric(
"abc",
function (data, ...)
standardGeneric("abc")
)
setMethod(
"abc",
signature=signature(data="missing"),
definition=function (...) {
reqd_arg("abc","data")
}
)
setMethod(
"abc",
signature=signature(data="ANY"),
definition=function (data, ...) {
undef_method("abc",data)
}
)
##' @rdname abc
##' @export
setMethod(
"abc",
signature=signature(data="data.frame"),
definition=function (
data,
...,
Nabc = 1, proposal, scale, epsilon,
probes,
params, rinit, rprocess, rmeasure, dprior,
verbose = getOption("verbose", FALSE)
) {
tryCatch(
abc_internal(
data,
...,
Nabc=Nabc,
proposal=proposal,
scale=scale,
epsilon=epsilon,
probes=probes,
params=params,
rinit=rinit,
rprocess=rprocess,
rmeasure=rmeasure,
dprior=dprior,
verbose=verbose
),
error = function (e) pStop(who="abc",conditionMessage(e))
)
}
)
##' @rdname abc
##' @export
setMethod(
"abc",
signature=signature(data="pomp"),
definition=function (
data,
...,
Nabc = 1, proposal, scale, epsilon,
probes,
verbose = getOption("verbose", FALSE)
) {
tryCatch(
abc_internal(
data,
...,
Nabc=Nabc,
proposal=proposal,
scale=scale,
epsilon=epsilon,
probes=probes,
verbose=verbose
),
error = function (e) pStop(who="abc",conditionMessage(e))
)
}
)
##' @rdname abc
##' @export
setMethod(
"abc",
signature=signature(data="probed_pomp"),
definition=function (
data,
...,
probes,
verbose = getOption("verbose", FALSE)
) {
if (missing(probes)) probes <- data@probes
abc(
as(data,"pomp"),
...,
probes=probes,
verbose=verbose
)
}
)
##' @rdname abc
##' @export
setMethod(
"abc",
signature=signature(data="abcd_pomp"),
definition=function (
data,
...,
Nabc, proposal, scale, epsilon,
probes,
verbose = getOption("verbose", FALSE)
) {
if (missing(Nabc)) Nabc <- data@Nabc
if (missing(proposal)) proposal <- data@proposal
if (missing(scale)) scale <- data@scale
if (missing(epsilon)) epsilon <- data@epsilon
if (missing(probes)) probes <- data@probes
abc(
as(data,"pomp"),
...,
Nabc=Nabc,
proposal=proposal,
scale=scale,
epsilon=epsilon,
probes=probes,
verbose=verbose
)
}
)
##' @rdname continue
##' @param Nabc positive integer; number of additional ABC iterations to perform
##' @export
setMethod(
"continue",
signature=signature(object="abcd_pomp"),
definition=function (
object,
...,
Nabc = 1
) {
ndone <- object@Nabc
accepts <- object@accepts
obj <- abc(object,...,Nabc=Nabc,.ndone=ndone,.accepts=accepts)
obj@traces <- rbind(
object@traces[,colnames(obj@traces)],
obj@traces[-1,]
)
names(dimnames(obj@traces)) <- c("iteration","name")
obj@Nabc <- as.integer(ndone+Nabc)
obj@accepts <- as.integer(accepts+obj@accepts)
obj
}
)
abc_internal <- function (
object,
...,
Nabc, proposal, scale, epsilon, probes,
verbose,
.ndone = 0L, .accepts = 0L, .gnsi = TRUE
) {
verbose <- as.logical(verbose)
object <- pomp(object,...,verbose=verbose)
if (undefined(object@rprocess) || undefined(object@rmeasure))
pStop_(paste(sQuote(c("rprocess","rmeasure")),collapse=", ")," are needed basic components.")
if (missing(proposal)) proposal <- NULL
if (missing(probes)) probes <- NULL
if (missing(scale)) scale <- NULL
if (missing(epsilon)) epsilon <- NULL
gnsi <- as.logical(.gnsi)
scale <- as.numeric(scale)
epsilon <- as.numeric(epsilon)
epssq <- epsilon*epsilon
.ndone <- as.integer(.ndone)
.accepts <- as.integer(.accepts)
params <- coef(object)
Nabc <- as.integer(Nabc)
if (!is.finite(Nabc) || Nabc < 0)
pStop_(sQuote("Nabc")," must be a positive integer.")
param.names <- names(params)
if (is.null(param.names) || !is.numeric(params))
pStop_(sQuote("params")," must be a named numeric vector.")
if (is.null(proposal))
pStop_(sQuote("proposal")," must be specified.")
if (!is.function(proposal))
pStop_(sQuote("proposal")," must be a function.")
if (is.null(probes))
pStop_(sQuote("probes")," must be specified.")
if (!is.list(probes)) probes <- list(probes)
if (!all(vapply(probes,is.function,logical(1L))))
pStop_(sQuote("probes")," must be a function or a list of functions.")
if (!all(vapply(probes,\(f)length(formals(f))==1L,logical(1L))))
pStop_("each probe must be a function of a single argument.")
if (length(scale)==0)
pStop_(sQuote("scale")," must be specified.")
if (length(epsilon)==0)
pStop_("abc match criterion, ",sQuote("epsilon"),", must be specified.")
pompLoad(object,verbose=verbose)
on.exit(pompUnload(object,verbose=verbose))
## test proposal distribution
theta <- tryCatch(
proposal(params,.n=0),
error = function (e)
pStop_("in proposal function: ",conditionMessage(e))
)
if (is.null(names(theta)) || !is.numeric(theta) || any(!nzchar(names(theta))))
pStop_(sQuote("proposal")," must return a named numeric vector.")
theta <- params
log.prior <-dprior(object,params=theta,log=TRUE,.gnsi=gnsi)
if (!is.finite(log.prior))
pStop_("non-finite log prior at starting parameters.")
## we suppose that theta is a "match",
## which does the right thing for continue() and
## should have negligible effect unless doing many short calls to continue()
traces <- matrix(
data=NA,
nrow=Nabc+1,
ncol=length(theta),
dimnames=list(
iteration=seq(from=0,to=Nabc,by=1),
name=names(theta)
)
)
## apply probes to data
datval <- tryCatch(
.Call(P_apply_probe_data,object,probes),
error = function (e) {
pStop_("applying probes to data: ",conditionMessage(e))
}
)
if (length(scale) != 1 && length(scale) != length(datval))
pStop_(sQuote("scale")," must have either length 1 or length equal to the",
" number of probes (here, ",length(datval),").")
traces[1,names(theta)] <- theta
for (n in seq_len(Nabc)) { # main loop
theta.prop <- tryCatch(
proposal(theta,.n=n+.ndone,.accepts=.accepts,verbose=verbose),
error = function (e)
pStop_("in proposal function: ",conditionMessage(e))
)
log.prior.prop <- dprior(object,params=theta.prop,log=TRUE,
.gnsi=gnsi)
if (is.finite(log.prior.prop) && runif(1) < exp(log.prior.prop-log.prior)) {
## compute the probes for the proposed new parameter values
simval <- tryCatch(
.Call(P_apply_probe_sim,object=object,nsim=1L,params=theta.prop,
probes=probes,datval=datval,gnsi=gnsi),
error = function (e)
pStop_("applying probes to simulations: ",conditionMessage(e))
)
## ABC update rule
distance <- sum(((datval-simval)/scale)^2)
if( (is.finite(distance)) && (distance<epssq) ){
theta <- theta.prop
log.prior <- log.prior.prop
.accepts <- .accepts+1L
}
}
## store a record of this iteration
traces[n+1,names(theta)] <- theta
if (verbose && (n%%5==0))
cat("ABC iteration",n+.ndone,"of",Nabc+.ndone,
"completed\nacceptance ratio:",
round(.accepts/(n+.ndone),3),"\n")
gnsi <- FALSE
}
pars <- apply(traces,2L,\(x)diff(range(x))>0)
pars <- names(pars[pars])
new(
"abcd_pomp",
object,
params=theta,
pars=pars,
Nabc=Nabc,
accepts=.accepts,
probes=probes,
scale=scale,
epsilon=epsilon,
proposal=proposal,
traces=traces
)
}
================================================
FILE: R/accumulators.R
================================================
##' accumulator variables
##'
##' Latent state variables that accumulate quantities through time.
##'
##' @name accumvars
##' @rdname accumvars
##' @family implementation information
##' @seealso \code{\link{sir}}
##' @details
##' In formulating models, one sometimes wishes to define a state variable that will accumulate some quantity over the interval between successive observations.
##' \pkg{pomp} provides a facility to make such features more convenient.
##' Specifically, if \eqn{a} is a state-variable named in the \code{pomp}'s \code{accumvars} argument, then for each interval \eqn{(t_k,t_{k+1})}{(t[k],t[k+1])}, \eqn{k=0,1,2,\dots}, \eqn{a} will be set to zero at prior to any \code{\link{rprocess}} computation over that interval.
##' Deterministic trajectory computation is handled slightly differently:
##' see \code{\link{flow}}.
##' For examples, see \code{\link{sir}} and the tutorials on the \href{https://kingaa.github.io/pomp/}{package website}.
##' @example examples/accumulators.R
##'
NULL
================================================
FILE: R/as_data_frame.R
================================================
##' Coerce to data frame
##'
##' All \pkg{pomp} model objects can be recast as data frames.
##' The contents of the resulting data frame depend on the nature of the object.
##'
##' @name as.data.frame
##' @docType methods
##' @keywords internal
##' @rdname as_data_frame
##' @include pomp_class.R pfilter.R bsmc2.R mif2.R pmcmc.R abc.R wpfilter.R
##' @include probe.R kalman.R melt.R
##'
NULL
setAs(
from="pomp",
to="data.frame",
def = function (from) {
x <- as.data.frame(cbind(from@times,t(from@data)))
names(x) <- c(from@timename,rownames(from@data))
if (length(from@states) > 0) {
nm <- c(names(x),rownames(from@states))
x <- cbind(x,t(from@states))
names(x) <- nm
}
cnames <- get_covariate_names(from@covar)
if (length(cnames) > 0) {
nm <- c(names(x),cnames) # see issue #56
y <- .Call(P_lookup_in_table,from@covar,from@times)
x <- cbind(x,t(y))
names(x) <- nm
}
x
}
)
##' @rdname as_data_frame
##' @inheritParams base::as.data.frame
##' @details
##' When \code{object} is a simple \sQuote{pomp} object,
##' \code{as(object,"data.frame")} or \code{as.data.frame(object)} results in a
##' data frame with the times, observables, states (if known), and
##' interpolated covariates (if any).
