New function convertData()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SOFIA
-Version: 1.1.0
-Date: 2022-02-20
+Version: 1.2.0
+Date: 2022-02-25
 Title: Tools to Work with SOFIA Analyses
 Authors@R: c(person("Rishi", "Sharma", role="aut"),
              person("Arni", "Magnusson", role=c("aut","cre"), email="[email protected]"))

NAMESPACE

@@ -4,6 +4,7 @@ export(addDriors)
 export(addEffort)
 export(calcCat)
 export(compCat)
+export(convertData)
 export(groupData)
 export(plotCat)
 export(plotProp)

NEWS.md

@@ -1,6 +1,17 @@
+# SOFIA 1.2.0 (2022-02-25)
+
+* Added function convertData() to convert primary data to combined data.
+
+* Improved groupData() so it exits gracefully when no CSV files are found.
+  Furthermore, it always creates a new set of empty subdirectories for the
+  output before copying files.
+
+
+
+
 # SOFIA 1.1.0 (2022-02-20)
 
-* Added function groupData() to group primary data into subdirectories.
+* Added function groupData() to group primary data in subdirectories.
 
 
 

R/SOFIA-package.R

@@ -12,9 +12,10 @@
 #' @details
 #' \emph{Prepare data:}
 #' \tabular{ll}{
-#'   \code{\link{addDriors}} \tab add driors column to stocks object\cr
-#'   \code{\link{addEffort}} \tab add effort column to catch data\cr
-#'   \code{\link{groupData}} \tab group primary data in subdirectories
+#'   \code{\link{addDriors}}   \tab add driors column to stocks object\cr
+#'   \code{\link{addEffort}}   \tab add effort column to catch data\cr
+#'   \code{\link{convertData}} \tab convert primary data to combined data\cr
+#'   \code{\link{groupData}}   \tab group primary data in subdirectories
 #' }
 #' \emph{Calculate:}
 #' \tabular{ll}{

R/convertData.R

@@ -0,0 +1,116 @@
+#' Convert Data
+#'
+#' Convert primary single-stock data files into combined data files ready for
+#' analysis, such \code{catches.csv}, \code{effort.csv}, and/or
+#' \code{indices.csv}.
+#'
+#' @param subdir is a directory containing the primary data files.
+#' @param min.catch is a small numeric constant to use instead of \code{NA} or
+#'        zero catches.
+#' @param quiet is whether to suppress screen output.
+#'
+#' @details
+#' \code{subdir} is usually one of \code{"both"}, \code{"effort"},
+#' \code{"index"}, or \code{"neither"}, generated by the \code{groupData}
+#' function.
+#'
+#' Pass any non-numeric value for \code{min.catch}, for example \code{FALSE}, to
+#' retain \code{NA} and zero catch values.
+#'
+#' @return
+#' Files are converted inside \code{subdir}. As a byproduct, a list is returned,
+#' describing the files after conversion.
+#'
+#' @note
+#' A primary data file can have a filename such as
+#' \file{Yellowtail_snapper_Mexico.csv} and columns such as
+#' \code{stockid|scientificname|commonname|year|catch|stocklong}.
+#'
+#' The combined data files, such as \code{catches.csv}, have the format
+#' \code{Year|Unique_Stock_Name_1|Unique_Stock_Name_2|...} where, for example,
+#' \code{Yellowtail_snapper_Mexico} is one column name.
+#'
+#' The output files created will depend on whether the data include effort
+#' and/or index data. If \code{subdir = "both"}, a full set of output files will
+#' be created: \code{catches.csv}, \code{effort.csv}, and \code{index.csv}.
+#'
+#' The functions \code{groupData} and \code{convertData} are used together:
+#' first group, then convert.
+#'
+#' @author Arni Magnusson.
+#'
+#' @seealso
+#' \code{\link{groupData}} groups primary data in subdirectories.
+#'
+#' \code{\link{SOFIA-package}} gives an overview of the package.
+#'
+#' @examples
+#' \dontrun{
+#' convertData("Data_files_Area_31_3/both")
+#' convertData("Data_files_Area_31_3/effort, quiet=TRUE")
+#' }
+#'
+#' @importFrom utils read.csv
+#'
+#' @export
+
+convertData <- function(subdir, min.catch=0.001, quiet=FALSE)
+{
+  ## 1  Import CSV files
+  files <- dir(subdir)
+  files <- files[!(files %in% c("catch.csv", "effort.csv", "index.csv"))]
+  if(length(files) == 0)
+  {
+    if(!quiet)
+      message("No CSV files to convert found in '", subdir, "'")
+    return(invisible(NULL))
+  }
+  csv <- lapply(file.path(subdir, files), read.csv)
+  names(csv) <- files
+
+  ## 2  Prepare data frames
+  years <- range(unlist(lapply(csv, "[[", "year")))
+  years <- seq(min(years), max(years))
+  catch <- effort <- index <- data.frame(year=years)
+
+  ## 3  Fill data frames
+  for(i in seq_along(files))
+  {
+    this <- csv[[i]]
+    names(this) <- tolower(names(this))
+    stock <- gsub("^Area[0-9]*_*", "", this$stockid[1])  # shave off prefix
+    if(!("year" %in% names(this)))
+      stop(files[i], " has no 'year' column")
+    if(!("catch" %in% names(this)))
+      stop(files[i], " has no 'catch' column")
+    c.vector <- merge(catch, this, all=TRUE)$catch
+    e.vector <- merge(effort, this, all=TRUE)$best_effort
+    i.vector <- merge(index, this, all=TRUE)$best_index
+    if(is.numeric(min.catch) && min.catch > 0)
+      c.vector[is.na(c.vector) | c.vector == 0] <- min.catch
+    catch[stock] <- c.vector
+    effort[stock] <- e.vector
+    index[stock] <- i.vector
+  }
+
+  ## 4  Write data frames
+  group <- basename(subdir)
+  write.taf(catch, dir=subdir)
+  if(group == "effort" || group == "both")
+    write.taf(effort, dir=subdir)
+  if(group == "index" || group == "both")
+    write.taf(index, dir=subdir)
+  if(!quiet)
+    message("Converted ", length(files), " files")
+
+  ## 5  Remove old files
+  file.remove(file.path(subdir, files))
+
+  ## 6  Return list
+  out <- list(catch=catch)
+  if(group == "effort" || group == "both")
+    out$effort <- effort
+  if(group == "index" || group == "both")
+    out$index <- index
+  invisible(out)
+}

R/groupData.R

@@ -37,9 +37,14 @@
 #'   both + (effort-both) + (index-both) + neither
 #' }
 #'
+#' The functions \code{groupData} and \code{convertData} are used together:
+#' first group, then convert.
+#'
 #' @author Arni Magnusson.
 #'
 #' @seealso
+#' \code{\link{convertData}} converts primary data to combined data.
+#'
 #' \code{\link{SOFIA-package}} gives an overview of the package.
 #'
 #' @examples