From 4cf22a2cfac7ff2a8a221d4f971946d7ca306b87 Mon Sep 17 00:00:00 2001 From: Rich FitzJohn Date: Fri, 16 Aug 2024 10:04:26 +0100 Subject: [PATCH] Update for new dust --- R/cpp11.R | 20 ++++++++++---------- src/cows.cpp | 20 ++++++++++---------- src/cpp11.cpp | 38 +++++++++++++++++++------------------- 3 files changed, 39 insertions(+), 39 deletions(-) diff --git a/R/cpp11.R b/R/cpp11.R index 98d95c8..36698a6 100644 --- a/R/cpp11.R +++ b/R/cpp11.R @@ -1,15 +1,15 @@ # Generated by cpp11: do not edit by hand -dust2_system_cows_alloc <- function(r_pars, r_time, r_dt, r_n_particles, r_n_groups, r_seed, r_deterministic) { - .Call(`_cowflu_dust2_system_cows_alloc`, r_pars, r_time, r_dt, r_n_particles, r_n_groups, r_seed, r_deterministic) +dust2_system_cows_alloc <- function(r_pars, r_time, r_dt, r_n_particles, r_n_groups, r_seed, r_deterministic, r_n_threads) { + .Call(`_cowflu_dust2_system_cows_alloc`, r_pars, r_time, r_dt, r_n_particles, r_n_groups, r_seed, r_deterministic, r_n_threads) } dust2_system_cows_run_to_time <- function(ptr, r_time) { .Call(`_cowflu_dust2_system_cows_run_to_time`, ptr, r_time) } -dust2_system_cows_state <- function(ptr, grouped) { - .Call(`_cowflu_dust2_system_cows_state`, ptr, grouped) +dust2_system_cows_state <- function(ptr, r_index_state, r_index_particle, r_index_group, preserve_particle_dimension, preserve_group_dimension) { + .Call(`_cowflu_dust2_system_cows_state`, ptr, r_index_state, r_index_particle, r_index_group, preserve_particle_dimension, preserve_group_dimension) } dust2_system_cows_time <- function(ptr) { @@ -20,8 +20,8 @@ dust2_system_cows_set_state_initial <- function(ptr) { .Call(`_cowflu_dust2_system_cows_set_state_initial`, ptr) } -dust2_system_cows_set_state <- function(ptr, r_state, grouped) { - .Call(`_cowflu_dust2_system_cows_set_state`, ptr, r_state, grouped) +dust2_system_cows_set_state <- function(ptr, r_state, preserve_group_dimension) { + .Call(`_cowflu_dust2_system_cows_set_state`, ptr, r_state, preserve_group_dimension) } dust2_system_cows_reorder <- function(ptr, r_index) { @@ -40,10 +40,10 @@ dust2_system_cows_set_time <- function(ptr, r_time) { .Call(`_cowflu_dust2_system_cows_set_time`, ptr, r_time) } -dust2_system_cows_update_pars <- function(ptr, pars, grouped) { - .Call(`_cowflu_dust2_system_cows_update_pars`, ptr, pars, grouped) +dust2_system_cows_update_pars <- function(ptr, pars) { + .Call(`_cowflu_dust2_system_cows_update_pars`, ptr, pars) } -dust2_system_cows_simulate <- function(ptr, r_times, r_index, grouped) { - .Call(`_cowflu_dust2_system_cows_simulate`, ptr, r_times, r_index, grouped) +dust2_system_cows_simulate <- function(ptr, r_times, r_index_state, preserve_particle_dimension, preserve_group_dimension) { + .Call(`_cowflu_dust2_system_cows_simulate`, ptr, r_times, r_index_state, preserve_particle_dimension, preserve_group_dimension) } diff --git a/src/cows.cpp b/src/cows.cpp index 46ac2a5..a050085 100644 --- a/src/cows.cpp +++ b/src/cows.cpp @@ -280,8 +280,8 @@ class cows { #include [[cpp11::register]] -SEXP