pomp
Inference for partially observed Markov processes
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Go to the source code of this file.
Functions | |
SEXP | bspline_basis (SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | periodic_bspline_basis (SEXP, SEXP, SEXP, SEXP, SEXP) |
void | bspline_basis_eval_deriv (double, double *, int, int, int, double *) |
void | periodic_bspline_basis_eval_deriv (double, double, int, int, int, double *) |
SEXP | do_dinit (SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | R_Euler_Multinom (SEXP, SEXP, SEXP, SEXP) |
SEXP | D_Euler_Multinom (SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | R_GammaWN (SEXP, SEXP, SEXP) |
SEXP | R_BetaBinom (SEXP, SEXP, SEXP, SEXP) |
SEXP | D_BetaBinom (SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | do_dmeasure (SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | do_dprior (SEXP, SEXP, SEXP, SEXP) |
SEXP | do_dprocess (SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | do_emeasure (SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | euler_simulator (SEXP, SEXP, SEXP, SEXP, SEXP, double, rprocmode, SEXP, SEXP, SEXP, SEXP) |
int | num_euler_steps (double, double, double *) |
int | num_map_steps (double, double, double) |
void | _gompertz_normal_dmeasure (double *, double *, double *, double *, int, int *, int *, int *, int *, double *, double) |
void | _gompertz_normal_rmeasure (double *, double *, double *, int *, int *, int *, int *, double *, double) |
void | _gompertz_normal_emeasure (double *, double *, double *, int *, int *, int *, int *, double *, double) |
void | _gompertz_normal_vmeasure (double *, double *, double *, int *, int *, int *, int *, double *, double) |
void | _gompertz_step (double *, const double *, const int *, const int *, const int *, const double *, double, double) |
void | _gompertz_skeleton (double *, double *, const double *, const int *, const int *, const int *, const double *, double) |
void | _gompertz_to_trans (double *, const double *, const int *) |
void | _gompertz_from_trans (double *, const double *, const int *) |
void | R_init_pomp (DllInfo *) |
SEXP | logmeanexp (const SEXP, const SEXP) |
SEXP | get_covariate_names (SEXP) |
lookup_table_t | make_covariate_table (SEXP, int *) |
SEXP | lookup_in_table (SEXP, SEXP) |
void | table_lookup (lookup_table_t *, double, double *) |
SEXP | randwalk_perturbation (SEXP, SEXP) |
void | _ou2_step (double *, const double *, const int *, const int *, const int *, const double *, double, double) |
void | _ou2_pdf (double *, double *, double *, double, double, const double *, const int *, const int *, const int *, const double *) |
void | _ou2_skel (double *, double *, double *, int *, int *, int *, double *, double) |
void | _ou2_dmeasure (double *, double *, double *, double *, int, int *, int *, int *, int *, double *, double) |
void | _ou2_rmeasure (double *, double *, double *, int *, int *, int *, int *, double *, double) |
void | _ou2_emeasure (double *, double *, double *, int *, int *, int *, int *, double *, double) |
void | _ou2_vmeasure (double *, double *, double *, int *, int *, int *, int *, double *, double) |
SEXP | do_partrans (SEXP, SEXP, SEXP, SEXP) |
SEXP | pfilter (SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | pomp_fun_handler (SEXP, SEXP, pompfunmode *, SEXP, SEXP, SEXP, SEXP) |
SEXP | load_stack_incr (SEXP) |
SEXP | load_stack_decr (SEXP) |
SEXP | apply_probe_data (SEXP, SEXP) |
SEXP | apply_probe_sim (SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | probe_acf (SEXP, SEXP, SEXP) |
SEXP | probe_ccf (SEXP, SEXP, SEXP, SEXP) |
SEXP | probe_marginal_setup (SEXP, SEXP, SEXP) |
