Merge pull request #306 from billdenney/helper-generate_data.R

Switch generate.data.R to be a helper file, using the testthat infrastructure to include the functions
billdenney · Jun 28, 2024 · 027ee95 · 027ee95
2 parents 67e1be4 + e6fe38b
commit 027ee95
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Showing 13 changed files with 1 addition and 22 deletions.
diff --git a/tests/testthat/generate.data.R → tests/testthat/helper-generate_data.R b/tests/testthat/generate.data.R → tests/testthat/helper-generate_data.R
diff --git a/tests/testthat/test-as_various.R b/tests/testthat/test-as_various.R
@@ -1,5 +1,3 @@
-source("generate.data.R")
-
 test_that("as_PKNCA*", {
   tmpconc <- generate.conc(2, 1, 0:24)
   tmpdose <- generate.dose(tmpconc)

diff --git a/tests/testthat/test-class-PKNCAconc.R b/tests/testthat/test-class-PKNCAconc.R
@@ -1,5 +1,3 @@
-source("generate.data.R")
-
 test_that("PKNCAconc expected errors", {
   tmp.conc <- generate.conc(nsub=1, ntreat=1, time.points=0:24)
   tmp.conc$foo <- "A"

diff --git a/tests/testthat/test-class-PKNCAdata.R b/tests/testthat/test-class-PKNCAdata.R
@@ -1,5 +1,3 @@
-source("generate.data.R")
-
 test_that("PKNCAdata", {
   tmp.conc <- generate.conc(nsub=5, ntreat=2, time.points=0:24)
   tmp.conc.analyte <- generate.conc(nsub=5, ntreat=2, time.points=0:24,

diff --git a/tests/testthat/test-class-PKNCAdose.R b/tests/testthat/test-class-PKNCAdose.R
@@ -1,5 +1,3 @@
-source("generate.data.R")
-
 test_that("PKNCAdose", {
   tmp.conc <- generate.conc(nsub=5, ntreat=2, time.points=0:24)
   tmp.conc.analyte <- generate.conc(nsub=5, ntreat=2, time.points=0:24,

diff --git a/tests/testthat/test-class-PKNCAresults.R b/tests/testthat/test-class-PKNCAresults.R
@@ -1,5 +1,3 @@
-source("generate.data.R")
-
 test_that("PKNCAresults object creation", {
   minimal_result <- PKNCAresults(data.frame(a=1), data=list())
   expect_equal(minimal_result$columns$exclude, "exclude")

diff --git a/tests/testthat/test-dplyr.R b/tests/testthat/test-dplyr.R
@@ -1,5 +1,3 @@
-source("generate.data.R")
-
 # based on purrr:::capture_output
 msg_grabber <- function(code) {
   messages <- character()

diff --git a/tests/testthat/test-exclude.R b/tests/testthat/test-exclude.R
@@ -1,5 +1,3 @@
-source("generate.data.R")
-
 test_that("setExcludeColumn", {
   # exclude argument not given
   expect_equal(

diff --git a/tests/testthat/test-impute.R b/tests/testthat/test-impute.R
@@ -1,5 +1,3 @@
-source("generate.data.R")
-
 test_that("PKNCA_impute_method_start_conc0", {
   # Time 0 is replaced
   expect_equal(

diff --git a/tests/testthat/test-pk.calc.all.R b/tests/testthat/test-pk.calc.all.R
@@ -1,5 +1,3 @@
-source("generate.data.R")
-
 test_that("pk.nca", {
   # Note that generate.conc sets the random seed, so it doesn't have to happen
   # here.

diff --git a/tests/testthat/test-pk.calc.dn.R b/tests/testthat/test-pk.calc.dn.R
@@ -7,7 +7,6 @@ test_that("pk.calc.dn", {
 
 test_that("pk.calc.cmax", {
   # Ensure that the formalsmap functionality works within pk.nca
-  source("generate.data.R")
   tmpconc <- generate.conc(2, 2, 0:24)
   tmpdose <- generate.dose(tmpconc)
   tmpconc <- merge(tmpconc, tmpdose[,c("ID", "treatment", "dose")])

diff --git a/tests/testthat/test-prepare_data.R b/tests/testthat/test-prepare_data.R
@@ -1,5 +1,3 @@
-source("generate.data.R")
-
 # prepare_* ####
 
 test_that("prepare_*", {

diff --git a/vignettes/v03-selection-of-calculation-intervals.Rmd b/vignettes/v03-selection-of-calculation-intervals.Rmd
@@ -19,7 +19,7 @@ library(cowplot)
 library(PKNCA)
 library(knitr)
 library(ggplot2)
-source("../tests/testthat/generate.data.R")
+source("../tests/testthat/helper-generate_data.R")
 scale_colour_discrete <- scale_colour_hue
 scale_fill_discrete <- scale_fill_hue
 ```