documentation examples updates

R/calc_age2length.R

@@ -24,15 +24,15 @@
 #' columns to include the length bin information.
 #'
 #' @examples
-#'
+#' \dontrun{
 #' directory <- system.file("extdata", "INIT_VMPA_Jan2015", package = "atlantisom")
 #' load(file.path(directory, "outputSETASrun_truth.RData"))
 #'
 #' lenout <- calc_age2length(
 #'   structn=result$structn, resn=result$resn, nums=result$nums,
 #'   biolprm = result$biolprm, fgs = result$fgs,
 #'   CVlenage = 0.1, remove.zeroes=TRUE)
-#'
+#' }
 calc_age2length <- function(structn, resn, nums,
   biolprm, fgs, maxbin = 150,
   CVlenage = 0.1, remove.zeroes = TRUE) {

R/calc_avgwtstage2age.R

@@ -14,26 +14,6 @@
 #'   with the other functions
 #'
 #' @export
-#'
-#' @examples
-#' dir <- system.file("extdata", "INIT_VMPA_Jan2015", package = "atlantisom")
-#' file_nc="outputSETAS.nc"
-#' fgs=load_fgs(dir = dir, "functionalGroups.csv")
-#' file_init="INIT_VMPA_Jan2015.nc"
-#' bps=load_bps(dir = dir, fgs, file_init)
-#' select_groups=fgs$Name[fgs$IsTurnedOn > 0]
-#' select_variable="Nums"
-#' box.info=load_box(dir = dir, file_bgm="VMPA_setas.bgm")
-#' bboxes=get_boundary(box.info)
-#' #when calc_stage2age is run in the run_truth, it will need to have the nums
-#' #data frame and the bioprm already read in:
-#' nums_data <- load_nc(dir = dir,
-#'                      file_nc="outputSETAS.nc",
-#'                      bps=bps, fgs=fgs, select_groups=select_groups,
-#'                      select_variable = "Nums",
-#'                      check_acronyms = TRUE, bboxes = bboxes)
-#' biolprm <- load_biolprm(dir, file_biolprm="VMPA_setas_biol_fishing_Trunk.prm")
-#' YOY <- load_yoy(dir, file_yoy="outputSETASYOY.txt")
 
 ## ACTUAL FUNCTION ##
 calc_avgwtstage2age <- function(wtagecl, annages, fgs) {

R/calc_biomass_age.R

@@ -20,7 +20,7 @@
 #' # Set up the example with input files
 #' d <- system.file("extdata", "INIT_VMPA_Jan2015", package = "atlantisom")
 #' fgs <- load_fgs(d, "functionalGroups.csv")
-#' bps <- load_bps(dir = d, fgs = fgs,
+#' bps <- load_bps(dir = d, fgs = "functionalGroups.csv",
 #'   file_init = paste0(tail(strsplit(d, "/")[[1]], 1), ".nc"))
 #' runprm <- load_runprm(d, "VMPA_setas_run_fishing_F_Trunk.xml")
 #' biolprm <- load_biolprm(dir = d,

R/calc_pred_diet.R

@@ -30,7 +30,7 @@
 #' @examples
 #' d <- system.file("extdata", "INIT_VMPA_Jan2015", package = "atlantisom")
 #' fgs <- load_fgs(d, "functionalGroups.csv")
-#' bps <- load_bps(dir = d, fgs = fgs,
+#' bps <- load_bps(dir = d, fgs = "functionalGroups.csv",
 #'   file_init = paste0(tail(strsplit(d, "/")[[1]], 1), ".nc"))
 #' runprm <- load_runprm(d, "VMPA_setas_run_fishing_F_Trunk.xml")
 #' dietcomp <- load_diet_comp(dir = d, file_diet = "outputSETASDietCheck.txt",

R/calc_stage2age.R

@@ -25,7 +25,7 @@
 #' file_nc="outputSETAS.nc"
 #' fgs=load_fgs(dir = dir, "functionalGroups.csv")
 #' file_init="INIT_VMPA_Jan2015.nc"
-#' bps=load_bps(dir = dir, fgs, file_init)
+#' bps=load_bps(dir = dir, "functionalGroups.csv", file_init)
 #' select_groups=fgs$Name[fgs$IsTurnedOn > 0]
 #' select_variable="Nums"
 #' box.info=load_box(dir = dir, file_bgm="VMPA_setas.bgm")