SEXP | probe_marginal_solve (SEXP, SEXP, SEXP) |
SEXP | probe_nlar (SEXP, SEXP, SEXP) |
SEXP | systematic_resampling (SEXP, SEXP) |
void | nosort_resamp (int, double *, int, int *, int) |
SEXP | do_rinit (SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | do_rmeasure (SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | do_rprior (SEXP, SEXP, SEXP) |
SEXP | do_rprocess (SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | do_simulate (SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | add_skel_args (SEXP, SEXP, SEXP, SEXP) |
void | eval_skeleton_R (double *, double *, double *, double *, SEXP, SEXP, SEXP, int, int, int, int, int, int, int, lookup_table_t *, double *) |
void | iterate_skeleton_R (double *, double, double, double *, double *, double *, SEXP, SEXP, SEXP, int, int, int, int, int, int, int, lookup_table_t *, int *, double *) |
void | eval_skeleton_native (double *, double *, double *, double *, int, int, int, int, int, int, int, int *, int *, int *, lookup_table_t *, pomp_skeleton *, SEXP, double *) |
void | iterate_skeleton_native (double *, double, double, double *, double *, double *, int, int, int, int, int, int, int, int *, int *, int *, lookup_table_t *, int *, pomp_skeleton *, SEXP, double *) |
SEXP | do_skeleton (SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | sobol_sequence (SEXP, SEXP) |
SEXP | SSA_simulator (SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | synth_loglik (SEXP, SEXP) |
SEXP | iterate_map (SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | pomp_desolve_setup (SEXP, SEXP, SEXP, SEXP) |
void | pomp_vf_eval (int *, double *, double *, double *, double *, int *) |
SEXP | pomp_desolve_takedown (void) |
SEXP | LogitTransform (SEXP) |
SEXP | ExpitTransform (SEXP) |
SEXP | LogBarycentricTransform (SEXP) |
SEXP | InverseLogBarycentricTransform (SEXP) |
SEXP | set_pomp_userdata (SEXP) |
const SEXP | get_userdata (const char *) |
const int * | get_userdata_int (const char *) |
const double * | get_userdata_double (const char *) |
SEXP | do_vmeasure (SEXP, SEXP, SEXP, SEXP, SEXP) |
SEXP | wpfilter (SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) |
void _gompertz_from_trans | ( | double * | __p, |
const double * | __pt, | ||
const int * | __parindex | ||
) |
Definition at line 113 of file gompertz.c.
void _gompertz_normal_dmeasure | ( | double * | lik, |
double * | y, | ||
double * | x, | ||
double * | p, | ||
int | give_log, | ||
int * | obsindex, | ||
int * | stateindex, | ||
int * | parindex, | ||
int * | covindex, | ||
double * | covars, | ||
double | t | ||
) |
Definition at line 20 of file gompertz.c.
void _gompertz_normal_emeasure | ( | double * | f, |
double * | x, | ||
double * | p, | ||
int * | obsindex, | ||
int * | stateindex, | ||
int * | parindex, | ||
int * | covindex, | ||
double * | covars, | ||
double | t | ||
) |
Definition at line 40 of file gompertz.c.
void _gompertz_normal_rmeasure | ( | double * | y, |
double * | x, | ||
double * | p, | ||
int * | obsindex, | ||
int * | stateindex, | ||
int * | parindex, | ||
int * | covindex, | ||
double * | covars, | ||
double | t | ||
) |
Definition at line 30 of file gompertz.c.
void _gompertz_normal_vmeasure | ( | double * | f, |
double * | x, | ||
double * | p, | ||
int * | vmatindex, | ||
int * | stateindex, | ||
int * | parindex, | ||
int * | covindex, | ||
double * | covars, | ||
double | t | ||
) |
Definition at line 50 of file gompertz.c.
void _gompertz_skeleton | ( | double * | f, |
double * | x, | ||
const double * | p, | ||
const int * | stateindex, | ||
const int * | parindex, | ||
const int * | covindex, | ||
const double * | covar, | ||
double | t | ||
) |
Definition at line 70 of file gompertz.c.
