SYMBOL INDEX (234 symbols across 41 files) FILE: inst/include/pomp.h type SEXP (line 26) | typedef const SEXP get_userdata_t (const char *name); function R_INLINE (line 109) | static R_INLINE function R_INLINE (line 114) | static R_INLINE function R_INLINE (line 119) | static R_INLINE function R_INLINE (line 128) | static R_INLINE function R_INLINE (line 156) | static R_INLINE function R_INLINE (line 191) | static R_INLINE function R_INLINE (line 233) | static R_INLINE function R_INLINE (line 268) | static R_INLINE function R_INLINE (line 278) | static R_INLINE function R_INLINE (line 288) | static R_INLINE function R_INLINE (line 297) | static R_INLINE function R_INLINE (line 304) | static R_INLINE function R_INLINE (line 311) | static R_INLINE function R_INLINE (line 321) | static R_INLINE function R_INLINE (line 329) | static R_INLINE FILE: inst/include/pomp_defines.h type pompfunmode (line 16) | typedef enum {undef=0,Rfun=1,native=2,regNative=3} pompfunmode; type rprocmode (line 17) | typedef enum {dflt=0,onestep=1,discrete=2,euler=3,gill=4} rprocmode; type lookup_table_t (line 20) | typedef struct { type SEXP (line 28) | typedef SEXP pomp_fun_handler_t (SEXP pfun, SEXP gnsi, pompfunmode *mode... type SEXP (line 29) | typedef SEXP load_stack_incr_t (SEXP pack); type SEXP (line 30) | typedef SEXP load_stack_decr_t (SEXP pack); type lookup_table_t (line 31) | typedef lookup_table_t make_covariate_table_t (SEXP object, int *ncovar); type SEXP (line 33) | typedef SEXP apply_probe_data_t (SEXP object, SEXP probes); type SEXP (line 34) | typedef SEXP apply_probe_sim_t (SEXP object, SEXP nsim, SEXP params, SEX... type SEXP (line 35) | typedef SEXP systematic_resampling_t (SEXP weights); type SEXP (line 38) | typedef SEXP get_covariate_names_t (SEXP object); function R_INLINE (line 40) | static R_INLINE SEXP makearray (int rank, const int *dim) { function R_INLINE (line 55) | static R_INLINE int invalid_names (SEXP names) { function R_INLINE (line 59) | static R_INLINE SEXP matchnames function R_INLINE (line 87) | static R_INLINE void fillrownames (SEXP x, SEXP names) { function R_INLINE (line 110) | static R_INLINE void setrownames (SEXP x, SEXP names, int rank) { function R_INLINE (line 121) | static R_INLINE void setcolnames (SEXP x, SEXP names) { function R_INLINE (line 129) | static R_INLINE void fixdimnames (SEXP x, const char **names, int n) { function R_INLINE (line 145) | static R_INLINE SEXP as_matrix (SEXP x) { function R_INLINE (line 183) | static R_INLINE SEXP as_state_array (SEXP x) { function R_INLINE (line 232) | static R_INLINE SEXP getListElement (SEXP list, const char *str) function R_INLINE (line 244) | static R_INLINE SEXP getPairListElement (SEXP list, const char *name) function Scalar (line 279) | inline Scalar& operator () (int d1) { function Scalar (line 282) | inline Scalar& operator () (int d1, int d2) { function Scalar (line 285) | inline Scalar& operator () (int d1, int d2, int d3) { FILE: src/bspline.c function bspline_eval (line 9) | static void bspline_eval function SEXP (line 51) | SEXP bspline_basis (SEXP range, SEXP x, SEXP nbasis, SEXP degree, SEXP d... function SEXP (line 85) | SEXP periodic_bspline_basis (SEXP x, SEXP nbasis, SEXP degree, SEXP period, function bspline_basis_eval_deriv (line 115) | void bspline_basis_eval_deriv (double x, double *knots, int degree, function periodic_bspline_basis_eval_deriv (line 122) | void periodic_bspline_basis_eval_deriv (double x, double period, int deg... FILE: src/dinit.c function R_INLINE (line 10) | static R_INLINE SEXP add_args function R_INLINE (line 59) | static R_INLINE SEXP eval_call function R_INLINE (line 86) | static R_INLINE SEXP ret_array (int nreps) function SEXP (line 97) | static SEXP init_density function SEXP (line 220) | SEXP do_dinit FILE: src/distributions.c function reulermultinom_multi (line 7) | static