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 # This file describes the settings to be used by the documentation system # 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 # iconv built into libc) for the transcoding. See # https://www.gnu.org/software/libiconv/ for the list of possible encodings. # The default value is: UTF-8. 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 = # Using the PROJECT_BRIEF tag one can provide an optional one line description # for a project that appears at the top of each page and should give viewer a # quick idea about the purpose of the project. Keep the description short. PROJECT_BRIEF = "Inference for partially observed Markov processes" # With the PROJECT_LOGO tag one can specify a logo or an icon that is included # in the documentation. The maximum height of the logo should not exceed 55 # pixels and the maximum width should not exceed 200 pixels. Doxygen will copy # the logo to the output directory. PROJECT_LOGO = # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path # 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. CREATE_SUBDIRS = NO # If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII # characters to appear in the names of generated files. If set to NO, non-ASCII # characters will be escaped, for example _xE3_x81_x84 will be used for Unicode # U+3044. # The default value is: NO. ALLOW_UNICODE_NAMES = NO # The OUTPUT_LANGUAGE tag is used to specify the language in which all # documentation generated by doxygen is written. Doxygen will use this # information to generate all constant output in the proper language. # Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese, # Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States), # Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian, # Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages), # Korean, Korean-en (Korean with English messages), Latvian, Lithuanian, # Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian, # Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish, # Ukrainian and Vietnamese. # The default value is: English. OUTPUT_LANGUAGE = English # The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all # documentation generated by doxygen is written. Doxygen will use this # information to generate all generated output in the proper direction. # Possible values are: None, LTR, RTL and Context. # The default value is: None. OUTPUT_TEXT_DIRECTION = None # If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member # descriptions after the members that are listed in the file and class # documentation (similar to Javadoc). Set to NO to disable this. # The default value is: YES. BRIEF_MEMBER_DESC = YES # If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief # description of a member or function before the detailed description # # Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the # brief descriptions will be completely suppressed. # The default value is: YES. REPEAT_BRIEF = YES # This tag implements a quasi-intelligent brief description abbreviator that is # used to form the text in various listings. Each string in this list, if found # as the leading text of the brief description, will be stripped from the text # and the result, after processing the whole list, is used as the annotated # text. Otherwise, the brief description is used as-is. If left blank, the # following values are used ($name is automatically replaced with the name of # the entity):The $name class, The $name widget, The $name file, is, provides, # specifies, contains, represents, a, an and the. ABBREVIATE_BRIEF = "The $name class" \ "The $name widget" \ "The $name file" \ is \ provides \ specifies \ contains \ represents \ a \ an \ the # If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then # doxygen will generate a detailed section even if there is only a brief # description. # The default value is: NO. ALWAYS_DETAILED_SEC = NO # If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all # inherited members of a class in the documentation of that class as if those # members were ordinary class members. Constructors, destructors and assignment # operators of the base classes will not be shown. # The default value is: NO. INLINE_INHERITED_MEMB = NO # If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path # before files name in the file list and in the header files. If set to NO the # shortest path that makes the file name unique will be used # The default value is: YES. FULL_PATH_NAMES = YES # The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. # Stripping is only done if one of the specified strings matches the left-hand # part of the path. The tag can be used to show relative paths in the file list. # If left blank the directory from which doxygen is run is used as the path to # strip. # # Note that you can specify absolute paths here, but also relative paths, which # will be relative from the directory where doxygen is started. # This tag requires that the tag FULL_PATH_NAMES is set to YES. STRIP_FROM_PATH = # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the # path mentioned in the documentation of a class, which tells the reader which # header file to include in order to use a class. If left blank only the name of # the header file containing the class definition is used. Otherwise one should # specify the list of include paths that are normally passed to the compiler # using the -I flag. STRIP_FROM_INC_PATH = # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but # less readable) file names. This can be useful is your file systems doesn't # support long names like on DOS, Mac, or CD-ROM. # The default value is: NO. SHORT_NAMES = NO # If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the # first line (until the first dot) of a Javadoc-style comment as the brief # description. If set to NO, the Javadoc-style will behave just like regular Qt- # style comments (thus requiring an explicit @brief command for a brief # description.) # The default value is: NO. JAVADOC_AUTOBRIEF = NO # If the JAVADOC_BANNER tag is set to YES then doxygen will interpret a line # such as # /*************** # as being the beginning of a Javadoc-style comment "banner". If set to NO, the # Javadoc-style will behave just like regular comments and it will not be # interpreted by doxygen. # The default value is: NO. JAVADOC_BANNER = NO # If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first # line (until the first dot) of a Qt-style comment as the brief description. If # set to NO, the Qt-style will behave just like regular Qt-style comments (thus # requiring an explicit \brief command for a brief description.) # The default value is: NO. QT_AUTOBRIEF = NO # The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a # multi-line C++ special comment block (i.e. a block of //! or /// comments) as # a brief description. This used to be the default behavior. The new default is # to treat a multi-line C++ comment block as a detailed description. Set this # tag to YES if you prefer the old behavior instead. # # Note that setting this tag to YES also means that rational rose comments are # not recognized any more. # The default value is: NO. MULTILINE_CPP_IS_BRIEF = NO # By default Python docstrings are displayed as preformatted text and doxygen's # special commands cannot be used. By setting PYTHON_DOCSTRING to NO the # doxygen's special commands can be used and the contents of the docstring # documentation blocks is shown as doxygen documentation. # The default value is: YES. PYTHON_DOCSTRING = YES # If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the # documentation from any documented member that it re-implements. # The default value is: YES. INHERIT_DOCS = YES # If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new # page for each member. If set to NO, the documentation of a member will be part # of the file/class/namespace that contains it. # The default value is: NO. SEPARATE_MEMBER_PAGES = NO # The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen # uses this value to replace tabs by spaces in code fragments. # Minimum value: 1, maximum value: 16, default value: 4. TAB_SIZE = 4 # This tag can be used to specify a number of aliases that act as commands in # the documentation. An alias has the form: # name=value # For example adding # "sideeffect=@par Side Effects:\n" # will allow you to put the command \sideeffect (or @sideeffect) in the # documentation, which will result in a user-defined paragraph with heading # "Side Effects:". You can put \n's in the value part of an alias to insert # newlines (in the resulting output). You can put ^^ in the value part of an # alias to insert a newline as if a physical newline was in the original file. # When you need a literal { or } or , in the value part of an alias you have to # escape them by means of a backslash (\), this can lead to conflicts with the # commands \{ and \} for these it is advised to use the version @{ and @} or use # a double escape (\\{ and \\}) ALIASES = # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources # only. Doxygen will then generate output that is more tailored for C. For # instance, some of the names that are used will be different. The list of all # members will be omitted, etc. # The default value is: NO. OPTIMIZE_OUTPUT_FOR_C = YES # Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or # Python sources only. Doxygen will then generate output that is more tailored # for that language. For instance, namespaces will be presented as packages, # qualified scopes will look different, etc. # The default value is: NO. OPTIMIZE_OUTPUT_JAVA = NO # Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran # sources. Doxygen will then generate output that is tailored for Fortran. # The default value is: NO. OPTIMIZE_FOR_FORTRAN = NO # Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL # sources. Doxygen will then generate output that is tailored for VHDL. # The default value is: NO. 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 ... \endif and \cond # ... \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: # # # # where is the value of the INPUT_FILTER tag, and 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 + S # (what the is depends on the OS and browser, but it is typically # , /