void _gompertz_step | ( | double * | x, |
const double * | p, | ||
const int * | stateindex, | ||
const int * | parindex, | ||
const int * | covindex, | ||
const double * | covar, | ||
double | t, | ||
double | deltat | ||
) |
Definition at line 58 of file gompertz.c.
void _gompertz_to_trans | ( | double * | __pt, |
const double * | __p, | ||
const int * | __parindex | ||
) |
void _ou2_dmeasure | ( | double * | lik, |
double * | y, | ||
double * | x, | ||
double * | p, | ||
int | give_log, | ||
int * | obsindex, | ||
int * | stateindex, | ||
int * | parindex, | ||
int * | covindex, | ||
double * | covar, | ||
double | t | ||
) |
void _ou2_emeasure | ( | double * | y, |
double * | x, | ||
double * | p, | ||
int * | obsindex, | ||
int * | stateindex, | ||
int * | parindex, | ||
int * | covindex, | ||
double * | covar, | ||
double | t | ||
) |
void _ou2_pdf | ( | double * | f, |
double * | x, | ||
double * | z, | ||
double | t1, | ||
double | t2, | ||
const double * | p, | ||
const int * | stateindex, | ||
const int * | parindex, | ||
const int * | covindex, | ||
const double * | covars | ||
) |
void _ou2_rmeasure | ( | double * | y, |
double * | x, | ||
double * | p, | ||
int * | obsindex, | ||
int * | stateindex, | ||
int * | parindex, | ||
int * | covindex, | ||
double * | covar, | ||
double | t | ||
) |
void _ou2_skel | ( | double * | f, |
double * | x, | ||
double * | p, | ||
int * | stateindex, | ||
int * | parindex, | ||
int * | covindex, | ||
double * | covars, | ||
double | t | ||
) |
void _ou2_step | ( | double * | x, |
const double * | p, | ||
const int * | stateindex, | ||
const int * | parindex, | ||
const int * | covindex, | ||
const double * | covars, | ||
double | t, | ||
double | deltat | ||
) |
void _ou2_vmeasure | ( | double * | f, |
double * | x, | ||
double * | p, | ||
int * | vmatindex, | ||
int * | stateindex, | ||
int * | parindex, | ||
int * | covindex, | ||
double * | covar, | ||
double | t | ||
) |
SEXP add_skel_args | ( | SEXP | args, |
SEXP | Snames, | ||
SEXP | Pnames, | ||
SEXP | Cnames | ||
) |
SEXP apply_probe_data | ( | SEXP | object, |
SEXP | probes | ||
) |
SEXP apply_probe_sim | ( | SEXP | object, |
SEXP | nsim, | ||
SEXP | params, | ||
SEXP | probes, | ||
SEXP | datval, | ||
SEXP | gnsi | ||
) |
Definition at line 29 of file probe.c.
SEXP bspline_basis | ( | SEXP | range, |
SEXP | x, | ||
SEXP | nbasis, | ||
SEXP | degree, | ||
SEXP | deriv | ||
) |
Definition at line 51 of file bspline.c.
void bspline_basis_eval_deriv | ( | double | x, |
double * | knots, | ||
int | degree, | ||
int | nbasis, | ||
int | deriv, | ||
double * | y | ||
) |
SEXP D_BetaBinom | ( | SEXP | x, |
SEXP | size, | ||
SEXP | prob, | ||
SEXP | theta, | ||
SEXP | log | ||
) |
Definition at line 121 of file distributions.c.
SEXP D_Euler_Multinom | ( | SEXP | x, |
SEXP | size, | ||
SEXP | rate, | ||
SEXP | deltat, | ||
SEXP | log | ||
) |
Definition at line 49 of file distributions.c.
SEXP do_dinit | ( | SEXP | object, |
SEXP | t0, | ||
SEXP | x, | ||
SEXP | params, | ||
SEXP | log, | ||
SEXP | gnsi | ||
) |
Definition at line 220 of file dinit.c.
