Merge branch 'FEAT-update-testing-fixtures' of https://github.com/PIF…

…SCstockassessments/ss3diags into FEAT-update-testing-fixtures

DESCRIPTION

@@ -2,57 +2,41 @@ Package: ss3diags
 Title: Stock Synthesis Model Diagnostics for Intergated Stock Assessments
 Version: 2.1.1
 Date: 2023-06-07
-Authors@R: 
-  c(person(given = "Henning",
-    family = "Winker",
-    role = c("aut"),
-    email = "henning.winker@ec.europa.eu"),
-    person(given = "Felipe",
-    family = "Carvalho",
-    role = c("aut"),
-    email = "felipe.carvalho@noaa.gov"),
-    person(given = "Massimiliano",
-    family = "Cardinale",
-    role = c("aut"),
-    email = "massimiliano.cardinale@slu.se"),
-    person(given = "Laurence",
-    family = "Kell",
-    role = c("aut"),
-    email = "laurie@seaplusplus.co.uk"),
-    person(given = "Megumi",
-    family = "Oshima",
-    role = c("aut","cre"),
-    email = "megumi.oshima@noaa.gov"),
-    person(given = "Eric",
-    family = "Fletcher",
-    role = c("aut"),
-    email = "eric.fletcher@noaa")
-  ) 
-Description: Compilation of diagnostic functions for Stock Synthesis models, which
-  developed for the manuscript "Using Model Diagnostics in Integrated Stock Assessments".
+Authors@R: c(
+    person("Henning", "Winker", , "henning.winker@ec.europa.eu", role = "aut"),
+    person("Felipe", "Carvalho", , "felipe.carvalho@noaa.gov", role = "aut"),
+    person("Massimiliano", "Cardinale", , "massimiliano.cardinale@slu.se", role = "aut"),
+    person("Laurence", "Kell", , "laurie@seaplusplus.co.uk", role = "aut"),
+    person("Megumi", "Oshima", , "megumi.oshima@noaa.gov", role = c("aut", "cre")),
+    person("Eric", "Fletcher", , "eric.fletcher@noaa", role = "aut")
+  )
+Description: Compilation of diagnostic functions for Stock Synthesis
+    models, which developed for the manuscript "Using Model Diagnostics in
+    Integrated Stock Assessments".
+License: EUPL
+URL: https://github.com/PIFSCstockassessments/ss3diags
+BugReports: https://github.com/PIFSCstockassessments/ss3diags/issues
 Depends:
-  R (>= 3.5)
+    R (>= 3.5)
 Imports:
-    reshape2,
-    mvtnorm,
-    randtests,
-    r4ss(>= 1.46.1),
+    dplyr,
     gplots,
+    lifecycle,
     magrittr,
-    dplyr,
-    rlang,
-    lifecycle
-Remotes: r4ss/r4ss#821
-License: EUPL
+    mvtnorm,
+    r4ss(>= 1.46.1),
+    randtests,
+    reshape2,
+    rlang
+Suggests:
+    knitr,
+    markdown,
+    rmarkdown,
+    testthat (>= 3.0.0)
+Remotes: 
+    r4ss/r4ss#821
 Encoding: UTF-8
 LazyData: True
 LazyDataCompression: gzip
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Suggests:
-  testthat (>= 3.0.0),
-  knitr,
-  rmarkdown,
-  markdown
-URL: https://github.com/PIFSCstockassessments/ss3diags
-BugReports: https://github.com/PIFSCstockassessments/ss3diags/issues

tests/testthat.R

@@ -13,7 +13,8 @@ if(file.exists(file.path(files_path, "ss"))|file.exists(file.path(files_path, "s
   r4ss::retro(dir = run_tmp, oldsubdir = "", newsubdir = "retrospectives", years = 0:-3, show_in_console = FALSE)
   # Creating retrospective object here so that multiple test files can access it without having to re-run retrospective for each test
   retroModels <- r4ss::SSgetoutput(
-    dirvec = file.path(run_tmp, "retrospectives",
+    dirvec = file.path(
+      run_tmp, "retrospectives",
       paste0("retro", 0:-3)
     )
   )

