refactor: changes suggested by IGT review

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: nwfscDiag
 Type: Package
 Title: Generate standard NWFSC assessment diagnostics
-Version: 2.0
+Version: 1.1.0
 Author: Chantel Wetzel
 Maintainer: Chantel Wetzel <[email protected]>
 Description: Package that can automates diagnositics for SS3 models by running jitters, retrospective, and profiles.  

R/get_settings.R

@@ -27,13 +27,13 @@ get_settings <- function(settings = NULL, verbose = FALSE) {
     profile_details = NULL,
     version = "3.30",
     exe = "ss",
+    verbose = FALSE,
 
   	# Jitter Settings
     extras = "-nohess",
     Njitter = 100,
     show_in_console = TRUE,
     printlikes = FALSE,
-    verbose = FALSE,
     jitter_fraction = 0.05,
     jitter_init_values_src = NULL,
 
@@ -59,8 +59,6 @@ get_settings <- function(settings = NULL, verbose = FALSE) {
     whichruns = NULL, 
     prior_check = FALSE,
     read_like = TRUE,
-    exe = "ss",
-    verbose = TRUE,
     init_values_src = 0      
   )
 

R/profile_wrapper.R

@@ -25,10 +25,6 @@ profile_wrapper <- function(mydir, model_settings){
   # plyr and dplyr.
   round_any <-  function(x, accuracy, f = round){
     f(x / accuracy) * accuracy}
-
-	OS <- "Mac" # don't know the version$os info for Mac
-  if(length(grep("linux", version$os)) > 0) OS <- "Linux"
-  if(length(grep("mingw", version$os)) > 0) OS <- "Windows"
 
   # figure out name of executable based on 'exe' input which may contain .exe
   if(length(grep(".exe", tolower(file.path(mydir, model_settings$base_name)))) == 1) {
@@ -39,12 +35,8 @@ profile_wrapper <- function(mydir, model_settings){
     exe <- paste(model_settings$exe, ifelse(OS == "Windows", ".exe", ""), sep="")
   }
   # check whether exe is in directory
-  if(OS == "Windows") {
-    if(!exe %in% list.files(file.path(mydir, model_settings$base_name))) 
-    		stop("Executable ", exe, " not found in ", file.path(mydir, model_settings$base_name))
-  } else {
-    if(!exe %in% list.files(file.path(mydir, model_settings$base_name))) 
-    	stop("Executable ", exe, " not found in ", file.path(mydir, model_settings$base_name))
+  if(!exe %in% list.files(file.path(mydir, model_settings$base_name))) {
+    stop("Executable ", exe, " not found in ", file.path(mydir, model_settings$base_name))
   }
 
   N <- nrow(model_settings$profile_details)
@@ -73,17 +65,9 @@ profile_wrapper <- function(mydir, model_settings){
     if (!file.exists(file.path(profile_dir, "control.ss_new"))) {
       orig_dir <- getwd()
       setwd(profile_dir)
-      command <- paste(model_settings$model, model_settings$extras)
-      if(OS != "windows") {
-        command <- paste( "./", command, sep="")
-      }
-      cat("Running model in directory:", getwd(), "\n")
-      cat("Using the command: '", command, "'\n", sep="")
-      if(OS == "windows" & !model_settings$systemcmd){
-        shell(cmd = command)
-      } else {
-        system(command)
-      }
+      r4ss::run(dir = profile_dir, 
+        exe = model_settings$exe, 
+        extras = model_settings$extras)
       setwd(orig_dir)
     }
 

R/retro_wrapper.R

@@ -62,7 +62,6 @@ retro_wrapper <- function(mydir,  model_settings) {
     dir = retro_dir, 
     oldsubdir = model_settings$oldsubdir, 
     newsubdir = model_settings$newsubdir,  	
-    subdirstart = "retro",
     years = model_settings$retro_yrs,
     overwrite = model_settings$overwrite,
     exe = model_settings$exe, 

R/run_diagnostics.R

@@ -15,24 +15,14 @@ run_diagnostics <- function(mydir, model_settings ){
 
   # Check for Report file
   model_dir <- file.path(mydir, paste0(model_settings$base_name))
-  OS <- "Mac" # don't know the version$os info for Mac
-  if(length(grep("linux", version$os)) > 0) OS <- "Linux"
-  if(length(grep("mingw", version$os)) > 0) OS <- "Windows"
 
   if (!file.exists(file.path(model_dir, "Report.sso"))) {
     orig_dir <- getwd()
     setwd(model_dir)
-    command <- paste(model_settings$exe, model_settings$extras)
-    if(OS != "windows") {
-      command <- paste( "./", command, sep="")
-    }
     cat("Running model in directory:", getwd(), "\n")
-    cat("Using the command: '", command, "'\n", sep="")
-    if(OS == "windows" & !model_settings$systemcmd){
-      shell(cmd = command)
-    } else {
-      system(command)
-    }
+    run(dir = model_dir, 
+      exe = model_settings$exe, 
+      extras = model_settings$extras)
     setwd(orig_dir)
   }