R/calc_timestep2time.R

@@ -21,13 +21,14 @@
 #'   is returned.
 #'
 #' @examples
+#' \dontrun{
 #' d <- system.file("extdata", "INIT_VMPA_Jan2015", package = "atlantisom")
 #' runprm <-
 #' load(file = file.path(d, "outputSETASrun_truth.RData"))
 #' test <- calc_timestep2time(dir = d, data = result$biomass_ages,
 #'   file_runprm = "VMPA_setas_run_fishing_F_Trunk.xml")
 #' rm(test)
-#'
+#' }
 calc_timestep2time <- function(dir = getwd(), data, file_runprm){
   if (!is.null(dir)) file_runprm <- file.path(dir, file_runprm)
 

R/load_bioind.R

@@ -18,8 +18,9 @@
 #'
 #' @examples
 #' d <- system.file("extdata", "INIT_VMPA_Jan2015", package = "atlantisom")
-#' file <- "outputSETAScatch.txt"
-#' test <- load_catch(dir = d, file_catch = file)
+#' file <- "outputSETASBiomIndx.txt"
+#' fgs <- load_fgs(dir = d, "functionalGroups.csv")
+#' test <- load_bioind(dir = d, file_bioind = file, fgs = fgs)
 load_bioind <- function(dir, file_bioind, fgs, verbose = FALSE) {
   file.bioind <- file.path(dir, file_bioind)
   truebio <- read.table(file.bioind, header = TRUE)

R/load_bps.R

@@ -1,11 +1,11 @@
 #' Extracts the names of the epibenthic biomasspools
 #' from the initial conditions file.
 #'
-#' Use \code{fgs} \code{data.frame} as read in by \code{\link{load_fgs}}
+#' Use \code{file_fgs} \code{data.frame} (this function will call \code{load_fgs})
 #' to get the biomass pool information.
 #'
 #' @template dir
-#' @template fgs
+#' @template file_fgs
 #' @template file_init
 #'
 #' @author Alexander Keth
@@ -17,8 +17,7 @@
 #'
 #' @examples
 #' d <- system.file("extdata", "INIT_VMPA_Jan2015", package = "atlantisom")
-#' fgs <- load_fgs(d, "functionalGroups.csv")
-#' bps <- load_bps(dir = d, fgs = fgs, file_init = "INIT_VMPA_Jan2015.nc")
+#' bps <- load_bps(dir = d, fgs = "functionalGroups.csv", file_init = "INIT_VMPA_Jan2015.nc")
 #'
 load_bps <- function(dir = getwd(), fgs, file_init){
   if (strsplit(file_init, "\\.")[[1]][2] != "nc") {

R/load_catch.R

@@ -15,13 +15,15 @@
 #'
 #' @examples
 #' d <- system.file("extdata", "INIT_VMPA_Jan2015", package = "atlantisom")
-#' file <- "outputSETAScatch.txt"
-#' test <- load_catch(dir = d, file_catch = file)
+#' file <- "outputSETASCatch.txt"
+#' fgs <- load_fgs(dir = d, "functionalGroups.csv")
+#' test <- load_catch(dir = d, fgs = fgs, file_catch = file)
 load_catch <- function(dir, file_catch, fgs, verbose = FALSE) {
   file.catch <- file.path(dir, file_catch)
   catchbio <- read.table(file.catch, header = TRUE)
   catchbio <- catchbio[, -grep("TsAct", colnames(catchbio))]
 
+  fgs <- fgs[fgs$IsTurnedOn > 0,]
   fishedlookup <- fgs[fgs$IsFished > 0,]
 
   names(catchbio)[match(fishedlookup$Code,names(catchbio))] <- fishedlookup$Name

R/load_fisheries.R

@@ -14,7 +14,7 @@
 #'
 #' @examples
 #' d <- system.file("extdata", "INIT_VMPA_Jan2015", package = "atlantisom")
-#' fleets <- load_fisheries(d, "fisheries.csv")
+#' fleets <- load_fisheries(d, "SETasFisheries.csv")
 #' rm(fleets)
 #'
 load_fisheries <- function(dir = getwd(), file_fish){