void reulermultinom_multi (int m, int n, double *size, double *ra... function deulermultinom_multi (line 15) | static void deulermultinom_multi (int m, int n, double *size, double *ra... function SEXP (line 23) | SEXP R_Euler_Multinom (SEXP n, SEXP size, SEXP rate, SEXP deltat) { function SEXP (line 49) | SEXP D_Euler_Multinom (SEXP x, SEXP size, SEXP rate, SEXP deltat, SEXP l... function SEXP (line 71) | SEXP E_Euler_Multinom (SEXP size, SEXP rate, SEXP deltat) { function SEXP (line 93) | SEXP R_GammaWN (SEXP n, SEXP sigma, SEXP deltat) { function SEXP (line 119) | SEXP R_BetaBinom (SEXP n, SEXP size, SEXP prob, SEXP theta) { function SEXP (line 137) | SEXP D_BetaBinom (SEXP x, SEXP size, SEXP prob, SEXP theta, SEXP log) { FILE: src/dmeasure.c function R_INLINE (line 10) | static R_INLINE SEXP add_args function R_INLINE (line 75) | static R_INLINE SEXP eval_call ( function R_INLINE (line 101) | static R_INLINE SEXP ret_array (int nreps, int ntimes) { function SEXP (line 111) | SEXP do_dmeasure (SEXP object, SEXP y, SEXP x, SEXP times, SEXP params, ... FILE: src/dprior.c function R_INLINE (line 10) | static R_INLINE SEXP add_args (SEXP names, SEXP log, SEXP args) function R_INLINE (line 34) | static R_INLINE SEXP eval_call (SEXP fn, SEXP args, double *p, int n) function SEXP (line 51) | SEXP do_dprior (SEXP object, SEXP params, SEXP log, SEXP gnsi) FILE: src/dprocess.c function R_INLINE (line 10) | static R_INLINE SEXP paste0 (SEXP a, SEXP b) { function R_INLINE (line 18) | static R_INLINE SEXP add_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP... function R_INLINE (line 86) | static R_INLINE SEXP eval_call function R_INLINE (line 115) | static R_INLINE SEXP ret_array (int nreps, int ntimes) function SEXP (line 127) | static SEXP onestep_density function SEXP (line 273) | SEXP do_dprocess (SEXP object, SEXP x, SEXP times, SEXP params, SEXP log... FILE: src/emeasure.c function R_INLINE (line 10) | static R_INLINE SEXP add_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP... function R_INLINE (line 60) | static R_INLINE SEXP eval_call ( function R_INLINE (line 84) | static R_INLINE SEXP ret_array (int n, int nreps, int ntimes, SEXP names) { function SEXP (line 98) | SEXP do_emeasure (SEXP object, SEXP x, SEXP times, SEXP params, SEXP gnsi) FILE: src/euler.c function R_INLINE (line 10) | static R_INLINE SEXP add_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP... function R_INLINE (line 67) | static R_INLINE SEXP eval_call ( function R_INLINE (line 92) | static R_INLINE SEXP ret_array (int n, int nreps, int ntimes, SEXP names) function SEXP (line 107) | SEXP euler_simulator function num_euler_steps (line 317) | int num_euler_steps (double t1, double t2, double *deltat) { function num_map_steps (line 342) | int num_map_steps (double t1, double t2, double deltat) { FILE: src/gompertz.c function _gompertz_normal_dmeasure (line 20) | void _gompertz_normal_dmeasure function _gompertz_normal_rmeasure (line 30) | void _gompertz_normal_rmeasure function _gompertz_normal_emeasure (line 40) | void _gompertz_normal_emeasure function _gompertz_normal_vmeasure (line 50) | void _gompertz_normal_vmeasure (double *f, double *x, double *p, function _gompertz_step (line 58) | void _gompertz_step function _gompertz_skeleton (line 70) | void _gompertz_skeleton function _gompertz_to_trans (line 102) | void _gompertz_to_trans function _gompertz_from_trans (line 113) | void _gompertz_from_trans FILE: src/init.c function R_init_pomp (line 54) | void R_init_pomp (DllInfo *info) { FILE: src/logmeanexp.c function SEXP (line 7) | SEXP logmeanexp (const SEXP X, const SEXP Drop) { FILE: src/lookup_table.c function SEXP (line 7) | SEXP get_covariate_names (SEXP object) { function lookup_table_t (line 11) | lookup_table_t make_covariate_table (SEXP object, int *ncovar) { function SEXP (line 24) | SEXP