##' @export
as.data.frame.pomp <- function (x, ...) as(x,"data.frame")
setAs(
from="pfilterd_pomp",
to="data.frame",
def = function (from) {
pm <- pred_mean(from)
pv <- pred_var(from)
fm <- filter_mean(from)
out <- cbind(
as(as(from,"pomp"),"data.frame"),
ess=eff_sample_size(from),
cond.logLik=cond_logLik(from)
)
if (length(pm)>0) {
pm <- as.data.frame(t(pm))
names(pm) <- paste0("pred.mean.",names(pm))
out <- cbind(out,pm)
}
if (length(pv)>0) {
pv <- as.data.frame(t(pv))
names(pv) <- paste0("pred.var.",names(pv))
out <- cbind(out,pv)
}
if (length(fm)>0) {
fm <- as.data.frame(t(fm))
names(fm) <- paste0("filter.mean.",names(fm))
out <- cbind(out,fm)
}
out
}
)
##' @rdname as_data_frame
##' @details When \code{object} is a \sQuote{pfilterd_pomp} object,
##' coercion to a data frame results in a data frame with the same content as for a simple \sQuote{pomp},
##' but with conditional log likelihood and effective sample size estimates included, as well as filtering means, prediction means, and prediction variances, if these have been computed.
##' @export
as.data.frame.pfilterd_pomp <- function (x, ...) as(x,"data.frame")
setAs(
from="probed_pomp",
to="data.frame",
def = function (from) {
x <- as.data.frame(rbind(from@datvals,from@simvals))
row.names(x) <- seq.int(from=0,to=nrow(x)-1)
x$.id <- factor(c("data",rep("sim",nrow(x)-1)))
x
}
)
##' @rdname as_data_frame
##' @details When \code{object} is a \sQuote{probed_pomp} object,
##' coercion to a data frame results in a data frame with the values of the probes computed on the data and on simulations.
##' @export
as.data.frame.probed_pomp <- function (x, ...)
as(x,"data.frame")
setAs(
from="kalmand_pomp",
to="data.frame",
def = function (from) {
pm <- pred_mean(from)
fm <- filter_mean(from)
fc <- forecast(from)
out <- cbind(
as(as(from,"pomp"),"data.frame"),
cond.logLik=cond_logLik(from)
)
if (length(pm)>0) {
pm <- as.data.frame(t(pm))
names(pm) <- paste0("pred.mean.",names(pm))
out <- cbind(out,pm)
}
if (length(fm)>0) {
fm <- as.data.frame(t(fm))
names(fm) <- paste0("filter.mean.",names(fm))
out <- cbind(out,fm)
}
if (length(fc)>0) {
fc <- as.data.frame(t(fc))
names(fc) <- paste0("forecast.",names(fc))
out <- cbind(out,fc)
}
out
}
)
##' @rdname as_data_frame
##' @details When \code{object} is a \sQuote{kalmand_pomp} object,
##' coercion to a data frame results in a data frame with prediction means, filter means and forecasts, in addition to the data.
##' @export
as.data.frame.kalmand_pomp <- function (x, ...) {
as(x,"data.frame")
}
setAs(
from="bsmcd_pomp",
to="data.frame",
def = function (from) {
prior <- as.data.frame(t(from@prior))
post <- as.data.frame(t(from@post))
prior$.id <- "prior"
post$.id <- "posterior"
rbind(prior,post)
}
)
##' @rdname as_data_frame
##' @details When \code{object} is a \sQuote{bsmcd_pomp} object,
##' coercion to a data frame results in a data frame with samples from the prior and posterior distribution.
##' The \code{.id} variable distinguishes them.
##' @export
as.data.frame.bsmcd_pomp <- function (x, ...) {
as(x,"data.frame")
}
setAs(
from="listie",
to="data.frame",
def = function (from) {
rbind_fill(
lapply(from,as,"data.frame"),
.id=".L1"
)
}
)
##' @rdname as_data_frame
##' @export
as.data.frame.pompList <- function (x, ...) {
as(x,"data.frame")
}
##' @rdname as_data_frame
##' @export
as.data.frame.pfilterList <- function (x, ...) {
as(x,"data.frame")
}
##' @rdname as_data_frame
##' @export
as.data.frame.abcList <- function (x, ...) {
as(x,"data.frame")
}
##' @rdname as_data_frame
##' @export
as.data.frame.mif2List <- function (x, ...) {
as(x,"data.frame")
}
##' @rdname as_data_frame
##' @export
as.data.frame.pmcmcList <- function (x, ...) {
as(x,"data.frame")
}
setAs(
from="wpfilterd_pomp",
to="data.frame",
def = function (from) {
cbind(
as(as(from,"pomp"),"data.frame"),
eff.sample.size=eff_sample_size(from),
cond.logLik=cond_logLik(from)
)
}
)
##' @rdname as_data_frame
##' @details When \code{object} is a \sQuote{wpfilterd_pomp} object,
##' coercion to a data frame results in a data frame with the same content as for a simple \sQuote{pomp},
##' but with conditional log likelihood and effective sample size estimates included.
##' @export
as.data.frame.wpfilterd_pomp <- function (x, ...) as(x,"data.frame")
================================================
FILE: R/as_pomp.R
================================================
##' as.pomp
##'
##' Coerce to a \sQuote{pomp} object
##'
##' @name as_pomp
##' @docType methods
##' @keywords internal
##' @rdname as_pomp
##' @include pomp_class.R
##'
##' @param object the object to be coerced
##' @param \dots additional arguments
##'
##' @export
as_pomp <- function (object, ...) {
as(object,"pomp")
}
================================================
FILE: R/bake.R
================================================
##' Tools for reproducible computations
##'
##' Archiving of computations and control of the random-number generator.
##'
##' @name reproducibility_tools
##' @rdname bake
##' @include package.R
##' @concept reproducibility
##' @author Aaron A. King
##' @details
##' On cooking shows, recipes requiring lengthy baking or stewing are prepared beforehand.
##' The \code{bake} and \code{stew} functions perform analogously:
##' an computation is performed and archived in a named file.
##' If the function is called again and the file is present, the computation is not executed.
##' Instead, the results are loaded from the archive.
##' Moreover, via their optional \code{seed} argument, \code{bake} and \code{stew} can control the pseudorandom-number generator (RNG) for greater reproducibility.
##' After the computation is finished, these functions restore the pre-existing RNG state to avoid side effects.
##'
##' The \code{freeze} function doesn't save results, but does set the RNG state to the specified value and restore it after the computation is complete.
##'
##' Both \code{bake} and \code{stew} first test to see whether \code{file} exists.
##' If it does, \code{bake} reads it using \code{\link{readRDS}} and returns the resulting object.
##' By contrast, \code{stew} loads the file using \code{\link{load}} and copies the objects it contains into the user's workspace (or the environment of the call to \code{stew}).
##'
##' If \code{file} does not exist, then both \code{bake} and \code{stew} evaluate the expression \code{expr};
##' they differ in the results that they save.
##' \code{bake} saves the value of the evaluated expression to \code{file} as a single object.
##' The name of that object is not saved.
##' By contrast, \code{stew} creates a local environment within which \code{expr} is evaluated; all objects in that environment are saved (by name) in \code{file}.
##' \code{bake} and \code{stew} also store information about the code executed, the dependencies, and the state of the random-number generator (if the latter is controlled) in the archive file.
##' Re-computation is triggered if any of these things change.
##' @section Avoid using \sQuote{pomp} objects as dependencies:
##' Note that when a \sQuote{pomp} object is built with one or more \link[=Csnippet]{C snippets}, the resulting code is \dQuote{salted} with a random element to prevent collisions in parallel computations.
##' As a result, two such \sQuote{pomp} objects will never match perfectly, even if the codes and data used to construct them are identical.
##' Therefore, avoid using \sQuote{pomp} objects as dependencies in \code{bake} and \code{stew}.
##' @param file Name of the archive file in which the result will be stored or retrieved, as appropriate.
##' For \code{bake}, this will contain a single object and hence be an RDS file (extension \sQuote{rds});
##' for \code{stew}, this will contain one or more named objects and hence be an RDA file (extension \sQuote{rda});
##' for \code{append_data}, this will be a CSV file.
##' @param dir Directory holding archive files;
##' by default, this is the current working directory.
##' This can also be set using the global option \code{pomp_archive_dir}.
##' If it does not exist, this directory will be created (with a message).
##' @param expr Expression to be evaluated.
##' @param seed,kind,normal.kind optional.
##' To set the state and of the RNG.
##' The default, \code{seed = NULL}, will not change the RNG state.
##' \code{seed} should be a single integer.
##' See \code{\link{set.seed}} for more information.
##' @param dependson arbitrary \R object (optional).
##' Variables on which the computation in \code{expr} depends.
##' A hash of these objects will be archived in \code{file}, along with the results of evaluation \code{expr}.
##' When \code{bake} or \code{stew} are called and \code{file} exists, the hash of these objects will be compared against the archived hash;
##' recomputation is forced when these do not match.
##' The dependencies should be specified as unquoted symbols:
##' use a list if there are multiple dependencies.
##' See the note below about avoiding using \sQuote{pomp} objects as dependencies.
##' @param timing logical.
##' If \code{TRUE}, the time required for the computation is returned.
##' This is returned as the \dQuote{system.time} attribute of the returned object.
##' @param info logical.
##' If \code{TRUE}, the \dQuote{ingredients} of the calculation are returned as a list.
##' In the case of \code{bake}, this list is the \dQuote{ingredients} attribute of the returned object.
##' In the case of \code{stew}, this list is a hidden object named \dQuote{.ingredients}, located in the environment within which \code{stew} was called.
##' @inheritParams base::eval
##' @section Compatibility with older versions:
##' With \pkg{pomp} version 3.4.4.2, the behavior of \code{bake} and \code{stew} changed.
##' In particular, older versions did no dependency checking, and did not check to see whether \code{expr} had changed.
