Merge pull request #130 from keaven/testthat-helper

Move independently programmed functions for validation to `helper.R`
keaven · Feb 21, 2024 · ae18ea5 · ae18ea5
2 parents 81837cd + 2dfdb32
commit ae18ea5
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Showing 38 changed files with 54 additions and 98 deletions.
diff --git a/tests/gsDesign_independent_code.R → tests/testthat/helper.R b/tests/gsDesign_independent_code.R → tests/testthat/helper.R
@@ -1,3 +1,5 @@
+# This file was formerly stored as `tests/gsDesign_independent_code.R` and is
+# now moved to `tests/testthat/helper.R` to follow testthat best practices.
 
 # This script contains independently programmed functions for validating some of 
 # the functions of the gsDesign package.

diff --git a/tests/testthat/test-independent-test-binomialSPRT.R b/tests/testthat/test-independent-test-binomialSPRT.R
@@ -5,8 +5,6 @@
 ## For such test cases,the tolerance is set to 1e-6 (= 0.000001), a sufficiently
 ## low value.
 
-source('../gsDesign_independent_code.R')
-
 validate_vd <- Validate_comp_sprt_bnd(
   alpha = 0.1, beta = 0.15, p0 = 0.05, p1 = 0.25,
   nmin = 10, nmax = 35
@@ -22,7 +20,7 @@ exct_des <- gsBinomialExact(
 
 
 testthat::test_that(desc = "Test binomialSPRT function
-                    source : independent R Program-gsDesign_independent_code.R", code = {
+                    source : independent R Program-helper.R", code = {
   binSPRT <- binomialSPRT(
     p0 = 0.05,
     p1 = 0.25,

diff --git a/tests/testthat/test-independent-test-eEvents.R b/tests/testthat/test-independent-test-eEvents.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 # #----------------------------------
 # ### Testing eEvents function 
 # For comparing floating-point numbers, an exact match cannot be expected. 
@@ -8,7 +7,7 @@ source('../gsDesign_independent_code.R')
 
 test_that(
   desc = "test: checking number of events on a single arm
-          source : gsDesign_independent_code.R",
+          source : helper.R",
   code = {
     nEv <- eEvents(
       lambda = 0.2, eta = 0.1, gamma = 1,

diff --git a/tests/testthat/test-independent-test-gsBoundCP.R b/tests/testthat/test-independent-test-gsBoundCP.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #---------------
 ##gsBoundCP
 #--------------
@@ -33,7 +32,7 @@ testthat::test_that(desc = "Test: out of range theta", code = {
 
 
 testthat::test_that(desc = "Test: output validation
-                          source: gsDesign_independent_code.R", 
+                          source: helper.R", 
                     code = {
   x = gsDesign(k =3, test.type=1, delta = 0.22)
   local_edition(3)

diff --git a/tests/testthat/test-independent-test-gsCPOS.R b/tests/testthat/test-independent-test-gsCPOS.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #------------
 ## gsCPOS
 #------------
@@ -33,7 +32,7 @@ testthat::test_that(desc = "Test: checking out of range i ", code = {
 
 
 testthat::test_that(desc = "Test: output validation 
-                    source: gsDesign_independent_code.R", code = {
+                    source: helper.R", code = {
   x <- gsDesign(k = 3, test.type = 2, n.fix = 800)
   theta = c(-1.50, -0.75, 0.00, 0.75, 1.50)
   wgts = c(0.064758798, 0.301137432, 0.199471140, 0.301137432, 0.064758798)

diff --git a/tests/testthat/test-independent-test-gsNormalGrid.R b/tests/testthat/test-independent-test-gsNormalGrid.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 # Testing gsNormalGrid() : normalGrid() is intended to be used for computation of
 # the expected value of a function of a normal random variable.
 # The function produces grid points and weights to be used for numerical integration.

diff --git a/tests/testthat/test-independent-test-gsPI.R b/tests/testthat/test-independent-test-gsPI.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #---------------
 ## gsPI
 
@@ -53,7 +52,7 @@ testthat::test_that(desc = "Test: checking variable type", code = {
 
 
 testthat::test_that(desc = "Test: checking output validation
-                    source: gsDesign_independent_code.R", 
+                    source: helper.R", 
                     code = {
 
     x <- gsDesign(k = 4, n.fix = 1371, timing = c(0.25,0.5, 0.7),

diff --git a/tests/testthat/test-independent-test-gsPP.R b/tests/testthat/test-independent-test-gsPP.R
@@ -1,11 +1,10 @@
-source('../gsDesign_independent_code.R')
 #---------------
 ### Testing gsPP:
 #---------------
 