R/load_meta.R

@@ -30,16 +30,16 @@ load_meta <- function(dir = getwd(), scenario, verbose = FALSE) {
     warning(paste("The function load_meta does not allow dir = NULL\n",
       "and dir will be set to\n", getwd(), "\nas determined using getwd()"))
   }
-  data <- list()
+  mdata <- list()
 
   # Main nc file
-  grepnc <- paste0("^output", scenario, "\\.nc")
+  grepnc <- paste0(scenario, "\\.nc")
   file <- dir(dir, pattern = grepnc, full.names = TRUE)
   connection <- RNetCDF::open.nc(file)
   on.exit(RNetCDF::close.nc(connection))
 
   # Get model name from the scenario argument
-  data$modelname <- scenario
+  mdata$modelname <- scenario
 
   # Get Atlantis version number
   file.log <- dir(dir, pattern = "^log", full.names = TRUE)
@@ -51,14 +51,14 @@ load_meta <- function(dir = getwd(), scenario, verbose = FALSE) {
       "load_meta will use the following log file:\n", tail(file.log, 1)))
     file.log <- tail(file.log, 1)
   }
-  if (!file.exists(file.log)) {
+  if (length(file.log)==0) {
     warning(paste("The log file does not exist in\n", dir, "\n",
       "and consequently the metadata will list the version number",
       "as NA."))
-    data$atlantisversion <- NA
+    mdata$atlantisversion <- NA
   } else {
-    data$atlantisversion <- readLines(file.log, n = 2)[2]
-    data$atlantisversion <- gsub("#", "", data$atlantisversion)
+    mdata$atlantisversion <- readLines(file.log, n = 2)[2]
+    mdata$atlantisversion <- gsub("#", "", mdata$atlantisversion)
   }
 
   # Get number of years, timestep, output interval,
@@ -81,20 +81,20 @@ load_meta <- function(dir = getwd(), scenario, verbose = FALSE) {
     warning(paste("The .prm file does not exist in\n", dir, "\n",
       "and consequently the metadata will list the number of years,",
       "timestep, and timestepunit as NA."))
-    data$toutstart <- NA
-    data$toutinc <- NA
-    data$toutfinc <- NA
-    data$tstop <- NA
-    data$nyears <- NA
-    data$timestep <- NA
-    data$timestepunit <- NA
-    data$outputstep <- NA
-    data$outputstepunit <- NA
-    data$hemisphere <- NA
-    data$nspp <- NA
-    data$nfleet <- NA
+    mdata$toutstart <- NA
+    mdata$toutinc <- NA
+    mdata$toutfinc <- NA
+    mdata$tstop <- NA
+    mdata$nyears <- NA
+    mdata$timestep <- NA
+    mdata$timestepunit <- NA
+    mdata$outputstep <- NA
+    mdata$outputstepunit <- NA
+    mdata$hemisphere <- NA
+    mdata$nspp <- NA
+    mdata$nfleet <- NA
   } else { # Only go here if the prm file is available
-    data <- append(data,
+    mdata <- append(mdata,
       load_runprm(dir = NULL, file.prm))
   } # Close if for prm file
 
@@ -108,18 +108,17 @@ load_meta <- function(dir = getwd(), scenario, verbose = FALSE) {
     warning(paste("The .bgm file does not exist in\n", dir, "\n",
       "and consequently the metadata will list the number",
       "of boxes and\n maximum depth as NA."))
-    data$nbox <- NA
-    data$depthmax <- NA
+    mdata$nbox <- NA
+    mdata$depthmax <- NA
   } else { # Only go here if the bgm file is available
     bgm <- readLines(file.bgm)
-    data$nbox <- grep("nbox", bgm, value = TRUE)
-    data$nbox <- gsub("nbox|[[:space:]]+", "", data$nbox)
-    data$nbox <- as.numeric(data$nbox)
+    mdata$nbox <- grep("nbox", bgm, value = TRUE)
+    mdata$nbox <- gsub("nbox|[[:space:]]+", "", mdata$nbox)
 
