diff --git a/DESCRIPTION b/DESCRIPTION index fa784635..2107d00b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,4 +1,4 @@ -Package: epiworldRfaster +Package: epiworldRdev Type: Package Title: Fast Agent-Based Epi Models Version: 0.0-3.9000 diff --git a/Makefile b/Makefile index a9796723..2516f3e8 100644 --- a/Makefile +++ b/Makefile @@ -11,9 +11,16 @@ docker-debug: EPI_CONFIG="-DEPI_DEBUG -Wall -pedantic -g" R CMD INSTALL \ --no-docs --build . -install: build - which R - cd ../ && R CMD INSTALL epiworldR_*.tar.gz +install-dev: clean + sed -i -E 's/^Package:.+/Package: epiworldRdev/g' DESCRIPTION + sed -i -E 's/^library\([a-zA-Z]+\)/library(epiworldRdev)/g' README.* + EPI_DEV=yes R CMD INSTALL . + +install: clean + sed -i -E 's/^Package:.+/Package: epiworldR/g' DESCRIPTION + sed -i -E 's/^library\([a-zA-Z]+\)/library(epiworldR)/g' README.* + R CMD INSTALL . + README.md: README.Rmd Rscript --vanilla -e 'rmarkdown::render("README.Rmd")' diff --git a/NAMESPACE b/NAMESPACE index 24a85cb1..84d2ff82 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -189,4 +189,4 @@ importFrom(stats,aggregate) importFrom(stats,quantile) importFrom(stats,sd) importFrom(utils,read.table) -useDynLib(epiworldRfaster, .registration = TRUE) +useDynLib(epiworldRdev, .registration = TRUE) diff --git a/R/cpp11.R b/R/cpp11.R index 49cfc685..207718cc 100644 --- a/R/cpp11.R +++ b/R/cpp11.R @@ -1,429 +1,429 @@ # Generated by cpp11: do not edit by hand globalaction_tool_logit_cpp <- function(tool, vars, coefs, name, day) { - .Call(`_epiworldRfaster_globalaction_tool_logit_cpp`, tool, vars, coefs, name, day) + .Call(`_epiworldR_globalaction_tool_logit_cpp`, tool, vars, coefs, name, day) } globalaction_tool_cpp <- function(tool, prob, name, day) { - .Call(`_epiworldRfaster_globalaction_tool_cpp`, tool, prob, name, day) + .Call(`_epiworldR_globalaction_tool_cpp`, tool, prob, name, day) } globalaction_set_param_cpp <- function(param, value, name, day) { - .Call(`_epiworldRfaster_globalaction_set_param_cpp`, param, value, name, day) + .Call(`_epiworldR_globalaction_set_param_cpp`, param, value, name, day) } print_global_action_cpp <- function(action) { - .Call(`_epiworldRfaster_print_global_action_cpp`, action) + .Call(`_epiworldR_print_global_action_cpp`, action) } add_global_action_cpp <- function(model, action) { - .Call(`_epiworldRfaster_add_global_action_cpp`, model, action) + .Call(`_epiworldR_add_global_action_cpp`, model, action) } rm_global_action_cpp <- function(model, name) { - .Call(`_epiworldRfaster_rm_global_action_cpp`, model, name) + .Call(`_epiworldR_rm_global_action_cpp`, model, name) } globalaction_fun_cpp <- function(fun, name, day) { - .Call(`_epiworldRfaster_globalaction_fun_cpp`, fun, name, day) + .Call(`_epiworldR_globalaction_fun_cpp`, fun, name, day) } get_agents_cpp <- function(model) { - .Call(`_epiworldRfaster_get_agents_cpp`, model) + .Call(`_epiworldR_get_agents_cpp`, model) } get_agent_cpp <- function(agents, i) { - .Call(`_epiworldRfaster_get_agent_cpp`, agents, i) + .Call(`_epiworldR_get_agent_cpp`, agents, i) } print_agent_cpp <- function(agent, model, compressed) { - .Call(`_epiworldRfaster_print_agent_cpp`, agent, model, compressed) + .Call(`_epiworldR_print_agent_cpp`, agent, model, compressed) } get_state_agent_cpp <- function(agent) { - .Call(`_epiworldRfaster_get_state_agent_cpp`, agent) + .Call(`_epiworldR_get_state_agent_cpp`, agent) } get_agents_states_cpp <- function(model) { - .Call(`_epiworldRfaster_get_agents_states_cpp`, model) + .Call(`_epiworldR_get_agents_states_cpp`, model) } add_virus_agent_cpp <- function(agent, model, virus, state_new, queue) { - .Call(`_epiworldRfaster_add_virus_agent_cpp`, agent, model, virus, state_new, queue) + .Call(`_epiworldR_add_virus_agent_cpp`, agent, model, virus, state_new, queue) } add_tool_agent_cpp <- function(agent, model, tool, state_new, queue) { - .Call(`_epiworldRfaster_add_tool_agent_cpp`, agent, model, tool, state_new, queue) + .Call(`_epiworldR_add_tool_agent_cpp`, agent, model, tool, state_new, queue) } has_virus_cpp <- function(agent, virus) { - .Call(`_epiworldRfaster_has_virus_cpp`, agent, virus) + .Call(`_epiworldR_has_virus_cpp`, agent, virus) } has_tool_cpp <- function(agent, tool) { - .Call(`_epiworldRfaster_has_tool_cpp`, agent, tool) + .Call(`_epiworldR_has_tool_cpp`, agent, tool) } change_state_cpp <- function(agent, model, new_state, queue) { - .Call(`_epiworldRfaster_change_state_cpp`, agent, model, new_state, queue) + .Call(`_epiworldR_change_state_cpp`, agent, model, new_state, queue) } get_hist_total_cpp <- function(model) { - .Call(`_epiworldRfaster_get_hist_total_cpp`, model) + .Call(`_epiworldR_get_hist_total_cpp`, model) } get_hist_virus_cpp <- function(model) { - .Call(`_epiworldRfaster_get_hist_virus_cpp`, model) + .Call(`_epiworldR_get_hist_virus_cpp`, model) } get_hist_tool_cpp <- function(model) { - .Call(`_epiworldRfaster_get_hist_tool_cpp`, model) + .Call(`_epiworldR_get_hist_tool_cpp`, model) } get_transition_probability_cpp <- function(model) { - .Call(`_epiworldRfaster_get_transition_probability_cpp`, model) + .Call(`_epiworldR_get_transition_probability_cpp`, model) } get_hist_transition_matrix_cpp <- function(model, skip_zeros) { - .Call(`_epiworldRfaster_get_hist_transition_matrix_cpp`, model, skip_zeros) + .Call(`_epiworldR_get_hist_transition_matrix_cpp`, model, skip_zeros) } get_reproductive_number_cpp <- function(model) { - .Call(`_epiworldRfaster_get_reproductive_number_cpp`, model) + .Call(`_epiworldR_get_reproductive_number_cpp`, model) } get_transmissions_cpp <- function(model) { - .Call(`_epiworldRfaster_get_transmissions_cpp`, model) + .Call(`_epiworldR_get_transmissions_cpp`, model) } get_generation_time_cpp <- function(model) { - .Call(`_epiworldRfaster_get_generation_time_cpp`, model) + .Call(`_epiworldR_get_generation_time_cpp`, model) } get_today_total_cpp <- function(model) { - .Call(`_epiworldRfaster_get_today_total_cpp`, model) + .Call(`_epiworldR_get_today_total_cpp`, model) } ModelSURV_cpp <- function(name, prevalence, efficacy_vax, latent_period, prob_symptoms, prop_vaccinated, prop_vax_redux_transm, infect_period, prop_vax_redux_infect, surveillance_prob, transmission_rate, prob_death, prob_noreinfect) { - .Call(`_epiworldRfaster_ModelSURV_cpp`, name, prevalence, efficacy_vax, latent_period, prob_symptoms, prop_vaccinated, prop_vax_redux_transm, infect_period, prop_vax_redux_infect, surveillance_prob, transmission_rate, prob_death, prob_noreinfect) + .Call(`_epiworldR_ModelSURV_cpp`, name, prevalence, efficacy_vax, latent_period, prob_symptoms, prop_vaccinated, prop_vax_redux_transm, infect_period, prop_vax_redux_infect, surveillance_prob, transmission_rate, prob_death, prob_noreinfect) } ModelSEIR_cpp <- function(name, prevalence, transmission_rate, incubation_days, recovery_rate) { - .Call(`_epiworldRfaster_ModelSEIR_cpp`, name, prevalence, transmission_rate, incubation_days, recovery_rate) + .Call(`_epiworldR_ModelSEIR_cpp`, name, prevalence, transmission_rate, incubation_days, recovery_rate) } ModelSIS_cpp <- function(name, prevalence, transmission_rate, recovery_rate) { - .Call(`_epiworldRfaster_ModelSIS_cpp`, name, prevalence, transmission_rate, recovery_rate) + .Call(`_epiworldR_ModelSIS_cpp`, name, prevalence, transmission_rate, recovery_rate) } ModelSIRCONN_cpp <- function(name, n, prevalence, contact_rate, transmission_rate, recovery_rate) { - .Call(`_epiworldRfaster_ModelSIRCONN_cpp`, name, n, prevalence, contact_rate, transmission_rate, recovery_rate) + .Call(`_epiworldR_ModelSIRCONN_cpp`, name, n, prevalence, contact_rate, transmission_rate, recovery_rate) } ModelSIR_cpp <- function(name, prevalence, transmission_rate, recovery_rate) { - .Call(`_epiworldRfaster_ModelSIR_cpp`, name, prevalence, transmission_rate, recovery_rate) + .Call(`_epiworldR_ModelSIR_cpp`, name, prevalence, transmission_rate, recovery_rate) } ModelSIRD_cpp <- function(name, prevalence, transmission_rate, recovery_rate, death_rate) { - .Call(`_epiworldRfaster_ModelSIRD_cpp`, name, prevalence, transmission_rate, recovery_rate, death_rate) + .Call(`_epiworldR_ModelSIRD_cpp`, name, prevalence, transmission_rate, recovery_rate, death_rate) } ModelSEIRD_cpp <- function(name, prevalence, transmission_rate, incubation_days, recovery_rate, death_rate) { - .Call(`_epiworldRfaster_ModelSEIRD_cpp`, name, prevalence, transmission_rate, incubation_days, recovery_rate, death_rate) + .Call(`_epiworldR_ModelSEIRD_cpp`, name, prevalence, transmission_rate, incubation_days, recovery_rate, death_rate) } ModelSISD_cpp <- function(name, prevalence, transmission_rate, recovery_rate, death_rate) { - .Call(`_epiworldRfaster_ModelSISD_cpp`, name, prevalence, transmission_rate, recovery_rate, death_rate) + .Call(`_epiworldR_ModelSISD_cpp`, name, prevalence, transmission_rate, recovery_rate, death_rate) } ModelSIRDCONN_cpp <- function(name, n, prevalence, contact_rate, transmission_rate, recovery_rate, death_rate) { - .Call(`_epiworldRfaster_ModelSIRDCONN_cpp`, name, n, prevalence, contact_rate, transmission_rate, recovery_rate, death_rate) + .Call(`_epiworldR_ModelSIRDCONN_cpp`, name, n, prevalence, contact_rate, transmission_rate, recovery_rate, death_rate) } ModelSEIRDCONN_cpp <- function(name, n, prevalence, contact_rate, transmission_rate, incubation_days, recovery_rate, death_rate) { - .Call(`_epiworldRfaster_ModelSEIRDCONN_cpp`, name, n, prevalence, contact_rate, transmission_rate, incubation_days, recovery_rate, death_rate) + .Call(`_epiworldR_ModelSEIRDCONN_cpp`, name, n, prevalence, contact_rate, transmission_rate, incubation_days, recovery_rate, death_rate) } ModelSEIRCONN_cpp <- function(name, n, prevalence, contact_rate, transmission_rate, incubation_days, recovery_rate) { - .Call(`_epiworldRfaster_ModelSEIRCONN_cpp`, name, n, prevalence, contact_rate, transmission_rate, incubation_days, recovery_rate) + .Call(`_epiworldR_ModelSEIRCONN_cpp`, name, n, prevalence, contact_rate, transmission_rate, incubation_days, recovery_rate) } ModelSIRLogit_cpp <- function(vname, data, ncols, coefs_infect, coefs_recover, coef_infect_cols, coef_recover_cols, prob_infection, recovery_rate, prevalence) { - .Call(`_epiworldRfaster_ModelSIRLogit_cpp`, vname, data, ncols, coefs_infect, coefs_recover, coef_infect_cols, coef_recover_cols, prob_infection, recovery_rate, prevalence) + .Call(`_epiworldR_ModelSIRLogit_cpp`, vname, data, ncols, coefs_infect, coefs_recover, coef_infect_cols, coef_recover_cols, prob_infection, recovery_rate, prevalence) } ModelDiffNet_cpp <- function(name, prevalence, prob_adopt, normalize_exposure, data, data_ncols, data_cols, params) { - .Call(`_epiworldRfaster_ModelDiffNet_cpp`, name, prevalence, prob_adopt, normalize_exposure, data, data_ncols, data_cols, params) + .Call(`_epiworldR_ModelDiffNet_cpp`, name, prevalence, prob_adopt, normalize_exposure, data, data_ncols, data_cols, params) } print_cpp <- function(m, lite) { - .Call(`_epiworldRfaster_print_cpp`, m, lite) + .Call(`_epiworldR_print_cpp`, m, lite) } agents_smallworld_cpp <- function(m, n, k, d, p) { - .Call(`_epiworldRfaster_agents_smallworld_cpp`, m, n, k, d, p) + .Call(`_epiworldR_agents_smallworld_cpp`, m, n, k, d, p) } agents_from_edgelist_cpp <- function(m, source, target, size, directed) { - .Call(`_epiworldRfaster_agents_from_edgelist_cpp`, m, source, target, size, directed) + .Call(`_epiworldR_agents_from_edgelist_cpp`, m, source, target, size, directed) } run_cpp <- function(m, ndays, seed) { - .Call(`_epiworldRfaster_run_cpp`, m, ndays, seed) + .Call(`_epiworldR_run_cpp`, m, ndays, seed) } make_saver_cpp <- function(fn, total_hist, virus_info, virus_hist, tool_info, tool_hist, transmission, transition, reproductive, generation) { - .Call(`_epiworldRfaster_make_saver_cpp`, fn, total_hist, virus_info, virus_hist, tool_info, tool_hist, transmission, transition, reproductive, generation) + .Call(`_epiworldR_make_saver_cpp`, fn, total_hist, virus_info, virus_hist, tool_info, tool_hist, transmission, transition, reproductive, generation) } run_multiple_cpp <- function(m, ndays, nsims, seed, saver, reset, verbose, nthreads) { - .Call(`_epiworldRfaster_run_multiple_cpp`, m, ndays, nsims, seed, saver, reset, verbose, nthreads) + .Call(`_epiworldR_run_multiple_cpp`, m, ndays, nsims, seed, saver, reset, verbose, nthreads) } queuing_on_cpp <- function(model) { - .Call(`_epiworldRfaster_queuing_on_cpp`, model) + .Call(`_epiworldR_queuing_on_cpp`, model) } queuing_off_cpp <- function(model) { - .Call(`_epiworldRfaster_queuing_off_cpp`, model) + .Call(`_epiworldR_queuing_off_cpp`, model) } get_param_cpp <- function(model, pname) { - .Call(`_epiworldRfaster_get_param_cpp`, model, pname) + .Call(`_epiworldR_get_param_cpp`, model, pname) } set_param_cpp <- function(model, pname, val) { - .Call(`_epiworldRfaster_set_param_cpp`, model, pname, val) + .Call(`_epiworldR_set_param_cpp`, model, pname, val) } set_name_cpp <- function(model, mname) { - .Call(`_epiworldRfaster_set_name_cpp`, model, mname) + .Call(`_epiworldR_set_name_cpp`, model, mname) } get_name_cpp <- function(model) { - .Call(`_epiworldRfaster_get_name_cpp`, model) + .Call(`_epiworldR_get_name_cpp`, model) } get_states_cpp <- function(model) { - .Call(`_epiworldRfaster_get_states_cpp`, model) + .Call(`_epiworldR_get_states_cpp`, model) } verbose_on_cpp <- function(model) { - .Call(`_epiworldRfaster_verbose_on_cpp`, model) + .Call(`_epiworldR_verbose_on_cpp`, model) } verbose_off_cpp <- function(model) { - .Call(`_epiworldRfaster_verbose_off_cpp`, model) + .Call(`_epiworldR_verbose_off_cpp`, model) } get_n_viruses_cpp <- function(model) { - .Call(`_epiworldRfaster_get_n_viruses_cpp`, model) + .Call(`_epiworldR_get_n_viruses_cpp`, model) } get_n_tools_cpp <- function(model) { - .Call(`_epiworldRfaster_get_n_tools_cpp`, model) + .Call(`_epiworldR_get_n_tools_cpp`, model) } get_ndays_cpp <- function(model) { - .Call(`_epiworldRfaster_get_ndays_cpp`, model) + .Call(`_epiworldR_get_ndays_cpp`, model) } get_n_replicates_cpp <- function(model) { - .Call(`_epiworldRfaster_get_n_replicates_cpp`, model) + .Call(`_epiworldR_get_n_replicates_cpp`, model) } size_cpp <- function(model) { - .Call(`_epiworldRfaster_size_cpp`, model) + .Call(`_epiworldR_size_cpp`, model) } set_agents_data_cpp <- function(model, data, ncols) { - .Call(`_epiworldRfaster_set_agents_data_cpp`, model, data, ncols) + .Call(`_epiworldR_set_agents_data_cpp`, model, data, ncols) } get_agents_data_ncols_cpp <- function(model) { - .Call(`_epiworldRfaster_get_agents_data_ncols_cpp`, model) + .Call(`_epiworldR_get_agents_data_ncols_cpp`, model) } get_virus_model_cpp <- function(model, virus_pos) { - .Call(`_epiworldRfaster_get_virus_model_cpp`, model, virus_pos) + .Call(`_epiworldR_get_virus_model_cpp`, model, virus_pos) } get_tool_model_cpp <- function(model, tool_pos) { - .Call(`_epiworldRfaster_get_tool_model_cpp`, model, tool_pos) + .Call(`_epiworldR_get_tool_model_cpp`, model, tool_pos) } get_network_cpp <- function(model) { - .Call(`_epiworldRfaster_get_network_cpp`, model) + .Call(`_epiworldR_get_network_cpp`, model) } tool_cpp <- function(name, susceptibility_reduction, transmission_reduction, recovery_enhancer, death_reduction) { - .Call(`_epiworldRfaster_tool_cpp`, name, susceptibility_reduction, transmission_reduction, recovery_enhancer, death_reduction) + .Call(`_epiworldR_tool_cpp`, name, susceptibility_reduction, transmission_reduction, recovery_enhancer, death_reduction) } add_tool_cpp <- function(m, t, preval) { - .Call(`_epiworldRfaster_add_tool_cpp`, m, t, preval) + .Call(`_epiworldR_add_tool_cpp`, m, t, preval) } add_tool_n_cpp <- function(m, t, preval) { - .Call(`_epiworldRfaster_add_tool_n_cpp`, m, t, preval) + .Call(`_epiworldR_add_tool_n_cpp`, m, t, preval) } rm_tool_cpp <- function(m, tool_pos) { - .Call(`_epiworldRfaster_rm_tool_cpp`, m, tool_pos) + .Call(`_epiworldR_rm_tool_cpp`, m, tool_pos) } tool_fun_logit_cpp <- function(vars, coefs, model) { - .Call(`_epiworldRfaster_tool_fun_logit_cpp`, vars, coefs, model) + .Call(`_epiworldR_tool_fun_logit_cpp`, vars, coefs, model) } set_transmission_reduction_cpp <- function(tool, prob) { - .Call(`_epiworldRfaster_set_transmission_reduction_cpp`, tool, prob) + .Call(`_epiworldR_set_transmission_reduction_cpp`, tool, prob) } set_transmission_reduction_ptr_cpp <- function(tool, model, param) { - .Call(`_epiworldRfaster_set_transmission_reduction_ptr_cpp`, tool, model, param) + .Call(`_epiworldR_set_transmission_reduction_ptr_cpp`, tool, model, param) } set_transmission_reduction_fun_cpp <- function(tool, model, tfun) { - .Call(`_epiworldRfaster_set_transmission_reduction_fun_cpp`, tool, model, tfun) + .Call(`_epiworldR_set_transmission_reduction_fun_cpp`, tool, model, tfun) } set_susceptibility_reduction_cpp <- function(tool, prob) { - .Call(`_epiworldRfaster_set_susceptibility_reduction_cpp`, tool, prob) + .Call(`_epiworldR_set_susceptibility_reduction_cpp`, tool, prob) } set_susceptibility_reduction_ptr_cpp <- function(tool, model, param) { - .Call(`_epiworldRfaster_set_susceptibility_reduction_ptr_cpp`, tool, model, param) + .Call(`_epiworldR_set_susceptibility_reduction_ptr_cpp`, tool, model, param) } set_susceptibility_reduction_fun_cpp <- function(tool, model, tfun) { - .Call(`_epiworldRfaster_set_susceptibility_reduction_fun_cpp`, tool, model, tfun) + .Call(`_epiworldR_set_susceptibility_reduction_fun_cpp`, tool, model, tfun) } set_recovery_enhancer_cpp <- function(tool, prob) { - .Call(`_epiworldRfaster_set_recovery_enhancer_cpp`, tool, prob) + .Call(`_epiworldR_set_recovery_enhancer_cpp`, tool, prob) } set_recovery_enhancer_ptr_cpp <- function(tool, model, param) { - .Call(`_epiworldRfaster_set_recovery_enhancer_ptr_cpp`, tool, model, param) + .Call(`_epiworldR_set_recovery_enhancer_ptr_cpp`, tool, model, param) } set_recovery_enhancer_fun_cpp <- function(tool, model, tfun) { - .Call(`_epiworldRfaster_set_recovery_enhancer_fun_cpp`, tool, model, tfun) + .Call(`_epiworldR_set_recovery_enhancer_fun_cpp`, tool, model, tfun) } set_death_reduction_cpp <- function(tool, prob) { - .Call(`_epiworldRfaster_set_death_reduction_cpp`, tool, prob) + .Call(`_epiworldR_set_death_reduction_cpp`, tool, prob) } set_death_reduction_ptr_cpp <- function(tool, model, param) { - .Call(`_epiworldRfaster_set_death_reduction_ptr_cpp`, tool, model, param) + .Call(`_epiworldR_set_death_reduction_ptr_cpp`, tool, model, param) } set_death_reduction_fun_cpp <- function(tool, model, tfun) { - .Call(`_epiworldRfaster_set_death_reduction_fun_cpp`, tool, model, tfun) + .Call(`_epiworldR_set_death_reduction_fun_cpp`, tool, model, tfun) } get_name_tool_cpp <- function(tool) { - .Call(`_epiworldRfaster_get_name_tool_cpp`, tool) + .Call(`_epiworldR_get_name_tool_cpp`, tool) } set_name_tool_cpp <- function(tool, name) { - .Call(`_epiworldRfaster_set_name_tool_cpp`, tool, name) + .Call(`_epiworldR_set_name_tool_cpp`, tool, name) } print_tool_cpp <- function(t) { - .Call(`_epiworldRfaster_print_tool_cpp`, t) + .Call(`_epiworldR_print_tool_cpp`, t) } get_agents_tools_cpp <- function(model) { - .Call(`_epiworldRfaster_get_agents_tools_cpp`, model) + .Call(`_epiworldR_get_agents_tools_cpp`, model) } print_agent_tools_cpp <- function(tools) { - .Call(`_epiworldRfaster_print_agent_tools_cpp`, tools) + .Call(`_epiworldR_print_agent_tools_cpp`, tools) } virus_cpp <- function(name, prob_infecting, prob_recovery, prob_death, post_immunity, incubation) { - .Call(`_epiworldRfaster_virus_cpp`, name, prob_infecting, prob_recovery, prob_death, post_immunity, incubation) + .Call(`_epiworldR_virus_cpp`, name, prob_infecting, prob_recovery, prob_death, post_immunity, incubation) } virus_set_state_cpp <- function(v, init, end, removed) { - .Call(`_epiworldRfaster_virus_set_state_cpp`, v, init, end, removed) + .Call(`_epiworldR_virus_set_state_cpp`, v, init, end, removed) } add_virus_cpp <- function(m, v, preval) { - .Call(`_epiworldRfaster_add_virus_cpp`, m, v, preval) + .Call(`_epiworldR_add_virus_cpp`, m, v, preval) } add_virus_n_cpp <- function(m, v, preval) { - .Call(`_epiworldRfaster_add_virus_n_cpp`, m, v, preval) + .Call(`_epiworldR_add_virus_n_cpp`, m, v, preval) } rm_virus_cpp <- function(m, virus_pos) { - .Call(`_epiworldRfaster_rm_virus_cpp`, m, virus_pos) + .Call(`_epiworldR_rm_virus_cpp`, m, virus_pos) } print_virus_cpp <- function(v) { - .Call(`_epiworldRfaster_print_virus_cpp`, v) + .Call(`_epiworldR_print_virus_cpp`, v) } virus_fun_logit_cpp <- function(vars, coefs, model) { - .Call(`_epiworldRfaster_virus_fun_logit_cpp`, vars, coefs, model) + .Call(`_epiworldR_virus_fun_logit_cpp`, vars, coefs, model) } set_prob_infecting_cpp <- function(virus, prob) { - .Call(`_epiworldRfaster_set_prob_infecting_cpp`, virus, prob) + .Call(`_epiworldR_set_prob_infecting_cpp`, virus, prob) } set_prob_infecting_ptr_cpp <- function(virus, model, param) { - .Call(`_epiworldRfaster_set_prob_infecting_ptr_cpp`, virus, model, param) + .Call(`_epiworldR_set_prob_infecting_ptr_cpp`, virus, model, param) } set_prob_infecting_fun_cpp <- function(virus, model, vfun) { - .Call(`_epiworldRfaster_set_prob_infecting_fun_cpp`, virus, model, vfun) + .Call(`_epiworldR_set_prob_infecting_fun_cpp`, virus, model, vfun) } set_prob_recovery_cpp <- function(virus, prob) { - .Call(`_epiworldRfaster_set_prob_recovery_cpp`, virus, prob) + .Call(`_epiworldR_set_prob_recovery_cpp`, virus, prob) } set_prob_recovery_ptr_cpp <- function(virus, model, param) { - .Call(`_epiworldRfaster_set_prob_recovery_ptr_cpp`, virus, model, param) + .Call(`_epiworldR_set_prob_recovery_ptr_cpp`, virus, model, param) } set_prob_recovery_fun_cpp <- function(virus, model, vfun) { - .Call(`_epiworldRfaster_set_prob_recovery_fun_cpp`, virus, model, vfun) + .Call(`_epiworldR_set_prob_recovery_fun_cpp`, virus, model, vfun) } set_prob_death_cpp <- function(virus, prob) { - .Call(`_epiworldRfaster_set_prob_death_cpp`, virus, prob) + .Call(`_epiworldR_set_prob_death_cpp`, virus, prob) } set_prob_death_ptr_cpp <- function(virus, model, param) { - .Call(`_epiworldRfaster_set_prob_death_ptr_cpp`, virus, model, param) + .Call(`_epiworldR_set_prob_death_ptr_cpp`, virus, model, param) } set_prob_death_fun_cpp <- function(virus, model, vfun) { - .Call(`_epiworldRfaster_set_prob_death_fun_cpp`, virus, model, vfun) + .Call(`_epiworldR_set_prob_death_fun_cpp`, virus, model, vfun) } set_incubation_cpp <- function(virus, prob) { - .Call(`_epiworldRfaster_set_incubation_cpp`, virus, prob) + .Call(`_epiworldR_set_incubation_cpp`, virus, prob) } set_incubation_ptr_cpp <- function(virus, model, param) { - .Call(`_epiworldRfaster_set_incubation_ptr_cpp`, virus, model, param) + .Call(`_epiworldR_set_incubation_ptr_cpp`, virus, model, param) } set_incubation_fun_cpp <- function(virus, model, vfun) { - .Call(`_epiworldRfaster_set_incubation_fun_cpp`, virus, model, vfun) + .Call(`_epiworldR_set_incubation_fun_cpp`, virus, model, vfun) } get_name_virus_cpp <- function(virus) { - .Call(`_epiworldRfaster_get_name_virus_cpp`, virus) + .Call(`_epiworldR_get_name_virus_cpp`, virus) } set_name_virus_cpp <- function(virus, name) { - .Call(`_epiworldRfaster_set_name_virus_cpp`, virus, name) + .Call(`_epiworldR_set_name_virus_cpp`, virus, name) } diff --git a/R/epiworldR-package.R b/R/epiworldR-package.R index 3127149d..1cedb328 100644 --- a/R/epiworldR-package.R +++ b/R/epiworldR-package.R @@ -1,5 +1,5 @@ -#' epiworldRfaster -#' @useDynLib epiworldRfaster, .registration = TRUE +#' epiworldRdev +#' @useDynLib epiworldRdev, .registration = TRUE #' @importFrom graphics boxplot plot "_PACKAGE" diff --git a/R/epiworldR-package.R.in b/R/epiworldR-package.R.in new file mode 100644 index 00000000..21204cbb --- /dev/null +++ b/R/epiworldR-package.R.in @@ -0,0 +1,5 @@ +#' @EPIWORLD_NAME@ +#' @useDynLib @EPIWORLD_NAME@, .registration = TRUE +#' @importFrom graphics boxplot plot +"_PACKAGE" + diff --git a/README.Rmd b/README.Rmd index 0856db1d..fd4291f3 100644 --- a/README.Rmd +++ b/README.Rmd @@ -67,7 +67,7 @@ This R package includes several popular epidemiological models including This Susceptible-Infected-Recovered model features a population of 100,000 agents simulated in a small-world network. Each agent is connected to ten other agents. One percent of the population has the virus, with a 70% chance of transmission. Infected individuals recover at a 0.3 rate: ```{r example} -library(epiworldRfaster) +library(epiworldRdev) # Creating a SIR model sir <- ModelSIR( @@ -204,8 +204,8 @@ sir <- ModelSIR( net <- get_transmissions(sir) # Plotting -library(netplot) -library(igraph) +library(epiworldRdev) +library(epiworldRdev) x <- graph_from_edgelist(as.matrix(net[,2:3]) + 1) nplot(x, edge.curvature = 0, edge.color = "gray", skip.vertex=TRUE) diff --git a/README.md b/README.md index 06b692f0..cb601ed0 100644 --- a/README.md +++ b/README.md @@ -87,7 +87,7 @@ virus, with a 70% chance of transmission. Infected individuals recover at a 0.3 rate: ``` r -library(epiworldRfaster) +library(epiworldRdev) # Creating a SIR model sir <- ModelSIR( @@ -345,9 +345,9 @@ sir <- ModelSIR( net <- get_transmissions(sir) # Plotting -library(netplot) +library(epiworldRdev) #> Loading required package: grid -library(igraph) +library(epiworldRdev) #> #> Attaching package: 'igraph' #> The following object is masked from 'package:netplot': diff --git a/configure b/configure index 4b715d07..d67d51b9 100755 --- a/configure +++ b/configure @@ -617,6 +617,7 @@ PACKAGE_URL='' ac_subst_vars='LTLIBOBJS LIBOBJS +EPIWORLD_NAME OPENMP_FLAG CXXCPP OBJEXT @@ -3365,11 +3366,29 @@ printf "%s\n" "found and suitable" >&6; } fi fi +# Checking if the development version is being built +{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether to build the dev version" >&5 +printf %s "checking whether to build the dev version... " >&6; } +epiworldname="epiworldR" +if test x"${EPI_DEV}" != x"" ; then + epiworldname="epiworldRdev" +fi ## now use all these OPENMP_FLAG="${openmp_flag}" -ac_config_files="$ac_config_files src/Makevars" +EPIWORLD_NAME="${epiworldname}" + +ac_config_files="$ac_config_files src/Makevars R/epiworldR-package.R" + + +# Use sed to replace the line useDynLib\([a-zA-Z]+ in the NAMESPACE +# file with useDynLib(${epiworldname} + + + + + cat >confcache <<\_ACEOF # This file is a shell script that caches the results of configure @@ -4072,6 +4091,7 @@ for ac_config_target in $ac_config_targets do case $ac_config_target in "src/Makevars") CONFIG_FILES="$CONFIG_FILES src/Makevars" ;; + "R/epiworldR-package.R") CONFIG_FILES="$CONFIG_FILES R/epiworldR-package.R" ;; *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;; esac @@ -4495,6 +4515,12 @@ ac_clean_files=$ac_clean_files_save test $ac_write_fail = 0 || as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5 +sed -i -E 's/^useDynLib\([a-zA-Z]+/useDynLib('"${epiworldname}"'/g' NAMESPACE + +sed -i -E 's/^Package:.+/Package: '"${epiworldname}"'/g' DESCRIPTION + +sed -i -E 's/^\\(name|alias|title)\{[a-zA-Z]+/\\\1{'"${epiworldname}"'/g' man/epiworldRfaster-package.Rd + # configure is writing to config.log, and then calls config.status. # config.status does its own redirection, appending to config.log. diff --git a/configure.ac b/configure.ac index 1a541949..990b1623 100644 --- a/configure.ac +++ b/configure.ac @@ -169,8 +169,30 @@ if test x"${can_use_openmp}" = x"yes"; then fi fi +# Checking if the development version is being built +AC_MSG_CHECKING([whether to build the dev version]) +epiworldname="epiworldR" +if test x"${EPI_DEV}" != x"" ; then + epiworldname="epiworldRdev" +fi ## now use all these AC_SUBST([OPENMP_FLAG], ["${openmp_flag}"]) -AC_CONFIG_FILES([src/Makevars]) +AC_SUBST([EPIWORLD_NAME], ["${epiworldname}"]) +AC_CONFIG_FILES([src/Makevars R/epiworldR-package.R]) + +# Use sed to replace the line useDynLib\([a-zA-Z]+ in the NAMESPACE +# file with useDynLib(${epiworldname} +AC_CONFIG_COMMANDS_POST( + [sed -i -E 's/^useDynLib\([[a-zA-Z]]+/useDynLib('"${epiworldname}"'/g' NAMESPACE] + ) + +AC_CONFIG_COMMANDS_POST( + [sed -i -E 's/^Package:.+/Package: '"${epiworldname}"'/g' DESCRIPTION] + ) + +AC_CONFIG_COMMANDS_POST( + [sed -i -E 's/^\\(name|alias|title)\{[[a-zA-Z]]+/\\\1{'"${epiworldname}"'/g' man/epiworldRfaster-package.Rd] + ) + AC_OUTPUT \ No newline at end of file diff --git a/man/epiworldRfaster-package.Rd b/man/epiworldRfaster-package.Rd deleted file mode 100644 index 7e59fe57..00000000 --- a/man/epiworldRfaster-package.Rd +++ /dev/null @@ -1,37 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/epiworldR-package.R -\docType{package} -\name{epiworldRfaster-package} -\alias{epiworldRfaster} -\alias{epiworldRfaster-package} -\title{epiworldRfaster} -\description{ -A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations. -} -\seealso{ -Useful links: -\itemize{ - \item \url{https://github.com/UofUEpiBio/epiworldR} - \item \url{https://uofuepibio.github.io/epiworldR/} - \item \url{https://uofuepibio.github.io/epiworldR-workshop/} - \item Report bugs at \url{https://github.com/UofUEpiBio/epiworldR/issues} -} - -} -\author{ -\strong{Maintainer}: Derek Meyer \email{derekmeyer37@gmail.com} (\href{https://orcid.org/0009-0005-1350-6988}{ORCID}) - -Authors: -\itemize{ - \item George Vega Yon \email{g.vegayon@gmail.com} (\href{https://orcid.org/0000-0002-3171-0844}{ORCID}) -} - -Other contributors: -\itemize{ - \item Susan Holmes (\href{https://orcid.org/0000-0002-2208-8168}{ORCID}) (JOSS reviewer) [reviewer] - \item Abinash Satapathy (\href{https://orcid.org/0000-0002-2955-2744}{ORCID}) (JOSS reviewer) [reviewer] - \item Carinogurjao [reviewer] - \item Centers for Disease Control and Prevention (Award number 1U01CK000585; 75D30121F00003) [funder] -} - -} diff --git a/src/cpp11.cpp b/src/cpp11.cpp index 919cb025..d9960ab4 100644 --- a/src/cpp11.cpp +++ b/src/cpp11.cpp @@ -7,749 +7,749 @@ // actions.cpp SEXP globalaction_tool_logit_cpp(SEXP tool, std::vector< int > vars, std::vector< double > coefs, std::string name, int day); -extern "C" SEXP _epiworldRfaster_globalaction_tool_logit_cpp(SEXP tool, SEXP vars, SEXP coefs, SEXP name, SEXP day) { +extern "C" SEXP _epiworldR_globalaction_tool_logit_cpp(SEXP tool, SEXP vars, SEXP coefs, SEXP name, SEXP day) { BEGIN_CPP11 return cpp11::as_sexp(globalaction_tool_logit_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>>(vars), cpp11::as_cpp>>(coefs), cpp11::as_cpp>(name), cpp11::as_cpp>(day))); END_CPP11 } // actions.cpp SEXP globalaction_tool_cpp(SEXP tool, double prob, std::string name, int day); -extern "C" SEXP _epiworldRfaster_globalaction_tool_cpp(SEXP tool, SEXP prob, SEXP name, SEXP day) { +extern "C" SEXP _epiworldR_globalaction_tool_cpp(SEXP tool, SEXP prob, SEXP name, SEXP day) { BEGIN_CPP11 return cpp11::as_sexp(globalaction_tool_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>(prob), cpp11::as_cpp>(name), cpp11::as_cpp>(day))); END_CPP11 } // actions.cpp SEXP globalaction_set_param_cpp(std::string param, double value, std::string name, int day); -extern "C" SEXP _epiworldRfaster_globalaction_set_param_cpp(SEXP param, SEXP value, SEXP name, SEXP day) { +extern "C" SEXP _epiworldR_globalaction_set_param_cpp(SEXP param, SEXP value, SEXP name, SEXP day) { BEGIN_CPP11 return cpp11::as_sexp(globalaction_set_param_cpp(cpp11::as_cpp>(param), cpp11::as_cpp>(value), cpp11::as_cpp>(name), cpp11::as_cpp>(day))); END_CPP11 } // actions.cpp SEXP print_global_action_cpp(SEXP action); -extern "C" SEXP _epiworldRfaster_print_global_action_cpp(SEXP action) { +extern "C" SEXP _epiworldR_print_global_action_cpp(SEXP action) { BEGIN_CPP11 return cpp11::as_sexp(print_global_action_cpp(cpp11::as_cpp>(action))); END_CPP11 } // actions.cpp SEXP add_global_action_cpp(SEXP model, SEXP action); -extern "C" SEXP _epiworldRfaster_add_global_action_cpp(SEXP model, SEXP action) { +extern "C" SEXP _epiworldR_add_global_action_cpp(SEXP model, SEXP action) { BEGIN_CPP11 return cpp11::as_sexp(add_global_action_cpp(cpp11::as_cpp>(model), cpp11::as_cpp>(action))); END_CPP11 } // actions.cpp SEXP rm_global_action_cpp(SEXP model, std::string name); -extern "C" SEXP _epiworldRfaster_rm_global_action_cpp(SEXP model, SEXP name) { +extern "C" SEXP _epiworldR_rm_global_action_cpp(SEXP model, SEXP name) { BEGIN_CPP11 return cpp11::as_sexp(rm_global_action_cpp(cpp11::as_cpp>(model), cpp11::as_cpp>(name))); END_CPP11 } // actions.cpp SEXP globalaction_fun_cpp(cpp11::function fun, std::string name, int day); -extern "C" SEXP _epiworldRfaster_globalaction_fun_cpp(SEXP fun, SEXP name, SEXP day) { +extern "C" SEXP _epiworldR_globalaction_fun_cpp(SEXP fun, SEXP name, SEXP day) { BEGIN_CPP11 return cpp11::as_sexp(globalaction_fun_cpp(cpp11::as_cpp>(fun), cpp11::as_cpp>(name), cpp11::as_cpp>(day))); END_CPP11 } // agents.cpp SEXP get_agents_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_agents_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_agents_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_agents_cpp(cpp11::as_cpp>(model))); END_CPP11 } // agents.cpp SEXP get_agent_cpp(SEXP agents, size_t i); -extern "C" SEXP _epiworldRfaster_get_agent_cpp(SEXP agents, SEXP i) { +extern "C" SEXP _epiworldR_get_agent_cpp(SEXP agents, SEXP i) { BEGIN_CPP11 return cpp11::as_sexp(get_agent_cpp(cpp11::as_cpp>(agents), cpp11::as_cpp>(i))); END_CPP11 } // agents.cpp SEXP print_agent_cpp(SEXP agent, SEXP model, bool compressed); -extern "C" SEXP _epiworldRfaster_print_agent_cpp(SEXP agent, SEXP model, SEXP compressed) { +extern "C" SEXP _epiworldR_print_agent_cpp(SEXP agent, SEXP model, SEXP compressed) { BEGIN_CPP11 return cpp11::as_sexp(print_agent_cpp(cpp11::as_cpp>(agent), cpp11::as_cpp>(model), cpp11::as_cpp>(compressed))); END_CPP11 } // agents.cpp int get_state_agent_cpp(SEXP agent); -extern "C" SEXP _epiworldRfaster_get_state_agent_cpp(SEXP agent) { +extern "C" SEXP _epiworldR_get_state_agent_cpp(SEXP agent) { BEGIN_CPP11 return cpp11::as_sexp(get_state_agent_cpp(cpp11::as_cpp>(agent))); END_CPP11 } // agents.cpp std::vector get_agents_states_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_agents_states_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_agents_states_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_agents_states_cpp(cpp11::as_cpp>(model))); END_CPP11 } // agents.cpp SEXP add_virus_agent_cpp(SEXP agent, SEXP model, SEXP virus, int state_new, int queue); -extern "C" SEXP _epiworldRfaster_add_virus_agent_cpp(SEXP agent, SEXP model, SEXP virus, SEXP state_new, SEXP queue) { +extern "C" SEXP _epiworldR_add_virus_agent_cpp(SEXP agent, SEXP model, SEXP virus, SEXP state_new, SEXP queue) { BEGIN_CPP11 return cpp11::as_sexp(add_virus_agent_cpp(cpp11::as_cpp>(agent), cpp11::as_cpp>(model), cpp11::as_cpp>(virus), cpp11::as_cpp>(state_new), cpp11::as_cpp>(queue))); END_CPP11 } // agents.cpp SEXP add_tool_agent_cpp(SEXP agent, SEXP model, SEXP tool, int state_new, int queue); -extern "C" SEXP _epiworldRfaster_add_tool_agent_cpp(SEXP agent, SEXP model, SEXP tool, SEXP state_new, SEXP queue) { +extern "C" SEXP _epiworldR_add_tool_agent_cpp(SEXP agent, SEXP model, SEXP tool, SEXP state_new, SEXP queue) { BEGIN_CPP11 return cpp11::as_sexp(add_tool_agent_cpp(cpp11::as_cpp>(agent), cpp11::as_cpp>(model), cpp11::as_cpp>(tool), cpp11::as_cpp>(state_new), cpp11::as_cpp>(queue))); END_CPP11 } // agents.cpp bool has_virus_cpp(SEXP agent, SEXP virus); -extern "C" SEXP _epiworldRfaster_has_virus_cpp(SEXP agent, SEXP virus) { +extern "C" SEXP _epiworldR_has_virus_cpp(SEXP agent, SEXP virus) { BEGIN_CPP11 return cpp11::as_sexp(has_virus_cpp(cpp11::as_cpp>(agent), cpp11::as_cpp>(virus))); END_CPP11 } // agents.cpp bool has_tool_cpp(SEXP agent, SEXP tool); -extern "C" SEXP _epiworldRfaster_has_tool_cpp(SEXP agent, SEXP tool) { +extern "C" SEXP _epiworldR_has_tool_cpp(SEXP agent, SEXP tool) { BEGIN_CPP11 return cpp11::as_sexp(has_tool_cpp(cpp11::as_cpp>(agent), cpp11::as_cpp>(tool))); END_CPP11 } // agents.cpp SEXP change_state_cpp(SEXP agent, SEXP model, int new_state, int queue); -extern "C" SEXP _epiworldRfaster_change_state_cpp(SEXP agent, SEXP model, SEXP new_state, SEXP queue) { +extern "C" SEXP _epiworldR_change_state_cpp(SEXP agent, SEXP model, SEXP new_state, SEXP queue) { BEGIN_CPP11 return cpp11::as_sexp(change_state_cpp(cpp11::as_cpp>(agent), cpp11::as_cpp>(model), cpp11::as_cpp>(new_state), cpp11::as_cpp>(queue))); END_CPP11 } // db.cpp cpp11::data_frame get_hist_total_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_hist_total_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_hist_total_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_hist_total_cpp(cpp11::as_cpp>(model))); END_CPP11 } // db.cpp cpp11::data_frame get_hist_virus_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_hist_virus_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_hist_virus_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_hist_virus_cpp(cpp11::as_cpp>(model))); END_CPP11 } // db.cpp cpp11::data_frame get_hist_tool_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_hist_tool_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_hist_tool_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_hist_tool_cpp(cpp11::as_cpp>(model))); END_CPP11 } // db.cpp doubles get_transition_probability_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_transition_probability_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_transition_probability_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_transition_probability_cpp(cpp11::as_cpp>(model))); END_CPP11 } // db.cpp cpp11::data_frame get_hist_transition_matrix_cpp(SEXP model, bool skip_zeros); -extern "C" SEXP _epiworldRfaster_get_hist_transition_matrix_cpp(SEXP model, SEXP skip_zeros) { +extern "C" SEXP _epiworldR_get_hist_transition_matrix_cpp(SEXP model, SEXP skip_zeros) { BEGIN_CPP11 return cpp11::as_sexp(get_hist_transition_matrix_cpp(cpp11::as_cpp>(model), cpp11::as_cpp>(skip_zeros))); END_CPP11 } // db.cpp cpp11::data_frame get_reproductive_number_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_reproductive_number_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_reproductive_number_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_reproductive_number_cpp(cpp11::as_cpp>(model))); END_CPP11 } // db.cpp cpp11::data_frame get_transmissions_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_transmissions_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_transmissions_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_transmissions_cpp(cpp11::as_cpp>(model))); END_CPP11 } // db.cpp cpp11::data_frame get_generation_time_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_generation_time_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_generation_time_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_generation_time_cpp(cpp11::as_cpp>(model))); END_CPP11 } // db.cpp cpp11::writable::doubles get_today_total_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_today_total_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_today_total_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_today_total_cpp(cpp11::as_cpp>(model))); END_CPP11 } // epimodels.cpp SEXP ModelSURV_cpp(std::string name, double prevalence, double efficacy_vax, double latent_period, double prob_symptoms, double prop_vaccinated, double prop_vax_redux_transm, double infect_period, double prop_vax_redux_infect, double surveillance_prob, double transmission_rate, double prob_death, double prob_noreinfect); -extern "C" SEXP _epiworldRfaster_ModelSURV_cpp(SEXP name, SEXP prevalence, SEXP efficacy_vax, SEXP latent_period, SEXP prob_symptoms, SEXP prop_vaccinated, SEXP prop_vax_redux_transm, SEXP infect_period, SEXP prop_vax_redux_infect, SEXP surveillance_prob, SEXP transmission_rate, SEXP prob_death, SEXP prob_noreinfect) { +extern "C" SEXP _epiworldR_ModelSURV_cpp(SEXP name, SEXP prevalence, SEXP efficacy_vax, SEXP latent_period, SEXP prob_symptoms, SEXP prop_vaccinated, SEXP prop_vax_redux_transm, SEXP infect_period, SEXP prop_vax_redux_infect, SEXP surveillance_prob, SEXP transmission_rate, SEXP prob_death, SEXP prob_noreinfect) { BEGIN_CPP11 return cpp11::as_sexp(ModelSURV_cpp(cpp11::as_cpp>(name), cpp11::as_cpp>(prevalence), cpp11::as_cpp>(efficacy_vax), cpp11::as_cpp>(latent_period), cpp11::as_cpp>(prob_symptoms), cpp11::as_cpp>(prop_vaccinated), cpp11::as_cpp>(prop_vax_redux_transm), cpp11::as_cpp>(infect_period), cpp11::as_cpp>(prop_vax_redux_infect), cpp11::as_cpp>(surveillance_prob), cpp11::as_cpp>(transmission_rate), cpp11::as_cpp>(prob_death), cpp11::as_cpp>(prob_noreinfect))); END_CPP11 } // epimodels.cpp SEXP ModelSEIR_cpp(std::string name, double prevalence, double transmission_rate, double incubation_days, double recovery_rate); -extern "C" SEXP _epiworldRfaster_ModelSEIR_cpp(SEXP name, SEXP prevalence, SEXP transmission_rate, SEXP incubation_days, SEXP recovery_rate) { +extern "C" SEXP _epiworldR_ModelSEIR_cpp(SEXP name, SEXP prevalence, SEXP transmission_rate, SEXP incubation_days, SEXP recovery_rate) { BEGIN_CPP11 return cpp11::as_sexp(ModelSEIR_cpp(cpp11::as_cpp>(name), cpp11::as_cpp>(prevalence), cpp11::as_cpp>(transmission_rate), cpp11::as_cpp>(incubation_days), cpp11::as_cpp>(recovery_rate))); END_CPP11 } // epimodels.cpp SEXP ModelSIS_cpp(std::string name, double prevalence, double transmission_rate, double recovery_rate); -extern "C" SEXP _epiworldRfaster_ModelSIS_cpp(SEXP name, SEXP prevalence, SEXP transmission_rate, SEXP recovery_rate) { +extern "C" SEXP _epiworldR_ModelSIS_cpp(SEXP name, SEXP prevalence, SEXP transmission_rate, SEXP recovery_rate) { BEGIN_CPP11 return cpp11::as_sexp(ModelSIS_cpp(cpp11::as_cpp>(name), cpp11::as_cpp>(prevalence), cpp11::as_cpp>(transmission_rate), cpp11::as_cpp>(recovery_rate))); END_CPP11 } // epimodels.cpp SEXP ModelSIRCONN_cpp(std::string name, unsigned int n, double prevalence, double contact_rate, double transmission_rate, double recovery_rate); -extern "C" SEXP _epiworldRfaster_ModelSIRCONN_cpp(SEXP name, SEXP n, SEXP prevalence, SEXP contact_rate, SEXP transmission_rate, SEXP recovery_rate) { +extern "C" SEXP _epiworldR_ModelSIRCONN_cpp(SEXP name, SEXP n, SEXP prevalence, SEXP contact_rate, SEXP transmission_rate, SEXP recovery_rate) { BEGIN_CPP11 return cpp11::as_sexp(ModelSIRCONN_cpp(cpp11::as_cpp>(name), cpp11::as_cpp>(n), cpp11::as_cpp>(prevalence), cpp11::as_cpp>(contact_rate), cpp11::as_cpp>(transmission_rate), cpp11::as_cpp>(recovery_rate))); END_CPP11 } // epimodels.cpp SEXP ModelSIR_cpp(std::string name, double prevalence, double transmission_rate, double recovery_rate); -extern "C" SEXP _epiworldRfaster_ModelSIR_cpp(SEXP name, SEXP prevalence, SEXP transmission_rate, SEXP recovery_rate) { +extern "C" SEXP _epiworldR_ModelSIR_cpp(SEXP name, SEXP prevalence, SEXP transmission_rate, SEXP recovery_rate) { BEGIN_CPP11 return cpp11::as_sexp(ModelSIR_cpp(cpp11::as_cpp>(name), cpp11::as_cpp>(prevalence), cpp11::as_cpp>(transmission_rate), cpp11::as_cpp>(recovery_rate))); END_CPP11 } // epimodels.cpp SEXP ModelSIRD_cpp(std::string name, double prevalence, double transmission_rate, double recovery_rate, double death_rate); -extern "C" SEXP _epiworldRfaster_ModelSIRD_cpp(SEXP name, SEXP prevalence, SEXP transmission_rate, SEXP recovery_rate, SEXP death_rate) { +extern "C" SEXP _epiworldR_ModelSIRD_cpp(SEXP name, SEXP prevalence, SEXP transmission_rate, SEXP recovery_rate, SEXP death_rate) { BEGIN_CPP11 return cpp11::as_sexp(ModelSIRD_cpp(cpp11::as_cpp>(name), cpp11::as_cpp>(prevalence), cpp11::as_cpp>(transmission_rate), cpp11::as_cpp>(recovery_rate), cpp11::as_cpp>(death_rate))); END_CPP11 } // epimodels.cpp SEXP ModelSEIRD_cpp(std::string name, double prevalence, double transmission_rate, double incubation_days, double recovery_rate, double death_rate); -extern "C" SEXP _epiworldRfaster_ModelSEIRD_cpp(SEXP name, SEXP prevalence, SEXP transmission_rate, SEXP incubation_days, SEXP recovery_rate, SEXP death_rate) { +extern "C" SEXP _epiworldR_ModelSEIRD_cpp(SEXP name, SEXP prevalence, SEXP transmission_rate, SEXP incubation_days, SEXP recovery_rate, SEXP death_rate) { BEGIN_CPP11 return cpp11::as_sexp(ModelSEIRD_cpp(cpp11::as_cpp>(name), cpp11::as_cpp>(prevalence), cpp11::as_cpp>(transmission_rate), cpp11::as_cpp>(incubation_days), cpp11::as_cpp>(recovery_rate), cpp11::as_cpp>(death_rate))); END_CPP11 } // epimodels.cpp SEXP ModelSISD_cpp(std::string name, double prevalence, double transmission_rate, double recovery_rate, double death_rate); -extern "C" SEXP _epiworldRfaster_ModelSISD_cpp(SEXP name, SEXP prevalence, SEXP transmission_rate, SEXP recovery_rate, SEXP death_rate) { +extern "C" SEXP _epiworldR_ModelSISD_cpp(SEXP name, SEXP prevalence, SEXP transmission_rate, SEXP recovery_rate, SEXP death_rate) { BEGIN_CPP11 return cpp11::as_sexp(ModelSISD_cpp(cpp11::as_cpp>(name), cpp11::as_cpp>(prevalence), cpp11::as_cpp>(transmission_rate), cpp11::as_cpp>(recovery_rate), cpp11::as_cpp>(death_rate))); END_CPP11 } // epimodels.cpp SEXP ModelSIRDCONN_cpp(std::string name, unsigned int n, double prevalence, double contact_rate, double transmission_rate, double recovery_rate, double death_rate); -extern "C" SEXP _epiworldRfaster_ModelSIRDCONN_cpp(SEXP name, SEXP n, SEXP prevalence, SEXP contact_rate, SEXP transmission_rate, SEXP recovery_rate, SEXP death_rate) { +extern "C" SEXP _epiworldR_ModelSIRDCONN_cpp(SEXP name, SEXP n, SEXP prevalence, SEXP contact_rate, SEXP transmission_rate, SEXP recovery_rate, SEXP death_rate) { BEGIN_CPP11 return cpp11::as_sexp(ModelSIRDCONN_cpp(cpp11::as_cpp>(name), cpp11::as_cpp>(n), cpp11::as_cpp>(prevalence), cpp11::as_cpp>(contact_rate), cpp11::as_cpp>(transmission_rate), cpp11::as_cpp>(recovery_rate), cpp11::as_cpp>(death_rate))); END_CPP11 } // epimodels.cpp SEXP ModelSEIRDCONN_cpp(std::string name, unsigned int n, double prevalence, double contact_rate, double transmission_rate, double incubation_days, double recovery_rate, double death_rate); -extern "C" SEXP _epiworldRfaster_ModelSEIRDCONN_cpp(SEXP name, SEXP n, SEXP prevalence, SEXP contact_rate, SEXP transmission_rate, SEXP incubation_days, SEXP recovery_rate, SEXP death_rate) { +extern "C" SEXP _epiworldR_ModelSEIRDCONN_cpp(SEXP name, SEXP n, SEXP prevalence, SEXP contact_rate, SEXP transmission_rate, SEXP incubation_days, SEXP recovery_rate, SEXP death_rate) { BEGIN_CPP11 return cpp11::as_sexp(ModelSEIRDCONN_cpp(cpp11::as_cpp>(name), cpp11::as_cpp>(n), cpp11::as_cpp>(prevalence), cpp11::as_cpp>(contact_rate), cpp11::as_cpp>(transmission_rate), cpp11::as_cpp>(incubation_days), cpp11::as_cpp>(recovery_rate), cpp11::as_cpp>(death_rate))); END_CPP11 } // epimodels.cpp SEXP ModelSEIRCONN_cpp(std::string name, unsigned int n, double prevalence, double contact_rate, double transmission_rate, double incubation_days, double recovery_rate); -extern "C" SEXP _epiworldRfaster_ModelSEIRCONN_cpp(SEXP name, SEXP n, SEXP prevalence, SEXP contact_rate, SEXP transmission_rate, SEXP incubation_days, SEXP recovery_rate) { +extern "C" SEXP _epiworldR_ModelSEIRCONN_cpp(SEXP name, SEXP n, SEXP prevalence, SEXP contact_rate, SEXP transmission_rate, SEXP incubation_days, SEXP recovery_rate) { BEGIN_CPP11 return