style and docs: run devtools::document() and styler::style_pkg()

tests/testthat.R

@@ -13,10 +13,11 @@ r4ss::retro(dir = run_tmp, oldsubdir = "", newsubdir = "retrospectives", years =
 on.exit(unlink(tmp_path, recursive = TRUE))
 # 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",
-      paste0("retro", 0:-3)
-    )
+  dirvec = file.path(
+    run_tmp, "retrospectives",
+    paste0("retro", 0:-3)
   )
+)
 retrosum.simple <- r4ss::SSsummarize(retroModels)
 
 test_check("ss3diags")

tests/testthat/SSmase_test.R

@@ -1,31 +1,31 @@
 ## File is deprecated by MOshima 6/12/23
 
-#library(ss3diags)
+# library(ss3diags)
 # Tests
 # sma = r4ss::SSsummarize(retro.sma)
 # Check joint MASE for indices
-#SSmase(retro.sma)
+# SSmase(retro.sma)
 # select indices
-#SSmase(retro.sma, indexselect = c(4))
+# SSmase(retro.sma, indexselect = c(4))
 # check for length comps
 # smaL = ss3diags::SSretroComps(retro.sma)
-#SSmase(retro.sma, quants = "len", indexselect = 2:4)
+# SSmase(retro.sma, quants = "len", indexselect = 2:4)
 
 # check manually
-#mase <- SSmase(retro.sma, residuals = T)
+# mase <- SSmase(retro.sma, residuals = T)
 # Joint mase from index 1, 3,4
-#mae <- apply(
+# mae <- apply(
 #  mase$Residuals[c("Pred.Res", "Naive.Res")], 2,
 #  function(x) mean(abs(x))
-#)
+# )
 # MASE
-#mae[1] / mae[2]
+# mae[1] / mae[2]
 # compare
-#SSmase(retro.sma)
+# SSmase(retro.sma)
 
 # Check hake
 # phk= r4ss::SSsummarize(retro.phk)
-#SSmase(retro.phk, verbose = T, indexselect = 1)
+# SSmase(retro.phk, verbose = T, indexselect = 1)
 # check for age comps
-#phkA <- ss3diags::SSretroComps(retro.phk)
-#SSmase(retro.phk, quants = "age")
+# phkA <- ss3diags::SSretroComps(retro.phk)
+# SSmase(retro.phk, quants = "age")

tests/testthat/test-HCxval.R

@@ -1,7 +1,7 @@
 ## Test script for hindcast cross validation and MASE
 
-#retroSimple <- ss3diags::retroSimple
-#retrosum.simple <- r4ss::SSsummarize(retroSimple)
+# retroSimple <- ss3diags::retroSimple
+# retrosum.simple <- r4ss::SSsummarize(retroSimple)
 
 path <- file.path(tempdir(), "test_runs")
 dir.create(path, showWarnings = FALSE)

tests/testthat/test-plotJABBA.R

@@ -1,5 +1,5 @@
 ## Test script for JABBA residual plot
-simple <- r4ss::SS_output(dir = test_example_path, verbose=FALSE, printstats = FALSE)
+simple <- r4ss::SS_output(dir = test_example_path, verbose = FALSE, printstats = FALSE)
 
 path <- file.path(tempdir(), "test_runs")
 dir.create(path, showWarnings = FALSE)
@@ -30,19 +30,19 @@ test_that("file of simple_len_jabbaresiduals plot exists", {
 })
 
 ## CAAL uncomment when con option is finished in function
-#test_that("file of simple_con_jabbaresiduals plot exists", {
-  #
-  #SSplotJABBAres(simple,
-    #use_png = TRUE,
-    #print_plot = TRUE,
-    #subplots = "con",
-    #plotdir = path,
-    #filenameprefix = "simple_con_"
-  #)
-
-  #expect_true(file.exists(file.path(path, "simple_con_jabbaresidual.png")))
-  #
-#})
+# test_that("file of simple_con_jabbaresiduals plot exists", {
+#
+# SSplotJABBAres(simple,
+# use_png = TRUE,
+# print_plot = TRUE,
+# subplots = "con",
+# plotdir = path,
+# filenameprefix = "simple_con_"
+# )
+
+# expect_true(file.exists(file.path(path, "simple_con_jabbaresidual.png")))
+#
+# })
 
 test_that("calculate RMSE for CPUE index", {
   rmse <- SSrmse(simple, quants = "cpue")

tests/testthat/test-runs-test.R

@@ -1,4 +1,4 @@
-simple <- r4ss::SS_output(dir = test_example_path, verbose=FALSE, printstats = FALSE)
+simple <- r4ss::SS_output(dir = test_example_path, verbose = FALSE, printstats = FALSE)
 
 #### Simple Model ###############################################################
 
@@ -127,11 +127,11 @@ test_that("runs test works with simple model", {
   run_cpue <- SSrunstest(simple, quants = "len", indexselect = 2)
   expect_match(run_cpue$Index, "SURVEY1")
 
-  # CAAL since switching to simple_small, there is no conditional-age-at-length data. 
-  #run_con <- SSrunstest(simple, quants = "con")
+  # CAAL since switching to simple_small, there is no conditional-age-at-length data.
+  # run_con <- SSrunstest(simple, quants = "con")
 
-  #expect_match(run_con$Index, "Fishery")
-  #expect_match(run_con$test, "Passed")
+  # expect_match(run_con$Index, "Fishery")
+  # expect_match(run_con$test, "Passed")
 })
 
 

tests/testthat/test-uncertainty.R

@@ -1,5 +1,5 @@
 # Test script for evaluating model uncertainty
-simple <- r4ss::SS_output(dir = test_example_path, verbose=FALSE, printstats = FALSE)
+simple <- r4ss::SS_output(dir = test_example_path, verbose = FALSE, printstats = FALSE)
 
 
 mvln.msy <- SSdeltaMVLN(simple, Fref = "MSY")