SEXP do_dmeasure | ( | SEXP | object, |
SEXP | y, | ||
SEXP | x, | ||
SEXP | times, | ||
SEXP | params, | ||
SEXP | log, | ||
SEXP | gnsi | ||
) |
Definition at line 111 of file dmeasure.c.
SEXP do_dprior | ( | SEXP | object, |
SEXP | params, | ||
SEXP | log, | ||
SEXP | gnsi | ||
) |
Definition at line 51 of file dprior.c.
SEXP do_dprocess | ( | SEXP | object, |
SEXP | x, | ||
SEXP | times, | ||
SEXP | params, | ||
SEXP | log, | ||
SEXP | gnsi | ||
) |
Definition at line 273 of file dprocess.c.
SEXP do_emeasure | ( | SEXP | object, |
SEXP | x, | ||
SEXP | times, | ||
SEXP | params, | ||
SEXP | gnsi | ||
) |
Definition at line 98 of file emeasure.c.
SEXP do_partrans | ( | SEXP | object, |
SEXP | params, | ||
SEXP | dir, | ||
SEXP | gnsi | ||
) |
Definition at line 49 of file partrans.c.
SEXP do_rinit | ( | SEXP | object, |
SEXP | params, | ||
SEXP | t0, | ||
SEXP | nsim, | ||
SEXP | gnsi | ||
) |
Definition at line 91 of file rinit.c.
SEXP do_rmeasure | ( | SEXP | object, |
SEXP | x, | ||
SEXP | times, | ||
SEXP | params, | ||
SEXP | gnsi | ||
) |
Definition at line 98 of file rmeasure.c.
SEXP do_rprior | ( | SEXP | object, |
SEXP | params, | ||
SEXP | gnsi | ||
) |
Definition at line 58 of file rprior.c.
SEXP do_rprocess | ( | SEXP | object, |
SEXP | xstart, | ||
SEXP | tstart, | ||
SEXP | times, | ||
SEXP | params, | ||
SEXP | gnsi | ||
) |
Definition at line 25 of file rprocess.c.
SEXP do_simulate | ( | SEXP | object, |
SEXP | params, | ||
SEXP | nsim, | ||
SEXP | rettype, | ||
SEXP | gnsi | ||
) |
Definition at line 6 of file simulate.c.
SEXP do_skeleton | ( | SEXP | object, |
SEXP | x, | ||
SEXP | t, | ||
SEXP | params, | ||
SEXP | gnsi | ||
) |
Definition at line 326 of file skeleton.c.
SEXP do_vmeasure | ( | SEXP | object, |
SEXP | x, | ||
SEXP | times, | ||
SEXP | params, | ||
SEXP | gnsi | ||
) |
Definition at line 99 of file vmeasure.c.
SEXP euler_simulator | ( | SEXP | func, |
SEXP | xstart, | ||
SEXP | tstart, | ||
SEXP | times, | ||
SEXP | params, | ||
double | deltat, | ||
rprocmode | method, | ||
SEXP | accumvars, | ||
SEXP | covar, | ||
SEXP | args, | ||
SEXP | gnsi | ||
) |
Definition at line 107 of file euler.c.
void eval_skeleton_native | ( | double * | f, |
double * | time, | ||
double * | x, | ||
double * | p, | ||
int | nvars, | ||
int | npars, | ||
int | ncovars, | ||
int | ntimes, | ||
int | nrepx, | ||
int | nrepp, | ||
int | nreps, | ||
int * | sidx, | ||
int * | pidx, | ||
int * | cidx, | ||
lookup_table_t * | covar_table, | ||
pomp_skeleton * | fun, | ||
SEXP | args, | ||
double * | cov | ||
) |
Definition at line 245 of file skeleton.c.
void eval_skeleton_R | ( | double * | f, |
double * | time, | ||
double * | x, | ||
double * | p, | ||
SEXP | fn, | ||
SEXP | args, | ||
SEXP | Snames, | ||
int | nvars, | ||
int | npars, | ||
int | ncovars, | ||
int | ntimes, | ||
int | nrepx, | ||
int | nrepp, | ||
int | nreps, | ||
lookup_table_t * | covar_table, | ||
double * | cov | ||
) |
Definition at line 93 of file skeleton.c.
