Style code and document

DESCRIPTION

@@ -40,7 +40,7 @@ Remotes:
     cran/assertive.types@master,
     r4ss/r4ss@main,
     ss3sim/ss3sim@main
+Config/roxygen2/version: 8.0.0
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -31,6 +31,7 @@ importFrom(r4ss,SS_writedat)
 importFrom(r4ss,SS_writeforecast)
 importFrom(r4ss,SS_writestarter)
 importFrom(ss3sim,get_results_all)
+importFrom(ss3sim,get_results_iter)
 importFrom(ss3sim,get_results_scenario)
 importFrom(stats,na.omit)
 importFrom(tidyr,gather)

R/MS_functions.R

@@ -484,7 +484,7 @@ get_no_EM_catch_df <- function(OM_dir, yrs, MS = "last_yr_catch") {
     # TODO: figure out what values should go here; probably not 0.
     Fcast_rec_line <- grep("^# Fcast_recruitments:$", par) + 1
     par[Fcast_rec_line] <- paste0(rep(0, fore[["Nforecastyrs"]]), collapse = " ")
-    # # Forecast implementation error parameters were included in earlier SS3 version 
+    # # Forecast implementation error parameters were included in earlier SS3 version
     # # whether specified by the user or not. These changes are not needed in 3.30.24.
     # Fcast_impl_err_line <- grep("^# Fcast_impl_error:$", par) + 1
     # par[Fcast_impl_err_line] <- paste0(rep(0, fore[["Nforecastyrs"]]), collapse = " ")
@@ -622,7 +622,7 @@ Interim <- function(EM_out_dir = NULL, EM_init_dir = NULL,
     temp_forecast[, 1] <- (Reference_dat[["endyr"]] + 1 - forecast_adjust):(Reference_dat[["endyr"]] + Reference_forecast[["Nforecastyrs"]])
     colnames(temp_forecast) <- c("year", "recdev")
     Reference_par[["recdev_forecast"]] <- as.data.frame(temp_forecast)
-    # # Forecast implementation error parameters were included in earlier SS3 version 
+    # # Forecast implementation error parameters were included in earlier SS3 version
     # # whether specified by the user or not. These changes are not needed in 3.30.24.
     # temp_impl_error <- matrix(0, nrow = (Reference_forecast[["Nforecastyrs"]]), ncol = 2)
     # temp_impl_error[, 1] <- (Reference_dat[["endyr"]] + 1):(Reference_dat[["endyr"]] + Reference_forecast[["Nforecastyrs"]])
@@ -839,7 +839,6 @@ Interim <- function(EM_out_dir = NULL, EM_init_dir = NULL,
       )
 
 
-
       if (!is.null(sample_struct)) {
         sample_struct_sub <- lapply(sample_struct,
           function(df, y) df[df[, 1] %in% y, ],

R/develop_OMs.R

@@ -170,7 +170,8 @@ develop_OMs <- function(
       } else {
         recdev_name <- "recdev2"
       }
-      new_parfile[[recdev_name]][, "recdev"] <- parfile[[recdev_name]][,
+      new_parfile[[recdev_name]][, "recdev"] <- parfile[[recdev_name]][
+        ,
         "recdev"
       ]
 

R/develtools.R

@@ -79,7 +79,7 @@ test_no_par <- function(orig_mod_dir, new_mod_dir) {
 }
 
 #' function for package developers to update SS3 input files
-#' 
+#'
 #' @param dir_models directory containing the model input files
 
 update_ss3_version <- function(dir_models = "inst/extdata/models") {
@@ -88,7 +88,7 @@ update_ss3_version <- function(dir_models = "inst/extdata/models") {
 
   # get current executable
   dir_exe <- r4ss::get_ss3_exe(dir = tempdir())
-  
+
   # run with current SS3 version without estimation
   for (i in 1:length(models)) {
     r4ss::run(

R/initOM.R

@@ -243,7 +243,6 @@ create_OM <- function(OM_out_dir,
   dat[["catch"]] <- new_catch
 
 
-
   default_F <- F_list[["F_rate"]][F_list[["F_rate"]][, "year"] == dat[["endyr"]], c("year", "seas", "fleet", "F")]
   new_F_rate <- rbind(F_list[["F_rate"]][, c("year", "seas", "fleet", "F")], F_list[["F_rate_fcast"]][, c("year", "seas", "fleet", "F")])
   rownames(new_F_rate) <- c(F_list[["F_rate"]][, c("name")], F_list[["F_rate_fcast"]][, c("name")])

R/single_extend_OM.R

@@ -374,8 +374,7 @@ add_OM_devs <- function(ctl, dat, parlist, timeseries, future_om_dat) {
           stop("Something is wrong, the number of temp selection parameters is not correct. This is likely a code bug not user error :(")
         }
 
-        if ((tv_size_length + tv_age_length + tv_age_length) == 0) {
-        } else if (!is.null(ctl[["dirichlet_parms"]])) {
+        if ((tv_size_length + tv_age_length + tv_age_length) == 0) {} else if (!is.null(ctl[["dirichlet_parms"]])) {
           insert_row <- which(names(ctl) == "dirichlet_parms")
         } else if (!is.null(ctl[["age_selex_parms"]])) {
           insert_row <- which(names(ctl) == "age_selex_parms")

R/utils.R

@@ -226,8 +226,6 @@ clean_init_mod_files <- function(OM_out_dir, EM_out_dir = NULL, MS = "EM",
   endyr <- OM_dat[["endyr"]]
 
 
-
-
   # get years in range function
   get_yrs_in_range <- function(list_name, dat, styr, endyr) {
     df <- dat[[list_name]]

tests/testthat/test-future_om.R

@@ -678,7 +678,6 @@ test_that("Tests a model with env link using historical values", {
 })
 
 
-
 test_that("Setting seeds works as intended", {
   # check replicate option works
   ext_files <- system.file(package = "SSMSE")