dust2_system_cows_alloc(cpp11::list r_pars, cpp11::sexp r_time, cpp11::sexp r_dt, cpp11::sexp r_n_particles, cpp11::sexp r_n_groups, cpp11::sexp r_seed, cpp11::sexp r_deterministic) { - return dust2::r::dust2_discrete_alloc(r_pars, r_time, r_dt, r_n_particles, r_n_groups, r_seed, r_deterministic); +SEXP dust2_system_cows_alloc(cpp11::list r_pars, cpp11::sexp r_time, cpp11::sexp r_dt, cpp11::sexp r_n_particles, cpp11::sexp r_n_groups, cpp11::sexp r_seed, cpp11::sexp r_deterministic, cpp11::sexp r_n_threads) { + return dust2::r::dust2_discrete_alloc(r_pars, r_time, r_dt, r_n_particles, r_n_groups, r_seed, r_deterministic, r_n_threads); } [[cpp11::register]] SEXP dust2_system_cows_run_to_time(cpp11::sexp ptr, cpp11::sexp r_time) { @@ -289,8 +289,8 @@ SEXP dust2_system_cows_run_to_time(cpp11::sexp ptr, cpp11::sexp r_time) { } [[cpp11::register]] -SEXP dust2_system_cows_state(cpp11::sexp ptr, bool grouped) { - return dust2::r::dust2_system_state>(ptr, grouped); +SEXP dust2_system_cows_state(cpp11::sexp ptr, cpp11::sexp r_index_state, cpp11::sexp r_index_particle, cpp11::sexp r_index_group, bool preserve_particle_dimension, bool preserve_group_dimension) { + return dust2::r::dust2_system_state>(ptr, r_index_state, r_index_particle, r_index_group, preserve_particle_dimension, preserve_group_dimension); } [[cpp11::register]] @@ -304,8 +304,8 @@ SEXP dust2_system_cows_set_state_initial(cpp11::sexp ptr) { } [[cpp11::register]] -SEXP dust2_system_cows_set_state(cpp11::sexp ptr, cpp11::sexp r_state, bool grouped) { - return dust2::r::dust2_system_set_state>(ptr, r_state, grouped); +SEXP dust2_system_cows_set_state(cpp11::sexp ptr, cpp11::sexp r_state, bool preserve_group_dimension) { + return dust2::r::dust2_system_set_state>(ptr, r_state, preserve_group_dimension); } [[cpp11::register]] @@ -329,11 +329,11 @@ SEXP dust2_system_cows_set_time(cpp11::sexp ptr, cpp11::sexp r_time) { } [[cpp11::register]] -SEXP dust2_system_cows_update_pars(cpp11::sexp ptr, cpp11::list pars, bool grouped) { - return dust2::r::dust2_system_update_pars>(ptr, pars, grouped); +SEXP dust2_system_cows_update_pars(cpp11::sexp ptr, cpp11::list pars) { + return dust2::r::dust2_system_update_pars>(ptr, pars); } [[cpp11::register]] -SEXP dust2_system_cows_simulate(cpp11::sexp ptr, cpp11::sexp r_times, cpp11::sexp r_index, bool grouped) { - return dust2::r::dust2_system_simulate>(ptr, r_times, r_index, grouped); +SEXP dust2_system_cows_simulate(cpp11::sexp ptr, cpp11::sexp r_times, cpp11::sexp r_index_state, bool preserve_particle_dimension, bool preserve_group_dimension) { + return dust2::r::dust2_system_simulate>(ptr, r_times, r_index_state, preserve_particle_dimension, preserve_group_dimension); } diff --git a/src/cpp11.cpp b/src/cpp11.cpp index 72ced6f..bef1d21 100644 --- a/src/cpp11.cpp +++ b/src/cpp11.cpp @@ -6,10 +6,10 @@ #include // cows.cpp -SEXP dust2_system_cows_alloc(cpp11::list r_pars, cpp11::sexp r_time, cpp11::sexp r_dt, cpp11::sexp r_n_particles, cpp11::sexp r_n_groups, cpp11::sexp r_seed, cpp11::sexp r_deterministic); -extern "C" SEXP _cowflu_dust2_system_cows_alloc(SEXP r_pars, SEXP r_time, SEXP r_dt, SEXP r_n_particles, SEXP r_n_groups, SEXP r_seed, SEXP r_deterministic) { +SEXP dust2_system_cows_alloc(cpp11::list r_pars, cpp11::sexp r_time, cpp11::sexp r_dt, cpp11::sexp r_n_particles, cpp11::sexp r_n_groups, cpp11::sexp r_seed, cpp11::sexp r_deterministic, cpp11::sexp r_n_threads); +extern "C" SEXP _cowflu_dust2_system_cows_alloc(SEXP r_pars, SEXP r_time, SEXP r_dt, SEXP r_n_particles, SEXP r_n_groups, SEXP r_seed, SEXP r_deterministic, SEXP r_n_threads) { BEGIN_CPP11 - return cpp11::as_sexp(dust2_system_cows_alloc(cpp11::as_cpp>(r_pars), cpp11::as_cpp>(r_time), cpp11::as_cpp>(r_dt), cpp11::as_cpp>(r_n_particles), cpp11::as_cpp>(r_n_groups), cpp11::as_cpp>(r_seed), cpp11::as_cpp>(r_deterministic))); + return cpp11::as_sexp(dust2_system_cows_alloc(cpp11::as_cpp>(r_pars), cpp11::as_cpp>(r_time), cpp11::as_cpp>(r_dt), cpp11::as_cpp>(r_n_particles), cpp11::as_cpp>(r_n_groups), cpp11::as_cpp>(r_seed), cpp11::as_cpp>(r_deterministic), cpp11::as_cpp>(r_n_threads))); END_CPP11 } // cows.cpp @@ -20,10 +20,10 @@ extern "C" SEXP _cowflu_dust2_system_cows_run_to_time(SEXP ptr, SEXP r_time) { END_CPP11 } // cows.cpp -SEXP dust2_system_cows_state(cpp11::sexp ptr, bool grouped); -extern "C" SEXP _cowflu_dust2_system_cows_state(SEXP ptr, SEXP grouped) { +SEXP dust2_system_cows_state(cpp11::sexp ptr, cpp11::sexp r_index_state, cpp11::sexp r_index_particle, cpp11::sexp r_index_group, bool preserve_particle_dimension, bool preserve_group_dimension); +extern "C" SEXP _cowflu_dust2_system_cows_state(SEXP ptr, SEXP r_index_state, SEXP r_index_particle, SEXP r_index_group, SEXP preserve_particle_dimension, SEXP preserve_group_dimension) { BEGIN_CPP11 - return cpp11::as_sexp(dust2_system_cows_state(cpp11::as_cpp>(ptr), cpp11::as_cpp>(grouped))); + return cpp11::as_sexp(dust2_system_cows_state(cpp11::as_cpp>(ptr), cpp11::as_cpp>(r_index_state), cpp11::as_cpp>(r_index_particle), cpp11::as_cpp>(r_index_group), cpp11::as_cpp>(preserve_particle_dimension), cpp11::as_cpp>(preserve_group_dimension))); END_CPP11 } // cows.cpp @@ -41,10 +41,10 @@ extern "C" SEXP _cowflu_dust2_system_cows_set_state_initial(SEXP ptr) { END_CPP11 } // cows.cpp -SEXP dust2_system_cows_set_state(cpp11::sexp ptr, cpp11::sexp r_state, bool grouped); -extern "C" SEXP _cowflu_dust2_system_cows_set_state(SEXP ptr, SEXP r_state, SEXP grouped) { +SEXP dust2_system_cows_set_state(cpp11::sexp ptr, cpp11::sexp r_state, bool preserve_group_dimension); +extern "C" SEXP _cowflu_dust2_system_cows_set_state(SEXP ptr, SEXP r_state, SEXP preserve_group_dimension) { BEGIN_CPP11 - return cpp11::as_sexp(dust2_system_cows_set_state(cpp11::as_cpp>(ptr), cpp11::as_cpp>(r_state), cpp11::as_cpp>(grouped))); + return cpp11::as_sexp(dust2_system_cows_set_state(cpp11::as_cpp>(ptr), cpp11::as_cpp>(r_state), cpp11::as_cpp>(preserve_group_dimension))); END_CPP11 } // cows.cpp @@ -76,23 +76,23 @@ extern "C" SEXP _cowflu_dust2_system_cows_set_time(SEXP ptr, SEXP r_time) { END_CPP11 } // cows.cpp -SEXP dust2_system_cows_update_pars(cpp11::sexp ptr, cpp11::list pars, bool grouped); -extern "C" SEXP _cowflu_dust2_system_cows_update_pars(SEXP ptr, SEXP pars, SEXP grouped) { +SEXP dust2_system_cows_update_pars(cpp11::sexp ptr, cpp11::list pars); +extern "C" SEXP _cowflu_dust2_system_cows_update_pars(SEXP ptr, SEXP pars) { BEGIN_CPP11 - return cpp11::as_sexp(dust2_system_cows_update_pars(cpp11::as_cpp>(ptr), cpp11::as_cpp>(pars), cpp11::as_cpp>(grouped))); + return cpp11::as_sexp(dust2_system_cows_update_pars(cpp11::as_cpp>(ptr), cpp11::as_cpp>(pars))); END_CPP11 } // cows.cpp -SEXP dust2_system_cows_simulate(cpp11::sexp ptr, cpp11::sexp r_times, cpp11::sexp r_index, bool grouped); -extern "C" SEXP _cowflu_dust2_system_cows_simulate(SEXP ptr, SEXP r_times, SEXP r_index, SEXP grouped) { +SEXP dust2_system_cows_simulate(cpp11::sexp ptr, cpp11::sexp r_times, cpp11::sexp r_index_state, bool preserve_particle_dimension, bool preserve_group_dimension); +extern "C" SEXP _cowflu_dust2_system_cows_simulate(SEXP ptr, SEXP r_times, SEXP r_index_state, SEXP preserve_particle_dimension, SEXP preserve_group_dimension) { BEGIN_CPP11 - return cpp11::as_sexp(dust2_system_cows_simulate(cpp11::as_cpp>(ptr), cpp11::as_cpp>(r_times), cpp11::as_cpp>(r_index), cpp11::as_cpp>(grouped))); + return cpp11::as_sexp(dust2_system_cows_simulate(cpp11::as_cpp>(ptr), cpp11::as_cpp>(r_times), cpp11::as_cpp>(r_index_state), cpp11::as_cpp>(preserve_particle_dimension), cpp11::as_cpp>(preserve_group_dimension))); END_CPP11 } extern "C" { static const R_CallMethodDef CallEntries[] = { - {"_cowflu_dust2_system_cows_alloc", (DL_FUNC) &_cowflu_dust2_system_cows_alloc, 7}, + {"_cowflu_dust2_system_cows_alloc", (DL_FUNC) &_cowflu_dust2_system_cows_alloc, 8}, {"_cowflu_dust2_system_cows_reorder", (DL_FUNC) &_cowflu_dust2_system_cows_reorder, 2}, {"_cowflu_dust2_system_cows_rng_state", (DL_FUNC) &_cowflu_dust2_system_cows_rng_state, 1}, {"_cowflu_dust2_system_cows_run_to_time", (DL_FUNC) &_cowflu_dust2_system_cows_run_to_time, 2}, @@ -100,10 +100,10 @@ static const R_CallMethodDef CallEntries[] = { {"_cowflu_dust2_system_cows_set_state", (DL_FUNC) &_cowflu_dust2_system_cows_set_state, 3}, {"_cowflu_dust2_system_cows_set_state_initial", (DL_FUNC) &_cowflu_dust2_system_cows_set_state_initial, 1}, {"_cowflu_dust2_system_cows_set_time", (DL_FUNC) &_cowflu_dust2_system_cows_set_time, 2}, - {"_cowflu_dust2_system_cows_simulate", (DL_FUNC) &_cowflu_dust2_system_cows_simulate, 4}, - {"_cowflu_dust2_system_cows_state", (DL_FUNC) &_cowflu_dust2_system_cows_state, 2}, + {"_cowflu_dust2_system_cows_simulate", (DL_FUNC) &_cowflu_dust2_system_cows_simulate, 5}, + {"_cowflu_dust2_system_cows_state", (DL_FUNC) &_cowflu_dust2_system_cows_state, 6}, {"_cowflu_dust2_system_cows_time", (DL_FUNC) &_cowflu_dust2_system_cows_time, 1}, - {"_cowflu_dust2_system_cows_update_pars", (DL_FUNC) &_cowflu_dust2_system_cows_update_pars, 3}, + {"_cowflu_dust2_system_cows_update_pars", (DL_FUNC) &_cowflu_dust2_system_cows_update_pars, 2}, {NULL, NULL, 0} }; }