tests/testthat/test-HCxval.R

@@ -9,8 +9,8 @@ dir.create(path, showWarnings = FALSE)
 ## Hindcast plotting of indices
 
 test_that("Hindcast plot is created for simple model indices", {
-    skip_if(
-    !exists("retrosum.simple") ,
+  skip_if(
+    !exists("retrosum.simple"),
     message = "skipping test that requires SS3 executable"
   )
   SSplotHCxval(retrosum.simple,
@@ -41,11 +41,11 @@ test_that("Hindcast plot is created for simple model indices", {
 #### note: function was too complicated to replicate in the test script so used values directly from running the function. If code for calculations changes, the values will change and it will error or if the SS3 input files change, the values will be different and it will error.
 
 test_that("MASE table gives expected values for simple model", {
-    skip_if(
-    !exists("retrosum.simple") ,
+  skip_if(
+    !exists("retrosum.simple"),
     message = "skipping test that requires SS3 executable"
   )
- 
+
   mase <- SSplotHCxval(retrosum.simple, add = T, verbose = F)
 
   expect_match(mase$Index[1], "SURVEY1")
@@ -55,9 +55,8 @@ test_that("MASE table gives expected values for simple model", {
 
 
 test_that("SSretroComps returns the correct comp data for simple model", {
-
-     skip_if(
-    !exists("retrosum.simple") ,
+  skip_if(
+    !exists("retrosum.simple"),
     message = "skipping test that requires SS3 executable"
   )
   retro_comps <- SSretroComps(retroSimple)
@@ -72,8 +71,8 @@ test_that("SSretroComps returns the correct comp data for simple model", {
 
 
 test_that("SSmase base.adj changes", {
-    skip_if(
-    !exists("retrosum.simple") ,
+  skip_if(
+    !exists("retrosum.simple"),
     message = "skipping test that requires SS3 executable"
   )
   ssmase <- SSmase(retrosum.simple, MAE.base.adj = 0.15)

tests/testthat/test-retro.R

@@ -6,8 +6,8 @@ dir.create(path, showWarnings = FALSE)
 
 ## SSB
 test_that("Retrospective plot is created for SSB (w/ deprecated parameters)", {
-    skip_if(
-    !exists("retrosum.simple") ,
+  skip_if(
+    !exists("retrosum.simple"),
     message = "skipping test that requires SS3 executable"
   )
   SSplotRetro(retrosum.simple,
@@ -23,8 +23,8 @@ test_that("Retrospective plot is created for SSB (w/ deprecated parameters)", {
 
 ## F
 test_that("Retrospective plot is created for F (w/ deprecated parameters)", {
-    skip_if(
-    !exists("retrosum.simple") ,
+  skip_if(
+    !exists("retrosum.simple"),
     message = "skipping test that requires SS3 executable"
   )
   SSplotRetro(retrosum.simple,
@@ -41,8 +41,8 @@ test_that("Retrospective plot is created for F (w/ deprecated parameters)", {
 ## Mohn's Rho table using SShcbias function. It's the same code used in SSplotRetro to make the table.
 ## SSB
 test_that("Mohn's Rho table is created for SSB", {
-    skip_if(
-    !exists("retrosum.simple") ,
+  skip_if(
+    !exists("retrosum.simple"),
     message = "skipping test that requires SS3 executable"
   )
   n <- retrosum.simple$n
@@ -70,8 +70,8 @@ test_that("Mohn's Rho table is created for SSB", {
 
 ## F
 test_that("Mohn's Rho table is created for F", {
-    skip_if(
-    !exists("retrosum.simple") ,
+  skip_if(
+    !exists("retrosum.simple"),
     message = "skipping test that requires SS3 executable"
   )
   n <- retrosum.simple$n