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

nmfs-fish-tools · Feb 2, 2024 · f594bb1 · f594bb1
1 parent 8073027
commit f594bb1
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Showing 5 changed files with 17 additions and 14 deletions.
diff --git a/R/calc_F.R b/R/calc_F.R
@@ -74,11 +74,11 @@ get_F <- function(timeseries, fleetnames, fleetnames_all) {
     # feed back as a named vector sorted by fleet, then season. Names are the
     # same as in the PARAMETERS section of report.sso
     init_F <- init_F[order(init_F[, "Fleet"], init_F[, "Seas"]), ]
-    
+
     # edit to account for fleets of type==3 in list of fleets
-    fleetnumbers = which(fleetnames_all %in% fleetnames)            
-    fleetnames_df<- data.frame(Fleet=fleetnumbers, fleetname=fleetnames)    
-    
+    fleetnumbers <- which(fleetnames_all %in% fleetnames)
+    fleetnames_df <- data.frame(Fleet = fleetnumbers, fleetname = fleetnames)
+
     init_F <- merge(init_F, fleetnames_df)
     init_F_names <- paste0(
       "InitF_seas_", init_F[["Seas"]], "_flt_", init_F[["Fleet"]],

diff --git a/R/initOM.R b/R/initOM.R
@@ -201,7 +201,7 @@ create_OM <- function(OM_out_dir,
     timeseries = outlist[["timeseries"]],
     fleetnames = dat[["fleetinfo"]][dat[["fleetinfo"]][["type"]] %in% c(1, 2), "fleetname"],
     fleetnames_all = dat[["fleetinfo"]][["fleetname"]] # add to account for fleets type=3
-  ) 
+  )
 
   # SINGLE_RUN_MODS:
   update_F_years <- (dat[["endyr"]] + 1):(dat[["endyr"]] + nyrs)

diff --git a/R/initOM_create_devs_list.R b/R/initOM_create_devs_list.R
@@ -153,9 +153,11 @@ match_parname <- function(list_pars, parlist) {
     )
   )
   ## Edit to allow for recdevs labeled recdev2 not recdev1
-  rdnme<-names(parlist)[grepl("recdev", names(parlist))][1]               
-  par_name_tbl <- rbind(par_name_tbl, data.frame(pars = "rec_devs",       
-                                                 obj = rdnme))      
+  rdnme <- names(parlist)[grepl("recdev", names(parlist))][1]
+  par_name_tbl <- rbind(par_name_tbl, data.frame(
+    pars = "rec_devs",
+    obj = rdnme
+  ))
   par_name_tbl <- rbind(par_name_tbl, data.frame(pars = "impl_error", obj = NA))
   if (isTRUE(list_pars == "all")) {
     # TODO: consider which parameters should be included in the "all" option.
@@ -444,11 +446,12 @@ calc_par_trend <- function(val_info,
   if (isTRUE(!is.na(val_info[val_info[["ts_param"]] == val_line, "first_yr_averaging"]) &
     !is.na(val_info[val_info[["ts_param"]] == val_line, "last_yr_averaging"]))) {
     if (parname == "rec_devs") {
-
       # EDITED bc par file labeled "recdev2" NOT "recdev1"
-      rdnme<-names(parlist)[grepl("recdev", names(parlist))][1]            
-      tmp_vals <- data.frame(yrs = parlist[[rdnme]][, 1],                  
-                             rec_devs = parlist[[rdnme]][, 2])              
+      rdnme <- names(parlist)[grepl("recdev", names(parlist))][1]
+      tmp_vals <- data.frame(
+        yrs = parlist[[rdnme]][, 1],
+        rec_devs = parlist[[rdnme]][, 2]
+      )
       tmp_vals_2 <- data.frame(yrs = vals_df[["yrs"]], rec_devs = vals_df[["rec_devs"]])
       tmp_vals <- rbind(tmp_vals, tmp_vals_2)
       to_include <- which(tmp_vals[["yrs"]] >= val_info[val_info[["ts_param"]] == val_line, "first_yr_averaging"] &

diff --git a/man/get_F.Rd b/man/get_F.Rd
diff --git a/tests/testthat/test-calc_F.R b/tests/testthat/test-calc_F.R
@@ -36,7 +36,7 @@ test_timeseries <- data.frame(
 test_fleetnames <- c("Fishery", "Survey")
 
 test_that("get_F works with multi yrs, fleets, and seasons", {
-  F_list <- get_F(timeseries = test_timeseries, fleetnames = test_fleetnames, fleetnames_all=test_fleetnames)
+  F_list <- get_F(timeseries = test_timeseries, fleetnames = test_fleetnames, fleetnames_all = test_fleetnames)
 
   expect_true(NROW(F_list[["F_df"]]) == nfleets * NROW(test_timeseries))
   expect_true(length(F_list) == 4) # b/c 4 components of output