From fdafe3ac3ef33a38c8fe3ecf61829ffe64afd7f9 Mon Sep 17 00:00:00 2001 From: Pratik Gupte Date: Wed, 23 Aug 2023 14:51:13 +0100 Subject: [PATCH] Add pkdown article in index, update docs and RcppExports --- R/RcppExports.R | 4 ++-- _pkgdown.yml | 1 + man/dot-epidemic_vacamole_cpp.Rd | 1 + src/RcppExports.cpp | 9 +++++---- 4 files changed, 9 insertions(+), 6 deletions(-) diff --git a/R/RcppExports.R b/R/RcppExports.R index 4e71cc19..f55aa3ea 100644 --- 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 index 1f5eea18..41289ecd 100644 --- 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 index 5582c1a8..c961b131 100644 --- a/man/dot-epidemic_vacamole_cpp.Rd +++ b/man/dot-epidemic_vacamole_cpp.Rd @@ -21,6 +21,7 @@ vax_time_begin, vax_time_end, vax_nu, + rate_interventions, time_end = 100, increment = 0.1 ) diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index 4180647f..8d3ff20d 100644 --- 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} };