Moved package loading in tests from individual test files

Author: droglenc

NEWS.md

@@ -6,7 +6,7 @@
   * Replaced many `expect_equivalent()` with `expect_equal(,ignore_attr=TRUE)` as `expect_equivalent()` was deprecated.
   * Had to correct many tests where I expected just `matrix` but the class was `c("matrix","array")`.
   * Had to handle multiple warnings for some tests (see [this article](https://testthat.r-lib.org/articles/third-edition.html#warnings)).
-  * Removed many `require()` that were not needed.
+  * Moved all `require()` in individual files to `testthat.R`. This removed many `require()` that were not needed.
 
 * `GompertzFuns()`: Accepted pull request related to [#112](https://github.com/fishR-Core-Team/FSA/issues/112) that fixed several typos and dead links in the documentation ... thanks Arni. Corrected the erroneous reference to t* (should have been t0) in the documentation for the Gompertz function (fixes [#113](https://github.com/fishR-Core-Team/FSA/issues/113) ... thanks again to Arni).
 

man/FSA.Rd

@@ -6,7 +6,18 @@
 # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
 # * https://testthat.r-lib.org/articles/special-files.html
 
-library(testthat)
-library(FSA)
+suppressPackageStartupMessages(library(testthat))
+suppressPackageStartupMessages(library(FSA))
 
+# packages used in tests (load here instead of in individual files)
+suppressPackageStartupMessages(library(FSAdata))
+suppressPackageStartupMessages(library(fishmethods))
+suppressPackageStartupMessages(library(DescTools))
+suppressPackageStartupMessages(library(dunn.test))
+suppressPackageStartupMessages(library(lmtest))
+suppressPackageStartupMessages(library(nlme))
+suppressPackageStartupMessages(library(psych))
+suppressPackageStartupMessages(library(tibble))
+
+# Test the package
 test_check("FSA")

man/growthModels.Rd

@@ -148,33 +148,31 @@ test_that("ageBias() symmetry tests match results in Evans and Hoenig (2008)",{
 })
 
 test_that("test ageBias() against compare2() with AlewifeLH data",{
-  if (require(FSAdata,quietly=TRUE) & require(fishmethods,quietly=TRUE)) {
-    data(AlewifeLH,package="FSAdata")
-    ab2 <- compare2(AlewifeLH,barplot=FALSE)
-    ## no continuity correction
-    suppressWarnings(ab1 <- ageBias(scales~otoliths,data=AlewifeLH,
-                                    ref.lab="Otolith Age",nref.lab="Scale Age"))
-    junk <- capture.output( ab1sum <- summary(ab1) )
-    expect_equal(ab1sum[ab1sum$symTest=="McNemar","chi.sq"], ab2$McNemar$Chisq)
-    expect_equal(ab1sum[ab1sum$symTest=="McNemar","p"], ab2$McNemar$pvalue)
-    expect_equal(ab1sum[ab1sum$symTest=="EvansHoenig","chi.sq"],
-                 ab2$Evans_Hoenig$Chisq)
-    expect_equal(ab1sum[ab1sum$symTest=="EvansHoenig","p"],
-                 ab2$Evans_Hoenig$pvalue)
-    expect_equal(ab1sum[ab1sum$symTest=="EvansHoenig","df"],
-                 ab2$Evans_Hoenig$df)
-    ## Yates continuity correction
-    junk <- capture.output( ab1sum2 <- summary(ab1,what="McNemar",
-                                               cont.corr="Yates") )
-    expect_equal(ab1sum2[1,"chi.sq"], ab2$McNemar_continuity_correction$Chisq)
-    expect_equal(ab1sum2[1,"p"], ab2$McNemar_continuity_correction$pvalue)
-    ## Edwards continuity correction
-    ab3 <- compare2(AlewifeLH,correct="Edwards",barplot=FALSE)
-    junk <- capture.output( ab1sum3 <- summary(ab1,what="McNemar",
-                                               cont.corr="Edwards") )
-    expect_equal(ab1sum3[1,"chi.sq"], ab3$McNemar_continuity_correction$Chisq)
-    expect_equal(ab1sum3[1,"p"], ab3$McNemar_continuity_correction$pvalue)
-  }
+  data(AlewifeLH,package="FSAdata")
+  ab2 <- fishmethods::compare2(AlewifeLH,barplot=FALSE)
+  ## no continuity correction
+  suppressWarnings(ab1 <- ageBias(scales~otoliths,data=AlewifeLH,
+                                  ref.lab="Otolith Age",nref.lab="Scale Age"))
+  junk <- capture.output( ab1sum <- summary(ab1) )
+  expect_equal(ab1sum[ab1sum$symTest=="McNemar","chi.sq"], ab2$McNemar$Chisq)
+  expect_equal(ab1sum[ab1sum$symTest=="McNemar","p"], ab2$McNemar$pvalue)
+  expect_equal(ab1sum[ab1sum$symTest=="EvansHoenig","chi.sq"],
+               ab2$Evans_Hoenig$Chisq)
+  expect_equal(ab1sum[ab1sum$symTest=="EvansHoenig","p"],
+               ab2$Evans_Hoenig$pvalue)
+  expect_equal(ab1sum[ab1sum$symTest=="EvansHoenig","df"],
+               ab2$Evans_Hoenig$df)
+  ## Yates continuity correction
+  junk <- capture.output( ab1sum2 <- summary(ab1,what="McNemar",
+                                             cont.corr="Yates") )
+  expect_equal(ab1sum2[1,"chi.sq"], ab2$McNemar_continuity_correction$Chisq)
+  expect_equal(ab1sum2[1,"p"], ab2$McNemar_continuity_correction$pvalue)
+  ## Edwards continuity correction
+  ab3 <- fishmethods::compare2(AlewifeLH,correct="Edwards",barplot=FALSE)
+  junk <- capture.output( ab1sum3 <- summary(ab1,what="McNemar",
+                                             cont.corr="Edwards") )
+  expect_equal(ab1sum3[1,"chi.sq"], ab3$McNemar_continuity_correction$Chisq)
+  expect_equal(ab1sum3[1,"p"], ab3$McNemar_continuity_correction$pvalue)
 })
 
 test_that("ageBias() compared to http://www.nefsc.noaa.gov/fbp/age-prec/ calculations for AlewifeLH data",{
@@ -285,4 +283,3 @@ test_that("agePrecision() differences for simple data with NA values",{
   ap135 <- agePrecision(~age1+age3+age5,data=tmp)
   expect_equal(round(ap135$PercAgree,4),50.0000)
 })
-