SEXP ExpitTransform | ( | SEXP | X | ) |
SEXP get_covariate_names | ( | SEXP | object | ) |
const SEXP get_userdata | ( | const char * | name | ) |
Definition at line 13 of file userdata.c.
const double* get_userdata_double | ( | const char * | name | ) |
Definition at line 26 of file userdata.c.
const int* get_userdata_int | ( | const char * | name | ) |
Definition at line 19 of file userdata.c.
SEXP InverseLogBarycentricTransform | ( | SEXP | Y | ) |
Definition at line 47 of file transformations.c.
SEXP iterate_map | ( | SEXP | object, |
SEXP | times, | ||
SEXP | t0, | ||
SEXP | x0, | ||
SEXP | params, | ||
SEXP | gnsi | ||
) |
Definition at line 19 of file trajectory.c.
void iterate_skeleton_native | ( | double * | X, |
double | t, | ||
double | deltat, | ||
double * | time, | ||
double * | x, | ||
double * | p, | ||
int | nvars, | ||
int | npars, | ||
int | ncovars, | ||
int | ntimes, | ||
int | nrepp, | ||
int | nreps, | ||
int | nzeros, | ||
int * | sidx, | ||
int * | pidx, | ||
int * | cidx, | ||
lookup_table_t * | covar_table, | ||
int * | zeroindex, | ||
pomp_skeleton * | fun, | ||
SEXP | args, | ||
double * | cov | ||
) |
Definition at line 274 of file skeleton.c.
void iterate_skeleton_R | ( | double * | X, |
double | t, | ||
double | deltat, | ||
double * | time, | ||
double * | x, | ||
double * | p, | ||
SEXP | fn, | ||
SEXP | args, | ||
SEXP | Snames, | ||
int | nvars, | ||
int | npars, | ||
int | ncovars, | ||
int | ntimes, | ||
int | nrepp, | ||
int | nreps, | ||
int | nzeros, | ||
lookup_table_t * | covar_table, | ||
int * | zeroindex, | ||
double * | cov | ||
) |
Definition at line 161 of file skeleton.c.
SEXP load_stack_decr | ( | SEXP | pack | ) |
SEXP load_stack_incr | ( | SEXP | pack | ) |
SEXP LogBarycentricTransform | ( | SEXP | X | ) |
Definition at line 38 of file transformations.c.
SEXP LogitTransform | ( | SEXP | P | ) |
SEXP logmeanexp | ( | const | SEXP, |
const | SEXP | ||
) |
Definition at line 7 of file logmeanexp.c.
SEXP lookup_in_table | ( | SEXP | covar, |
SEXP | t | ||
) |
Definition at line 24 of file lookup_table.c.
lookup_table_t make_covariate_table | ( | SEXP | object, |
int * | ncovar | ||
) |
void nosort_resamp | ( | int | nw, |
double * | w, | ||
int | np, | ||
int * | p, | ||
int | offset | ||
) |
int num_euler_steps | ( | double | t1, |
double | t2, | ||
double * | deltat | ||
) |
int num_map_steps | ( | double | t1, |
double | t2, | ||
double | deltat | ||
) |
SEXP periodic_bspline_basis | ( | SEXP | x, |
SEXP | nbasis, | ||
SEXP | degree, | ||
SEXP | period, | ||
SEXP | deriv | ||
) |
Definition at line 85 of file bspline.c.
void periodic_bspline_basis_eval_deriv | ( | double | x, |
double | period, | ||
int | degree, | ||
int | nbasis, | ||
int | deriv, | ||
double * | y | ||
) |
SEXP pfilter | ( | SEXP | x, |
SEXP | params, | ||
SEXP | Np, | ||
SEXP | predmean, | ||
SEXP | predvar, | ||
SEXP | filtmean, | ||
SEXP | trackancestry, | ||
SEXP | doparRS, | ||
SEXP | weights, | ||
SEXP | wave | ||
) |
Definition at line 16 of file pfilter.c.
