fixed wrong argument name and arguments for verbose = FALSE

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: FLakeR
 Type: Package
 Title: Work with FLake in R
-Version: 0.0.9
+Version: 0.0.10
 Authors@R: person("Tadhg", "Moore", email = "tadhg.moore@dkit.ie", role = c("aut", "cre"))
 Maintainer: The package maintainer <tadhg.moore@dkit.ie>
 Description: Run the FLake model within R. Comes with a compiled version of FLake and example files.
 License: GPL3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.2

R/run_flake.R

@@ -5,63 +5,63 @@
 #'The specified \code{sim_folder} must contain valid NML files.
 #'
 #'@param sim_folder the directory where simulation files are contained
-#'@param nml_file filepath; to file with FLake setup. Defaults to 'flake.nml'
+#'@param nml_file filepath; to file with FLake setup. Defaults to "flake.nml"
 #'@param verbose Save output as character vector. Defaults to FALSE
 #'
 #'@keywords methods
 #'@author
 #'Tadhg Moore
 #'@examples
-#'sim_folder <- system.file('extdata', package = 'FLakeR')
-#'run_flake(sim_folder, nml_file = 'Heiligensee80-96.nml')
+#'sim_folder <- system.file("extdata", package = "FLakeR")
+#'run_flake(sim_folder, nml_file = "flake.nml")
 #'@export
 #'@importFrom utils packageName
-run_flake <- function (sim_folder = ".", nml_file = NULL, verbose = FALSE)
+run_flake <- function (sim_folder = ".", nml_file = "flake.nml", verbose = FALSE)
 {
   if (is.null(nml_file)) {
-    files <- list.files(sim_folder)[grep('nml', list.files(sim_folder))]
+    files <- list.files(sim_folder)[grep("nml", list.files(sim_folder))]
     if(length(files) > 1){
       stop("You must select one FLake namelist file in your sim_folder: ",
            sim_folder)
     }else if(length(files) < 1){
       stop("You must have a valid FLake namelist file in your sim_folder: ",
            sim_folder)
     }else{
-      nml = files
+      nml <- files
     }
   }else{
-    nml = nml_file
+    nml <- nml_file
   }
   if (.Platform$pkgType == "win.binary") {
     return(run_flakeWin(sim_folder, nml_file = nml, verbose = verbose))
   }
 
   ### macOS ###
-  if (grepl('mac.binary',.Platform$pkgType)) {
-    # stop('No FLake executable available for your machine yet...')
+  if (grepl("mac.binary",.Platform$pkgType)) {
+    # stop("No FLake executable available for your machine yet...")
     maj_v_number <- as.numeric(strsplit(
-      Sys.info()["release"][[1]],'.', fixed = TRUE)[[1]][1])
+      Sys.info()["release"][[1]],".", fixed = TRUE)[[1]][1])
 
     if (maj_v_number < 13.0) {
-      stop('pre-mavericks mac OSX is not supported. Consider upgrading')
+      stop("pre-mavericks mac OSX is not supported. Consider upgrading")
     }
 
     return(run_flakeOSx(sim_folder, nml_file = nml, verbose = verbose))
 
   }
 
   if (.Platform$pkgType == "source") {
-    #stop('No FLake executable available for your machine yet...')
+    #stop("No FLake executable available for your machine yet...")
     return(run_flakeNIX(sim_folder, nml_file = nml, verbose = verbose))
   }
 }
 
 run_flakeWin <- function(sim_folder, nml_file, verbose = FALSE){
 
-  if(.Platform$r_arch == 'x64'){
-    flake_path <- system.file('extbin/win/flake.exe', package = packageName()) 
+  if(.Platform$r_arch == "x64"){
+    flake_path <- system.file("extbin/win/flake.exe", package = packageName()) 
   }else{
-    stop('No FLake executable available for your machine yet...')
+    stop("No FLake executable available for your machine yet...")
   }
 
   origin <- getwd()
@@ -72,8 +72,8 @@ run_flakeWin <- function(sim_folder, nml_file, verbose = FALSE){
       out <- system2(flake_path, wait = TRUE, stdout = TRUE,
                      stderr = "", args=nml_file)
     } else {
-      out <- system2(flake_path, stdout = NULL,
-                     stderr = NULL, args=nml_file)
+      out <- system2(flake_path, args=nml_file, wait = TRUE, stdout = NULL,
+                     stderr = NULL)
     }
     setwd(origin)
     return(out)
@@ -85,18 +85,18 @@ run_flakeWin <- function(sim_folder, nml_file, verbose = FALSE){
 