##' Accordingly, the archive files written by older versions have a format that is not compat
gitextract_mv8sofvg/
├── .Rbuildignore
├── .Rprofile
├── .github/
│ ├── ISSUE_TEMPLATE/
│ │ ├── bug_report.md
│ │ └── feature_request.md
│ └── workflows/
│ ├── binary-build.yml
│ ├── r-cmd-check.yml
│ └── test-coverage.yml
├── .gitignore
├── BUILD.md
├── CRAN.md
├── DESCRIPTION
├── Doxyfile
├── LICENSE.md
├── Makefile
├── NAMESPACE
├── R/
│ ├── abc.R
│ ├── accumulators.R
│ ├── as_data_frame.R
│ ├── as_pomp.R
│ ├── bake.R
│ ├── basic_components.R
│ ├── basic_probes.R
│ ├── betabinom.R
│ ├── blowflies.R
│ ├── bsflu.R
│ ├── bsmc2.R
│ ├── bsplines.R
│ ├── builder.R
│ ├── childhood.R
│ ├── coef.R
│ ├── conc.R
│ ├── concat.R
│ ├── cond_logLik.R
│ ├── continue.R
│ ├── covariate_table.R
│ ├── covmat.R
│ ├── csnippet.R
│ ├── dacca.R
│ ├── design.R
│ ├── dinit_spec.R
│ ├── dmeasure_spec.R
│ ├── dprocess_spec.R
│ ├── ebola.R
│ ├── eff_sample_size.R
│ ├── elementary_algorithms.R
│ ├── emeasure_spec.R
│ ├── estimation_algorithms.R
│ ├── eulermultinom.R
│ ├── extract.R
│ ├── filter_mean.R
│ ├── filter_traj.R
│ ├── flow.R
│ ├── forecast.R
│ ├── gompertz.R
│ ├── kalman.R
│ ├── kf.R
│ ├── listie.R
│ ├── load.R
│ ├── loglik.R
│ ├── logmeanexp.R
│ ├── lookup.R
│ ├── mcap.R
│ ├── melt.R
│ ├── mif2.R
│ ├── nlf.R
│ ├── objfun.R
│ ├── obs.R
│ ├── ou2.R
│ ├── package.R
│ ├── parameter_trans.R
│ ├── parmat.R
│ ├── parus.R
│ ├── pfilter.R
│ ├── plot.R
│ ├── pmcmc.R
│ ├── pomp.R
│ ├── pomp_class.R
│ ├── pomp_examp.R
│ ├── pomp_fun.R
│ ├── pred_mean.R
│ ├── pred_var.R
│ ├── print.R
│ ├── prior_spec.R
│ ├── probe.R
│ ├── probe_match.R
│ ├── profile_design.R
│ ├── proposals.R
│ ├── pstop.R
│ ├── resample.R
│ ├── ricker.R
│ ├── rinit_spec.R
│ ├── rmeasure_spec.R
│ ├── rprocess_spec.R
│ ├── runif_design.R
│ ├── rw2.R
│ ├── safecall.R
│ ├── sannbox.R
│ ├── saved_states.R
│ ├── show.R
│ ├── simulate.R
│ ├── sir.R
│ ├── skeleton_spec.R
│ ├── slice_design.R
│ ├── sobol_design.R
│ ├── spect.R
│ ├── spect_match.R
│ ├── spy.R
│ ├── states.R
│ ├── summary.R
│ ├── templates.R
│ ├── time.R
│ ├── timezero.R
│ ├── traces.R
│ ├── traj_match.R
│ ├── trajectory.R
│ ├── transformations.R
│ ├── undefined.R
│ ├── userdata.R
│ ├── verhulst.R
│ ├── vmeasure_spec.R
│ ├── window.R
│ ├── workhorses.R
│ ├── wpfilter.R
│ └── wquant.R
├── README.md
├── TODO.md
├── codecov.yml
├── data/
│ ├── LondonYorke.rda
│ ├── blowflies.csv
│ ├── bsflu.rda
│ ├── ebolaWA2014.rda
│ ├── ewcitmeas.rda
│ ├── ewmeas.rda
│ └── parus.csv
├── examples/
│ ├── accumulators.R
│ ├── bake.R
│ ├── bsflu.R
│ ├── concat.R
│ ├── dacca.R
│ ├── design.R
│ ├── dmeasure_spec.R
│ ├── ebola.R
│ ├── eulermultinom.R
│ ├── kf.R
│ ├── logmeanexp.R
│ ├── nlf.R
│ ├── ou2.R
│ ├── parus.R
│ ├── pfilter.R
│ ├── pmcmc.R
│ ├── prior_spec.R
│ ├── probe_match.R
│ ├── ricker-bifdiag.R
│ ├── ricker.R
│ ├── rinit_spec.R
│ ├── rmeasure_spec.R
│ ├── rw2.R
│ ├── sir.R
│ ├── skeleton_spec.R
│ ├── spect_match.R
│ ├── spy.R
│ ├── traj_match.R
│ ├── trajectory.R
│ ├── userdata.R
│ └── verhulst.R
├── inst/
│ ├── CITATION
│ ├── GPL
│ ├── NEWS
│ ├── NEWS.Rd
│ ├── doc/
│ │ ├── Makefile
│ │ ├── index.html
│ │ └── index.md
│ └── include/
│ ├── pomp.h
│ └── pomp_defines.h
├── man/
│ ├── abc.Rd
│ ├── accumvars.Rd
│ ├── as_data_frame.Rd
│ ├── as_pomp.Rd
│ ├── bake.Rd
│ ├── basic_components.Rd
│ ├── basic_probes.Rd
│ ├── betabinom.Rd
│ ├── blowflies.Rd
│ ├── bsflu.Rd
│ ├── bsmc2.Rd
│ ├── bsplines.Rd
│ ├── childhood.Rd
│ ├── coef.Rd
│ ├── conc.Rd
│ ├── concat.Rd
│ ├── cond_logLik.Rd
│ ├── continue.Rd
│ ├── covariate_table.Rd
│ ├── covmat.Rd
│ ├── csnippet.Rd
│ ├── dacca.Rd
│ ├── design.Rd
│ ├── dinit.Rd
│ ├── dinit_spec.Rd
│ ├── dmeasure.Rd
│ ├── dmeasure_spec.Rd
│ ├── dprior.Rd
│ ├── dprocess.Rd
│ ├── dprocess_spec.Rd
│ ├── ebola.Rd
│ ├── eff_sample_size.Rd
│ ├── elementary_algorithms.Rd
│ ├── emeasure.Rd
│ ├── emeasure_spec.Rd
│ ├── estimation_algorithms.Rd
│ ├── eulermultinom.Rd
│ ├── filter_mean.Rd
│ ├── filter_traj.Rd
│ ├── flow.Rd
│ ├── forecast.Rd
│ ├── gompertz.Rd
│ ├── hitch.Rd
│ ├── kalman.Rd
│ ├── kf.Rd
│ ├── listie.Rd
│ ├── load.Rd
│ ├── loglik.Rd
│ ├── logmeanexp.Rd
│ ├── lookup.Rd
│ ├── macros/
│ │ └── citations.Rd
│ ├── mcap.Rd
│ ├── melt.Rd
│ ├── mif2.Rd
│ ├── nlf.Rd
│ ├── objfun.Rd
│ ├── obs.Rd
│ ├── ou2.Rd
│ ├── pStop.Rd
│ ├── parameter_trans.Rd
│ ├── parmat.Rd
│ ├── partrans.Rd
│ ├── parus.Rd
│ ├── pfilter.Rd
│ ├── plot.Rd
│ ├── pmcmc.Rd
│ ├── pomp-package.Rd
│ ├── pomp.Rd
│ ├── pomp_class.Rd
│ ├── pomp_examp.Rd
│ ├── pomp_fun.Rd
│ ├── pred_mean.Rd
│ ├── pred_var.Rd
│ ├── print.Rd
│ ├── prior_spec.Rd
│ ├── probe.Rd
│ ├── probe_match.Rd
│ ├── proposals.Rd
│ ├── resample.Rd
│ ├── ricker.Rd
│ ├── rinit.Rd
│ ├── rinit_spec.Rd
│ ├── rmeasure.Rd
│ ├── rmeasure_spec.Rd
│ ├── roxygen/
│ │ └── meta.R
│ ├── rprior.Rd
│ ├── rprocess.Rd
│ ├── rprocess_spec.Rd
│ ├── rw2.Rd
│ ├── rw_sd.Rd
│ ├── sannbox.Rd
│ ├── saved_states.Rd
│ ├── show.Rd
│ ├── simulate.Rd
│ ├── sir.Rd
│ ├── skeleton.Rd
│ ├── skeleton_spec.Rd
│ ├── spect.Rd
│ ├── spect_match.Rd
│ ├── spy.Rd
│ ├── states.Rd
│ ├── summary.Rd
│ ├── time.Rd
│ ├── timezero.Rd
│ ├── traces.Rd
│ ├── traj_match.Rd
│ ├── trajectory.Rd
│ ├── transformations.Rd
│ ├── undefined.Rd
│ ├── userdata.Rd
│ ├── verhulst.Rd
│ ├── vmeasure.Rd
│ ├── vmeasure_spec.Rd
│ ├── window.Rd
│ ├── workhorses.Rd
│ ├── wpfilter.Rd
│ └── wquant.Rd
├── revdep/
│ ├── .gitignore
│ ├── Makefile
│ └── timings.tab
├── rules.mk
├── src/
│ ├── Makevars
│ ├── backports.h
│ ├── bspline.c
│ ├── decls.h
│ ├── dinit.c
│ ├── distributions.c
│ ├── dmeasure.c
│ ├── dprior.c
│ ├── dprocess.c
│ ├── emeasure.c
│ ├── euler.c
│ ├── gompertz.c
│ ├── init.c
│ ├── internal.h
│ ├── logmeanexp.c
│ ├── lookup_table.c
│ ├── mif2.c
│ ├── ou2.c
│ ├── partrans.c
│ ├── pfilter.c
│ ├── pomp.h
│ ├── pomp_defines.h
│ ├── pomp_fun.c
│ ├── pomp_mat.h
│ ├── probe.c
│ ├── probe_acf.c
│ ├── probe_marginal.c
│ ├── probe_nlar.c
│ ├── resample.c
│ ├── rinit.c
│ ├── rmeasure.c
│ ├── rprior.c
│ ├── rprocess.c
│ ├── simulate.c
│ ├── skeleton.c
│ ├── soboldata.h
│ ├── sobolseq.c
│ ├── ssa.c
│ ├── synth_lik.c
│ ├── trajectory.c
│ ├── transformations.c
│ ├── userdata.c
│ ├── vmeasure.c
│ └── wpfilter.c
├── tests/
│ ├── Makefile
│ ├── R_v_C.R
│ ├── R_v_C.Rout
│ ├── abc.R
│ ├── abc.Rout.save
│ ├── baddm.R
│ ├── baddm.Rout.save
│ ├── bake.R
│ ├── bake.Rout.save
│ ├── basic_probes.R
│ ├── basic_probes.Rout.save
│ ├── betabinom.R
│ ├── betabinom.Rout.save
│ ├── blowflies.R
│ ├── blowflies.Rout.save
│ ├── bsmc2.R
│ ├── bsmc2.Rout.save
│ ├── bsplines1.R
│ ├── bsplines1.Rout.save
│ ├── bsplines2.R
│ ├── bsplines2.Rout.save
│ ├── concat.R
│ ├── concat.Rout.save
│ ├── covmat.R
│ ├── covmat.Rout.save
│ ├── csnippet.R
│ ├── csnippet.Rout.save
│ ├── dacca.R
│ ├── dacca.Rout.save
│ ├── dinit.R
│ ├── dinit.Rout.save
│ ├── dp.R
│ ├── dp.Rout.save
│ ├── dprocess.R
│ ├── dprocess.Rout.save
│ ├── ebola.R
│ ├── ebola.Rout.save
│ ├── emeasure.R
│ ├── emeasure.Rout.save
│ ├── eulermultinom.R
│ ├── eulermultinom.Rout.save
│ ├── flow.R
│ ├── flow.Rout.save
│ ├── gillespie.R
│ ├── gillespie.Rout.save
│ ├── gompertz.R
│ ├── gompertz.Rout.save
│ ├── helpers.R
│ ├── helpers.Rout.save
│ ├── hitch.R
│ ├── hitch.Rout.save
│ ├── issue109.R
│ ├── issue109.Rout.save
│ ├── issue222.R
│ ├── issue222.Rout.save
│ ├── issue56.R
│ ├── issue56.Rout.save
