Release 1.1-0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: icesTAF
-Version: 1.0-0
-Date: 2017-02-17
+Version: 1.1-0
+Date: 2017-04-27
 Title: Functions to Support the ICES Transparent Assessment Framework
 Authors@R: c(person("Arni", "Magnusson", role=c("aut","cre"), email="[email protected]"),
              person("Colin", "Millar", role="aut"))

NAMESPACE

@@ -2,6 +2,8 @@
 
 export(dir.remove)
 export(dos2unix)
+export(flr2taf)
 export(readDLS)
+export(taf2long)
 export(unix2dos)
 export(writeDLS)

NEWS

@@ -1,3 +1,11 @@
+--------------------------------------------------------------------------------
+icesTAF 1.1-0 (2017-04-27)
+--------------------------------------------------------------------------------
+o Added functions flr2taf() and taf2long() to convert between table formats.
+
+
+
+
 --------------------------------------------------------------------------------
 icesTAF 1.0-0 (2017-02-17)
 --------------------------------------------------------------------------------

R/flr2taf.R

@@ -0,0 +1,44 @@
+#' Convert FLR table to TAF format
+#'
+#' Convert a simple crosstab table from FLR format to TAF format.
+#'
+#' @param x a table of class \code{FLQuant}.
+#' @param na a value that should be converted to NA.
+#' @param year whether the year should be stored in the first column, instead of
+#' row names.
+#'
+#' @note
+#' FLR uses the \code{FLQuant} class to store tables as 6-dimensional arrays,
+#' while TAF crosstabs are stored as data frames with a year column.
+#'
+#' @seealso
+#' \code{\link{as.data.frame}} is a method provided by the \pkg{FLCore} package
+#' to convert \code{FLQuant} tables to a 7-column long format.
+#'
+#' \code{\link{taf2long}} converts TAF tables to long format.
+#'
+#' \code{\link{icesTAF-package}} gives an overview of the package.
+#'
+#' @examples
+#' x <- array(round(runif(70)/3, 1), dim=c(7,10,1,1,1,1))
+#' dimnames(x) <- list(age=2:8, year=1991:2000,
+#'                     unit="unique", season="all", area="unique", iter=1)
+#' flr2taf(x)
+#' flr2taf(x, na=0, year=FALSE)
+#'
+#' @export
+
+flr2taf <- function(x, na=NULL, year=TRUE)
+{
+  y <- as.data.frame(t(drop(unclass(x))))
+  if(year)
+  {
+    y <- cbind(Year=as.integer(row.names(y)), y)
+    row.names(y) <- NULL
+  }
+  if(!is.null(na))
+  {
+    y[y==na] <- NA
+  }
+  y
+}

R/icesTAF-package.R

@@ -16,6 +16,11 @@
 #'   \code{\link{readDLS}}  \tab read \code{DLS3.2} output from file\cr
 #'   \code{\link{writeDLS}} \tab write \code{DLS3.2} output to file
 #' }
+#' \emph{Table converters:}
+#' \tabular{ll}{
+#'   \code{\link{flr2taf}}  \tab from FLR to TAF format\cr
+#'   \code{\link{taf2long}} \tab from TAF to long format
+#' }
 #' \emph{File management:}
 #' \tabular{ll}{
 #'   \code{\link{dir.remove}} \tab remove empty directories\cr

R/taf2long.R

@@ -0,0 +1,41 @@
+#' Convert TAF table to long format
+#'
+#' Convert a table from TAF crosstab format to a 3-column long format.
+#'
+#' @param x a data frame containing crosstab data.
+#' @param names a vector of three column names for the resulting data frame.
+#' @param year whether the input table has year in the first column, instead of
+#' row names.
+#'
+#' @note
+#' TAF stores crosstab tables as data frames with a year column, as seen in
+#' stock assessment reports. The long format is practical for analysis and
+#' producing plots.
+#'
+#' @seealso
+#' \code{\link{flr2taf}} converts tables from FLR to TAF format.
+#'
+#' \code{\link{icesTAF-package}} gives an overview of the package.
+#'
+#' @examples
+#' fish <- matrix(round(runif(30),3), 5)
+#' fish <- data.frame(Year=2001:2005, fish, check.names=FALSE)
+#' taf2long(fish)
+#'
+#' alt <- fish[-1]
+#' row.names(alt) <- fish$Year
+#' taf2long(alt, names=c("Year","Age","Weight"), year=FALSE)
+#'
+#' @export
+
+taf2long <- function(x, names=c("Year","Age","Value"), year=TRUE)
+{
+  if(year)
+  {
+    row.names(x) <- x[[1]]
+    x <- x[-1]
+  }
+  y <- as.data.frame(as.table(as.matrix(x)))
+  names(y) <- names
+  y
+}