Add pkdown article in index, update docs and RcppExports

epiverse-trace · Aug 23, 2023 · fdafe3a · fdafe3a
1 parent 0832278
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Showing 4 changed files with 9 additions and 6 deletions.
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -132,8 +132,8 @@
 #' as specified in the initial conditions matrix (see [population()]).
 #' The second list element is a vector of timesteps.
 #' @keywords internal
-.epidemic_vacamole_cpp <- function(initial_state, beta, beta_v, alpha, omega, omega_v, eta, eta_v, gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, time_end = 100.0, increment = 0.1) {
-    .Call(`_epidemics_epidemic_vacamole_cpp_internal`, initial_state, beta, beta_v, alpha, omega, omega_v, eta, eta_v, gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, time_end, increment)
+.epidemic_vacamole_cpp <- function(initial_state, beta, beta_v, alpha, omega, omega_v, eta, eta_v, gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_end = 100.0, increment = 0.1) {
+    .Call(`_epidemics_epidemic_vacamole_cpp_internal`, initial_state, beta, beta_v, alpha, omega, omega_v, eta, eta_v, gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_end, increment)
 }
 
 #' @title Compute the discrete probability of the truncated Erlang distribution

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -20,6 +20,7 @@ articles:
   - modelling_vaccination
   - modelling_interventions
   - multiple_interventions
+  - rate_interventions
 - title: Guides to library models
   navbar: Guides to library models
   contents:

diff --git a/man/dot-epidemic_vacamole_cpp.Rd b/man/dot-epidemic_vacamole_cpp.Rd
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -55,8 +55,8 @@ BEGIN_RCPP
 END_RCPP
 }
 // epidemic_vacamole_cpp_internal
-Rcpp::List epidemic_vacamole_cpp_internal(const Eigen::MatrixXd& initial_state, const double& beta, const double& beta_v, const double& alpha, const double& omega, const double& omega_v, const double& eta, const double& eta_v, const double& gamma, const Eigen::MatrixXd& contact_matrix, const Rcpp::NumericVector& npi_time_begin, const Rcpp::NumericVector& npi_time_end, const Rcpp::NumericMatrix& npi_cr, const Eigen::MatrixXd& vax_time_begin, const Eigen::MatrixXd& vax_time_end, const Eigen::MatrixXd& vax_nu, const double& time_end, const double& increment);
-RcppExport SEXP _epidemics_epidemic_vacamole_cpp_internal(SEXP initial_stateSEXP, SEXP betaSEXP, SEXP beta_vSEXP, SEXP alphaSEXP, SEXP omegaSEXP, SEXP omega_vSEXP, SEXP etaSEXP, SEXP eta_vSEXP, SEXP gammaSEXP, SEXP contact_matrixSEXP, SEXP npi_time_beginSEXP, SEXP npi_time_endSEXP, SEXP npi_crSEXP, SEXP vax_time_beginSEXP, SEXP vax_time_endSEXP, SEXP vax_nuSEXP, SEXP time_endSEXP, SEXP incrementSEXP) {
+Rcpp::List epidemic_vacamole_cpp_internal(const Eigen::MatrixXd& initial_state, const double& beta, const double& beta_v, const double& alpha, const double& omega, const double& omega_v, const double& eta, const double& eta_v, const double& gamma, const Eigen::MatrixXd& contact_matrix, const Rcpp::NumericVector& npi_time_begin, const Rcpp::NumericVector& npi_time_end, const Rcpp::NumericMatrix& npi_cr, const Eigen::MatrixXd& vax_time_begin, const Eigen::MatrixXd& vax_time_end, const Eigen::MatrixXd& vax_nu, const Rcpp::List& rate_interventions, const double& time_end, const double& increment);
+RcppExport SEXP _epidemics_epidemic_vacamole_cpp_internal(SEXP initial_stateSEXP, SEXP betaSEXP, SEXP beta_vSEXP, SEXP alphaSEXP, SEXP omegaSEXP, SEXP omega_vSEXP, SEXP etaSEXP, SEXP eta_vSEXP, SEXP gammaSEXP, SEXP contact_matrixSEXP, SEXP npi_time_beginSEXP, SEXP npi_time_endSEXP, SEXP npi_crSEXP, SEXP vax_time_beginSEXP, SEXP vax_time_endSEXP, SEXP vax_nuSEXP, SEXP rate_interventionsSEXP, SEXP time_endSEXP, SEXP incrementSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
@@ -76,9 +76,10 @@ BEGIN_RCPP
     Rcpp::traits::input_parameter< const Eigen::MatrixXd& >::type vax_time_begin(vax_time_beginSEXP);
     Rcpp::traits::input_parameter< const Eigen::MatrixXd& >::type vax_time_end(vax_time_endSEXP);
     Rcpp::traits::input_parameter< const Eigen::MatrixXd& >::type vax_nu(vax_nuSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::List& >::type rate_interventions(rate_interventionsSEXP);
     Rcpp::traits::input_parameter< const double& >::type time_end(time_endSEXP);
     Rcpp::traits::input_parameter< const double& >::type increment(incrementSEXP);
-    rcpp_result_gen = Rcpp::wrap(epidemic_vacamole_cpp_internal(initial_state, beta, beta_v, alpha, omega, omega_v, eta, eta_v, gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, time_end, increment));
+    rcpp_result_gen = Rcpp::wrap(epidemic_vacamole_cpp_internal(initial_state, beta, beta_v, alpha, omega, omega_v, eta, eta_v, gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_end, increment));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -98,7 +99,7 @@ END_RCPP
 static const R_CallMethodDef CallEntries[] = {
     {"_epidemics_epidemic_default_cpp_internal", (DL_FUNC) &_epidemics_epidemic_default_cpp_internal, 14},
     {"_epidemics_epidemic_ebola_cpp_internal", (DL_FUNC) &_epidemics_epidemic_ebola_cpp_internal, 8},
-    {"_epidemics_epidemic_vacamole_cpp_internal", (DL_FUNC) &_epidemics_epidemic_vacamole_cpp_internal, 18},
+    {"_epidemics_epidemic_vacamole_cpp_internal", (DL_FUNC) &_epidemics_epidemic_vacamole_cpp_internal, 19},
     {"_epidemics_prob_discrete_erlang_cpp", (DL_FUNC) &_epidemics_prob_discrete_erlang_cpp, 2},
     {NULL, NULL, 0}
 };