Use touchstone

Add benchmarking vignette

Fix touchstone script

Fix touchstone script

Fix touchstone script

Fix touchstone script

Fix touchstone script

Author: pratikunterwegs

.Rbuildignore

@@ -18,3 +18,4 @@
 ^.*\.log$
 ^touchstone$
 ^README\.Rmd$
+^touchstone$

DESCRIPTION

@@ -44,5 +44,5 @@ Encoding: UTF-8
 Language: en-GB
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.2
 SystemRequirements: C++14

NAMESPACE

@@ -17,6 +17,7 @@ export(make_parameter_file)
 export(run_pathomove)
 export(use_cluster)
 exportClasses(pathomove_output)
+import(RcppEigen)
 import(data.table)
 importFrom(Rcpp,sourceCpp)
 importFrom(RcppParallel,RcppParallelLibs)

tests/spelling.R

@@ -1,3 +1,6 @@
-if(requireNamespace('spelling', quietly = TRUE))
-  spelling::spell_check_test(vignettes = TRUE, error = FALSE,
-                             skip_on_cran = TRUE)
+if (requireNamespace('spelling', quietly = TRUE))
+  spelling::spell_check_test(
+    vignettes = TRUE,
+    error = FALSE,
+    skip_on_cran = TRUE
+  )

touchstone/script.R

@@ -1,25 +1,21 @@
 # see `help(run_script, package = 'touchstone')` on how to run this
 # interactively
 
-# TODO OPTIONAL Add directories you want to be available in this file or during the
-# benchmarks.
-# touchstone::pin_assets("some/dir")
-
 # installs branches to benchmark
 touchstone::branch_install()
 
 # some setup
-genmax <- 10L
-g_patho_init <- genmax / 2
-initial_infections <- 5L
-tmax = 100
-popsize = 100
-scenario = 1
-
 # benchmark a function call from your package (two calls per branch)
 touchstone::benchmark_run(
-  # expr_before_benchmark = source("dir/data.R"), #<-- TODO OTPIONAL setup before benchmark
-  random_test = pathomove::run_pathomove(
+  expr_before_benchmark = {
+    genmax <- 100L
+    g_patho_init <- genmax / 2
+    initial_infections <- 5L
+    tmax = 100
+    popsize = 100
+    scenario = 1
+  }, #<-- TODO OTPIONAL setup before benchmark
+  simple_case = pathomove::run_pathomove(
     scenario = scenario,
     popsize = popsize,
     initialInfections = initial_infections,
@@ -30,16 +26,5 @@ touchstone::benchmark_run(
   n = 2
 )
 
-# TODO OPTIONAL benchmark any R expression (six calls per branch)
-# touchstone::benchmark_run(
-#   more = {
-#     if (TRUE) {
-#       y <- yourpkg::f2(x = 3)
-#     }
-#   }, #<- TODO put the call you want to benchmark here
-#   n = 6
-# )
-
-
 # create artifacts used downstream in the GitHub Action
 touchstone::benchmark_analyze()

vignettes/.gitignore

@@ -0,0 +1,2 @@
+*.html
+*.R

vignettes/benchmarking.Rmd

@@ -0,0 +1,40 @@
+---
+title: "benchmarking"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{benchmarking}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup}
+library(pathomove)
+```
+
+```{r}
+# some setup
+genmax <- 10L
+g_patho_init <- genmax / 2
+initial_infections <- 5L
+tmax = 100
+popsize = 100
+scenario = 1
+
+microbenchmark::microbenchmark(
+  simple_case = run_pathomove(
+    scenario = scenario,
+    popsize = popsize,
+    initialInfections = initial_infections,
+    tmax = tmax,
+    genmax = genmax,
+    g_patho_init = g_patho_init
+  )
+)
+```