     # Get maximum depth
-    data$depthmax <- grep("maxwcbotz", bgm, value = TRUE)
-    data$depthmax <- gsub("maxwcbotz|[[:space:]]+", "", data$depthmax)
-    data$depthmax <- as.numeric(data$depthmax)
+    mdata$depthmax <- grep("maxwcbotz", bgm, value = TRUE)
+    mdata$depthmax <- gsub("maxwcbotz|[[:space:]]+", "", mdata$depthmax)
+    mdata$depthmax <- as.numeric(mdata$depthmax)
   } # Close if for bgm file
 
   # Get the size of the study area in kilometers^2
@@ -130,8 +129,8 @@ load_meta <- function(dir = getwd(), scenario, verbose = FALSE) {
   area <- volume[dim(volume)[1], , ] / dz[dim(dz)[1], 1, 1]
   # If the assumption of the lowest box having a height of 1 m is false you
   # would need to divide by the sum of meters of sediment here
-  data$area <- sum(area[2:dim(area)[1], 1]) / 1000000
-  data$areaunit <- "km^2"
+  mdata$area <- sum(area[2:dim(area)[1], 1]) / 1000000
+  mdata$areaunit <- "km^2"
 
-  invisible(data)
+  invisible(mdata)
 }

R/load_nc.R

@@ -29,7 +29,7 @@
 #' @examples
 #' d <- system.file("extdata", "INIT_VMPA_Jan2015", package = "atlantisom")
 #' fgs <- load_fgs(d, "functionalGroups.csv")
-#' bps <- load_bps(dir = d, fgs = fgs, file_init = "INIT_VMPA_Jan2015.nc")
+#' bps <- load_bps(dir = d, "functionalGroups.csv", file_init = "INIT_VMPA_Jan2015.nc")
 #' test <- load_nc(dir = d, file_nc = "outputSETASCATCH.nc",
 #'   fgs = fgs, bps = bps,
 #'   select_variable = "Catch",

R/load_nc_annage.R

@@ -27,17 +27,6 @@
 #' @keywords gen
 #' @author Alexander Keth, modified by Sarah Gaichas
 #'
-#' @examples
-#' d <- system.file("extdata", "INIT_VMPA_Jan2015", package = "atlantisom")
-#' fgs <- load_fgs(d, "functionalGroups.csv")
-#' bps <- load_bps(dir = d, fgs = fgs, file_init = "INIT_VMPA_Jan2015.nc")
-#' test <- load_nc(dir = d, file_nc = "outputSETASCATCH.nc",
-#'   fgs = fgs, bps = bps,
-#'   select_variable = "Catch",
-#'   select_groups = "Pisciv_T_Fish",
-#'   check_acronyms = TRUE)
-#' str(test)
-#' rm(test)
 #'
 #' @importFrom magrittr %>%
 #' @export
@@ -65,7 +54,7 @@ load_nc_annage <- function(dir = getwd(), file_nc, file_fish, bps, fgs, biolprm,
 
   # Check input of select_variable as only one value is allowed
   select_variable <- match.arg(select_variable, several.ok = FALSE)
-  
+
   # select_variable gets renamed for fishery data, save input
   input_select_variable <- select_variable
 
@@ -140,7 +129,7 @@ load_nc_annage <- function(dir = getwd(), file_nc, file_fish, bps, fgs, biolprm,
     dplyr::mutate(maxage = nagecl * ageperagecl) %>%
     dplyr::mutate(name = fgs$Name[match(code, fgs$Code)]) %>%
     dplyr::filter(!is.na(maxage))
-  
+
   #limit to groups that have ages
   select_groups <- select_groups[select_groups %in% maxage$name]
 
@@ -179,7 +168,7 @@ load_nc_annage <- function(dir = getwd(), file_nc, file_fish, bps, fgs, biolprm,
   final_agecl <- maxage$maxage[
     sapply(final_species, function(x) which(x == maxage$name))]
 
