Speedup render by avoiding repeated vector copies.

.github/workflows/pkgdown.yml

@@ -13,9 +13,9 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |

R/RcppExports.R

@@ -437,6 +437,18 @@ integer_ragged_variable_queue_shrink_bitset <- function(variable, index) {
     invisible(.Call(`_individual_integer_ragged_variable_queue_shrink_bitset`, variable, index))
 }
 
+create_render_vector <- function(data) {
+    .Call(`_individual_create_render_vector`, data)
+}
+
+render_vector_update <- function(v, index, value) {
+    invisible(.Call(`_individual_render_vector_update`, v, index, value))
+}
+
+render_vector_data <- function(v) {
+    .Call(`_individual_render_vector_data`, v)
+}
+
 execute_process <- function(process, timestep) {
     invisible(.Call(`_individual_execute_process`, process, timestep))
 }
@@ -455,5 +467,5 @@ variable_resize <- function(variable) {
 
 # Register entry points for exported C++ functions
 methods::setLoadAction(function(ns) {
-    .Call('_individual_RcppExport_registerCCallable', PACKAGE = 'individual')
+    .Call(`_individual_RcppExport_registerCCallable`)
 })

R/render.R

@@ -16,7 +16,7 @@ Render <- R6Class(
     #' @param timesteps number of timesteps in the simulation.
     initialize = function(timesteps) {
       private$.timesteps = timesteps
-      private$.vectors[['timestep']] <- seq_len(timesteps)
+      private$.vectors[['timestep']] <- create_render_vector(seq_len(timesteps))
     },
 
     #' @description
@@ -28,7 +28,7 @@ Render <- R6Class(
       if (name == 'timestep') {
         stop("Cannot set default value for variable 'timestep'")
       }
-      private$.vectors[[name]] = rep(value, private$.timesteps)
+      private$.vectors[[name]] = create_render_vector(rep(value, private$.timesteps))
     },
 
     #' @description
@@ -41,15 +41,15 @@ Render <- R6Class(
         stop("Please don't name your variable 'timestep'")
       }
       if (!(name %in% names(private$.vectors))) {
-        private$.vectors[[name]] = rep(NA, private$.timesteps)
+        private$.vectors[[name]] = create_render_vector(rep(NA, private$.timesteps))
       }
-      private$.vectors[[name]][[timestep]] = value
+      render_vector_update(private$.vectors[[name]], timestep, value)
     },
 
     #' @description
     #' Return the render as a \code{\link[base]{data.frame}}.
     to_dataframe = function() {
-      data.frame(private$.vectors)
+      data.frame(lapply(private$.vectors, render_vector_data))
     }
   )
 )

README.md

@@ -1,7 +1,7 @@
-# Individual <img src='man/figures/logo.png' align="right" height="139" />
+# Individual <img src='man/figures/logo.png' align="right" style="height:139px !important" />
 
 <!-- badges: start -->
-[![R build status](https://github.com/mrc-ide/individual/workflows/R-CMD-check/badge.svg)](https://github.com/mrc-ide/individual/actions)
+[![R build status](https://github.com/mrc-ide/individual/actions/workflows/R-CMD-check.yaml/badge.svg?branch=dev)](https://github.com/mrc-ide/individual/actions)
 [![codecov.io](https://codecov.io/github/mrc-ide/individual/coverage.svg)](https://codecov.io/github/mrc-ide/individual)
 [![CRAN](https://www.r-pkg.org/badges/version/individual)](https://cran.r-project.org/package=individual)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

inst/include/RenderVector.h

@@ -0,0 +1,36 @@
+/*
+ *  RenderVector.h
+ *
+ *  Created on: 21 Dec 2023
+ *      Author: pl2113
+ */
+
+#ifndef INST_INCLUDE_RENDER_VECTOR_H_
+#define INST_INCLUDE_RENDER_VECTOR_H_
+
+#include <Rcpp.h>
+
+/**
+ * A thin wrapper around a NumericVector, used to provide by-reference
+ * semantics and guaranteed in-place mutation in the Render class.
+ *
+ */
+struct RenderVector {
+    RenderVector(Rcpp::NumericVector data) : _data(data) { }
+
+    void update(size_t index, float value) {
+        if (index < 1 || index > _data.size()) {
+            Rcpp::stop("index out-of-bounds");
+        }
+        _data[index - 1] = value;
+    }
+
+    const Rcpp::NumericVector& data() const {
+        return _data;
+    }
+
+    private:
+        Rcpp::NumericVector _data;
+};
+
+#endif /* INST_INCLUDE_RENDER_VECTOR_H_ */

inst/include/individual_types.h

@@ -15,5 +15,6 @@
 #include "RaggedInteger.h"
 #include "RaggedDouble.h"
 #include "Event.h"
+#include "RenderVector.h"
 
