From f594bb1d826a0cc3264c0f7ed975c72906f42a6a Mon Sep 17 00:00:00 2001 From: k-doering-NOAA Date: Fri, 2 Feb 2024 16:40:27 +0000 Subject: [PATCH] style and docs: run devtools::document() and styler::style_pkg() --- R/calc_F.R | 8 ++++---- R/initOM.R | 2 +- R/initOM_create_devs_list.R | 17 ++++++++++------- man/get_F.Rd | 2 +- tests/testthat/test-calc_F.R | 2 +- 5 files changed, 17 insertions(+), 14 deletions(-) diff --git a/R/calc_F.R b/R/calc_F.R index d459e78e..fa204e6c 100644 --- 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 index d29dd2bd..f732fd8d 100644 --- 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 index 36287ea3..92a69fe3 100644 --- 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 index f3b3f541..179bcf84 100644 --- a/man/get_F.Rd +++ b/man/get_F.Rd @@ -4,7 +4,7 @@ \alias{get_F} \title{Get the Fishing mortality from the timeseries Report.sso table} \usage{ -get_F(timeseries, fleetnames) +get_F(timeseries, fleetnames, fleetnames_all) } \arguments{ \item{timeseries}{The timeseries table from \code{r4ss::SS_output()}.} diff --git a/tests/testthat/test-calc_F.R b/tests/testthat/test-calc_F.R index a6323f3a..f30fb7c0 100644 --- 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