│ ├── kalman.R
│ ├── kalman.Rout.save
│ ├── kalman2.R
│ ├── kalman2.Rout.save
│ ├── link.R
│ ├── link.Rout.save
│ ├── load.R
│ ├── load.Rout.save
│ ├── logmeanexp.R
│ ├── logmeanexp.Rout.save
│ ├── lookup.R
│ ├── lookup.Rout.save
│ ├── map.R
│ ├── map.Rout.save
│ ├── mcap.R
│ ├── mcap.Rout.save
│ ├── measure.R
│ ├── measure.Rout.save
│ ├── mif2.R
│ ├── mif2.Rout.save
│ ├── mif2_index.R
│ ├── mif2_index.Rout.save
│ ├── mif2_kf.R
│ ├── mif2_kf.Rout.save
│ ├── nlf.R
│ ├── nlf.Rout.save
│ ├── nullcases.R
│ ├── nullcases.Rout.save
│ ├── ou2.R
│ ├── ou2.Rout.save
│ ├── parmat.R
│ ├── parmat.Rout.save
│ ├── partrans.R
│ ├── partrans.Rout.save
│ ├── pfilter.R
│ ├── pfilter.Rout.save
│ ├── pfilter2.R
│ ├── pfilter2.Rout.save
│ ├── pmcmc.R
│ ├── pmcmc.Rout.save
│ ├── pomp.R
│ ├── pomp.Rout.save
│ ├── pomp_fun.R
│ ├── pomp_fun.Rout.save
│ ├── pomp_methods.R
│ ├── pomp_methods.Rout.save
│ ├── prior.R
│ ├── prior.Rout.save
│ ├── probe.R
│ ├── probe.Rout.save
│ ├── probe_match.R
│ ├── probe_match.Rout.save
│ ├── process.R
│ ├── process.Rout.save
│ ├── profile_design.R
│ ├── profile_design.Rout.save
│ ├── proposals.R
│ ├── proposals.Rout.save
│ ├── resample.R
│ ├── resample.Rout.save
│ ├── rgammawn.R
│ ├── rgammawn.Rout.save
│ ├── ricker.R
│ ├── ricker.Rout.save
│ ├── rinit.R
│ ├── rinit.Rout.save
│ ├── runif_design.R
│ ├── runif_design.Rout.save
│ ├── rw2.R
│ ├── rw2.Rout.save
│ ├── sannbox.R
│ ├── sannbox.Rout.save
│ ├── save.R
│ ├── save.Rout.save
│ ├── simulate.R
│ ├── simulate.Rout.save
│ ├── simulate_data_frame.R
│ ├── simulate_data_frame.Rout.save
│ ├── sir.R
│ ├── sir.Rout.save
│ ├── sir2.R
│ ├── sir2.Rout.save
│ ├── skeleton.R
│ ├── skeleton.Rout.save
│ ├── slice_design.R
│ ├── slice_design.Rout.save
│ ├── sobol.R
│ ├── sobol.Rout.save
│ ├── spect.R
│ ├── spect.Rout.save
│ ├── spect_match.R
│ ├── spect_match.Rout.save
│ ├── spy.R
│ ├── spy.Rout
│ ├── steps.R
│ ├── steps.Rout.save
│ ├── synlik.R
│ ├── synlik.Rout.save
│ ├── traj_match.R
│ ├── traj_match.Rout.save
│ ├── trajectory.R
│ ├── trajectory.Rout.save
│ ├── transformations.R
│ ├── transformations.Rout.save
│ ├── undefined.R
│ ├── undefined.Rout.save
│ ├── userdata.R
│ ├── userdata.Rout.save
│ ├── verhulst.R
│ ├── verhulst.Rout.save
│ ├── vmeasure.R
│ ├── vmeasure.Rout.save
│ ├── wpfilter.R
│ ├── wpfilter.Rout.save
│ ├── wquant.R
│ └── wquant.Rout.save
└── tools/
└── check.env
SYMBOL INDEX (234 symbols across 41 files)
FILE: inst/include/pomp.h
type SEXP (line 26) | typedef const SEXP get_userdata_t (const char *name);
function R_INLINE (line 109) | static R_INLINE
function R_INLINE (line 114) | static R_INLINE
function R_INLINE (line 119) | static R_INLINE
function R_INLINE (line 128) | static R_INLINE
function R_INLINE (line 156) | static R_INLINE
function R_INLINE (line 191) | static R_INLINE
function R_INLINE (line 233) | static R_INLINE
function R_INLINE (line 268) | static R_INLINE
function R_INLINE (line 278) | static R_INLINE
function R_INLINE (line 288) | static R_INLINE
function R_INLINE (line 297) | static R_INLINE
function R_INLINE (line 304) | static R_INLINE
function R_INLINE (line 311) | static R_INLINE
function R_INLINE (line 321) | static R_INLINE
function R_INLINE (line 329) | static R_INLINE
FILE: inst/include/pomp_defines.h
type pompfunmode (line 16) | typedef enum {undef=0,Rfun=1,native=2,regNative=3} pompfunmode;
type rprocmode (line 17) | typedef enum {dflt=0,onestep=1,discrete=2,euler=3,gill=4} rprocmode;
type lookup_table_t (line 20) | typedef struct {
type SEXP (line 28) | typedef SEXP pomp_fun_handler_t (SEXP pfun, SEXP gnsi, pompfunmode *mode...
type SEXP (line 29) | typedef SEXP load_stack_incr_t (SEXP pack);
type SEXP (line 30) | typedef SEXP load_stack_decr_t (SEXP pack);
type lookup_table_t (line 31) | typedef lookup_table_t make_covariate_table_t (SEXP object, int *ncovar);
type SEXP (line 33) | typedef SEXP apply_probe_data_t (SEXP object, SEXP probes);
type SEXP (line 34) | typedef SEXP apply_probe_sim_t (SEXP object, SEXP nsim, SEXP params, SEX...
type SEXP (line 35) | typedef SEXP systematic_resampling_t (SEXP weights);
type SEXP (line 38) | typedef SEXP get_covariate_names_t (SEXP object);
function R_INLINE (line 40) | static R_INLINE SEXP makearray (int rank, const int *dim) {
function R_INLINE (line 55) | static R_INLINE int invalid_names (SEXP names) {
function R_INLINE (line 59) | static R_INLINE SEXP matchnames
function R_INLINE (line 87) | static R_INLINE void fillrownames (SEXP x, SEXP names) {
function R_INLINE (line 110) | static R_INLINE void setrownames (SEXP x, SEXP names, int rank) {
function R_INLINE (line 121) | static R_INLINE void setcolnames (SEXP x, SEXP names) {
function R_INLINE (line 129) | static R_INLINE void fixdimnames (SEXP x, const char **names, int n) {
function R_INLINE (line 145) | static R_INLINE SEXP as_matrix (SEXP x) {
function R_INLINE (line 183) | static R_INLINE SEXP as_state_array (SEXP x) {
function R_INLINE (line 232) | static R_INLINE SEXP getListElement (SEXP list, const char *str)
function R_INLINE (line 244) | static R_INLINE SEXP getPairListElement (SEXP list, const char *name)
function Scalar (line 279) | inline Scalar& operator () (int d1) {
function Scalar (line 282) | inline Scalar& operator () (int d1, int d2) {
function Scalar (line 285) | inline Scalar& operator () (int d1, int d2, int d3) {
FILE: src/bspline.c
function bspline_eval (line 9) | static void bspline_eval
function SEXP (line 51) | SEXP bspline_basis (SEXP range, SEXP x, SEXP nbasis, SEXP degree, SEXP d...
function SEXP (line 85) | SEXP periodic_bspline_basis (SEXP x, SEXP nbasis, SEXP degree, SEXP period,
function bspline_basis_eval_deriv (line 115) | void bspline_basis_eval_deriv (double x, double *knots, int degree,
function periodic_bspline_basis_eval_deriv (line 122) | void periodic_bspline_basis_eval_deriv (double x, double period, int deg...
FILE: src/dinit.c
function R_INLINE (line 10) | static R_INLINE SEXP add_args
function R_INLINE (line 59) | static R_INLINE SEXP eval_call
function R_INLINE (line 86) | static R_INLINE SEXP ret_array (int nreps)
function SEXP (line 97) | static SEXP init_density
function SEXP (line 220) | SEXP do_dinit
FILE: src/distributions.c
function reulermultinom_multi (line 7) | static void reulermultinom_multi (int m, int n, double *size, double *ra...
function deulermultinom_multi (line 15) | static void deulermultinom_multi (int m, int n, double *size, double *ra...
function SEXP (line 23) | SEXP R_Euler_Multinom (SEXP n, SEXP size, SEXP rate, SEXP deltat) {
function SEXP (line 49) | SEXP D_Euler_Multinom (SEXP x, SEXP size, SEXP rate, SEXP deltat, SEXP l...
function SEXP (line 71) | SEXP E_Euler_Multinom (SEXP size, SEXP rate, SEXP deltat) {
function SEXP (line 93) | SEXP R_GammaWN (SEXP n, SEXP sigma, SEXP deltat) {
function SEXP (line 119) | SEXP R_BetaBinom (SEXP n, SEXP size, SEXP prob, SEXP theta) {
function SEXP (line 137) | SEXP D_BetaBinom (SEXP x, SEXP size, SEXP prob, SEXP theta, SEXP log) {
FILE: src/dmeasure.c
function R_INLINE (line 10) | static R_INLINE SEXP add_args
function R_INLINE (line 75) | static R_INLINE SEXP eval_call (
function R_INLINE (line 101) | static R_INLINE SEXP ret_array (int nreps, int ntimes) {
function SEXP (line 111) | SEXP do_dmeasure (SEXP object, SEXP y, SEXP x, SEXP times, SEXP params, ...