cpp11::as_sexp(ModelSEIRCONN_cpp(cpp11::as_cpp>(name), cpp11::as_cpp>(n), cpp11::as_cpp>(prevalence), cpp11::as_cpp>(contact_rate), cpp11::as_cpp>(transmission_rate), cpp11::as_cpp>(incubation_days), cpp11::as_cpp>(recovery_rate))); END_CPP11 } // epimodels.cpp SEXP ModelSIRLogit_cpp(std::string vname, SEXP data, int ncols, std::vector< double > coefs_infect, std::vector< double > coefs_recover, std::vector< int > coef_infect_cols, std::vector< int > coef_recover_cols, double prob_infection, double recovery_rate, double prevalence); -extern "C" SEXP _epiworldRfaster_ModelSIRLogit_cpp(SEXP vname, SEXP data, SEXP ncols, SEXP coefs_infect, SEXP coefs_recover, SEXP coef_infect_cols, SEXP coef_recover_cols, SEXP prob_infection, SEXP recovery_rate, SEXP prevalence) { +extern "C" SEXP _epiworldR_ModelSIRLogit_cpp(SEXP vname, SEXP data, SEXP ncols, SEXP coefs_infect, SEXP coefs_recover, SEXP coef_infect_cols, SEXP coef_recover_cols, SEXP prob_infection, SEXP recovery_rate, SEXP prevalence) { BEGIN_CPP11 return cpp11::as_sexp(ModelSIRLogit_cpp(cpp11::as_cpp>(vname), cpp11::as_cpp>(data), cpp11::as_cpp>(ncols), cpp11::as_cpp>>(coefs_infect), cpp11::as_cpp>>(coefs_recover), cpp11::as_cpp>>(coef_infect_cols), cpp11::as_cpp>>(coef_recover_cols), cpp11::as_cpp>(prob_infection), cpp11::as_cpp>(recovery_rate), cpp11::as_cpp>(prevalence))); END_CPP11 } // epimodels.cpp SEXP ModelDiffNet_cpp(std::string name, double prevalence, double prob_adopt, bool normalize_exposure, SEXP data, int data_ncols, std::vector< int > data_cols, std::vector params); -extern "C" SEXP _epiworldRfaster_ModelDiffNet_cpp(SEXP name, SEXP prevalence, SEXP prob_adopt, SEXP normalize_exposure, SEXP data, SEXP data_ncols, SEXP data_cols, SEXP params) { +extern "C" SEXP _epiworldR_ModelDiffNet_cpp(SEXP name, SEXP prevalence, SEXP prob_adopt, SEXP normalize_exposure, SEXP data, SEXP data_ncols, SEXP data_cols, SEXP params) { BEGIN_CPP11 return cpp11::as_sexp(ModelDiffNet_cpp(cpp11::as_cpp>(name), cpp11::as_cpp>(prevalence), cpp11::as_cpp>(prob_adopt), cpp11::as_cpp>(normalize_exposure), cpp11::as_cpp>(data), cpp11::as_cpp>(data_ncols), cpp11::as_cpp>>(data_cols), cpp11::as_cpp>>(params))); END_CPP11 } // model.cpp SEXP print_cpp(SEXP m, bool lite); -extern "C" SEXP _epiworldRfaster_print_cpp(SEXP m, SEXP lite) { +extern "C" SEXP _epiworldR_print_cpp(SEXP m, SEXP lite) { BEGIN_CPP11 return cpp11::as_sexp(print_cpp(cpp11::as_cpp>(m), cpp11::as_cpp>(lite))); END_CPP11 } // model.cpp SEXP agents_smallworld_cpp(SEXP m, unsigned int n, unsigned int k, bool d, double p); -extern "C" SEXP _epiworldRfaster_agents_smallworld_cpp(SEXP m, SEXP n, SEXP k, SEXP d, SEXP p) { +extern "C" SEXP _epiworldR_agents_smallworld_cpp(SEXP m, SEXP n, SEXP k, SEXP d, SEXP p) { BEGIN_CPP11 return cpp11::as_sexp(agents_smallworld_cpp(cpp11::as_cpp>(m), cpp11::as_cpp>(n), cpp11::as_cpp>(k), cpp11::as_cpp>(d), cpp11::as_cpp>(p))); END_CPP11 } // model.cpp SEXP agents_from_edgelist_cpp(SEXP m, const std::vector & source, const std::vector & target, int size, bool directed); -extern "C" SEXP _epiworldRfaster_agents_from_edgelist_cpp(SEXP m, SEXP source, SEXP target, SEXP size, SEXP directed) { +extern "C" SEXP _epiworldR_agents_from_edgelist_cpp(SEXP m, SEXP source, SEXP target, SEXP size, SEXP directed) { BEGIN_CPP11 return cpp11::as_sexp(agents_from_edgelist_cpp(cpp11::as_cpp>(m), cpp11::as_cpp &>>(source), cpp11::as_cpp &>>(target), cpp11::as_cpp>(size), cpp11::as_cpp>(directed))); END_CPP11 } // model.cpp SEXP run_cpp(SEXP m, int ndays, int seed); -extern "C" SEXP _epiworldRfaster_run_cpp(SEXP m, SEXP ndays, SEXP seed) { +extern "C" SEXP _epiworldR_run_cpp(SEXP m, SEXP ndays, SEXP seed) { BEGIN_CPP11 return cpp11::as_sexp(run_cpp(cpp11::as_cpp>(m), cpp11::as_cpp>(ndays), cpp11::as_cpp>(seed))); END_CPP11 } // model.cpp SEXP make_saver_cpp(std::string fn, bool total_hist, bool virus_info, bool virus_hist, bool tool_info, bool tool_hist, bool transmission, bool transition, bool reproductive, bool generation); -extern "C" SEXP _epiworldRfaster_make_saver_cpp(SEXP fn, SEXP total_hist, SEXP virus_info, SEXP virus_hist, SEXP tool_info, SEXP tool_hist, SEXP transmission, SEXP transition, SEXP reproductive, SEXP generation) { +extern "C" SEXP _epiworldR_make_saver_cpp(SEXP fn, SEXP total_hist, SEXP virus_info, SEXP virus_hist, SEXP tool_info, SEXP tool_hist, SEXP transmission, SEXP transition, SEXP reproductive, SEXP generation) { BEGIN_CPP11 return cpp11::as_sexp(make_saver_cpp(cpp11::as_cpp>(fn), cpp11::as_cpp>(total_hist), cpp11::as_cpp>(virus_info), cpp11::as_cpp>(virus_hist), cpp11::as_cpp>(tool_info), cpp11::as_cpp>(tool_hist), cpp11::as_cpp>(transmission), cpp11::as_cpp>(transition), cpp11::as_cpp>(reproductive), cpp11::as_cpp>(generation))); END_CPP11 } // model.cpp SEXP run_multiple_cpp(SEXP m, int ndays, int nsims, int seed, SEXP saver, bool reset, bool verbose, int nthreads); -extern "C" SEXP _epiworldRfaster_run_multiple_cpp(SEXP m, SEXP ndays, SEXP nsims, SEXP seed, SEXP saver, SEXP reset, SEXP verbose, SEXP nthreads) { +extern "C" SEXP _epiworldR_run_multiple_cpp(SEXP m, SEXP ndays, SEXP nsims, SEXP seed, SEXP saver, SEXP reset, SEXP verbose, SEXP nthreads) { BEGIN_CPP11 return cpp11::as_sexp(run_multiple_cpp(cpp11::as_cpp>(m), cpp11::as_cpp>(ndays), cpp11::as_cpp>(nsims), cpp11::as_cpp>(seed), cpp11::as_cpp>(saver), cpp11::as_cpp>(reset), cpp11::as_cpp>(verbose), cpp11::as_cpp>(nthreads))); END_CPP11 } // model.cpp SEXP queuing_on_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_queuing_on_cpp(SEXP model) { +extern "C" SEXP _epiworldR_queuing_on_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(queuing_on_cpp(cpp11::as_cpp>(model))); END_CPP11 } // model.cpp SEXP queuing_off_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_queuing_off_cpp(SEXP model) { +extern "C" SEXP _epiworldR_queuing_off_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(queuing_off_cpp(cpp11::as_cpp>(model))); END_CPP11 } // model.cpp double get_param_cpp(SEXP model, std::string pname); -extern "C" SEXP _epiworldRfaster_get_param_cpp(SEXP model, SEXP pname) { +extern "C" SEXP _epiworldR_get_param_cpp(SEXP model, SEXP pname) { BEGIN_CPP11 return cpp11::as_sexp(get_param_cpp(cpp11::as_cpp>(model), cpp11::as_cpp>(pname))); END_CPP11 } // model.cpp SEXP set_param_cpp(SEXP model, std::string pname, double val); -extern "C" SEXP _epiworldRfaster_set_param_cpp(SEXP model, SEXP pname, SEXP val) { +extern "C" SEXP _epiworldR_set_param_cpp(SEXP model, SEXP pname, SEXP val) { BEGIN_CPP11 return cpp11::as_sexp(set_param_cpp(cpp11::as_cpp>(model), cpp11::as_cpp>(pname), cpp11::as_cpp>(val))); END_CPP11 } // model.cpp SEXP set_name_cpp(SEXP model, std::string mname); -extern "C" SEXP _epiworldRfaster_set_name_cpp(SEXP model, SEXP mname) { +extern "C" SEXP _epiworldR_set_name_cpp(SEXP model, SEXP mname) { BEGIN_CPP11 return cpp11::as_sexp(set_name_cpp(cpp11::as_cpp>(model), cpp11::as_cpp>(mname))); END_CPP11 } // model.cpp std::string get_name_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_name_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_name_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_name_cpp(cpp11::as_cpp>(model))); END_CPP11 } // model.cpp strings get_states_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_states_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_states_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_states_cpp(cpp11::as_cpp>(model))); END_CPP11 } // model.cpp SEXP verbose_on_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_verbose_on_cpp(SEXP model) { +extern "C" SEXP _epiworldR_verbose_on_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(verbose_on_cpp(cpp11::as_cpp>(model))); END_CPP11 } // model.cpp SEXP verbose_off_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_verbose_off_cpp(SEXP model) { +extern "C" SEXP _epiworldR_verbose_off_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(verbose_off_cpp(cpp11::as_cpp>(model))); END_CPP11 } // model.cpp int get_n_viruses_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_n_viruses_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_n_viruses_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_n_viruses_cpp(cpp11::as_cpp>(model))); END_CPP11 } // model.cpp int get_n_tools_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_n_tools_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_n_tools_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_n_tools_cpp(cpp11::as_cpp>(model))); END_CPP11 } // model.cpp int get_ndays_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_ndays_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_ndays_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_ndays_cpp(cpp11::as_cpp>(model))); END_CPP11 } // model.cpp int get_n_replicates_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_n_replicates_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_n_replicates_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_n_replicates_cpp(cpp11::as_cpp>(model))); END_CPP11 } // model.cpp int size_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_size_cpp(SEXP model) { +extern "C" SEXP _epiworldR_size_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(size_cpp(cpp11::as_cpp>(model))); END_CPP11 } // model.cpp SEXP set_agents_data_cpp(SEXP model, SEXP data, int ncols); -extern "C" SEXP _epiworldRfaster_set_agents_data_cpp(SEXP model, SEXP data, SEXP ncols) { +extern "C" SEXP _epiworldR_set_agents_data_cpp(SEXP model, SEXP data, SEXP ncols) { BEGIN_CPP11 return cpp11::as_sexp(set_agents_data_cpp(cpp11::as_cpp>(model), cpp11::as_cpp>(data), cpp11::as_cpp>(ncols))); END_CPP11 } // model.cpp int get_agents_data_ncols_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_agents_data_ncols_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_agents_data_ncols_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_agents_data_ncols_cpp(cpp11::as_cpp>(model))); END_CPP11 } // model.cpp SEXP get_virus_model_cpp(SEXP model, int virus_pos); -extern "C" SEXP _epiworldRfaster_get_virus_model_cpp(SEXP model, SEXP virus_pos) { +extern "C" SEXP _epiworldR_get_virus_model_cpp(SEXP model, SEXP virus_pos) { BEGIN_CPP11 return cpp11::as_sexp(get_virus_model_cpp(cpp11::as_cpp>(model), cpp11::as_cpp>(virus_pos))); END_CPP11 } // model.cpp SEXP get_tool_model_cpp(SEXP model, int tool_pos); -extern "C" SEXP _epiworldRfaster_get_tool_model_cpp(SEXP model, SEXP tool_pos) { +extern "C" SEXP _epiworldR_get_tool_model_cpp(SEXP model, SEXP tool_pos) { BEGIN_CPP11 return cpp11::as_sexp(get_tool_model_cpp(cpp11::as_cpp>(model), cpp11::as_cpp>(tool_pos))); END_CPP11 } // model.cpp cpp11::data_frame get_network_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_network_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_network_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_network_cpp(cpp11::as_cpp>(model))); END_CPP11 } // tool.cpp SEXP tool_cpp(std::string name, double susceptibility_reduction, double transmission_reduction, double recovery_enhancer, double death_reduction); -extern "C" SEXP _epiworldRfaster_tool_cpp(SEXP name, SEXP susceptibility_reduction, SEXP transmission_reduction, SEXP recovery_enhancer, SEXP death_reduction) { +extern "C" SEXP _epiworldR_tool_cpp(SEXP name, SEXP susceptibility_reduction, SEXP transmission_reduction, SEXP recovery_enhancer, SEXP death_reduction) { BEGIN_CPP11 return cpp11::as_sexp(tool_cpp(cpp11::as_cpp>(name), cpp11::as_cpp>(susceptibility_reduction), cpp11::as_cpp>(transmission_reduction), cpp11::as_cpp>(recovery_enhancer), cpp11::as_cpp>(death_reduction))); END_CPP11 } // tool.cpp int add_tool_cpp(SEXP m, SEXP t, double preval); -extern "C" SEXP _epiworldRfaster_add_tool_cpp(SEXP m, SEXP t, SEXP preval) { +extern "C" SEXP _epiworldR_add_tool_cpp(SEXP