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

ss3sim · Mar 15, 2023 · 26b57b9 · 26b57b9
1 parent 47cffba
commit 26b57b9
Show file tree

Hide file tree

Showing 19 changed files with 2 additions and 32 deletions.
diff --git a/tests/testthat/test-change-e.R b/tests/testthat/test-change-e.R
@@ -1,4 +1,3 @@
-
 wd.old <- getwd()
 temp_path <- file.path(tempdir(), "pars")
 dir.create(temp_path, showWarnings = FALSE)

diff --git a/tests/testthat/test-change-o.R b/tests/testthat/test-change-o.R
@@ -1,4 +1,3 @@
-
 # set up temp directory
 temp_path <- file.path(tempdir(), "ss3sim-test")
 dir.create(temp_path, showWarnings = FALSE)

diff --git a/tests/testthat/test-change-q.R b/tests/testthat/test-change-q.R
@@ -1,4 +1,3 @@
-
 test_that("Automatic errors in change_q", {
   expect_error(change_q(string_add = "Fishery"))
   expect_error(change_q())

diff --git a/tests/testthat/test-change-tv.R b/tests/testthat/test-change-tv.R
@@ -1,4 +1,3 @@
-
 d <- system.file("extdata", package = "ss3sim")
 om <- paste0(d, "/models/cod-om")
 

diff --git a/tests/testthat/test-change_catch.R b/tests/testthat/test-change_catch.R
@@ -1,4 +1,3 @@
-
 d <- system.file("extdata", "models", "cod-om", package = "ss3sim")
 dat <- r4ss::SS_readdat(
   file = file.path(d, "codOM.dat"),

diff --git a/tests/testthat/test-change_f.R b/tests/testthat/test-change_f.R
@@ -1,4 +1,3 @@
-
 om <- system.file("extdata", "models", "cod-om", package = "ss3sim")
 em <- system.file("extdata", "models", "cod-em", package = "ss3sim")
 dat_list <- r4ss::SS_readdat(file.path(om, "codOM.dat"), verbose = FALSE)

diff --git a/tests/testthat/test-clean-data.R b/tests/testthat/test-clean-data.R
@@ -1,5 +1,3 @@
-
-
 d <- system.file("extdata", package = "ss3sim")
 om_dir <- file.path(d, "models", "cod-om")
 

diff --git a/tests/testthat/test-forecast.R b/tests/testthat/test-forecast.R
@@ -1,5 +1,3 @@
-
-
 test_that("check_forecast is working", {
   file <- system.file(
     package = "ss3sim",

diff --git a/tests/testthat/test-get-results.R b/tests/testthat/test-get-results.R
@@ -1,4 +1,3 @@
-
 temp_path <- file.path(tempdir(), "ss3sim-test")
 dir.create(temp_path, showWarnings = FALSE)
 wd <- getwd()

diff --git a/tests/testthat/test-model-setup.r b/tests/testthat/test-model-setup.r
@@ -1,5 +1,3 @@
-
-
 wd.old <- getwd()
 temp_path <- file.path(tempdir(), "verify_input")
 dir.create(temp_path, showWarnings = FALSE)

diff --git a/tests/testthat/test-plot_functions.R b/tests/testthat/test-plot_functions.R
@@ -1,5 +1,3 @@
-
-
 test_that("plot_cummean works", {
   data("scalar_dat", package = "ss3sim")
 

diff --git a/tests/testthat/test-recdevs.R b/tests/testthat/test-recdevs.R
@@ -1,4 +1,3 @@
-
 # .
 # get_recdevs() is pretty simple, so does not need a test for now.
 

diff --git a/tests/testthat/test-run-ss3sim.R b/tests/testthat/test-run-ss3sim.R
@@ -1,5 +1,3 @@
-
-
 # Tests are skipped on CRAN because the Stock Synthesis executable is no available.
 
 temp_path <- file.path(tempdir(), "run-ss3sim-test")

diff --git a/tests/testthat/test-run-ss3simwseas.R b/tests/testthat/test-run-ss3simwseas.R
@@ -1,5 +1,3 @@
-
-
 # Tests are skipped on CRAN because the Stock Synthesis executable is no available.
 
 library(magrittr)

diff --git a/tests/testthat/test-sample-cal.R b/tests/testthat/test-sample-cal.R
@@ -1,5 +1,3 @@
-
-
 temp_path <- file.path(tempdir(), "run-CAAL-test")
 dir.create(temp_path, showWarnings = FALSE)
 wd <- getwd()

diff --git a/tests/testthat/test-sample-comp.R b/tests/testthat/test-sample-comp.R
@@ -1,5 +1,3 @@
-
-
 d <- system.file("extdata", package = "ss3sim")
 exp_dat_path <- file.path(d, "example-om", "ss3_exp_vals_comps.dat")
 

diff --git a/tests/testthat/test-sample-index.R b/tests/testthat/test-sample-index.R
@@ -1,5 +1,3 @@
-
-
 temp_path <- file.path(tempdir(), "ss3sim-test")
 dir.create(temp_path, showWarnings = FALSE)
 wd <- getwd()

diff --git a/tests/testthat/test-setup_scenarios.R b/tests/testthat/test-setup_scenarios.R
@@ -1,7 +1,3 @@
-
-
-
-
 test_that("Default setup_scenarios work", {
   input <- setup_scenarios_defaults()
   scenario_list <- setup_scenarios(input)

diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd
@@ -611,7 +611,7 @@ Use the long data to create a multi-panel plot with {ggplot2}.
 p <- plot_boxplot(
   scalar_dat_long[
     scalar_dat_long$parameter %in% c("depletion", "SSB_MSY") &
-    grepl("E10[0-1]", scalar_dat_long[, "scenario"]),
+      grepl("E10[0-1]", scalar_dat_long[, "scenario"]),
   ],
   x = "E", y = "RE", re = FALSE,
   horiz = "parameter", print = FALSE
@@ -642,7 +642,7 @@ print(p)
 p <- plot_boxplot(
   scalar_dat_long[
     scalar_dat_long$parameter %in% c("depletion", "SSB_MSY") &
-    grepl("E[0-1]-", scalar_dat_long$scenario),
+      grepl("E[0-1]-", scalar_dat_long$scenario),
   ],
   x = "D", y = "RE", re = FALSE,
   vert = "E", horiz = "parameter", print = FALSE