-  # Get final fleets for full age structure fishery output 
+  # Get final fleets for full age structure fishery output
   if(input_select_variable %in% c("Catch", "Discard")){
     final_fleet <- fleetnames$Code[sapply(
       lapply(select_variable, grepl, x = search_clean), any)]
@@ -249,22 +238,22 @@ load_nc_annage <- function(dir = getwd(), file_nc, file_fish, bps, fgs, biolprm,
 
   int_fs <- final_species
   int_fa <- final_agecl
-  
+
   if(input_select_variable %in% c("Catch", "Discard")){
     # how many unique fleets per select_group in search_clean?
     # lookup of species and fleet names
     splitfleets <- search_clean %>%
       str_replace(paste0("\\d+_*",input_select_variable,"_"), "-")
     sp_fleet <- as.data.frame(unique(splitfleets)) %>%
       rename(spfleet = "unique(splitfleets)") %>%
-      separate(spfleet, c("species", "fleet"), sep = "-") 
+      separate(spfleet, c("species", "fleet"), sep = "-")
     # lookup of number of fleets per species
     sp_nfleet <- as.data.frame(table(sp_fleet$species)) %>%
       rename(species = Var1, nfleet = Freq)
     # for indexing fleets
     int_ff <- sp_nfleet$nfleet
   }
-  
+
   if (length(at_data3d) >= 1) {
     # Remove biomasspools if selected variable is "N"!
     if (select_variable == "N") {
@@ -322,18 +311,18 @@ load_nc_annage <- function(dir = getwd(), file_nc, file_fish, bps, fgs, biolprm,
     }
 
     # Order of the data in value column = "atoutput".
-    # 1. species  --> rep each with the number of 
+    # 1. species  --> rep each with the number of
     #                 ageclasses * fleets and n_timesteps * boxes
     # 2. age      --> rep each (1:maxage for each species) with n_timesteps * boxes
     # 3. timestep --> rep each timestep (1:n_timesteps)
     #                 with the number of boxes and final_agecl
     #                 (num ages per species)
     # 4. polygon  --> rep boxes times n_timesteps * final_agecl
     #                 (num ages per species)
-    # 5. fleet    --> 
+    # 5. fleet    -->
 
     if(input_select_variable %in% c("Nums", "Weight")){
-      
+
     result2d <- data.frame(species = unlist(sapply(
       X = mapply(FUN = rep, x = int_fs, each = int_fa, SIMPLIFY = FALSE,
                  USE.NAMES = FALSE),
@@ -349,18 +338,18 @@ load_nc_annage <- function(dir = getwd(), file_nc, file_fish, bps, fgs, biolprm,
       stringsAsFactors = F)
       if (select_variable == "N") result2d$layer <- n_layers - 1
     }
-    
+
     #should now work properly for multiple fleets
     if(input_select_variable %in% c("Catch", "Discard")){
-      result2d <- data.frame(species = unlist(sapply(X = mapply(FUN = rep, x = int_fs, 
+      result2d <- data.frame(species = unlist(sapply(X = mapply(FUN = rep, x = int_fs,
                    each = (int_fa * int_ff),SIMPLIFY = FALSE,USE.NAMES = FALSE),
         FUN = rep, each = length(boxes) * n_timesteps, simplify = FALSE)),
         agecl = unlist(sapply(X = sapply(X = rep(int_fa, int_ff), FUN = seq, from = 1,
                                          by = 1, simplify = FALSE, USE.NAMES = FALSE),
                               FUN = rep, each = (length(boxes) * n_timesteps), simplify = FALSE)),
         polygon = unlist(sapply(X = n_timesteps * int_fa * int_ff,
                                 FUN = rep, x = boxes, simplify = FALSE, USE.NAMES = FALSE)),
-        fleet = unlist(sapply(X = mapply(FUN = rep, x = sp_fleet$fleet, 
+        fleet = unlist(sapply(X = mapply(FUN = rep, x = sp_fleet$fleet,
                                          each = (rep(int_fa, int_ff)),SIMPLIFY = FALSE,USE.NAMES = FALSE),
           FUN = rep, each = (length(boxes) * n_timesteps), simplify = FALSE)),
         time = unlist(sapply(X = int_fa * int_ff , FUN = rep, x = rep(0:(n_timesteps - 1),
@@ -369,7 +358,7 @@ load_nc_annage <- function(dir = getwd(), file_nc, file_fish, bps, fgs, biolprm,
         stringsAsFactors = F)
       #if (select_variable == "N") result2d$layer <- n_layers - 1
     }
-    
+
   }
 
   # Combine dataframes if necessary!