 # testing TestCase1_gsPP test.type = 2
 testthat::test_that(desc = "Test: checking output validation,
-                    source: gsDesign_independent_code.R", 
+                    source: helper.R", 
                     code = {
   x <- gsDesign(k = 4, test.type = 2, n.fix = 800)
   zi <- 1
@@ -25,7 +24,7 @@ testthat::test_that(desc = "Test: checking output validation,
 
 # testing TestCase1_gsPP test.type = 1
 testthat::test_that(desc = "Test: checking output validation,
-                    source: gsDesign_independent_code.R", 
+                    source: helper.R", 
                     code = {
   x <- gsDesign(k = 4, test.type = 1, n.fix = 800)
   zi <- 0

diff --git a/tests/testthat/test-independent-test-gsPosterior.R b/tests/testthat/test-independent-test-gsPosterior.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #--------------------------------------------
 ### Testing gsPosterior:
 #---------------------------------------------
@@ -101,7 +100,7 @@ testthat::test_that(desc = "Test: checking z variable types.", code = {
 
 testthat::test_that(
   desc = "Test: checking Output validation, 
-          source: /tests/cytel/gsDesign_independent_code.R",
+          source: helper.R",
   code = {
     x <- gsDesign(k = 3, test.type = 1, n.fix = 800)
     theta <- seq(-3, 3, 0.75)

diff --git a/tests/testthat/test-independent-test-gsZ.R b/tests/testthat/test-independent-test-gsZ.R
@@ -1,12 +1,11 @@
-source('../gsDesign_independent_code.R')
 #---------------
 ### Testing gsZ:
 #---------------
 
 
 testthat::test_that(
   desc = "test: checking output validation density = 0, 
-                    source independent R Program gsDesign_independent_code.R",
+                    source independent R Program helper.R",
   code = {
     x <- gsDesign(k = 3, test.type = 1, n.fix = 800)
     theta <- c(0, 0.5)
@@ -33,7 +32,7 @@ testthat::test_that(desc = "test: checking error x$n.I", code = {
 
 testthat::test_that(
   desc = "test : checking output validation,
-                    source : independent R Program gsDesign_independent_code.R",
+                    source : independent R Program helper.R",
   code = {
     x <- gsDesign(k = 3, test.type = 1, n.fix = 800)
     theta <- c(0, 2, 0.5)
@@ -52,7 +51,7 @@ testthat::test_that(
 
 testthat::test_that(
   desc = "test : checking output validation, 
-  source : independent R Program gsDesign_independent_code.R",
+  source : independent R Program helper.R",
   code = {
     x <- gsDesign(k = 4, test.type = 2, n.fix = 800)
     theta <- c(0, 0.1, 0.05)

diff --git a/tests/testthat/test-independent-test-hGraph.R b/tests/testthat/test-independent-test-hGraph.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #-------------------------------------------------------------------------------
 # hGraph : hGraph() plots a multiplicity graph defined by user inputs. The graph
 #          can also be used with the **gMCPLite** package to evaluate a set of 

diff --git a/tests/testthat/test-independent-test-plot.binomialSPRT.R b/tests/testthat/test-independent-test-plot.binomialSPRT.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 # --------------------------------------------
 # Test plot.binomialSPRT function
 #----------------------------------------------

diff --git a/tests/testthat/test-independent-test-plot.gsBinomialExact.R b/tests/testthat/test-independent-test-plot.gsBinomialExact.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 # --------------------------------------------
 # Test plot.gsBinomialExact function
 #----------------------------------------------

diff --git a/tests/testthat/test-independent-test-plot.gsDesign.R b/tests/testthat/test-independent-test-plot.gsDesign.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 # --------------------------------------------
 # Test plot.gsDesign function
 ## save_gg_plot() is used for storing plots created using ggplot2 package,

diff --git a/tests/testthat/test-independent-test-plot.gsProbability.R b/tests/testthat/test-independent-test-plot.gsProbability.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 # --------------------------------------------
 # Test plot.gsProbability function
 ## save_gg_plot() is used for storing plots created using ggplot2 package,