 
 
-# run_flakeOSx <- function(sim_folder, nml = TRUE, nml_file = 'flake.nml', verbose = TRUE, args){
-#   #lib_path <- system.file('extbin/macFLake/bin', package=packageName()) #Not sure if libraries needed for FLake
+# run_flakeOSx <- function(sim_folder, nml = TRUE, nml_file = "flake.nml", verbose = TRUE, args){
+#   #lib_path <- system.file("extbin/macFLake/bin", package=packageName()) #Not sure if libraries needed for FLake
 #
-#   flake_path <- system.file('exec/macflake', package=packageName())
+#   flake_path <- system.file("exec/macflake", package=packageName())
 #
 #   # ship flake and libs to sim_folder
 #   #Sys.setenv(DYLD_FALLBACK_LIBRARY_PATH=lib_path) #Libraries?
 #
 #   if(nml){
 #     args <- c(args, nml_file)
 #   }else{
-#     args <- c(args,'--read_nml')
+#     args <- c(args,"--read_nml")
 #   }
 #
 #   origin <- getwd()
@@ -121,56 +121,58 @@ run_flakeWin <- function(sim_folder, nml_file, verbose = FALSE){
 #   })
 # }
 
-run_flakeOSx <- function(sim_folder, nml_file = 'flake.nml', verbose=FALSE){
-  flake_path <- system.file('exec/macflake', package='FLakeR')
+run_flakeOSx <- function(sim_folder, nml_file = "flake.nml", verbose=FALSE){
+  flake_path <- system.file("exec/macflake", package="FLakeR")
 
 
   origin <- getwd()
   setwd(sim_folder)
-  Sys.setenv(LD_LIBRARY_PATH = paste(system.file('extbin/nix',
+  old_ld_path <- Sys.getenv("LD_LIBRARY_PATH")
+  on.exit(expr = {Sys.setenv(LD_LIBRARY_PATH = old_ld_path)})
+  Sys.setenv(LD_LIBRARY_PATH = paste(system.file("extbin/nix",
                                                  package = packageName()),
-                                     Sys.getenv('LD_LIBRARY_PATH'),
+                                     Sys.getenv("LD_LIBRARY_PATH"),
                                      sep = ":"))
   tryCatch({
     if (verbose){
       out <- system2(flake_path, wait = TRUE, stdout = TRUE,
                      stderr = "", args=nml_file)
     } else {
-      out <- system2(flake_path, stdout = NULL,
-                     stderr = NULL, args=nml_file)
+      out <- system2(flake_path, args=nml_file, wait = TRUE, stdout = NULL,
+                     stderr = NULL)
     }
     setwd(origin)
     return(out)
   }, error = function(err) {
     print(paste("FLake_ERROR:  ",err))
     setwd(origin)
   })
-
 }
 
-run_flakeNIX <- function(sim_folder, nml_file = 'flake.nml', verbose=FALSE){
-  flake_path <- system.file('exec/nixflake', package=packageName())
+run_flakeNIX <- function(sim_folder, nml_file = "flake.nml", verbose=FALSE){
+  flake_path <- system.file("exec/nixflake", package=packageName())
 