FILE: src/dprior.c
function R_INLINE (line 10) | static R_INLINE SEXP add_args (SEXP names, SEXP log, SEXP args)
function R_INLINE (line 34) | static R_INLINE SEXP eval_call (SEXP fn, SEXP args, double *p, int n)
function SEXP (line 51) | SEXP do_dprior (SEXP object, SEXP params, SEXP log, SEXP gnsi)
FILE: src/dprocess.c
function R_INLINE (line 10) | static R_INLINE SEXP paste0 (SEXP a, SEXP b) {
function R_INLINE (line 18) | static R_INLINE SEXP add_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP...
function R_INLINE (line 86) | static R_INLINE SEXP eval_call
function R_INLINE (line 115) | static R_INLINE SEXP ret_array (int nreps, int ntimes)
function SEXP (line 127) | static SEXP onestep_density
function SEXP (line 273) | SEXP do_dprocess (SEXP object, SEXP x, SEXP times, SEXP params, SEXP log...
FILE: src/emeasure.c
function R_INLINE (line 10) | static R_INLINE SEXP add_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP...
function R_INLINE (line 60) | static R_INLINE SEXP eval_call (
function R_INLINE (line 84) | static R_INLINE SEXP ret_array (int n, int nreps, int ntimes, SEXP names) {
function SEXP (line 98) | SEXP do_emeasure (SEXP object, SEXP x, SEXP times, SEXP params, SEXP gnsi)
FILE: src/euler.c
function R_INLINE (line 10) | static R_INLINE SEXP add_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP...
function R_INLINE (line 67) | static R_INLINE SEXP eval_call (
function R_INLINE (line 92) | static R_INLINE SEXP ret_array (int n, int nreps, int ntimes, SEXP names)
function SEXP (line 107) | SEXP euler_simulator
function num_euler_steps (line 317) | int num_euler_steps (double t1, double t2, double *deltat) {
function num_map_steps (line 342) | int num_map_steps (double t1, double t2, double deltat) {
FILE: src/gompertz.c
function _gompertz_normal_dmeasure (line 20) | void _gompertz_normal_dmeasure
function _gompertz_normal_rmeasure (line 30) | void _gompertz_normal_rmeasure
function _gompertz_normal_emeasure (line 40) | void _gompertz_normal_emeasure
function _gompertz_normal_vmeasure (line 50) | void _gompertz_normal_vmeasure (double *f, double *x, double *p,
function _gompertz_step (line 58) | void _gompertz_step
function _gompertz_skeleton (line 70) | void _gompertz_skeleton
function _gompertz_to_trans (line 102) | void _gompertz_to_trans
function _gompertz_from_trans (line 113) | void _gompertz_from_trans
FILE: src/init.c
function R_init_pomp (line 54) | void R_init_pomp (DllInfo *info) {
FILE: src/logmeanexp.c
function SEXP (line 7) | SEXP logmeanexp (const SEXP X, const SEXP Drop) {
FILE: src/lookup_table.c
function SEXP (line 7) | SEXP get_covariate_names (SEXP object) {
function lookup_table_t (line 11) | lookup_table_t make_covariate_table (SEXP object, int *ncovar) {
function SEXP (line 24) | SEXP lookup_in_table (SEXP covar, SEXP t) {
function table_lookup (line 53) | void table_lookup (lookup_table_t *tab, double x, double *y)
FILE: src/mif2.c
function SEXP (line 6) | SEXP randwalk_perturbation (SEXP params, SEXP rw_sd)
FILE: src/ou2.c
function sim_ou2 (line 9) | static void sim_ou2
function dens_ou2 (line 29) | static double dens_ou2
function _ou2_step (line 71) | void _ou2_step
function _ou2_pdf (line 82) | void _ou2_pdf
function _ou2_skel (line 95) | void _ou2_skel
function _ou2_dmeasure (line 106) | void _ou2_dmeasure
function _ou2_rmeasure (line 120) | void _ou2_rmeasure
function _ou2_emeasure (line 132) | void _ou2_emeasure
function _ou2_vmeasure (line 143) | void _ou2_vmeasure
FILE: src/partrans.c
type direction_t (line 10) | typedef enum {to = 1, from = -1} direction_t;
function R_INLINE (line 12) | static R_INLINE SEXP add_args (SEXP args, SEXP names)
function R_INLINE (line 33) | static R_INLINE SEXP eval_call (SEXP fn, SEXP args, double *p, int n)
function SEXP (line 49) | SEXP do_partrans (SEXP object, SEXP params, SEXP dir, SEXP gnsi)
FILE: src/pfilter.c
function SEXP (line 16) | SEXP pfilter (SEXP x, SEXP params, SEXP Np,
function pred_mean_var (line 266) | static void pred_mean_var (int nvars, int nreps, int do_pv,
function filt_mean (line 294) | static void filt_mean (int nvars, int nreps, int all_fail, long double w...
FILE: src/pomp.h
type SEXP (line 34) | typedef const SEXP get_userdata_t (const char *name);
function R_INLINE (line 117) | static R_INLINE
function R_INLINE (line 122) | static R_INLINE
function R_INLINE (line 127) | static R_INLINE
function R_INLINE (line 136) | static R_INLINE
function R_INLINE (line 164) | static R_INLINE
function R_INLINE (line 199) | static R_INLINE
function R_INLINE (line 241) | static R_INLINE
function R_INLINE (line 276) | static R_INLINE
function R_INLINE (line 286) | static R_INLINE
function R_INLINE (line 296) | static R_INLINE
function R_INLINE (line 305) | static R_INLINE
function R_INLINE (line 312) | static R_INLINE
function R_INLINE (line 319) | static R_INLINE
function R_INLINE (line 329) | static R_INLINE
function R_INLINE (line 337) | static R_INLINE
FILE: src/pomp_defines.h
type pompfunmode (line 16) | typedef enum {undef=0,Rfun=1,native=2,regNative=3} pompfunmode;
type rprocmode (line 17) | typedef enum {dflt=0,onestep=1,discrete=2,euler=3,gill=4} rprocmode;
type lookup_table_t (line 20) | typedef struct {
type SEXP (line 28) | typedef SEXP pomp_fun_handler_t (SEXP pfun, SEXP gnsi, pompfunmode *mode...
type SEXP (line 29) | typedef SEXP load_stack_incr_t (SEXP pack);
type SEXP (line 30) | typedef SEXP load_stack_decr_t (SEXP pack);
type lookup_table_t (line 31) | typedef lookup_table_t make_covariate_table_t (SEXP object, int *ncovar);
type SEXP (line 33) | typedef SEXP apply_probe_data_t (SEXP object, SEXP probes);
type SEXP (line 34) | typedef SEXP apply_probe_sim_t (SEXP object, SEXP nsim, SEXP params, SEX...
type SEXP (line 35) | typedef SEXP systematic_resampling_t (SEXP weights);
type SEXP (line 38) | typedef SEXP get_covariate_names_t (SEXP object);
function R_INLINE (line 40) | static R_INLINE SEXP makearray (int rank, const int *dim) {
function R_INLINE (line 55) | static R_INLINE int invalid_names (SEXP names) {
function R_INLINE (line 59) | static R_INLINE SEXP matchnames
function R_INLINE (line 87) | static R_INLINE void fillrownames (SEXP x, SEXP names) {
function R_INLINE (line 110) | static R_INLINE void setrownames (SEXP x, SEXP names, int rank) {
function R_INLINE (line 121) | static R_INLINE void setcolnames (SEXP x, SEXP names) {
function R_INLINE (line 129) | static R_INLINE void fixdimnames (SEXP x, const char **names, int n) {
function R_INLINE (line 145) | static R_INLINE SEXP as_matrix (SEXP x) {
function R_INLINE (line 183) | static R_INLINE SEXP as_state_array (SEXP x) {
function R_INLINE (line 232) | static R_INLINE SEXP getListElement (SEXP list, const char *str)
function R_INLINE (line 244) | static R_INLINE SEXP getPairListElement (SEXP list, const char *name)
function Scalar (line 279) | inline Scalar& operator () (int d1) {
function Scalar (line 282) | inline Scalar& operator () (int d1, int d2) {
function Scalar (line 285) | inline Scalar& operator () (int d1, int d2, int d3) {
FILE: src/pomp_fun.c
function R_INLINE (line 10) | static R_INLINE SEXP name_index (SEXP provided, SEXP object, const char ...
function SEXP (line 30) | SEXP pomp_fun_handler (SEXP pfun, SEXP gnsi, pompfunmode *mode,
function SEXP (line 121) | SEXP load_stack_incr (SEXP pack) {
function SEXP (line 130) | SEXP load_stack_decr (SEXP pack) {
FILE: src/pomp_mat.h
function R_INLINE (line 11) | static R_INLINE void pomp_backsolve
function R_INLINE (line 27) | static R_INLINE void pomp_qr
function R_INLINE (line 46) | static R_INLINE void pomp_qrqy
FILE: src/probe.c
function SEXP (line 4) | SEXP apply_probe_data (SEXP object, SEXP probes) {
function SEXP (line 29) | SEXP apply_probe_sim (SEXP object, SEXP nsim, SEXP params,
FILE: src/probe_acf.c
function pomp_acf_compute (line 11) | static void pomp_acf_compute (double *acf, double *x, int n, int nvars, ...
function pomp_ccf_compute (line 47) | static void pomp_ccf_compute (double *ccf, double *x, double *y, int n, ...
function SEXP (line 100) | SEXP probe_acf (SEXP x, SEXP lags, SEXP corr) {
function SEXP (line 145) | SEXP probe_ccf (SEXP x, SEXP y, SEXP lags, SEXP corr) {
FILE: src/probe_marginal.c
function SEXP (line 10) | SEXP probe_marginal_setup (SEXP ref, SEXP order, SEXP diff) {
function SEXP (line 43) | SEXP probe_marginal_solve (SEXP x, SEXP setup, SEXP diff) {
function order_reg_model_matrix (line 78) | static void order_reg_model_matrix (double *z, double *X, double *tau, i...
function order_reg_solve (line 117) | static void order_reg_solve (double *beta, double *x, double *mm, double...