SEXP pomp_desolve_setup | ( | SEXP | object, |
SEXP | x0, | ||
SEXP | params, | ||
SEXP | gnsi | ||
) |
SEXP pomp_desolve_takedown | ( | void | ) |
Definition at line 292 of file trajectory.c.
SEXP pomp_fun_handler | ( | SEXP | pfun, |
SEXP | gnsi, | ||
pompfunmode * | mode, | ||
SEXP | S, | ||
SEXP | P, | ||
SEXP | O, | ||
SEXP | C | ||
) |
Definition at line 30 of file pomp_fun.c.
void pomp_vf_eval | ( | int * | neq, |
double * | t, | ||
double * | y, | ||
double * | ydot, | ||
double * | yout, | ||
int * | ip | ||
) |
Definition at line 260 of file trajectory.c.
SEXP probe_acf | ( | SEXP | x, |
SEXP | lags, | ||
SEXP | corr | ||
) |
Definition at line 100 of file probe_acf.c.
SEXP probe_ccf | ( | SEXP | x, |
SEXP | y, | ||
SEXP | lags, | ||
SEXP | corr | ||
) |
Definition at line 145 of file probe_acf.c.
SEXP probe_marginal_setup | ( | SEXP | ref, |
SEXP | order, | ||
SEXP | diff | ||
) |
Definition at line 10 of file probe_marginal.c.
SEXP probe_marginal_solve | ( | SEXP | x, |
SEXP | setup, | ||
SEXP | diff | ||
) |
Definition at line 43 of file probe_marginal.c.
SEXP probe_nlar | ( | SEXP | x, |
SEXP | lags, | ||
SEXP | powers | ||
) |
Definition at line 9 of file probe_nlar.c.
SEXP R_BetaBinom | ( | SEXP | n, |
SEXP | size, | ||
SEXP | prob, | ||
SEXP | theta | ||
) |
Definition at line 103 of file distributions.c.
SEXP R_Euler_Multinom | ( | SEXP | n, |
SEXP | size, | ||
SEXP | rate, | ||
SEXP | deltat | ||
) |
Definition at line 23 of file distributions.c.
SEXP R_GammaWN | ( | SEXP | n, |
SEXP | sigma, | ||
SEXP | deltat | ||
) |
void R_init_pomp | ( | DllInfo * | info | ) |
Definition at line 53 of file init.c.
SEXP randwalk_perturbation | ( | SEXP | params, |
SEXP | rw_sd | ||
) |
SEXP set_pomp_userdata | ( | SEXP | userdata | ) |
Definition at line 8 of file userdata.c.
SEXP sobol_sequence | ( | SEXP | dim, |
SEXP | length | ||
) |
Definition at line 234 of file sobolseq.c.
SEXP SSA_simulator | ( | SEXP | func, |
SEXP | xstart, | ||
SEXP | tstart, | ||
SEXP | times, | ||
SEXP | params, | ||
SEXP | vmatrix, | ||
SEXP | covar, | ||
SEXP | accumvars, | ||
SEXP | hmax, | ||
SEXP | args, | ||
SEXP | gnsi | ||
) |
Definition at line 228 of file ssa.c.
SEXP synth_loglik | ( | SEXP | ysim, |
SEXP | ydat | ||
) |
Definition at line 104 of file synth_lik.c.
SEXP systematic_resampling | ( | SEXP | weights, |
SEXP | np | ||
) |
Definition at line 9 of file resample.c.
void table_lookup | ( | lookup_table_t * | tab, |
double | x, | ||
double * | y | ||
) |
SEXP wpfilter | ( | SEXP | X, |
SEXP | Params, | ||
SEXP | Weights, | ||
SEXP | W, | ||
SEXP | Trigger, | ||
SEXP | Target, | ||
SEXP | Np | ||
) |