diff --git a/tests/testthat/test-independent-test-plot.ssrCP.R b/tests/testthat/test-independent-test-plot.ssrCP.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #----------------------
 # plot.ssrCP
 #---------------------

diff --git a/tests/testthat/test-independent-test-plotHR.R b/tests/testthat/test-independent-test-plotHR.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #################################################
 # Test plotHR function
 #################################################

diff --git a/tests/testthat/test-independent-test-plotRR.R b/tests/testthat/test-independent-test-plotRR.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #################################################
 # Test plotRR function
 #################################################

diff --git a/tests/testthat/test-independent-test-plotgsCP.R b/tests/testthat/test-independent-test-plotgsCP.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #-------------------------------------------------------------------------------
 # expected CP Calculations done using East 6.5
 # source file : tests/benchmarks/gsqplot.cywx

diff --git a/tests/testthat/test-independent-test-plotgsPower.R b/tests/testthat/test-independent-test-plotgsPower.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #-------------------------------------------------------------------------------
 # Probability Calculations done using East 6.5', 
 # source : tests/benchmarks/gsqplot.cywx

diff --git a/tests/testthat/test-independent-test-plotgsZ.R b/tests/testthat/test-independent-test-plotgsZ.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #################################################
 # Test plotgsZ function
 #################################################

diff --git a/tests/testthat/test-independent-test-plotsf.R b/tests/testthat/test-independent-test-plotsf.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #------------
 ## plotsf
 #-----------

diff --git a/tests/testthat/test-independent-test-sfBetaDist.R b/tests/testthat/test-independent-test-sfBetaDist.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #-----------------------------------
 ### Testing sfBetaDist function
 #-----------------------------------
@@ -134,7 +133,7 @@ testthat::test_that("Test: param - Checking Variable Type, Out-of-Range,
 
 
 testthat::test_that("Test: output validation for param of length 2 :
-                    Source: gsDesign_independent_code.R)", {
+                    Source: helper.R)", {
 
   t <- c(.01, .05, .1, .25, .5,1)
   param<-c(0.25,0.1)
@@ -148,7 +147,7 @@ testthat::test_that("Test: output validation for param of length 2 :
 
 
 testthat::test_that("Test: for param of length 2, t of length 5 :
-                     Source: gsDesign_independent_code.R)", {
+                     Source: helper.R)", {
 
   t <- c(.01, .05, .1, .25, .5)
   param<-c(0.25,0.1)
@@ -162,7 +161,7 @@ testthat::test_that("Test: for param of length 2, t of length 5 :
 
 
 testthat::test_that("Test: for param of length 2, t of length 7 :
-                    Source: gsDesign_independent_code.R)", {
+                    Source: helper.R)", {
 
   t <- c(.01, .05, .1, .25, .5, 1, 1.02)
   param<-c(0.25,0.1)

diff --git a/tests/testthat/test-independent-test-sfCauchy.R b/tests/testthat/test-independent-test-sfCauchy.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #----------------------------------
 ### Testing sfCauchy function
 #----------------------------------
@@ -144,7 +143,7 @@ testthat::test_that("Test: param - Testing incorrect variable type,
 
 
 testthat::test_that("Test: output validation param length as 2, 
-                    Source: gsDesign_independent_code.R", {
+                    Source: helper.R", {
 
   t <- c(0.25, 0.5, 0.75, 1)
   param <- c(1, 2)
@@ -158,7 +157,7 @@ testthat::test_that("Test: output validation param length as 2,
 
 
 testthat::test_that("Test: output validation param length as 4, 
-                    Source: gsDesign_independent_code.R", {
+                    Source: helper.R", {
   t <- c(0.25, 0.5, .75, 1)
   param <- c(0.2, 0.4, 0.1, 0.3)
   alpha <- 0.05

diff --git a/tests/testthat/test-independent-test-sfExtremeValue.R b/tests/testthat/test-independent-test-sfExtremeValue.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #-----------------------------------
 ### Testing sfExtremeValue function
 #-----------------------------------
@@ -139,7 +138,7 @@ testthat::test_that("Test: param - Testing incorrect variable type,
 
 
 testthat::test_that("Test: output validation param length as 2,  
-                    Source: gsDesign_independent_code.R",  {
+                    Source: helper.R",  {
 