FILE: src/probe_nlar.c
function SEXP (line 9) | SEXP probe_nlar (SEXP x, SEXP lags, SEXP powers) {
function poly_nlar_fit (line 39) | static void poly_nlar_fit (double *beta, double *y, int n,
FILE: src/resample.c
function SEXP (line 9) | SEXP systematic_resampling (SEXP weights, SEXP np)
function nosort_resamp (line 25) | void nosort_resamp (int nw, double *w, int np, int *p, int offset)
FILE: src/rinit.c
function R_INLINE (line 10) | static R_INLINE SEXP paste0 (SEXP a, SEXP b, SEXP c) {
function R_INLINE (line 21) | static R_INLINE SEXP add_args (SEXP args, SEXP Pnames, SEXP Cnames)
function R_INLINE (line 58) | static R_INLINE SEXP eval_call
function R_INLINE (line 79) | static R_INLINE SEXP ret_array (int m, int n, SEXP names)
function SEXP (line 91) | SEXP do_rinit (SEXP object, SEXP params, SEXP t0, SEXP nsim, SEXP gnsi)
function SEXP (line 254) | static SEXP pomp_default_rinit (SEXP params, SEXP Pnames,
FILE: src/rmeasure.c
function R_INLINE (line 10) | static R_INLINE SEXP add_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP...
function R_INLINE (line 60) | static R_INLINE SEXP eval_call (
function R_INLINE (line 84) | static R_INLINE SEXP ret_array (int n, int nreps, int ntimes, SEXP names) {
function SEXP (line 98) | SEXP do_rmeasure (SEXP object, SEXP x, SEXP times, SEXP params, SEXP gnsi)
FILE: src/rprior.c
function R_INLINE (line 10) | static R_INLINE SEXP add_args (SEXP args, SEXP names)
function R_INLINE (line 31) | static R_INLINE SEXP eval_call (SEXP fn, SEXP args, double *p, int n)
function R_INLINE (line 47) | static R_INLINE SEXP ret_array (SEXP params)
function SEXP (line 58) | SEXP do_rprior (SEXP object, SEXP params, SEXP gnsi)
FILE: src/rprocess.c
function SEXP (line 10) | static SEXP pomp_default_rprocess (SEXP xstart, int nvars, int nreps, in...
function SEXP (line 25) | SEXP do_rprocess (SEXP object, SEXP xstart, SEXP tstart, SEXP times, SEX...
FILE: src/simulate.c
function SEXP (line 6) | SEXP do_simulate (SEXP object, SEXP params, SEXP nsim, SEXP rettype, SEX...
FILE: src/skeleton.c
function SEXP (line 10) | SEXP add_skel_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP Cnames)
function R_INLINE (line 57) | static R_INLINE SEXP eval_call (
function R_INLINE (line 81) | static R_INLINE SEXP ret_array (int nvars, int nreps, int ntimes, SEXP S...
function eval_skeleton_R (line 93) | void eval_skeleton_R
function iterate_skeleton_R (line 161) | void iterate_skeleton_R (
function eval_skeleton_native (line 245) | void eval_skeleton_native (
function iterate_skeleton_native (line 274) | void iterate_skeleton_native (
function SEXP (line 326) | SEXP do_skeleton (SEXP object, SEXP x, SEXP t, SEXP params, SEXP gnsi)
FILE: src/sobolseq.c
type Int32 (line 59) | typedef Int32 uint32_t;
type nlopt_soboldata_s (line 60) | struct nlopt_soboldata_s
type soboldata (line 65) | typedef struct nlopt_soboldata_s {
function rightzero32 (line 84) | static unsigned rightzero32 (uint32_t n)
function sobol_gen (line 96) | static int sobol_gen (soboldata *sd, double *x)
function sobol_init (line 122) | static int sobol_init (soboldata *sd, unsigned sdim)
function sobol_destroy (line 177) | static void sobol_destroy (soboldata *sd)
function nlopt_sobol (line 188) | static nlopt_sobol nlopt_sobol_create (unsigned sdim)
function nlopt_sobol_destroy (line 196) | static void nlopt_sobol_destroy (nlopt_sobol s)
function nlopt_sobol_skip (line 225) | static void nlopt_sobol_skip(nlopt_sobol s, unsigned n, double *x)
function SEXP (line 234) | SEXP sobol_sequence (SEXP dim, SEXP length)
FILE: src/ssa.c
function R_INLINE (line 9) | static R_INLINE SEXP add_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP...
function gillespie (line 66) | static void gillespie (double *t, double tmax, double *f, double *y,
function SSA (line 118) | static void SSA (pomp_ssa_rate_fn *ratefun, int irep,
function __pomp_Rfun_ssa_ratefn (line 199) | static double __pomp_Rfun_ssa_ratefn (int j, double t, const double *x, ...
function SEXP (line 226) | SEXP SSA_simulator (SEXP func, SEXP xstart, SEXP tstart, SEXP times, SEX...
FILE: src/synth_lik.c
function robust_synth_loglik (line 11) | static void robust_synth_loglik (double *y, int *dim, double *ydat, doub...
function SEXP (line 104) | SEXP synth_loglik (SEXP ysim, SEXP ydat) {
FILE: src/trajectory.c
function R_INLINE (line 6) | static R_INLINE SEXP ret_array (int nvars, int nreps, int ntimes, SEXP S...
function SEXP (line 19) | SEXP iterate_map (SEXP object, SEXP times, SEXP t0, SEXP x0, SEXP params...
function SEXP (line 156) | SEXP pomp_desolve_setup (SEXP object, SEXP x0, SEXP params, SEXP gnsi) {
function pomp_vf_eval (line 260) | void pomp_vf_eval (int *neq, double *t, double *y, double *ydot, double ...
function SEXP (line 292) | SEXP pomp_desolve_takedown (void) {
FILE: src/transformations.c
function SEXP (line 14) | SEXP LogitTransform (SEXP P) {
function SEXP (line 26) | SEXP ExpitTransform (SEXP X) {
function SEXP (line 38) | SEXP LogBarycentricTransform (SEXP X) {
function SEXP (line 47) | SEXP InverseLogBarycentricTransform (SEXP Y) {
FILE: src/userdata.c
function SEXP (line 8) | SEXP set_pomp_userdata (SEXP userdata) {
function SEXP (line 13) | const SEXP get_userdata (const char *name) {
FILE: src/vmeasure.c
function R_INLINE (line 10) | static R_INLINE SEXP add_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP...
function R_INLINE (line 60) | static R_INLINE SEXP eval_call (
function R_INLINE (line 84) | static R_INLINE SEXP ret_array (int n, int nreps, int ntimes, SEXP names) {
function SEXP (line 99) | SEXP do_vmeasure (SEXP object, SEXP x, SEXP times, SEXP params, SEXP gnsi)
FILE: src/wpfilter.c
function SEXP (line 10) | SEXP wpfilter (SEXP X, SEXP Params, SEXP Weights, SEXP W, SEXP Trigger, ...
Condensed preview — 513 files, each showing path, character count, and a content snippet. Download the .json file or copy for the full structured content (2,341K chars).
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"preview": "Package: pomp\nType: Package\nTitle: Statistical Inference for Partially Observed Markov Processes\nVersion: 6.4.0.0\nDate: "
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"preview": "##' Tools for reproducible computations\n##'\n##' Archiving of computations and control of the random-number generator.\n##"
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"preview": "##' Basic POMP model components.\n##'\n##' Mathematically, the parts of a \\acronym{POMP} model include the latent-state pr"
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"chars": 7032,
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"preview": "##' Nicholson's blowflies.\n##'\n##' \\code{blowflies} is a data frame containing the data from several of Nicholson's clas"
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"preview": "##' The Liu and West Bayesian particle filter\n##'\n##' Modified version of the Liu & West (2001) algorithm.\n##'\n##' \\code"
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"preview": "##' B-spline bases\n##'\n##' These functions generate B-spline basis functions.\n##' \\code{bspline_basis} gives a basis of "
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"chars": 2112,
"preview": "##' Historical childhood disease incidence data\n##'\n##' @description\n##' \\code{LondonYorke} is a data frame containing t"
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"preview": "##' Extract, set, or alter coefficients\n##'\n##' Extract, set, or modify the estimated parameters from a fitted model.\n##"
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"path": "R/ou2.R",
"chars": 2284,
"preview": "##' Two-dimensional discrete-time Ornstein-Uhlenbeck process\n##'\n##' \\code{ou2()} constructs a \\sQuote{pomp} object enco"
},
{
"path": "R/package.R",
"chars": 5196,
"preview": "##' Inference for partially observed Markov processes\n##'\n##' The \\pkg{pomp} package provides facilities for inference o"
},
{
"path": "R/parameter_trans.R",
"chars": 9227,
"preview": "##' parameter transformations\n##'\n##' Equipping models with parameter transformations to facilitate searches in constrai"
},
{
"path": "R/parmat.R",
"chars": 3108,
"preview": "##' Create a matrix of parameters\n##'\n##' \\code{parmat} is a utility that makes a vector of parameters suitable for\n##' "
},
{
"path": "R/parus.R",
"chars": 589,
"preview": "##' Parus major population dynamics\n##'\n##' Size of a population of great tits (\\emph{Parus major}) from Wytham Wood, ne"
},
{
"path": "R/pfilter.R",
"chars": 14431,
"preview": "##' Particle filter\n##'\n##' A plain vanilla sequential Monte Carlo (particle filter) algorithm.\n##' Resampling is perfor"
},
{
"path": "R/plot.R",
"chars": 15494,
"preview": "##' pomp plotting facilities\n##'\n##' Diagnostic plots.\n##'\n##' @name plot\n##' @rdname plot\n##' @include pomp_class.R\n##'"
},
{
"path": "R/pmcmc.R",
"chars": 10200,
"preview": "##' The particle Markov chain Metropolis-Hastings algorithm\n##'\n##' The Particle MCMC algorithm for estimating the param"
},
{
"path": "R/pomp.R",
"chars": 25450,
"preview": "##' Constructor of the basic pomp object\n##'\n##' This function constructs a \\sQuote{pomp} object, encoding a partially-o"
},
{
"path": "R/pomp_class.R",
"chars": 2930,
"preview": "##' The basic pomp class\n##'\n##' The basic class implementing a \\acronym{POMP} model with data\n##'\n##' @rdname pomp_clas"
},
{
"path": "R/pomp_examp.R",
"chars": 2510,