lookup_in_table (SEXP covar, SEXP t) { function table_lookup (line 53) | void table_lookup (lookup_table_t *tab, double x, double *y) FILE: src/mif2.c function SEXP (line 6) | SEXP randwalk_perturbation (SEXP params, SEXP rw_sd) FILE: src/ou2.c function sim_ou2 (line 9) | static void sim_ou2 function dens_ou2 (line 29) | static double dens_ou2 function _ou2_step (line 71) | void _ou2_step function _ou2_pdf (line 82) | void _ou2_pdf function _ou2_skel (line 95) | void _ou2_skel function _ou2_dmeasure (line 106) | void _ou2_dmeasure function _ou2_rmeasure (line 120) | void _ou2_rmeasure function _ou2_emeasure (line 132) | void _ou2_emeasure function _ou2_vmeasure (line 143) | void _ou2_vmeasure FILE: src/partrans.c type direction_t (line 10) | typedef enum {to = 1, from = -1} direction_t; function R_INLINE (line 12) | static R_INLINE SEXP add_args (SEXP args, SEXP names) function R_INLINE (line 33) | static R_INLINE SEXP eval_call (SEXP fn, SEXP args, double *p, int n) function SEXP (line 49) | SEXP do_partrans (SEXP object, SEXP params, SEXP dir, SEXP gnsi) FILE: src/pfilter.c function SEXP (line 16) | SEXP pfilter (SEXP x, SEXP params, SEXP Np, function pred_mean_var (line 266) | static void pred_mean_var (int nvars, int nreps, int do_pv, function filt_mean (line 294) | static void filt_mean (int nvars, int nreps, int all_fail, long double w... FILE: src/pomp.h type SEXP (line 34) | typedef const SEXP get_userdata_t (const char *name); function R_INLINE (line 117) | static R_INLINE function R_INLINE (line 122) | static R_INLINE function R_INLINE (line 127) | static R_INLINE function R_INLINE (line 136) | static R_INLINE function R_INLINE (line 164) | static R_INLINE function R_INLINE (line 199) | static R_INLINE function R_INLINE (line 241) | static R_INLINE function R_INLINE (line 276) | static R_INLINE function R_INLINE (line 286) | static R_INLINE function R_INLINE (line 296) | static R_INLINE function R_INLINE (line 305) | static R_INLINE function R_INLINE (line 312) | static R_INLINE function R_INLINE (line 319) | static R_INLINE function R_INLINE (line 329) | static R_INLINE function R_INLINE (line 337) | static R_INLINE FILE: src/pomp_defines.h type pompfunmode (line 16) | typedef enum {undef=0,Rfun=1,native=2,regNative=3} pompfunmode; type rprocmode (line 17) | typedef enum {dflt=0,onestep=1,discrete=2,euler=3,gill=4} rprocmode; type lookup_table_t (line 20) | typedef struct { type SEXP (line 28) | typedef SEXP pomp_fun_handler_t (SEXP pfun, SEXP gnsi, pompfunmode *mode... type SEXP (line 29) | typedef SEXP load_stack_incr_t (SEXP pack); type SEXP (line 30) | typedef SEXP load_stack_decr_t (SEXP pack); type lookup_table_t (line 31) | typedef lookup_table_t make_covariate_table_t (SEXP object, int *ncovar); type SEXP (line 33) | typedef SEXP apply_probe_data_t (SEXP object, SEXP probes); type SEXP (line 34) | typedef SEXP apply_probe_sim_t (SEXP object, SEXP nsim, SEXP params, SEX... type SEXP (line 35) | typedef SEXP systematic_resampling_t (SEXP weights); type SEXP (line 38) | typedef SEXP get_covariate_names_t (SEXP object); function R_INLINE (line 40) | static R_INLINE SEXP makearray (int rank, const int *dim) { function R_INLINE (line 55) | static R_INLINE int invalid_names (SEXP names) { function R_INLINE (line 59) | static R_INLINE SEXP matchnames function R_INLINE (line 87) | static R_INLINE void fillrownames (SEXP x, SEXP names) { function R_INLINE (line 110) | static R_INLINE void setrownames (SEXP x, SEXP names, int rank) { function R_INLINE (line 121) | static R_INLINE void setcolnames (SEXP x, SEXP names) { function R_INLINE (line 129) | static R_INLINE void fixdimnames (SEXP x, const char **names, int n) { function R_INLINE (line 145) | static R_INLINE SEXP as_matrix (SEXP x) { function R_INLINE (line 183) | static R_INLINE SEXP as_state_array (SEXP x) { function R_INLINE (line 