   t <- c(0.2, 0.15, .75, 1)
   param<-c(0.1, 0.2)
@@ -153,7 +152,7 @@ testthat::test_that("Test: output validation param length as 2,
 
 
 testthat::test_that("Test: output validation param length as 4,  
-                     Source: gsDesign_independent_code.R",  {
+                     Source: helper.R",  {
 
   t <- c(0.2, 0.15, 0.75, 1)
   param<-c(0.1, 0.2, 0.2, 0.3)

diff --git a/tests/testthat/test-independent-test-sfExtremeValue2.R b/tests/testthat/test-independent-test-sfExtremeValue2.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 ### Testing sfExtremeValue2 function
 #-----------------------------------
 
@@ -136,7 +135,7 @@ testthat::test_that("Test: param - Testing incorrect variable type,
 
 
 testthat::test_that("Test: output validation param length as 2,  
-                     Source: gsDesign_independent_code.R)",  {
+                     Source: helper.R)",  {
 
   t <- c(.25, .5, .75, 1)
   param <- c(.1,  .2)
@@ -150,7 +149,7 @@ testthat::test_that("Test: output validation param length as 2,
 
 
 testthat::test_that("Test: output validation param length as 4,  
-                     Source: gsDesign_independent_code.R",  {
+                     Source: helper.R",  {
 
   t <- c(.25,.5,.75,1)
   param <- c(.4, .5,.2,.3)

diff --git a/tests/testthat/test-independent-test-sfGapped.R b/tests/testthat/test-independent-test-sfGapped.R
@@ -1,5 +1,3 @@
-source('../gsDesign_independent_code.R')
-
 #-----------------------------------
 ### Testing sfGapped function
 #-----------------------------------
@@ -145,7 +143,7 @@ testthat::test_that("Test: param - Checking Variable Type,
 
 
 testthat::test_that("Test: sfNormal, 
-                    Source: gsDesign_independent_code.R", {
+                    Source: helper.R", {
   tx <- c(0.167,0.333,0.5,0.667,0.833,1)
   param <- list(trange = c(.2, .8), sf = gsDesign::sfNormal, param = c(1,2))
   alpha<-0.05 
@@ -157,7 +155,7 @@ testthat::test_that("Test: sfNormal,
 
 
 testthat::test_that("Test: sfExponential: Output verification, 
-                    Source: gsDesign_independent_code.R", {
+                    Source: helper.R", {
 
   tx <- c(0.167,0.333,0.5,0.667,0.833,1)
   param <- list(trange = c(.2, .8), sf = gsDesign::sfExponential, param = 1.5 )
@@ -170,7 +168,7 @@ testthat::test_that("Test: sfExponential: Output verification,
 
 
 testthat::test_that("Test:  sfLDPocock: Output verification, 
-                    Source: gsDesign_independent_code.R", {
+                    Source: helper.R", {
 
 
   tx <- c(0.167,0.333,0.5,0.667,0.833,1)

diff --git a/tests/testthat/test-independent-test-sfLogistic.R b/tests/testthat/test-independent-test-sfLogistic.R
@@ -1,4 +1,3 @@
-source('../gsDesign_independent_code.R')
 #-----------------------------------
 # Test sfLogistic function
 #-----------------------------------
@@ -152,7 +151,7 @@ testthat::test_that("Test: param - Checking Variable Type,
 
 
 testthat::test_that("Test: output validation param of length 2,  
-                    Source: gsDesign_independent_code.R",  {
+                    Source: helper.R",  {
 
   t <- c(0.33, 0.67, 1)
   param<-c(0, 1)
@@ -164,7 +163,7 @@ testthat::test_that("Test: output validation param of length 2,
 })
 
 testthat::test_that("Test: output validation param of length 2,  t of length 4,  
-                    Source: gsDesign_independent_code.R",  {
+                    Source: helper.R",  {
 
   t <- c(0.2, 0.5, 0.7, 1)
   param<-c(1, 1)
@@ -177,7 +176,7 @@ testthat::test_that("Test: output validation param of length 2,  t of length 4,
 
 
 testthat::test_that("Test: output validation param of length 4,  
-                    Source: gsDesign_independent_code.R",  {
+                    Source: helper.R",  {
 
   t <- c(0.33, 0.67, 1)
   param<-c(0.01, .1, .1, 0.4)