"preview": "##' pre-built pomp examples\n##'\n##' Examples of pomp objects containing models and data.\n##'\n##' @name pomp_examples\n##'"
},
{
"path": "R/pomp_fun.R",
"chars": 4909,
"preview": "##' The \"pomp_fun\" class\n##'\n##' Definition and methods of the \\sQuote{pomp_fun} class.\n##'\n##' The \\sQuote{pomp_fun} cl"
},
{
"path": "R/pred_mean.R",
"chars": 2172,
"preview": "##' Prediction mean\n##'\n##' The mean of the prediction distribution\n##'\n##' The prediction distribution is that of\n##' \\"
},
{
"path": "R/pred_var.R",
"chars": 1686,
"preview": "##' Prediction variance\n##'\n##' The variance of the prediction distribution\n##'\n##' The prediction distribution is that "
},
{
"path": "R/print.R",
"chars": 687,
"preview": "##' Print methods\n##'\n##' These methods print their argument and return it *invisibly*.\n##'\n##' @name print\n##' @rdname "
},
{
"path": "R/prior_spec.R",
"chars": 2755,
"preview": "##' prior specification\n##'\n##' Specification of prior distributions via the rprior and dprior components.\n##'\n##' @name"
},
{
"path": "R/probe.R",
"chars": 7774,
"preview": "##' Probes (AKA summary statistics)\n##'\n##' Probe a partially-observed Markov process by computing summary statistics\n##"
},
{
"path": "R/probe_match.R",
"chars": 7961,
"preview": "##' Probe matching\n##'\n##' Estimation of parameters by maximum synthetic likelihood\n##'\n##' In probe-matching, one attem"
},
{
"path": "R/profile_design.R",
"chars": 1549,
"preview": "##' @description\n##' \\code{profile_design} generates a data-frame where each row can be used as the starting point for a"
},
{
"path": "R/proposals.R",
"chars": 6050,
"preview": "##' MCMC proposal distributions\n##'\n##' Functions to construct proposal distributions for use with MCMC methods.\n##'\n##'"
},
{
"path": "R/pstop.R",
"chars": 1994,
"preview": "##' pStop, pWarn, pMess\n##'\n##' Custom error, warning, and message functions.\n##' @name pStop\n##' @rdname pStop\n##' @key"
},
{
"path": "R/resample.R",
"chars": 507,
"preview": "##' Resample\n##'\n##' Systematic resampling.\n##'\n##' @return\n##' A vector of integers containing the indices of the resam"
},
{
"path": "R/ricker.R",
"chars": 2290,
"preview": "##' Ricker model with Poisson observations.\n##'\n##' \\code{ricker} is a \\sQuote{pomp} object encoding a stochastic Ricker"
},
{
"path": "R/rinit_spec.R",
"chars": 2611,
"preview": "##' rinit specification\n##'\n##' Specification of the initial-state distribution simulator, rinit.\n##'\n##' @name rinit_sp"
},
{
"path": "R/rmeasure_spec.R",
"chars": 2258,
"preview": "##' rmeasure specification\n##'\n##' Specification of the measurement-model simulator, rmeasure.\n##'\n##' @name rmeasure_sp"
},
{
"path": "R/rprocess_spec.R",
"chars": 15193,
"preview": "##' rprocess specification\n##'\n##' Specification of the latent state process simulator, rprocess.\n##'\n##' @name rprocess"
},
{
"path": "R/runif_design.R",
"chars": 1116,
"preview": "##' @description\n##' \\code{runif_design} generates a design based on random samples from a multivariate uniform distribu"
},
{
"path": "R/rw2.R",
"chars": 1733,
"preview": "##' Two-dimensional random-walk process\n##'\n##' \\code{rw2} constructs a \\sQuote{pomp} object encoding a 2-D Gaussian ran"
},
{
"path": "R/safecall.R",
"chars": 276,
"preview": "## a class to hold unevaluated function calls\n\nsetClass(\n \"safecall\",\n slots=c(\n call=\"call\",\n envir=\"environmen"
},
{
"path": "R/sannbox.R",
"chars": 7519,
"preview": "##' Simulated annealing with box constraints.\n##'\n##' A straightforward implementation of simulated annealing with box c"
},
{
"path": "R/saved_states.R",
"chars": 3794,
"preview": "##' Saved states\n##'\n##' Retrieve latent state trajectories from a particle filter calculation.\n##'\n##' When one calls \\"
},
{
"path": "R/show.R",
"chars": 5007,
"preview": "##' Show methods\n##'\n##' Display the object, according to its class.\n##'\n##' @name show\n##' @rdname show\n##' @docType me"
},
{
"path": "R/simulate.R",
"chars": 7942,
"preview": "##' Simulations of a partially-observed Markov process\n##'\n##' \\code{simulate} generates simulations of the state and me"
},
{
"path": "R/sir.R",
"chars": 9464,
"preview": "##' Compartmental epidemiological models\n##'\n##' Simple SIR-type models implemented in various ways.\n##'\n##' \\code{sir()"
},
{
"path": "R/skeleton_spec.R",
"chars": 5414,
"preview": "##' skeleton specification\n##'\n##' Specification of the deterministic skeleton.\n##'\n##' @name skeleton_spec\n##' @rdname "
},
{
"path": "R/slice_design.R",
"chars": 1481,
"preview": "##' @description\n##' \\code{slice_design} generates points along slices through a specified point.\n##' @rdname design\n##'"
},
{
"path": "R/sobol_design.R",
"chars": 1733,
"preview": "##' @description\n##' \\code{sobol_design} generates a Latin hypercube design based on the Sobol' low-discrepancy sequence"
},
{
"path": "R/spect.R",
"chars": 10445,
"preview": "##' Power spectrum\n##'\n##' Power spectrum computation and spectrum-matching for partially-observed\n##' Markov processes."
},
{
"path": "R/spect_match.R",
"chars": 10160,
"preview": "##' Spectrum matching\n##'\n##' Estimation of parameters by matching power spectra\n##'\n##' In spectrum matching, one attem"
},
{
"path": "R/spy.R",
"chars": 3229,
"preview": "##' Spy\n##'\n##' Peek into the inside of one of \\pkg{pomp}'s objects.\n##'\n##' @name spy\n##' @rdname spy\n##' @include pomp"
},
{
"path": "R/states.R",
"chars": 2013,
"preview": "##' Latent states\n##'\n##' Extract the latent states from a \\sQuote{pomp} object.\n##'\n##' @name states\n##' @aliases state"
},
{
"path": "R/summary.R",
"chars": 279,
"preview": "##' Summary methods\n##'\n##' Display a summary of a fitted model object.\n##'\n##' @name summary\n##' @rdname summary\n##' @p"
},
{
"path": "R/templates.R",
"chars": 12496,
"preview": "## default templates for pomp's own C snippets.\n## This is used in 'pomp.R' and 'builder.R'.\n\n## BASIC TEMPLATES\n\npomp_t"
},
{
"path": "R/time.R",
"chars": 3027,
"preview": "##' Methods to extract and manipulate the obseration times\n##'\n##' Get and set the vector of observation times.\n##'\n##' "
},
{
"path": "R/timezero.R",
"chars": 1402,
"preview": "##' The zero time\n##'\n##' Get and set the zero-time.\n##'\n##' @name timezero\n##' @rdname timezero\n##' @docType methods\n##"
},
{
"path": "R/traces.R",
"chars": 3925,
"preview": "##' Traces\n##'\n##' Retrieve the history of an iterative calculation.\n##'\n##' @name traces\n##' @rdname traces\n##' @aliase"
},
{
"path": "R/traj_match.R",
"chars": 6830,
"preview": "##' Trajectory matching\n##'\n##' Estimation of parameters for deterministic \\acronym{POMP} models via trajectory matching"
},
{
"path": "R/trajectory.R",
"chars": 6527,
"preview": "##' Trajectory of a deterministic model\n##'\n##' Compute trajectories of the deterministic skeleton of a Markov process.\n"
},
{
"path": "R/transformations.R",
"chars": 2502,
"preview": "##' Transformations\n##'\n##' Some useful parameter transformations.\n##'\n##' Parameter transformations can be used in many"
},
{
"path": "R/undefined.R",
"chars": 792,
"preview": "##' Undefined\n##'\n##' Check for undefined methods.\n##'\n##' @name undefined\n##' @rdname undefined\n##' @return\n##' Returns"
},
{
"path": "R/userdata.R",
"chars": 4488,
"preview": "##' Facilities for making additional information available to basic model components\n##'\n##' When \\acronym{POMP} basic c"
},
{
"path": "R/verhulst.R",
"chars": 2140,
"preview": "##' Verhulst-Pearl model\n##'\n##' The Verhulst-Pearl (logistic) model of population growth.\n##'\n##' A stochastic version "
},
{
"path": "R/vmeasure_spec.R",
"chars": 2524,
"preview": "##' vmeasure specification\n##'\n##' Specification of the measurement-model covariance matrix, vmeasure.\n##'\n##' @name vm"
},
{
"path": "R/window.R",
"chars": 1064,
"preview": "##' Window\n##'\n##' Restrict to a portion of a time series.\n##'\n##' @name window\n##' @docType methods\n##' @rdname window\n"
},
{
"path": "R/workhorses.R",
"chars": 24930,
"preview": "##' Workhorse functions for the \\pkg{pomp} algorithms.\n##'\n##' These functions mediate the interface between the user's "
},
{
"path": "R/wpfilter.R",
"chars": 5962,
"preview": "##' Weighted particle filter\n##'\n##' A sequential importance sampling (particle filter) algorithm.\n##' Unlike in \\code{p"
},
{
"path": "R/wquant.R",
"chars": 2186,
"preview": "##' Weighted quantile function\n##'\n##' Estimate weighted quantiles.\n##'\n##' \\code{wquant} estimates quantiles of weighte"
},
{
"path": "README.md",
"chars": 2702,
"preview": "# **pomp**\n\n## an *R* package for statistical inference on partially observed Markov processes\n\n[![Project Status: Activ"
},
{
"path": "TODO.md",
"chars": 3256,
"preview": "-------------\n\n# pomp to-do list\n\n## For pomp:\n\n- References using new bibtex support for Rd files.\n[R-exts.html#Bibliog"
},
{
"path": "codecov.yml",
"chars": 218,
"preview": "coverage:\n precision: 2\n round: nearest\n range: \"90...100\"\ncomment:\n layout: \"header, diff, changes, sunburst, uncov"
},
{
"path": "data/blowflies.csv",
"chars": 8931,
"preview": "day;count;set\n40;3721;1\n41;3373;1\n42;2880;1\n43;1805;1\n44;1195;1\n45;557;1\n46;267;1\n47;239;1\n48;182;1\n49;270;1\n50;300;1\n51"
},
{
"path": "data/parus.csv",
"chars": 817,
"preview": "## Parus major (Great Tit) census (all individuals)\n## Wytham Wood, Oxfordshire\n## Global Population Dynamics Database d"
},
{
"path": "examples/accumulators.R",
"chars": 3712,