232) | static R_INLINE SEXP getListElement (SEXP list, const char *str) function R_INLINE (line 244) | static R_INLINE SEXP getPairListElement (SEXP list, const char *name) function Scalar (line 279) | inline Scalar& operator () (int d1) { function Scalar (line 282) | inline Scalar& operator () (int d1, int d2) { function Scalar (line 285) | inline Scalar& operator () (int d1, int d2, int d3) { FILE: src/pomp_fun.c function R_INLINE (line 10) | static R_INLINE SEXP name_index (SEXP provided, SEXP object, const char ... function SEXP (line 30) | SEXP pomp_fun_handler (SEXP pfun, SEXP gnsi, pompfunmode *mode, function SEXP (line 121) | SEXP load_stack_incr (SEXP pack) { function SEXP (line 130) | SEXP load_stack_decr (SEXP pack) { FILE: src/pomp_mat.h function R_INLINE (line 11) | static R_INLINE void pomp_backsolve function R_INLINE (line 27) | static R_INLINE void pomp_qr function R_INLINE (line 46) | static R_INLINE void pomp_qrqy FILE: src/probe.c function SEXP (line 4) | SEXP apply_probe_data (SEXP object, SEXP probes) { function SEXP (line 29) | SEXP apply_probe_sim (SEXP object, SEXP nsim, SEXP params, FILE: src/probe_acf.c function pomp_acf_compute (line 11) | static void pomp_acf_compute (double *acf, double *x, int n, int nvars, ... function pomp_ccf_compute (line 47) | static void pomp_ccf_compute (double *ccf, double *x, double *y, int n, ... function SEXP (line 100) | SEXP probe_acf (SEXP x, SEXP lags, SEXP corr) { function SEXP (line 145) | SEXP probe_ccf (SEXP x, SEXP y, SEXP lags, SEXP corr) { FILE: src/probe_marginal.c function SEXP (line 10) | SEXP probe_marginal_setup (SEXP ref, SEXP order, SEXP diff) { function SEXP (line 43) | SEXP probe_marginal_solve (SEXP x, SEXP setup, SEXP diff) { function order_reg_model_matrix (line 78) | static void order_reg_model_matrix (double *z, double *X, double *tau, i... function order_reg_solve (line 117) | static void order_reg_solve (double *beta, double *x, double *mm, double... FILE: src/probe_nlar.c function SEXP (line 9) | SEXP probe_nlar (SEXP x, SEXP lags, SEXP powers) { function poly_nlar_fit (line 39) | static void poly_nlar_fit (double *beta, double *y, int n, FILE: src/resample.c function SEXP (line 9) | SEXP systematic_resampling (SEXP weights, SEXP np) function nosort_resamp (line 25) | void nosort_resamp (int nw, double *w, int np, int *p, int offset) FILE: src/rinit.c function R_INLINE (line 10) | static R_INLINE SEXP paste0 (SEXP a, SEXP b, SEXP c) { function R_INLINE (line 21) | static R_INLINE SEXP add_args (SEXP args, SEXP Pnames, SEXP Cnames) function R_INLINE (line 58) | static R_INLINE SEXP eval_call function R_INLINE (line 79) | static R_INLINE SEXP ret_array (int m, int n, SEXP names) function SEXP (line 91) | SEXP do_rinit (SEXP object, SEXP params, SEXP t0, SEXP nsim, SEXP gnsi) function SEXP (line 254) | static SEXP pomp_default_rinit (SEXP params, SEXP Pnames, FILE: src/rmeasure.c function R_INLINE (line 10) | static R_INLINE SEXP add_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP... function R_INLINE (line 60) | static R_INLINE SEXP eval_call ( function R_INLINE (line 84) | static R_INLINE SEXP ret_array (int n, int nreps, int ntimes, SEXP names) { function SEXP (line 98) | SEXP do_rmeasure (SEXP object, SEXP x, SEXP times, SEXP params, SEXP gnsi) FILE: src/rprior.c function R_INLINE (line 10) | static R_INLINE SEXP add_args (SEXP args, SEXP names) function R_INLINE (line 31) | static R_INLINE SEXP eval_call (SEXP fn, SEXP args, double *p, int n) function R_INLINE (line 47) | static R_INLINE SEXP ret_array (SEXP params) function SEXP (line 58) | SEXP do_rprior (SEXP object, SEXP params, SEXP gnsi) FILE: src/rprocess.c function SEXP (line 10) | static SEXP pomp_default_rprocess (SEXP xstart, int nvars, int nreps, in... function SEXP (line 25) | SEXP do_rprocess (SEXP object, SEXP xstart, SEXP tstart, SEXP