 
   origin <- getwd()
   setwd(sim_folder)
-  Sys.setenv(LD_LIBRARY_PATH = paste(system.file('extbin/nix',
+  old_ld_path <- Sys.getenv("LD_LIBRARY_PATH")
+  on.exit(expr = {Sys.setenv(LD_LIBRARY_PATH = old_ld_path)})
+  Sys.setenv(LD_LIBRARY_PATH = paste(system.file("extbin/nix",
                                                  package = packageName()),
-                                     Sys.getenv('LD_LIBRARY_PATH'), 
+                                     Sys.getenv("LD_LIBRARY_PATH"), 
                                      sep = ":"))
   tryCatch({
     if (verbose){
       out <- system2(flake_path, wait = TRUE, stdout = TRUE,
                      stderr = "", args=nml_file)
     } else {
-      out <- system2(flake_path, stdout = NULL,
-                     stderr = NULL, args=nml_file)
+      out <- system2(flake_path, args=nml_file, wait = TRUE, stdout = NULL,
+                     stderr = NULL)
     }
     setwd(origin)
     return(out)
   }, error = function(err) {
     print(paste("FLake_ERROR:  ",err))
     setwd(origin)
   })
-
 }

README.md

@@ -18,9 +18,6 @@ devtools::install_github("aemon-j/FLakeR")
 
 ```{r example, eval=FALSE}
 library(FLakeR)
-sim_folder <- system.file('extdata', package = 'FLakeR')
-run_flake(sim_folder, nml_file = 'Heiligensee80-96.nml')
+sim_folder <- system.file("extdata", package = "FLakeR")
+run_flake(sim_folder, nml_file = "flake.nml")
 ```
-
-### Output
-Suite of tools for working with FLake output coming soon...

inst/extdata/feeagh.nml → inst/extdata/flake.nml

@@ -6,7 +6,7 @@
 
 &SIMULATION_PARAMS
 del_time_lk   = 86400,! Time step [s]
-time_step_number = 210,! /LER/ The total number of time steps (17 years 1980-1996)
+time_step_number = 200,! /LER/ The total number of time steps (17 years 1980-1996)
 save_interval_n  = 1        ! Saving interval in time steps
 T_wML_in = 6.128,! /LER/ initial temperature of the upper mixed layer
 T_bot_in = 6.255,! /LER/ initial temperature at the bottom
@@ -31,10 +31,11 @@ outputfile    = 'output/output.dat',
 !------------------------------------------------------------------------------
 &LAKE_PARAMS
 depth_w_lk  = 16.05,! /LER/ Lake depth [m]
-fetch_lk    = 2.0E+03,      ! Typical wind fetch [m]
+fetch_lk    = 2000,      ! Typical wind fetch [m]
 depth_bs_lk =  5.0,         ! Depth of the thermally active layer of the bottom sediments [m]
 T_bs_lk     =  4.0,         ! Temperature at the outer edge of the thermally active layer of the bottom sediments [C]
 latitude_lk = 53.9,! /LER/ Geographical latitude [dgr]
+c_relax_C = 0.0030, ! Adjustable constant in the relaxation equation for the shape factor
 /
 
 
@@ -49,10 +50,10 @@ extincoef_optic = 0.98,! /LER/ Extinction coefficients
 /
 
 &inflow
-DTinflow = 0.0,    ! not relevant if Qfromfile = .true.
-DTfixed  = .true., ! not relevant if Qfromfile = .true.
-QS       = 0.0,    ! inflow rate per lake area [m/s], not relevant if Qfromfile = .true.
-Qfromfile = .true.,
-Qfile='Tinflow',   ! a filename with inflow data should be subsituted for 'Tinflow'
-time_step_number = 209 ! number of the model time steps, should be less than or equal to the number of rows in Qfile
+DTinflow = 0.0,    ! not relevant if inflows are not used
+DTfixed  = .true., ! not relevant if inflows are not used
+QS       = 0.0,    ! inflow rate per lake area [m/s], not relevant if inflows are not used
+Qfromfile = .true.,! /LER/
+Qfile='Tinflow',   ! a filename with inflow data should be substituted for 'Tinflow'
+time_step_number = 200 ! number of the model time steps, should be less than or equal to the number of rows in Qfile
 /