Add minor change to convert_output arg defaults and format latin name…

… in title (#88)

* update(convert_output): change dir args to wd

*Specific output data file columns set to numeric

* update(create_title): improve formatting in title - make latin name italicized

* Update(documentation): for convert_output changes to args

R/convert_output.R

@@ -4,7 +4,8 @@
 #'
 #' @param output_file Assessment model output file (e.g., the
 #'  Report.sso file for SS3, the rdat file for BAM, etc.)
-#' @param outdir Directory of the assessment model output file.
+#' @param outdir Directory of the assessment model output file. Defaults to
+#' working directory.
 #' @param model Assessment model used in evaluation ("ss3", "bam",
 #'  "asap", "fims", "amak", "ms-java", "wham", "mas").
 #' @param fleet_names Names of fleets in the assessment model as
@@ -13,7 +14,8 @@
 #' @param file_save TRUE/FALSE; Save the formatted object rather
 #'  than calling the function and adding the formatted object to
 #'  the global environment? Default is false.
-#' @param savedir Directory to save the converted output file.
+#' @param savedir Directory to save the converted output file. Defaults to
+#' working directory.
 #' @param save_name Name of the converted output file (do not use
 #'  spaces).
 #'
@@ -32,11 +34,11 @@
 #'
 convert_output <- function(
     output_file = NULL,
-    outdir = NULL,
+    outdir = getwd(),
     model = NULL,
     fleet_names = NULL,
     file_save = FALSE,
-    savedir = NULL,
+    savedir = getwd(),
     save_name = "std_model_output") {
   #### out_new ####
   # Blank dataframe and set up to mold output into
@@ -80,15 +82,15 @@ convert_output <- function(
   out_new <- out_new[-1, ]
 
   # pull together path
-  if (!is.null(outdir)) {
-    output_file <- paste(outdir, "/", output_file, sep = "")
-  } else {
+  if(file.exists(output_file)) {
     output_file <- output_file
+  } else {
+    output_file <- file.path(outdir, output_file)
   }
 
-  # Check if can locate output file
+  # check path
   if (!file.exists(output_file)) {
-    stop("output file path is invalid.")
+    stop("File not found.")
   }
 
   #### SS3 ####
@@ -1164,10 +1166,11 @@ convert_output <- function(
 
   #### Exporting ####
   # Combind DFs into one
-  out_new <- Reduce(rbind, out_list) # |>
-  # dplyr::mutate(estimate = as.numeric(estimate),
-  #               uncertainty = as.numeric(uncertainty),
-  #               initial = as.numeric(initial))
+  out_new <- Reduce(rbind, out_list) |>
+    dplyr::mutate(estimate = as.numeric(estimate),
+                  uncertainty = as.numeric(uncertainty),
+                  initial = as.numeric(initial)) |>
+    suppressWarnings()
   if (tolower(model) == "ss3") {
     con_file <- system.file("resources", "ss3_var_names.xlsx", package = "asar", mustWork = TRUE)
     var_names_sheet <- openxlsx::read.xlsx(con_file)

R/create_title.R

@@ -21,6 +21,9 @@ create_title <- function(
     year <- format(Sys.Date(), "%Y")
   }
 
+  # Species latin name with italics latex fxn
+  spp_latin <- paste("\\textit{", spp_latin, "}", sep = "")
+
   # Create title dependent on regional language
   if (office == "AFSC") {
     if (is.null(complex)) {