times, SEX... FILE: src/simulate.c function SEXP (line 6) | SEXP do_simulate (SEXP object, SEXP params, SEXP nsim, SEXP rettype, SEX... FILE: src/skeleton.c function SEXP (line 10) | SEXP add_skel_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP Cnames) function R_INLINE (line 57) | static R_INLINE SEXP eval_call ( function R_INLINE (line 81) | static R_INLINE SEXP ret_array (int nvars, int nreps, int ntimes, SEXP S... function eval_skeleton_R (line 93) | void eval_skeleton_R function iterate_skeleton_R (line 161) | void iterate_skeleton_R ( function eval_skeleton_native (line 245) | void eval_skeleton_native ( function iterate_skeleton_native (line 274) | void iterate_skeleton_native ( function SEXP (line 326) | SEXP do_skeleton (SEXP object, SEXP x, SEXP t, SEXP params, SEXP gnsi) FILE: src/sobolseq.c type Int32 (line 59) | typedef Int32 uint32_t; type nlopt_soboldata_s (line 60) | struct nlopt_soboldata_s type soboldata (line 65) | typedef struct nlopt_soboldata_s { function rightzero32 (line 84) | static unsigned rightzero32 (uint32_t n) function sobol_gen (line 96) | static int sobol_gen (soboldata *sd, double *x) function sobol_init (line 122) | static int sobol_init (soboldata *sd, unsigned sdim) function sobol_destroy (line 177) | static void sobol_destroy (soboldata *sd) function nlopt_sobol (line 188) | static nlopt_sobol nlopt_sobol_create (unsigned sdim) function nlopt_sobol_destroy (line 196) | static void nlopt_sobol_destroy (nlopt_sobol s) function nlopt_sobol_skip (line 225) | static void nlopt_sobol_skip(nlopt_sobol s, unsigned n, double *x) function SEXP (line 234) | SEXP sobol_sequence (SEXP dim, SEXP length) FILE: src/ssa.c function R_INLINE (line 9) | static R_INLINE SEXP add_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP... function gillespie (line 66) | static void gillespie (double *t, double tmax, double *f, double *y, function SSA (line 118) | static void SSA (pomp_ssa_rate_fn *ratefun, int irep, function __pomp_Rfun_ssa_ratefn (line 199) | static double __pomp_Rfun_ssa_ratefn (int j, double t, const double *x, ... function SEXP (line 226) | SEXP SSA_simulator (SEXP func, SEXP xstart, SEXP tstart, SEXP times, SEX... FILE: src/synth_lik.c function robust_synth_loglik (line 11) | static void robust_synth_loglik (double *y, int *dim, double *ydat, doub... function SEXP (line 104) | SEXP synth_loglik (SEXP ysim, SEXP ydat) { FILE: src/trajectory.c function R_INLINE (line 6) | static R_INLINE SEXP ret_array (int nvars, int nreps, int ntimes, SEXP S... function SEXP (line 19) | SEXP iterate_map (SEXP object, SEXP times, SEXP t0, SEXP x0, SEXP params... function SEXP (line 156) | SEXP pomp_desolve_setup (SEXP object, SEXP x0, SEXP params, SEXP gnsi) { function pomp_vf_eval (line 260) | void pomp_vf_eval (int *neq, double *t, double *y, double *ydot, double ... function SEXP (line 292) | SEXP pomp_desolve_takedown (void) { FILE: src/transformations.c function SEXP (line 14) | SEXP LogitTransform (SEXP P) { function SEXP (line 26) | SEXP ExpitTransform (SEXP X) { function SEXP (line 38) | SEXP LogBarycentricTransform (SEXP X) { function SEXP (line 47) | SEXP InverseLogBarycentricTransform (SEXP Y) { FILE: src/userdata.c function SEXP (line 8) | SEXP set_pomp_userdata (SEXP userdata) { function SEXP (line 13) | const SEXP get_userdata (const char *name) { FILE: src/vmeasure.c function R_INLINE (line 10) | static R_INLINE SEXP add_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP... function R_INLINE (line 60) | static R_INLINE SEXP eval_call ( function R_INLINE (line 84) | static R_INLINE SEXP ret_array (int n, int nreps, int ntimes, SEXP names) { function SEXP (line 99) | SEXP do_vmeasure (SEXP object, SEXP x, SEXP times, SEXP params, SEXP gnsi) FILE: src/wpfilter.c function SEXP (line 10) | SEXP wpfilter (SEXP X, SEXP Params, SEXP Weights, SEXP W, SEXP Trigger, ...