m, SEXP t, SEXP preval) { BEGIN_CPP11 return cpp11::as_sexp(add_tool_cpp(cpp11::as_cpp>(m), cpp11::as_cpp>(t), cpp11::as_cpp>(preval))); END_CPP11 } // tool.cpp int add_tool_n_cpp(SEXP m, SEXP t, size_t preval); -extern "C" SEXP _epiworldRfaster_add_tool_n_cpp(SEXP m, SEXP t, SEXP preval) { +extern "C" SEXP _epiworldR_add_tool_n_cpp(SEXP m, SEXP t, SEXP preval) { BEGIN_CPP11 return cpp11::as_sexp(add_tool_n_cpp(cpp11::as_cpp>(m), cpp11::as_cpp>(t), cpp11::as_cpp>(preval))); END_CPP11 } // tool.cpp SEXP rm_tool_cpp(SEXP m, size_t tool_pos); -extern "C" SEXP _epiworldRfaster_rm_tool_cpp(SEXP m, SEXP tool_pos) { +extern "C" SEXP _epiworldR_rm_tool_cpp(SEXP m, SEXP tool_pos) { BEGIN_CPP11 return cpp11::as_sexp(rm_tool_cpp(cpp11::as_cpp>(m), cpp11::as_cpp>(tool_pos))); END_CPP11 } // tool.cpp SEXP tool_fun_logit_cpp(integers vars, doubles coefs, SEXP model); -extern "C" SEXP _epiworldRfaster_tool_fun_logit_cpp(SEXP vars, SEXP coefs, SEXP model) { +extern "C" SEXP _epiworldR_tool_fun_logit_cpp(SEXP vars, SEXP coefs, SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(tool_fun_logit_cpp(cpp11::as_cpp>(vars), cpp11::as_cpp>(coefs), cpp11::as_cpp>(model))); END_CPP11 } // tool.cpp SEXP set_transmission_reduction_cpp(SEXP tool, double prob); -extern "C" SEXP _epiworldRfaster_set_transmission_reduction_cpp(SEXP tool, SEXP prob) { +extern "C" SEXP _epiworldR_set_transmission_reduction_cpp(SEXP tool, SEXP prob) { BEGIN_CPP11 return cpp11::as_sexp(set_transmission_reduction_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>(prob))); END_CPP11 } // tool.cpp SEXP set_transmission_reduction_ptr_cpp(SEXP tool, SEXP model, std::string param); -extern "C" SEXP _epiworldRfaster_set_transmission_reduction_ptr_cpp(SEXP tool, SEXP model, SEXP param) { +extern "C" SEXP _epiworldR_set_transmission_reduction_ptr_cpp(SEXP tool, SEXP model, SEXP param) { BEGIN_CPP11 return cpp11::as_sexp(set_transmission_reduction_ptr_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>(model), cpp11::as_cpp>(param))); END_CPP11 } // tool.cpp SEXP set_transmission_reduction_fun_cpp(SEXP tool, SEXP model, SEXP tfun); -extern "C" SEXP _epiworldRfaster_set_transmission_reduction_fun_cpp(SEXP tool, SEXP model, SEXP tfun) { +extern "C" SEXP _epiworldR_set_transmission_reduction_fun_cpp(SEXP tool, SEXP model, SEXP tfun) { BEGIN_CPP11 return cpp11::as_sexp(set_transmission_reduction_fun_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>(model), cpp11::as_cpp>(tfun))); END_CPP11 } // tool.cpp SEXP set_susceptibility_reduction_cpp(SEXP tool, double prob); -extern "C" SEXP _epiworldRfaster_set_susceptibility_reduction_cpp(SEXP tool, SEXP prob) { +extern "C" SEXP _epiworldR_set_susceptibility_reduction_cpp(SEXP tool, SEXP prob) { BEGIN_CPP11 return cpp11::as_sexp(set_susceptibility_reduction_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>(prob))); END_CPP11 } // tool.cpp SEXP set_susceptibility_reduction_ptr_cpp(SEXP tool, SEXP model, std::string param); -extern "C" SEXP _epiworldRfaster_set_susceptibility_reduction_ptr_cpp(SEXP tool, SEXP model, SEXP param) { +extern "C" SEXP _epiworldR_set_susceptibility_reduction_ptr_cpp(SEXP tool, SEXP model, SEXP param) { BEGIN_CPP11 return cpp11::as_sexp(set_susceptibility_reduction_ptr_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>(model), cpp11::as_cpp>(param))); END_CPP11 } // tool.cpp SEXP set_susceptibility_reduction_fun_cpp(SEXP tool, SEXP model, SEXP tfun); -extern "C" SEXP _epiworldRfaster_set_susceptibility_reduction_fun_cpp(SEXP tool, SEXP model, SEXP tfun) { +extern "C" SEXP _epiworldR_set_susceptibility_reduction_fun_cpp(SEXP tool, SEXP model, SEXP tfun) { BEGIN_CPP11 return cpp11::as_sexp(set_susceptibility_reduction_fun_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>(model), cpp11::as_cpp>(tfun))); END_CPP11 } // tool.cpp SEXP set_recovery_enhancer_cpp(SEXP tool, double prob); -extern "C" SEXP _epiworldRfaster_set_recovery_enhancer_cpp(SEXP tool, SEXP prob) { +extern "C" SEXP _epiworldR_set_recovery_enhancer_cpp(SEXP tool, SEXP prob) { BEGIN_CPP11 return cpp11::as_sexp(set_recovery_enhancer_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>(prob))); END_CPP11 } // tool.cpp SEXP set_recovery_enhancer_ptr_cpp(SEXP tool, SEXP model, std::string param); -extern "C" SEXP _epiworldRfaster_set_recovery_enhancer_ptr_cpp(SEXP tool, SEXP model, SEXP param) { +extern "C" SEXP _epiworldR_set_recovery_enhancer_ptr_cpp(SEXP tool, SEXP model, SEXP param) { BEGIN_CPP11 return cpp11::as_sexp(set_recovery_enhancer_ptr_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>(model), cpp11::as_cpp>(param))); END_CPP11 } // tool.cpp SEXP set_recovery_enhancer_fun_cpp(SEXP tool, SEXP model, SEXP tfun); -extern "C" SEXP _epiworldRfaster_set_recovery_enhancer_fun_cpp(SEXP tool, SEXP model, SEXP tfun) { +extern "C" SEXP _epiworldR_set_recovery_enhancer_fun_cpp(SEXP tool, SEXP model, SEXP tfun) { BEGIN_CPP11 return cpp11::as_sexp(set_recovery_enhancer_fun_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>(model), cpp11::as_cpp>(tfun))); END_CPP11 } // tool.cpp SEXP set_death_reduction_cpp(SEXP tool, double prob); -extern "C" SEXP _epiworldRfaster_set_death_reduction_cpp(SEXP tool, SEXP prob) { +extern "C" SEXP _epiworldR_set_death_reduction_cpp(SEXP tool, SEXP prob) { BEGIN_CPP11 return cpp11::as_sexp(set_death_reduction_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>(prob))); END_CPP11 } // tool.cpp SEXP set_death_reduction_ptr_cpp(SEXP tool, SEXP model, std::string param); -extern "C" SEXP _epiworldRfaster_set_death_reduction_ptr_cpp(SEXP tool, SEXP model, SEXP param) { +extern "C" SEXP _epiworldR_set_death_reduction_ptr_cpp(SEXP tool, SEXP model, SEXP param) { BEGIN_CPP11 return cpp11::as_sexp(set_death_reduction_ptr_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>(model), cpp11::as_cpp>(param))); END_CPP11 } // tool.cpp SEXP set_death_reduction_fun_cpp(SEXP tool, SEXP model, SEXP tfun); -extern "C" SEXP _epiworldRfaster_set_death_reduction_fun_cpp(SEXP tool, SEXP model, SEXP tfun) { +extern "C" SEXP _epiworldR_set_death_reduction_fun_cpp(SEXP tool, SEXP model, SEXP tfun) { BEGIN_CPP11 return cpp11::as_sexp(set_death_reduction_fun_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>(model), cpp11::as_cpp>(tfun))); END_CPP11 } // tool.cpp std::string get_name_tool_cpp(SEXP tool); -extern "C" SEXP _epiworldRfaster_get_name_tool_cpp(SEXP tool) { +extern "C" SEXP _epiworldR_get_name_tool_cpp(SEXP tool) { BEGIN_CPP11 return cpp11::as_sexp(get_name_tool_cpp(cpp11::as_cpp>(tool))); END_CPP11 } // tool.cpp SEXP set_name_tool_cpp(SEXP tool, std::string name); -extern "C" SEXP _epiworldRfaster_set_name_tool_cpp(SEXP tool, SEXP name) { +extern "C" SEXP _epiworldR_set_name_tool_cpp(SEXP tool, SEXP name) { BEGIN_CPP11 return cpp11::as_sexp(set_name_tool_cpp(cpp11::as_cpp>(tool), cpp11::as_cpp>(name))); END_CPP11 } // tool.cpp SEXP print_tool_cpp(SEXP t); -extern "C" SEXP _epiworldRfaster_print_tool_cpp(SEXP t) { +extern "C" SEXP _epiworldR_print_tool_cpp(SEXP t) { BEGIN_CPP11 return cpp11::as_sexp(print_tool_cpp(cpp11::as_cpp>(t))); END_CPP11 } // tool.cpp cpp11::writable::list get_agents_tools_cpp(SEXP model); -extern "C" SEXP _epiworldRfaster_get_agents_tools_cpp(SEXP model) { +extern "C" SEXP _epiworldR_get_agents_tools_cpp(SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(get_agents_tools_cpp(cpp11::as_cpp>(model))); END_CPP11 } // tool.cpp SEXP print_agent_tools_cpp(SEXP tools); -extern "C" SEXP _epiworldRfaster_print_agent_tools_cpp(SEXP tools) { +extern "C" SEXP _epiworldR_print_agent_tools_cpp(SEXP tools) { BEGIN_CPP11 return cpp11::as_sexp(print_agent_tools_cpp(cpp11::as_cpp>(tools))); END_CPP11 } // virus.cpp SEXP virus_cpp(std::string name, double prob_infecting, double prob_recovery, double prob_death, double post_immunity, double incubation); -extern "C" SEXP _epiworldRfaster_virus_cpp(SEXP name, SEXP prob_infecting, SEXP prob_recovery, SEXP prob_death, SEXP post_immunity, SEXP incubation) { +extern "C" SEXP _epiworldR_virus_cpp(SEXP name, SEXP prob_infecting, SEXP prob_recovery, SEXP prob_death, SEXP post_immunity, SEXP incubation) { BEGIN_CPP11 return cpp11::as_sexp(virus_cpp(cpp11::as_cpp>(name), cpp11::as_cpp>(prob_infecting), cpp11::as_cpp>(prob_recovery), cpp11::as_cpp>(prob_death), cpp11::as_cpp>(post_immunity), cpp11::as_cpp>(incubation))); END_CPP11 } // virus.cpp SEXP virus_set_state_cpp(SEXP v, size_t init, size_t end, size_t removed); -extern "C" SEXP _epiworldRfaster_virus_set_state_cpp(SEXP v, SEXP init, SEXP end, SEXP removed) { +extern "C" SEXP _epiworldR_virus_set_state_cpp(SEXP v, SEXP init, SEXP end, SEXP removed) { BEGIN_CPP11 return cpp11::as_sexp(virus_set_state_cpp(cpp11::as_cpp>(v), cpp11::as_cpp>(init), cpp11::as_cpp>(end), cpp11::as_cpp>(removed))); END_CPP11 } // virus.cpp SEXP add_virus_cpp(SEXP m, SEXP v, double preval); -extern "C" SEXP _epiworldRfaster_add_virus_cpp(SEXP m, SEXP v, SEXP preval) { +extern "C" SEXP _epiworldR_add_virus_cpp(SEXP m, SEXP v, SEXP preval) { BEGIN_CPP11 return cpp11::as_sexp(add_virus_cpp(cpp11::as_cpp>(m), cpp11::as_cpp>(v), cpp11::as_cpp>(preval))); END_CPP11 } // virus.cpp SEXP add_virus_n_cpp(SEXP m, SEXP v, size_t preval); -extern "C" SEXP _epiworldRfaster_add_virus_n_cpp(SEXP m, SEXP v, SEXP preval) { +extern "C" SEXP _epiworldR_add_virus_n_cpp(SEXP m, SEXP v, SEXP preval) { BEGIN_CPP11 return cpp11::as_sexp(add_virus_n_cpp(cpp11::as_cpp>(m), cpp11::as_cpp>(v), cpp11::as_cpp>(preval))); END_CPP11 } // virus.cpp SEXP rm_virus_cpp(SEXP m, size_t virus_pos); -extern "C" SEXP _epiworldRfaster_rm_virus_cpp(SEXP m, SEXP virus_pos) { +extern "C" SEXP _epiworldR_rm_virus_cpp(SEXP m, SEXP virus_pos) { BEGIN_CPP11 return cpp11::as_sexp(rm_virus_cpp(cpp11::as_cpp>(m), cpp11::as_cpp>(virus_pos))); END_CPP11 } // virus.cpp SEXP print_virus_cpp(SEXP v); -extern "C" SEXP _epiworldRfaster_print_virus_cpp(SEXP v) { +extern "C" SEXP _epiworldR_print_virus_cpp(SEXP v) { BEGIN_CPP11 return cpp11::as_sexp(print_virus_cpp(cpp11::as_cpp>(v))); END_CPP11 } // virus.cpp SEXP virus_fun_logit_cpp(integers vars, doubles coefs, SEXP model); -extern "C" SEXP _epiworldRfaster_virus_fun_logit_cpp(SEXP vars, SEXP coefs, SEXP model) { +extern "C" SEXP _epiworldR_virus_fun_logit_cpp(SEXP vars, SEXP coefs, SEXP model) { BEGIN_CPP11 return cpp11::as_sexp(virus_fun_logit_cpp(cpp11::as_cpp>(vars), cpp11::as_cpp>(coefs), cpp11::as_cpp>(model))); END_CPP11 } // virus.cpp SEXP set_prob_infecting_cpp(SEXP virus, double prob); -extern "C" SEXP _epiworldRfaster_set_prob_infecting_cpp(SEXP virus, SEXP prob) { +extern "C" SEXP _epiworldR_set_prob_infecting_cpp(SEXP virus, SEXP prob) { BEGIN_CPP11 return cpp11::as_sexp(set_prob_infecting_cpp(cpp11::as_cpp>(virus), cpp11::as_cpp>(prob))); END_CPP11 } // virus.cpp SEXP set_prob_infecting_ptr_cpp(SEXP virus, SEXP model, std::string param); -extern "C" SEXP _epiworldRfaster_set_prob_infecting_ptr_cpp(SEXP virus, SEXP model, SEXP param) { +extern "C" SEXP _epiworldR_set_prob_infecting_ptr_cpp(SEXP virus, SEXP model, SEXP param) { BEGIN_CPP11 return cpp11::as_sexp(set_prob_infecting_ptr_cpp(cpp11::as_cpp>(virus), cpp11::as_cpp>(model), cpp11::as_cpp>(param))); END_CPP11 } // virus.cpp SEXP set_prob_infecting_fun_cpp(SEXP virus, SEXP model, SEXP vfun); -extern "C" SEXP _epiworldRfaster_set_prob_infecting_fun_cpp(SEXP virus, SEXP model, SEXP vfun) { +extern "C" SEXP _epiworldR_set_prob_infecting_fun_cpp(SEXP virus, SEXP model, SEXP vfun) { BEGIN_CPP11 return cpp11::as_sexp(set_prob_infecting_fun_cpp(cpp11::as_cpp>(virus), cpp11::as_cpp>(model), cpp11::as_cpp>(vfun))); END_CPP11 } // virus.cpp SEXP set_prob_recovery_cpp(SEXP virus, double prob); -extern "C" SEXP _epiworldRfaster_set_prob_recovery_cpp(SEXP virus, SEXP prob) { +extern "C" SEXP _epiworldR_set_prob_recovery_cpp(SEXP virus, SEXP prob) { BEGIN_CPP11 return cpp11::as_sexp(set_prob_recovery_cpp(cpp11::as_cpp>(virus), cpp11::as_cpp>(prob))); END_CPP11 } // virus.cpp SEXP set_prob_recovery_ptr_cpp(SEXP virus, SEXP model, std::string param); -extern "C" SEXP _epiworldRfaster_set_prob_recovery_ptr_cpp(SEXP virus, SEXP model, SEXP param) { +extern "C" SEXP _epiworldR_set_prob_recovery_ptr_cpp(SEXP virus, SEXP model, SEXP param) { BEGIN_CPP11 return cpp11::as_sexp(set_prob_recovery_ptr_cpp(cpp11::as_cpp>(virus), cpp11::as_cpp>(model), cpp11::as_cpp>(param))); END_CPP11 } // virus.cpp SEXP set_prob_recovery_fun_cpp(SEXP virus, SEXP model, SEXP vfun); -extern "C" SEXP _epiworldRfaster_set_prob_recovery_fun_cpp(SEXP virus, SEXP model, SEXP vfun) { +extern "C" SEXP _epiworldR_set_prob_recovery_fun_cpp(SEXP virus, SEXP model, SEXP vfun) { BEGIN_CPP11 return cpp11::as_sexp(set_prob_recovery_fun_cpp(cpp11::as_cpp>(virus), cpp11::as_cpp>(model), cpp11::as_cpp>(vfun))); END_CPP11 } // virus.cpp SEXP set_prob_death_cpp(SEXP virus, double prob); -extern "C" SEXP _epiworldRfaster_set_prob_death_cpp(SEXP virus, SEXP prob) { +extern "C" SEXP _epiworldR_set_prob_death_cpp(SEXP virus, SEXP prob) { BEGIN_CPP11 return cpp11::as_sexp(set_prob_death_cpp(cpp11::as_cpp>(virus), cpp11::as_cpp>(prob))); END_CPP11 } // virus.cpp SEXP set_prob_death_ptr_cpp(SEXP virus, SEXP model, std::string param); -extern "C" SEXP _epiworldRfaster_set_prob_death_ptr_cpp(SEXP virus, SEXP model, SEXP param) { +extern "C" SEXP _epiworldR_set_prob_death_ptr_cpp(SEXP virus, SEXP model, SEXP param) { BEGIN_CPP11 return cpp11::as_sexp(set_prob_death_ptr_cpp(cpp11::as_cpp>(virus), cpp11::as_cpp>(model), cpp11::as_cpp>(param))); END_CPP11 } // virus.cpp SEXP set_prob_death_fun_cpp(SEXP virus, SEXP model, SEXP vfun); -extern "C" SEXP _epiworldRfaster_set_prob_death_fun_cpp(SEXP virus, SEXP model, SEXP vfun) { +extern "C" SEXP _epiworldR_set_prob_death_fun_cpp(SEXP virus, SEXP model, SEXP vfun) { BEGIN_CPP11 return cpp11::as_sexp(set_prob_death_fun_cpp(cpp11::as_cpp>(virus), cpp11::as_cpp>(model), cpp11::as_cpp>(vfun))); END_CPP11 } // virus.cpp SEXP set_incubation_cpp(SEXP virus, double prob); -extern "C" SEXP _epiworldRfaster_set_incubation_cpp(SEXP virus, SEXP prob) { +extern "C" SEXP _epiworldR_set_incubation_cpp(SEXP virus, SEXP prob) { BEGIN_CPP11 return cpp11::as_sexp(set_incubation_cpp(cpp11::as_cpp>(virus), cpp11::as_cpp>(prob))); END_CPP11 } // virus.cpp SEXP set_incubation_ptr_cpp(SEXP virus, SEXP model, std::string param); -extern "C" SEXP _epiworldRfaster_set_incubation_ptr_cpp(SEXP virus, SEXP model, SEXP param) { +extern "C" SEXP _epiworldR_set_incubation_ptr_cpp(SEXP virus, SEXP model, SEXP param) { BEGIN_CPP11 return cpp11::as_sexp(set_incubation_ptr_cpp(cpp11::as_cpp>(virus), cpp11::as_cpp>(model), cpp11::as_cpp>(param))); END_CPP11 } // virus.cpp SEXP set_incubation_fun_cpp(SEXP virus, SEXP model, SEXP vfun); -extern "C" SEXP _epiworldRfaster_set_incubation_fun_cpp(SEXP virus, SEXP model, SEXP vfun) { +extern "C" SEXP _epiworldR_set_incubation_fun_cpp(SEXP virus, SEXP model, SEXP vfun) { BEGIN_CPP11 return cpp11::as_sexp(set_incubation_fun_cpp(cpp11::as_cpp>(virus), cpp11::as_cpp>(model), cpp11::as_cpp>(vfun))); END_CPP11 } // virus.cpp std::string get_name_virus_cpp(SEXP virus); -extern "C" SEXP _epiworldRfaster_get_name_virus_cpp(SEXP virus) { +extern "C" SEXP _epiworldR_get_name_virus_cpp(SEXP virus) { BEGIN_CPP11 return cpp11::as_sexp(get_name_virus_cpp(cpp11::as_cpp>(virus))); END_CPP11 } // virus.cpp SEXP set_name_virus_cpp(SEXP virus, std::string name); -extern "C" SEXP _epiworldRfaster_set_name_virus_cpp(SEXP virus, SEXP name) { +extern "C" SEXP _epiworldR_set_name_virus_cpp(SEXP virus, SEXP name) { BEGIN_CPP11 return cpp11::as_sexp(set_name_virus_cpp(cpp11::as_cpp>(virus), cpp11::as_cpp>(name))); END_CPP11 @@ -757,118 +757,118 @@ extern "C" SEXP _epiworldRfaster_set_name_virus_cpp(SEXP virus, SEXP name) { extern "C" { static const R_CallMethodDef CallEntries[] = { - {"_epiworldRfaster_ModelDiffNet_cpp", (DL_FUNC) &_epiworldRfaster_ModelDiffNet_cpp, 8}, - {"_epiworldRfaster_ModelSEIRCONN_cpp", (DL_FUNC) &_epiworldRfaster_ModelSEIRCONN_cpp, 7}, - {"_epiworldRfaster_ModelSEIRDCONN_cpp", (DL_FUNC) &_epiworldRfaster_ModelSEIRDCONN_cpp, 8}, - {"_epiworldRfaster_ModelSEIRD_cpp", (DL_FUNC) &_epiworldRfaster_ModelSEIRD_cpp, 6}, - {"_epiworldRfaster_ModelSEIR_cpp", (DL_FUNC) &_epiworldRfaster_ModelSEIR_cpp, 5}, - {"_epiworldRfaster_ModelSIRCONN_cpp", (DL_FUNC) &_epiworldRfaster_ModelSIRCONN_cpp, 6}, - {"_epiworldRfaster_ModelSIRDCONN_cpp", (DL_FUNC) &_epiworldRfaster_ModelSIRDCONN_cpp, 7}, - {"_epiworldRfaster_ModelSIRD_cpp", (DL_FUNC) &_epiworldRfaster_ModelSIRD_cpp, 5}, - {"_epiworldRfaster_ModelSIRLogit_cpp", (DL_FUNC) &_epiworldRfaster_ModelSIRLogit_cpp, 10}, - {"_epiworldRfaster_ModelSIR_cpp", (DL_FUNC) &_epiworldRfaster_ModelSIR_cpp, 4}, - {"_epiworldRfaster_ModelSISD_cpp", (DL_FUNC) &_epiworldRfaster_ModelSISD_cpp, 5}, - {"_epiworldRfaster_ModelSIS_cpp", (DL_FUNC) &_epiworldRfaster_ModelSIS_cpp, 4}, - {"_epiworldRfaster_ModelSURV_cpp", (DL_FUNC) &_epiworldRfaster_ModelSURV_cpp, 13}, - {"_epiworldRfaster_add_global_action_cpp", (DL_FUNC) &_epiworldRfaster_add_global_action_cpp, 2}, - {"_epiworldRfaster_add_tool_agent_cpp", (DL_FUNC) &_epiworldRfaster_add_tool_agent_cpp, 5}, - {"_epiworldRfaster_add_tool_cpp", (DL_FUNC) &_epiworldRfaster_add_tool_cpp, 3}, - {"_epiworldRfaster_add_tool_n_cpp", (DL_FUNC) &_epiworldRfaster_add_tool_n_cpp, 3}, - {"_epiworldRfaster_add_virus_agent_cpp", (DL_FUNC) &_epiworldRfaster_add_virus_agent_cpp, 5}, - {"_epiworldRfaster_add_virus_cpp", (DL_FUNC) &_epiworldRfaster_add_virus_cpp, 3}, - {"_epiworldRfaster_add_virus_n_cpp", (DL_FUNC) &_epiworldRfaster_add_virus_n_cpp, 3}, - {"_epiworldRfaster_agents_from_edgelist_cpp", (DL_FUNC) &_epiworldRfaster_agents_from_edgelist_cpp, 5}, - {"_epiworldRfaster_agents_smallworld_cpp", (DL_FUNC) &_epiworldRfaster_agents_smallworld_cpp, 5}, - {"_epiworldRfaster_change_state_cpp", (DL_FUNC) &_epiworldRfaster_change_state_cpp, 4}, - {"_epiworldRfaster_get_agent_cpp", (DL_FUNC) &_epiworldRfaster_get_agent_cpp, 2}, - {"_epiworldRfaster_get_agents_cpp", (DL_FUNC) &_epiworldRfaster_get_agents_cpp, 1}, - {"_epiworldRfaster_get_agents_data_ncols_cpp", (DL_FUNC) &_epiworldRfaster_get_agents_data_ncols_cpp, 1}, - {"_epiworldRfaster_get_agents_states_cpp", (DL_FUNC) &_epiworldRfaster_get_agents_states_cpp, 1}, - {"_epiworldRfaster_get_agents_tools_cpp", (DL_FUNC) &_epiworldRfaster_get_agents_tools_cpp, 1}, - {"_epiworldRfaster_get_generation_time_cpp", (DL_FUNC) &_epiworldRfaster_get_generation_time_cpp, 1}, - {"_epiworldRfaster_get_hist_tool_cpp", (DL_FUNC) &_epiworldRfaster_get_hist_tool_cpp, 1}, - {"_epiworldRfaster_get_hist_total_cpp", (DL_FUNC) &_epiworldRfaster_get_hist_total_cpp, 1}, - {"_epiworldRfaster_get_hist_transition_matrix_cpp", (DL_FUNC) &_epiworldRfaster_get_hist_transition_matrix_cpp, 2}, - {"_epiworldRfaster_get_hist_virus_cpp", (DL_FUNC) &_epiworldRfaster_get_hist_virus_cpp, 1}, - {"_epiworldRfaster_get_n_replicates_cpp", (DL_FUNC) &_epiworldRfaster_get_n_replicates_cpp, 1}, - {"_epiworldRfaster_get_n_tools_cpp", (DL_FUNC) &_epiworldRfaster_get_n_tools_cpp, 1}, - {"_epiworldRfaster_get_n_viruses_cpp", (DL_FUNC) &_epiworldRfaster_get_n_viruses_cpp, 1}, - {"_epiworldRfaster_get_name_cpp", (DL_FUNC) &_epiworldRfaster_get_name_cpp, 1}, - {"_epiworldRfaster_get_name_tool_cpp", (DL_FUNC) &_epiworldRfaster_get_name_tool_cpp, 1}, - {"_epiworldRfaster_get_name_virus_cpp", (DL_FUNC) &_epiworldRfaster_get_name_virus_cpp, 1}, - {"_epiworldRfaster_get_ndays_cpp", (DL_FUNC) &_epiworldRfaster_get_ndays_cpp, 1}, - {"_epiworldRfaster_get_network_cpp", (DL_FUNC) &_epiworldRfaster_get_network_cpp, 1}, - {"_epiworldRfaster_get_param_cpp", (DL_FUNC) &_epiworldRfaster_get_param_cpp, 2}, - {"_epiworldRfaster_get_reproductive_number_cpp", (DL_FUNC) &_epiworldRfaster_get_reproductive_number_cpp, 1}, - {"_epiworldRfaster_get_state_agent_cpp", (DL_FUNC) &_epiworldRfaster_get_state_agent_cpp, 1}, - {"_epiworldRfaster_get_states_cpp", (DL_FUNC) &_epiworldRfaster_get_states_cpp, 1}, - {"_epiworldRfaster_get_today_total_cpp", (DL_FUNC) &_epiworldRfaster_get_today_total_cpp, 1}, - {"_epiworldRfaster_get_tool_model_cpp", (DL_FUNC) &_epiworldRfaster_get_tool_model_cpp, 2}, - {"_epiworldRfaster_get_transition_probability_cpp", (DL_FUNC) &_epiworldRfaster_get_transition_probability_cpp, 1}, - {"_epiworldRfaster_get_transmissions_cpp", (DL_FUNC) &_epiworldRfaster_get_transmissions_cpp, 1}, - {"_epiworldRfaster_get_virus_model_cpp", (DL_FUNC) &_epiworldRfaster_get_virus_model_cpp, 2}, - {"_epiworldRfaster_globalaction_fun_cpp", (DL_FUNC) &_epiworldRfaster_globalaction_fun_cpp, 3}, - {"_epiworldRfaster_globalaction_set_param_cpp", (DL_FUNC) &_epiworldRfaster_globalaction_set_param_cpp, 4}, - {"_epiworldRfaster_globalaction_tool_cpp", (DL_FUNC) &_epiworldRfaster_globalaction_tool_cpp, 4}, - {"_epiworldRfaster_globalaction_tool_logit_cpp", (DL_FUNC) &_epiworldRfaster_globalaction_tool_logit_cpp, 5}, - {"_epiworldRfaster_has_tool_cpp", (DL_FUNC) &_epiworldRfaster_has_tool_cpp, 2}, - {"_epiworldRfaster_has_virus_cpp", (DL_FUNC) &_epiworldRfaster_has_virus_cpp, 2}, - {"_epiworldRfaster_make_saver_cpp", (DL_FUNC) &_epiworldRfaster_make_saver_cpp, 10}, - {"_epiworldRfaster_print_agent_cpp", (DL_FUNC) &_epiworldRfaster_print_agent_cpp, 3}, - {"_epiworldRfaster_print_agent_tools_cpp", (DL_FUNC) &_epiworldRfaster_print_agent_tools_cpp, 1}, - {"_epiworldRfaster_print_cpp", (DL_FUNC) &_epiworldRfaster_print_cpp, 2}, - {"_epiworldRfaster_print_global_action_cpp", (DL_FUNC) &_epiworldRfaster_print_global_action_cpp, 1}, - {"_epiworldRfaster_print_tool_cpp", (DL_FUNC) &_epiworldRfaster_print_tool_cpp, 1}, - {"_epiworldRfaster_print_virus_cpp", (DL_FUNC) &_epiworldRfaster_print_virus_cpp, 1}, - {"_epiworldRfaster_queuing_off_cpp", (DL_FUNC) &_epiworldRfaster_queuing_off_cpp, 1}, - {"_epiworldRfaster_queuing_on_cpp", (DL_FUNC) &_epiworldRfaster_queuing_on_cpp, 1}, - {"_epiworldRfaster_rm_global_action_cpp", (DL_FUNC) &_epiworldRfaster_rm_global_action_cpp, 2}, - {"_epiworldRfaster_rm_tool_cpp", (DL_FUNC) &_epiworldRfaster_rm_tool_cpp, 2}, - {"_epiworldRfaster_rm_virus_cpp", (DL_FUNC) &_epiworldRfaster_rm_virus_cpp, 2}, - {"_epiworldRfaster_run_cpp", (DL_FUNC) &_epiworldRfaster_run_cpp, 3}, - {"_epiworldRfaster_run_multiple_cpp", (DL_FUNC) &_epiworldRfaster_run_multiple_cpp, 8}, - {"_epiworldRfaster_set_agents_data_cpp", (DL_FUNC) &_epiworldRfaster_set_agents_data_cpp, 3}, - {"_epiworldRfaster_set_death_reduction_cpp", (DL_FUNC) &_epiworldRfaster_set_death_reduction_cpp, 2}, - {"_epiworldRfaster_set_death_reduction_fun_cpp", (DL_FUNC) &_epiworldRfaster_set_death_reduction_fun_cpp, 3}, - {"_epiworldRfaster_set_death_reduction_ptr_cpp", (DL_FUNC) &_epiworldRfaster_set_death_reduction_ptr_cpp, 3}, - {"_epiworldRfaster_set_incubation_cpp", (DL_FUNC) &_epiworldRfaster_set_incubation_cpp, 2}, - {"_epiworldRfaster_set_incubation_fun_cpp", (DL_FUNC) &_epiworldRfaster_set_incubation_fun_cpp, 3}, - {"_epiworldRfaster_set_incubation_ptr_cpp", (DL_FUNC) &_epiworldRfaster_set_incubation_ptr_cpp, 3}, - {"_epiworldRfaster_set_name_cpp", (DL_FUNC) &_epiworldRfaster_set_name_cpp, 2}, - {"_epiworldRfaster_set_name_tool_cpp", (DL_FUNC) &_epiworldRfaster_set_name_tool_cpp, 2}, - {"_epiworldRfaster_set_name_virus_cpp", (DL_FUNC) &_epiworldRfaster_set_name_virus_cpp, 2}, - {"_epiworldRfaster_set_param_cpp", (DL_FUNC) &_epiworldRfaster_set_param_cpp, 3}, - {"_epiworldRfaster_set_prob_death_cpp", (DL_FUNC) &_epiworldRfaster_set_prob_death_cpp, 2}, - {"_epiworldRfaster_set_prob_death_fun_cpp", (DL_FUNC) &_epiworldRfaster_set_prob_death_fun_cpp, 