 #endif /* INDIVIDUAL_TYPES_H_ */

src/RcppExports.cpp

@@ -1303,6 +1303,40 @@ BEGIN_RCPP
     return R_NilValue;
 END_RCPP
 }
+// create_render_vector
+Rcpp::XPtr<RenderVector> create_render_vector(Rcpp::NumericVector data);
+RcppExport SEXP _individual_create_render_vector(SEXP dataSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::NumericVector >::type data(dataSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_render_vector(data));
+    return rcpp_result_gen;
+END_RCPP
+}
+// render_vector_update
+void render_vector_update(Rcpp::XPtr<RenderVector> v, size_t index, float value);
+RcppExport SEXP _individual_render_vector_update(SEXP vSEXP, SEXP indexSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RenderVector> >::type v(vSEXP);
+    Rcpp::traits::input_parameter< size_t >::type index(indexSEXP);
+    Rcpp::traits::input_parameter< float >::type value(valueSEXP);
+    render_vector_update(v, index, value);
+    return R_NilValue;
+END_RCPP
+}
+// render_vector_data
+Rcpp::NumericVector render_vector_data(Rcpp::XPtr<RenderVector> v);
+RcppExport SEXP _individual_render_vector_data(SEXP vSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RenderVector> >::type v(vSEXP);
+    rcpp_result_gen = Rcpp::wrap(render_vector_data(v));
+    return rcpp_result_gen;
+END_RCPP
+}
 // execute_process
 void execute_process(Rcpp::XPtr<process_t> process, size_t timestep);
 RcppExport SEXP _individual_execute_process(SEXP processSEXP, SEXP timestepSEXP) {
@@ -1362,7 +1396,7 @@ RcppExport SEXP _individual_RcppExport_registerCCallable() {
     return R_NilValue;
 }
 
-RcppExport SEXP run_testthat_tests(SEXP);
+RcppExport SEXP run_testthat_tests(void *);
 
 static const R_CallMethodDef CallEntries[] = {
     {"_individual_create_bitset", (DL_FUNC) &_individual_create_bitset, 1},
@@ -1475,6 +1509,9 @@ static const R_CallMethodDef CallEntries[] = {
     {"_individual_integer_ragged_variable_queue_extend", (DL_FUNC) &_individual_integer_ragged_variable_queue_extend, 2},
     {"_individual_integer_ragged_variable_queue_shrink", (DL_FUNC) &_individual_integer_ragged_variable_queue_shrink, 2},
     {"_individual_integer_ragged_variable_queue_shrink_bitset", (DL_FUNC) &_individual_integer_ragged_variable_queue_shrink_bitset, 2},
+    {"_individual_create_render_vector", (DL_FUNC) &_individual_create_render_vector, 1},
+    {"_individual_render_vector_update", (DL_FUNC) &_individual_render_vector_update, 3},
+    {"_individual_render_vector_data", (DL_FUNC) &_individual_render_vector_data, 1},
     {"_individual_execute_process", (DL_FUNC) &_individual_execute_process, 2},
     {"_individual_variable_get_size", (DL_FUNC) &_individual_variable_get_size, 1},
     {"_individual_variable_update", (DL_FUNC) &_individual_variable_update, 1},

src/render_vector.cpp

@@ -0,0 +1,26 @@
+/*
+ * render_vector.cpp
+ *
+ *  Created on: 21 Dec 2023
+ *      Author: pl2113
+ */
+
+
+#include "../inst/include/RenderVector.h"
+#include <Rcpp.h>
+
+
+//[[Rcpp::export]]
+Rcpp::XPtr<RenderVector> create_render_vector(Rcpp::NumericVector data) {
+    return Rcpp::XPtr<RenderVector>(new RenderVector(data), true);
+}
+
+//[[Rcpp::export]]
+void render_vector_update(Rcpp::XPtr<RenderVector> v, size_t index, float value) {
+    v->update(index, value);
+}
+
+//[[Rcpp::export]]
+Rcpp::NumericVector render_vector_data(Rcpp::XPtr<RenderVector> v) {
+    return v->data();
+}