"preview": "\\donttest{\n ## A simple SIR model.\n\n ewmeas |>\n subset(time < 1952) |>\n pomp(\n times=\"time\",t0=1948,\n "
},
{
"path": "examples/bake.R",
"chars": 543,
"preview": "\\dontrun{\n bake(file=\"example1.rds\",{\n x <- runif(1000)\n mean(x)\n })\n\n bake(file=\"example1.rds\",{\n x <- runi"
},
{
"path": "examples/bsflu.R",
"chars": 245,
"preview": "if (require(tidyr) && require(ggplot2)) {\n\n bsflu |>\n gather(variable,value,-date,-day) |>\n ggplot(aes(x=date,y=v"
},
{
"path": "examples/concat.R",
"chars": 208,
"preview": "gompertz(sigma=2,tau=1) -> g\nNp <- c(low=100,med=1000,high=10000)\nlapply(\n Np,\n \\(np) pfilter(g,Np=np)\n) |>\n concat()"
},
{
"path": "examples/dacca.R",
"chars": 115,
"preview": "\\donttest{ # takes too long for R CMD check\n po <- dacca()\n plot(po)\n ## MLE:\n coef(po)\n plot(simulate(po))\n}\n"
},
{
"path": "examples/design.R",
"chars": 912,
"preview": "## Sobol' low-discrepancy design\nplot(sobol_design(lower=c(a=0,b=100),upper=c(b=200,a=1),nseq=100))\n\n## Uniform random d"
},
{
"path": "examples/dmeasure_spec.R",
"chars": 645,
"preview": "\\donttest{\n ## We start with the pre-built Ricker example:\n ricker() -> po\n\n ## To change the measurement model densi"
},
{
"path": "examples/ebola.R",
"chars": 453,
"preview": "\\donttest{ # takes too long for R CMD check\n if (require(ggplot2) && require(tidyr)) {\n \n ebolaWA2014 |>\n pi"
},
{
"path": "examples/eulermultinom.R",
"chars": 513,
"preview": "## Simulate 5 realizations of Euler-multinomial random variable:\n\ndn <- reulermultinom(5,size=100,rate=c(a=1,b=2,c=3),dt"
},
{
"path": "examples/kf.R",
"chars": 409,
"preview": "if (require(dplyr)) {\n\n gompertz() -> po\n\n po |>\n as.data.frame() |>\n mutate(\n logY=log(Y)\n ) |>\n sel"
},
{
"path": "examples/logmeanexp.R",
"chars": 291,
"preview": "\\donttest{ # takes too long for R CMD check\n ## an estimate of the log likelihood:\n ricker() |>\n pfilter(Np=1000) |"
},
{
"path": "examples/nlf.R",
"chars": 391,
"preview": "\\donttest{\n\n if (require(subplex)) {\n\n ricker() |>\n nlf_objfun(est=c(\"r\",\"sigma\",\"N_0\"),lags=c(4,6),\n pa"
},
{
"path": "examples/ou2.R",
"chars": 93,
"preview": "po <- ou2()\nplot(po)\ncoef(po)\nx <- simulate(po)\nplot(x)\npf <- pfilter(po,Np=1000)\nlogLik(pf)\n"
},
{
"path": "examples/parus.R",
"chars": 748,
"preview": "\\donttest{ # takes too long for R CMD check\n parus |>\n pfilter(Np=1000,times=\"year\",t0=1960,\n params=c(K=190,r="
},
{
"path": "examples/pfilter.R",
"chars": 592,
"preview": "pf <- pfilter(gompertz(),Np=1000)\t## use 1000 particles\n\nplot(pf)\nlogLik(pf)\ncond_logLik(pf)\t\t\t## conditional log-likeli"
},
{
"path": "examples/pmcmc.R",
"chars": 407,
"preview": "\\donttest{\nsir(\n times=seq(from=0,to=1,by=1/26),\n t0=-1/26\n) |>\n pmcmc(\n Np = 1000,\n Nmcmc = 50,\n dprior = f"
},
{
"path": "examples/prior_spec.R",
"chars": 1606,
"preview": "\\donttest{ # takes too long for R CMD check\n ## Starting with an existing pomp object:\n verhulst() |> window(end=30) -"
},
{
"path": "examples/probe_match.R",
"chars": 1301,
"preview": "\\donttest{\n gompertz() -> po\n \n ## A list of probes:\n plist <- list(\n mean=probe_mean(\"Y\",trim=0.1,transform=sqrt"
},
{
"path": "examples/ricker-bifdiag.R",
"chars": 391,
"preview": "\\donttest{ # takes too long for R CMD check\n ## generate a bifurcation diagram for the Ricker map\n p <- parmat(coef(ri"
},
{
"path": "examples/ricker.R",
"chars": 56,
"preview": "po <- ricker()\nplot(po)\ncoef(po)\nsimulate(po) |> plot()\n"
},
{
"path": "examples/rinit_spec.R",
"chars": 624,
"preview": "\\donttest{\n ## Starting with an existing pomp object\n\n verhulst() -> po\n \n ## we add or change the initial-state sim"
},
{
"path": "examples/rmeasure_spec.R",
"chars": 605,
"preview": "\\donttest{\n ## We start with the pre-built Ricker example:\n \n ricker() -> po\n\n ## To change the measurement model si"
},
{
"path": "examples/rw2.R",
"chars": 249,
"preview": "\\donttest{\n\n if (require(ggplot2)) {\n\n rw2() |> plot()\n\n rw2(s1=1,s2=1,tau=0.1) |>\n simulate(nsim=10,format="
},
{
"path": "examples/sir.R",
"chars": 161,
"preview": "\\donttest{\n po <- sir()\n plot(po)\n coef(po)\n \n po <- sir2()\n plot(po)\n plot(simulate(window(po,end=3)))\n coef(po"
},
{
"path": "examples/skeleton_spec.R",
"chars": 1229,
"preview": "\\donttest{\n ## Starting with an existing pomp object,\n ## e.g., the continuous-time Verhulst-Pearl model,\n\n verhulst("
},
{
"path": "examples/spect_match.R",
"chars": 536,
"preview": "\\donttest{\n\n ricker() |>\n spect_objfun(\n est=c(\"r\",\"sigma\",\"N_0\"),\n partrans=parameter_trans(log=c(\"r\",\"si"
},
{
"path": "examples/spy.R",
"chars": 72,
"preview": "\\donttest{\n\n ricker() |> spy()\n\n sir() |> spy()\n\n sir2() |> spy()\n\n}\n"
},
{
"path": "examples/traj_match.R",
"chars": 547,
"preview": "\\donttest{\n\n ricker() |>\n traj_objfun(\n est=c(\"r\",\"sigma\",\"N_0\"),\n partrans=parameter_trans(log=c(\"r\",\"sig"
},
{
"path": "examples/trajectory.R",
"chars": 1013,
"preview": "\\donttest{\n ## The basic components needed to compute trajectories\n ## of a deterministic dynamical system are\n ## ri"
},
{
"path": "examples/userdata.R",
"chars": 1524,
"preview": "\\donttest{\n ## The familiar Ricker example.\n ## Suppose that for some reason we wish to pass 'phi'\n ## via the userda"
},
{
"path": "examples/verhulst.R",
"chars": 148,
"preview": "\\donttest{ # takes too long for R CMD check\n verhulst() -> po\n plot(po)\n plot(simulate(po))\n pfilter(po,Np=1000) -> "
},
{
"path": "inst/CITATION",
"chars": 2117,
"preview": "year <- sub(\"-.*\", \"\", meta$Date)\nnote1 <- sprintf(\"{R}~package, version~%s\", meta$Version)\nnote2 <- sprintf(\"(R package"
},
{
"path": "inst/GPL",
"chars": 35147,
"preview": " GNU GENERAL PUBLIC LICENSE\n Version 3, 29 June 2007\n\n Copyright (C) 2007 Free "
},
{
"path": "inst/NEWS",
"chars": 77762,
"preview": "_\bN_\be_\bw_\bs _\bf_\bo_\br _\bp_\ba_\bc_\bk_\ba_\bg_\be '_\bp_\bo_\bm_\bp'\n\n_\bC_\bh_\ba_\bn_\bg_\be_\bs _\bi_\bn '_\bp_\bo_\bm_\bp' _\bv_\be_\br_\bs_\bi"
},
{
"path": "inst/NEWS.Rd",
"chars": 73114,
"preview": "\\name{NEWS}\n\\title{News for package `pomp'}\n\\section{Changes in \\pkg{pomp} version 6.3.1}{\n \\itemize{\n \\item \\code{c"
},
{
"path": "inst/doc/Makefile",
"chars": 658,
"preview": "RM = rm -f\nCP = cp\nTOUCH = touch\nINSTALL = install\nPANDOC = pandoc\n\ndefault: index.html\n\n%.tex: %.Rnw\n\t$(RSCRIPT) -e \"li"
},
{
"path": "inst/doc/index.html",
"chars": 2389,
"preview": "<style>\nhtml {\n overflow-y: scroll;\n}\n\nbody {\n color: #000000;\n background: #ffffff;\n font-family: \"DejaVu S"
},
{
"path": "inst/doc/index.md",
"chars": 2157,
"preview": "---\ntitle: \"pomp\"\nsubtitle: \"user guides, vignettes, and tutorials\"\n---\n\n<style>\nhtml {\n overflow-y: scroll;\n}\n\nbody "
},
{
"path": "inst/include/pomp.h",
"chars": 8154,
"preview": "// -*- C++ -*-\n// Header for the C API for pomp.\n// Documentation: https://kingaa.github.io/pomp/C_API.html\n\n\n#ifndef _P"
},
{
"path": "inst/include/pomp_defines.h",
"chars": 7849,
"preview": "// -*- C++ -*-\n\n#ifndef _POMP_DEFINES_H_\n#define _POMP_DEFINES_H_\n\n#include <R.h>\n#include <Rmath.h>\n#include <Rdefines."
},
{
"path": "man/abc.Rd",
"chars": 6839,
"preview": "% Generated by roxygen2: do not edit by hand\n% Please edit documentation in R/abc.R\n\\docType{methods}\n\\name{abc}\n\\alias{"
},
{
"path": "man/accumvars.Rd",
"chars": 5360,
"preview": "% Generated by roxygen2: do not edit by hand\n% Please edit documentation in R/accumulators.R\n\\name{accumvars}\n\\alias{acc"
},
{
"path": "man/as_data_frame.Rd",
"chars": 2687,
"preview": "% Generated by roxygen2: do not edit by hand\n% Please edit documentation in R/as_data_frame.R\n\\docType{methods}\n\\name{as"
},
{
"path": "man/as_pomp.Rd",
"chars": 342,
"preview": "% Generated by roxygen2: do not edit by hand\n% Please edit documentation in R/as_pomp.R\n\\docType{methods}\n\\name{as_pomp}"
},
{
"path": "man/bake.Rd",
"chars": 8744,
"preview": "% Generated by roxygen2: do not edit by hand\n% Please edit documentation in R/bake.R\n\\name{reproducibility_tools}\n\\alias"
},
{
"path": "man/basic_components.Rd",
"chars": 3680,
"preview": "% Generated by roxygen2: do not edit by hand\n% Please edit documentation in R/basic_components.R\n\\name{basic_components}"
},
{
"path": "man/basic_probes.Rd",
"chars": 3464,
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{
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{
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{
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},
{
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},
{
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},
{
"path": "man/dprocess_spec.Rd",
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},
{
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}
]
// ... and 313 more files (download for full content)
About this extraction
This page contains the full source code of the kingaa/pomp GitHub repository, extracted and formatted as plain text for AI agents and large language models (LLMs). The extraction includes 513 files (2.1 MB), approximately 573.1k tokens, and a symbol index with 234 extracted functions, classes, methods, constants, and types. Use this with OpenClaw, Claude, ChatGPT, Cursor, Windsurf, or any other AI tool that accepts text input. You can copy the full output to your clipboard or download it as a .txt file.
Extracted by GitExtract — free GitHub repo to text converter for AI. Built by Nikandr Surkov.