3}, - {"_epiworldRfaster_set_prob_death_ptr_cpp", (DL_FUNC) &_epiworldRfaster_set_prob_death_ptr_cpp, 3}, - {"_epiworldRfaster_set_prob_infecting_cpp", (DL_FUNC) &_epiworldRfaster_set_prob_infecting_cpp, 2}, - {"_epiworldRfaster_set_prob_infecting_fun_cpp", (DL_FUNC) &_epiworldRfaster_set_prob_infecting_fun_cpp, 3}, - {"_epiworldRfaster_set_prob_infecting_ptr_cpp", (DL_FUNC) &_epiworldRfaster_set_prob_infecting_ptr_cpp, 3}, - {"_epiworldRfaster_set_prob_recovery_cpp", (DL_FUNC) &_epiworldRfaster_set_prob_recovery_cpp, 2}, - {"_epiworldRfaster_set_prob_recovery_fun_cpp", (DL_FUNC) &_epiworldRfaster_set_prob_recovery_fun_cpp, 3}, - {"_epiworldRfaster_set_prob_recovery_ptr_cpp", (DL_FUNC) &_epiworldRfaster_set_prob_recovery_ptr_cpp, 3}, - {"_epiworldRfaster_set_recovery_enhancer_cpp", (DL_FUNC) &_epiworldRfaster_set_recovery_enhancer_cpp, 2}, - {"_epiworldRfaster_set_recovery_enhancer_fun_cpp", (DL_FUNC) &_epiworldRfaster_set_recovery_enhancer_fun_cpp, 3}, - {"_epiworldRfaster_set_recovery_enhancer_ptr_cpp", (DL_FUNC) &_epiworldRfaster_set_recovery_enhancer_ptr_cpp, 3}, - {"_epiworldRfaster_set_susceptibility_reduction_cpp", (DL_FUNC) &_epiworldRfaster_set_susceptibility_reduction_cpp, 2}, - {"_epiworldRfaster_set_susceptibility_reduction_fun_cpp", (DL_FUNC) &_epiworldRfaster_set_susceptibility_reduction_fun_cpp, 3}, - {"_epiworldRfaster_set_susceptibility_reduction_ptr_cpp", (DL_FUNC) &_epiworldRfaster_set_susceptibility_reduction_ptr_cpp, 3}, - {"_epiworldRfaster_set_transmission_reduction_cpp", (DL_FUNC) &_epiworldRfaster_set_transmission_reduction_cpp, 2}, - {"_epiworldRfaster_set_transmission_reduction_fun_cpp", (DL_FUNC) &_epiworldRfaster_set_transmission_reduction_fun_cpp, 3}, - {"_epiworldRfaster_set_transmission_reduction_ptr_cpp", (DL_FUNC) &_epiworldRfaster_set_transmission_reduction_ptr_cpp, 3}, - {"_epiworldRfaster_size_cpp", (DL_FUNC) &_epiworldRfaster_size_cpp, 1}, - {"_epiworldRfaster_tool_cpp", (DL_FUNC) &_epiworldRfaster_tool_cpp, 5}, - {"_epiworldRfaster_tool_fun_logit_cpp", (DL_FUNC) &_epiworldRfaster_tool_fun_logit_cpp, 3}, - {"_epiworldRfaster_verbose_off_cpp", (DL_FUNC) &_epiworldRfaster_verbose_off_cpp, 1}, - {"_epiworldRfaster_verbose_on_cpp", (DL_FUNC) &_epiworldRfaster_verbose_on_cpp, 1}, - {"_epiworldRfaster_virus_cpp", (DL_FUNC) &_epiworldRfaster_virus_cpp, 6}, - {"_epiworldRfaster_virus_fun_logit_cpp", (DL_FUNC) &_epiworldRfaster_virus_fun_logit_cpp, 3}, - {"_epiworldRfaster_virus_set_state_cpp", (DL_FUNC) &_epiworldRfaster_virus_set_state_cpp, 4}, + {"_epiworldR_ModelDiffNet_cpp", (DL_FUNC) &_epiworldR_ModelDiffNet_cpp, 8}, + {"_epiworldR_ModelSEIRCONN_cpp", (DL_FUNC) &_epiworldR_ModelSEIRCONN_cpp, 7}, + {"_epiworldR_ModelSEIRDCONN_cpp", (DL_FUNC) &_epiworldR_ModelSEIRDCONN_cpp, 8}, + {"_epiworldR_ModelSEIRD_cpp", (DL_FUNC) &_epiworldR_ModelSEIRD_cpp, 6}, + {"_epiworldR_ModelSEIR_cpp", (DL_FUNC) &_epiworldR_ModelSEIR_cpp, 5}, + {"_epiworldR_ModelSIRCONN_cpp", (DL_FUNC) &_epiworldR_ModelSIRCONN_cpp, 6}, + {"_epiworldR_ModelSIRDCONN_cpp", (DL_FUNC) &_epiworldR_ModelSIRDCONN_cpp, 7}, + {"_epiworldR_ModelSIRD_cpp", (DL_FUNC) &_epiworldR_ModelSIRD_cpp, 5}, + {"_epiworldR_ModelSIRLogit_cpp", (DL_FUNC) &_epiworldR_ModelSIRLogit_cpp, 10}, + {"_epiworldR_ModelSIR_cpp", (DL_FUNC) &_epiworldR_ModelSIR_cpp, 4}, + {"_epiworldR_ModelSISD_cpp", (DL_FUNC) &_epiworldR_ModelSISD_cpp, 5}, + {"_epiworldR_ModelSIS_cpp", (DL_FUNC) &_epiworldR_ModelSIS_cpp, 4}, + {"_epiworldR_ModelSURV_cpp", (DL_FUNC) &_epiworldR_ModelSURV_cpp, 13}, + {"_epiworldR_add_global_action_cpp", (DL_FUNC) &_epiworldR_add_global_action_cpp, 2}, + {"_epiworldR_add_tool_agent_cpp", (DL_FUNC) &_epiworldR_add_tool_agent_cpp, 5}, + {"_epiworldR_add_tool_cpp", (DL_FUNC) &_epiworldR_add_tool_cpp, 3}, + {"_epiworldR_add_tool_n_cpp", (DL_FUNC) &_epiworldR_add_tool_n_cpp, 3}, + {"_epiworldR_add_virus_agent_cpp", (DL_FUNC) &_epiworldR_add_virus_agent_cpp, 5}, + {"_epiworldR_add_virus_cpp", (DL_FUNC) &_epiworldR_add_virus_cpp, 3}, + {"_epiworldR_add_virus_n_cpp", (DL_FUNC) &_epiworldR_add_virus_n_cpp, 3}, + {"_epiworldR_agents_from_edgelist_cpp", (DL_FUNC) &_epiworldR_agents_from_edgelist_cpp, 5}, + {"_epiworldR_agents_smallworld_cpp", (DL_FUNC) &_epiworldR_agents_smallworld_cpp, 5}, + {"_epiworldR_change_state_cpp", (DL_FUNC) &_epiworldR_change_state_cpp, 4}, + {"_epiworldR_get_agent_cpp", (DL_FUNC) &_epiworldR_get_agent_cpp, 2}, + {"_epiworldR_get_agents_cpp", (DL_FUNC) &_epiworldR_get_agents_cpp, 1}, + {"_epiworldR_get_agents_data_ncols_cpp", (DL_FUNC) &_epiworldR_get_agents_data_ncols_cpp, 1}, + {"_epiworldR_get_agents_states_cpp", (DL_FUNC) &_epiworldR_get_agents_states_cpp, 1}, + {"_epiworldR_get_agents_tools_cpp", (DL_FUNC) &_epiworldR_get_agents_tools_cpp, 1}, + {"_epiworldR_get_generation_time_cpp", (DL_FUNC) &_epiworldR_get_generation_time_cpp, 1}, + {"_epiworldR_get_hist_tool_cpp", (DL_FUNC) &_epiworldR_get_hist_tool_cpp, 1}, + {"_epiworldR_get_hist_total_cpp", (DL_FUNC) &_epiworldR_get_hist_total_cpp, 1}, + {"_epiworldR_get_hist_transition_matrix_cpp", (DL_FUNC) &_epiworldR_get_hist_transition_matrix_cpp, 2}, + {"_epiworldR_get_hist_virus_cpp", (DL_FUNC) &_epiworldR_get_hist_virus_cpp, 1}, + {"_epiworldR_get_n_replicates_cpp", (DL_FUNC) &_epiworldR_get_n_replicates_cpp, 1}, + {"_epiworldR_get_n_tools_cpp", (DL_FUNC) &_epiworldR_get_n_tools_cpp, 1}, + {"_epiworldR_get_n_viruses_cpp", (DL_FUNC) &_epiworldR_get_n_viruses_cpp, 1}, + {"_epiworldR_get_name_cpp", (DL_FUNC) &_epiworldR_get_name_cpp, 1}, + {"_epiworldR_get_name_tool_cpp", (DL_FUNC) &_epiworldR_get_name_tool_cpp, 1}, + {"_epiworldR_get_name_virus_cpp", (DL_FUNC) &_epiworldR_get_name_virus_cpp, 1}, + {"_epiworldR_get_ndays_cpp", (DL_FUNC) &_epiworldR_get_ndays_cpp, 1}, + {"_epiworldR_get_network_cpp", (DL_FUNC) &_epiworldR_get_network_cpp, 1}, + {"_epiworldR_get_param_cpp", (DL_FUNC) &_epiworldR_get_param_cpp, 2}, + {"_epiworldR_get_reproductive_number_cpp", (DL_FUNC) &_epiworldR_get_reproductive_number_cpp, 1}, + {"_epiworldR_get_state_agent_cpp", (DL_FUNC) &_epiworldR_get_state_agent_cpp, 1}, + {"_epiworldR_get_states_cpp", (DL_FUNC) &_epiworldR_get_states_cpp, 1}, + {"_epiworldR_get_today_total_cpp", (DL_FUNC) &_epiworldR_get_today_total_cpp, 1}, + {"_epiworldR_get_tool_model_cpp", (DL_FUNC) &_epiworldR_get_tool_model_cpp, 2}, + {"_epiworldR_get_transition_probability_cpp", (DL_FUNC) &_epiworldR_get_transition_probability_cpp, 1}, + {"_epiworldR_get_transmissions_cpp", (DL_FUNC) &_epiworldR_get_transmissions_cpp, 1}, + {"_epiworldR_get_virus_model_cpp", (DL_FUNC) &_epiworldR_get_virus_model_cpp, 2}, + {"_epiworldR_globalaction_fun_cpp", (DL_FUNC) &_epiworldR_globalaction_fun_cpp, 3}, + {"_epiworldR_globalaction_set_param_cpp", (DL_FUNC) &_epiworldR_globalaction_set_param_cpp, 4}, + {"_epiworldR_globalaction_tool_cpp", (DL_FUNC) &_epiworldR_globalaction_tool_cpp, 4}, + {"_epiworldR_globalaction_tool_logit_cpp", (DL_FUNC) &_epiworldR_globalaction_tool_logit_cpp, 5}, + {"_epiworldR_has_tool_cpp", (DL_FUNC) &_epiworldR_has_tool_cpp, 2}, + {"_epiworldR_has_virus_cpp", (DL_FUNC) &_epiworldR_has_virus_cpp, 2}, + {"_epiworldR_make_saver_cpp", (DL_FUNC) &_epiworldR_make_saver_cpp, 10}, + {"_epiworldR_print_agent_cpp", (DL_FUNC) &_epiworldR_print_agent_cpp, 3}, + {"_epiworldR_print_agent_tools_cpp", (DL_FUNC) &_epiworldR_print_agent_tools_cpp, 1}, + {"_epiworldR_print_cpp", (DL_FUNC) &_epiworldR_print_cpp, 2}, + {"_epiworldR_print_global_action_cpp", (DL_FUNC) &_epiworldR_print_global_action_cpp, 1}, + {"_epiworldR_print_tool_cpp", (DL_FUNC) &_epiworldR_print_tool_cpp, 1}, + {"_epiworldR_print_virus_cpp", (DL_FUNC) &_epiworldR_print_virus_cpp, 1}, + {"_epiworldR_queuing_off_cpp", (DL_FUNC) &_epiworldR_queuing_off_cpp, 1}, + {"_epiworldR_queuing_on_cpp", (DL_FUNC) &_epiworldR_queuing_on_cpp, 1}, + {"_epiworldR_rm_global_action_cpp", (DL_FUNC) &_epiworldR_rm_global_action_cpp, 2}, + {"_epiworldR_rm_tool_cpp", (DL_FUNC) &_epiworldR_rm_tool_cpp, 2}, + {"_epiworldR_rm_virus_cpp", (DL_FUNC) &_epiworldR_rm_virus_cpp, 2}, + {"_epiworldR_run_cpp", (DL_FUNC) &_epiworldR_run_cpp, 3}, + {"_epiworldR_run_multiple_cpp", (DL_FUNC) &_epiworldR_run_multiple_cpp, 8}, + {"_epiworldR_set_agents_data_cpp", (DL_FUNC) &_epiworldR_set_agents_data_cpp, 3}, + {"_epiworldR_set_death_reduction_cpp", (DL_FUNC) &_epiworldR_set_death_reduction_cpp, 2}, + {"_epiworldR_set_death_reduction_fun_cpp", (DL_FUNC) &_epiworldR_set_death_reduction_fun_cpp, 3}, + {"_epiworldR_set_death_reduction_ptr_cpp", (DL_FUNC) &_epiworldR_set_death_reduction_ptr_cpp, 3}, + {"_epiworldR_set_incubation_cpp", (DL_FUNC) &_epiworldR_set_incubation_cpp, 2}, + {"_epiworldR_set_incubation_fun_cpp", (DL_FUNC) &_epiworldR_set_incubation_fun_cpp, 3}, + {"_epiworldR_set_incubation_ptr_cpp", (DL_FUNC) &_epiworldR_set_incubation_ptr_cpp, 3}, + {"_epiworldR_set_name_cpp", (DL_FUNC) &_epiworldR_set_name_cpp, 2}, + {"_epiworldR_set_name_tool_cpp", (DL_FUNC) &_epiworldR_set_name_tool_cpp, 2}, + {"_epiworldR_set_name_virus_cpp", (DL_FUNC) &_epiworldR_set_name_virus_cpp, 2}, + {"_epiworldR_set_param_cpp", (DL_FUNC) &_epiworldR_set_param_cpp, 3}, + {"_epiworldR_set_prob_death_cpp", (DL_FUNC) &_epiworldR_set_prob_death_cpp, 2}, + {"_epiworldR_set_prob_death_fun_cpp", (DL_FUNC) &_epiworldR_set_prob_death_fun_cpp, 3}, + {"_epiworldR_set_prob_death_ptr_cpp", (DL_FUNC) &_epiworldR_set_prob_death_ptr_cpp, 3}, + {"_epiworldR_set_prob_infecting_cpp", (DL_FUNC) &_epiworldR_set_prob_infecting_cpp, 2}, + {"_epiworldR_set_prob_infecting_fun_cpp", (DL_FUNC) &_epiworldR_set_prob_infecting_fun_cpp, 3}, + {"_epiworldR_set_prob_infecting_ptr_cpp", (DL_FUNC) &_epiworldR_set_prob_infecting_ptr_cpp, 3}, + {"_epiworldR_set_prob_recovery_cpp", (DL_FUNC) &_epiworldR_set_prob_recovery_cpp, 2}, + {"_epiworldR_set_prob_recovery_fun_cpp", (DL_FUNC) &_epiworldR_set_prob_recovery_fun_cpp, 3}, + {"_epiworldR_set_prob_recovery_ptr_cpp", (DL_FUNC) &_epiworldR_set_prob_recovery_ptr_cpp, 3}, + {"_epiworldR_set_recovery_enhancer_cpp", (DL_FUNC) &_epiworldR_set_recovery_enhancer_cpp, 2}, + {"_epiworldR_set_recovery_enhancer_fun_cpp", (DL_FUNC) &_epiworldR_set_recovery_enhancer_fun_cpp, 3}, + {"_epiworldR_set_recovery_enhancer_ptr_cpp", (DL_FUNC) &_epiworldR_set_recovery_enhancer_ptr_cpp, 3}, + {"_epiworldR_set_susceptibility_reduction_cpp", (DL_FUNC) &_epiworldR_set_susceptibility_reduction_cpp, 2}, + {"_epiworldR_set_susceptibility_reduction_fun_cpp", (DL_FUNC) &_epiworldR_set_susceptibility_reduction_fun_cpp, 3}, + {"_epiworldR_set_susceptibility_reduction_ptr_cpp", (DL_FUNC) &_epiworldR_set_susceptibility_reduction_ptr_cpp, 3}, + {"_epiworldR_set_transmission_reduction_cpp", (DL_FUNC) &_epiworldR_set_transmission_reduction_cpp, 2}, + {"_epiworldR_set_transmission_reduction_fun_cpp", (DL_FUNC) &_epiworldR_set_transmission_reduction_fun_cpp, 3}, + {"_epiworldR_set_transmission_reduction_ptr_cpp", (DL_FUNC) &_epiworldR_set_transmission_reduction_ptr_cpp, 3}, + {"_epiworldR_size_cpp", (DL_FUNC) &_epiworldR_size_cpp, 1}, + {"_epiworldR_tool_cpp", (DL_FUNC) &_epiworldR_tool_cpp, 5}, + {"_epiworldR_tool_fun_logit_cpp", (DL_FUNC) &_epiworldR_tool_fun_logit_cpp, 3}, + {"_epiworldR_verbose_off_cpp", (DL_FUNC) &_epiworldR_verbose_off_cpp, 1}, + {"_epiworldR_verbose_on_cpp", (DL_FUNC) &_epiworldR_verbose_on_cpp, 1}, + {"_epiworldR_virus_cpp", (DL_FUNC) &_epiworldR_virus_cpp, 6}, + {"_epiworldR_virus_fun_logit_cpp", (DL_FUNC) &_epiworldR_virus_fun_logit_cpp, 3}, + {"_epiworldR_virus_set_state_cpp", (DL_FUNC) &_epiworldR_virus_set_state_cpp, 4}, {NULL, NULL, 0} }; } -extern "C" attribute_visible void R_init_epiworldRfaster(DllInfo* dll){ +extern "C" attribute_visible void R_init_epiworldR(DllInfo* dll){ R_registerRoutines(dll, NULL, CallEntries, NULL, NULL); R_useDynamicSymbols(dll, FALSE); R_forceSymbols(dll, TRUE);