Add references to help files

R/ply-array.r

@@ -23,6 +23,9 @@
 #'   backend provided by foreach
 #' @return if results are atomic with same type and dimensionality, a vector, matrix or array; otherwise, a list-array (a list with dimensions)
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 #' @examples
 #' laply(baseball, is.factor)
 #' # cf
@@ -67,6 +70,9 @@ laply <-  function(.data, .fun = NULL, ..., .progress = "none", .drop = TRUE, .p
 #'   backend provided by foreach
 #' @return if results are atomic with same type and dimensionality, a vector, matrix or array; otherwise, a list-array (a list with dimensions)
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 #' @examples
 #' daply(baseball, .(year), nrow)
 #'
@@ -114,6 +120,9 @@ daply <- function(.data, .variables, .fun = NULL, ..., .progress = "none", .drop
 #'   backend provided by foreach
 #' @return if results are atomic with same type and dimensionality, a vector, matrix or array; otherwise, a list-array (a list with dimensions)
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 #' @examples
 #' dim(ozone)
 #' aaply(ozone, 1, mean)

R/ply-data-frame.r

@@ -24,6 +24,9 @@
 #'   backend provided by foreach
 #' @return a data frame
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 ldply <- function(.data, .fun = NULL, ..., .progress = "none", .parallel = FALSE) {
   if (!inherits(.data, "split")) .data <- as.list(.data)
   res <- llply(.data = .data, .fun = .fun, ..., 
@@ -61,6 +64,9 @@ ldply <- function(.data, .fun = NULL, ..., .progress = "none", .parallel = FALSE
 #'   backend provided by foreach
 #' @return a data frame
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 #' @examples
 #' ddply(baseball, .(year), "nrow") 
 #' ddply(baseball, .(lg), c("nrow", "ncol")) 
@@ -103,6 +109,9 @@ ddply <- function(.data, .variables, .fun = NULL, ..., .progress = "none", .drop
 #'   backend provided by foreach
 #' @return a data frame
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 adply <- function(.data, .margins, .fun = NULL, ..., .expand = TRUE, .progress = "none", .parallel = FALSE) {
   pieces <- splitter_a(.data, .margins, .expand)
 

R/ply-list.r

@@ -23,6 +23,9 @@
 #'   backend provided by foreach
 #' @return list of results
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 #' @examples
 #' llply(llply(mtcars, round), table)
 #' llply(baseball, summary)
@@ -123,6 +126,9 @@ llply <- function(.data, .fun = NULL, ..., .progress = "none", .inform = FALSE,
 #'   backend provided by foreach
 #' @return if results are atomic with same type and dimensionality, a vector, matrix or array; otherwise, a list-array (a list with dimensions)
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 #' @examples
 #' linmod <- function(df) lm(rbi ~ year, data = mutate(df, year = year - min(year)))
 #' models <- dlply(baseball, .(id), linmod)
@@ -156,6 +162,9 @@ dlply <- function(.data, .variables, .fun = NULL, ..., .progress = "none", .drop
 #' 
 #' @keywords manip
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 #' @param .data matrix, array or data frame to be processed
 #' @param .margins a vector giving the subscripts to split up \code{data} by.  1 splits up by rows, 2 by columns and c(1,2) by rows and columns, and so on for higher dimensions
 #' @param .fun function to apply to each piece

R/ply-mapply.r

@@ -23,6 +23,9 @@
 #'   backend provided by foreach
 #' @return a data frame
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 #' @examples
 #' mdply(data.frame(mean = 1:5, sd = 1:5), rnorm, n = 2)
 #' mdply(expand.grid(mean = 1:5, sd = 1:5), rnorm, n = 2)
@@ -59,6 +62,9 @@ mdply <- function(.data, .fun = NULL, ..., .expand = TRUE, .progress = "none", .
 #'   backend provided by foreach
 #' @return if results are atomic with same type and dimensionality, a vector, matrix or array; otherwise, a list-array (a list with dimensions)
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 #' @examples
 #' maply(cbind(mean = 1:5, sd = 1:5), rnorm, n = 5)
 #' maply(expand.grid(mean = 1:5, sd = 1:5), rnorm, n = 5)
@@ -94,6 +100,9 @@ maply <- function(.data, .fun = NULL, ..., .expand = TRUE, .progress = "none", .
 #'   backend provided by foreach
 #' @return list of results
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 #' @examples
 #' mlply(cbind(1:4, 4:1), rep)
 #' mlply(cbind(1:4, times = 4:1), rep)
@@ -128,6 +137,9 @@ mlply <- function(.data, .fun = NULL, ..., .expand = TRUE, .progress = "none", .
 #'   each row; or nd (expand = TRUE), with a dimension for each variable.
 #' @param .progress name of the progress bar to use, see \code{\link{create_progress_bar}}
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 m_ply <- function(.data, .fun = NULL, ..., .expand = TRUE, .progress = "none") {
   if (is.matrix(.data) & !is.list(.data)) .data <- .matrix_to_df(.data)
 

R/ply-null.r

@@ -15,6 +15,9 @@
 #' @param .progress name of the progress bar to use, see \code{\link{create_progress_bar}}
 #' @param .print automatically print each result? (default: \code{FALSE})
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 l_ply <- function(.data, .fun = NULL, ..., .progress = "none", .print = FALSE) {
   if (is.character(.fun)) .fun <- do.call("each", as.list(.fun))
   if (!is.function(.fun)) stop(".fun is not a function.")
@@ -52,6 +55,9 @@ l_ply <- function(.data, .fun = NULL, ..., .progress = "none", .print = FALSE) {
 #' @param .progress name of the progress bar to use, see \code{\link{create_progress_bar}}
 #' @param .print automatically print each result? (default: \code{FALSE})
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 d_ply <- function(.data, .variables, .fun = NULL, ..., .progress = "none", .print = FALSE) {
   .variables <- as.quoted(.variables)
   pieces <- splitter_d(.data, .variables)
@@ -81,6 +87,9 @@ d_ply <- function(.data, .variables, .fun = NULL, ..., .progress = "none", .prin
 #' @param .progress name of the progress bar to use, see \code{\link{create_progress_bar}}
 #' @param .print automatically print each result? (default: \code{FALSE})
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 a_ply <- function(.data, .margins, .fun = NULL, ..., .expand = TRUE, .progress = "none", .print = FALSE) {
   pieces <- splitter_a(.data, .margins, .expand)
 

R/ply-replicate.r

@@ -13,6 +13,9 @@
 #' @param .progress name of the progress bar to use, see \code{\link{create_progress_bar}}
 #' @return list of results
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 #' @examples
 #' mods <- rlply(100, lm(y ~ x, data=data.frame(x=rnorm(100), y=rnorm(100))))
 #' hist(laply(mods, function(x) summary(x)$r.squared))
@@ -53,6 +56,9 @@ rlply <- function(.n, .expr, .progress = "none") {
 #' @param .progress name of the progress bar to use, see \code{\link{create_progress_bar}}
 #' @return a data frame
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 #' @examples
 #' rdply(20, mean(runif(100)))
 #' rdply(20, each(mean, var)(runif(100)))
@@ -86,6 +92,9 @@ rdply <- function(.n, .expr, .progress = "none") {
 #' @return if results are atomic with same type and dimensionality, a vector, matrix or array; otherwise, a list-array (a list with dimensions)
 #' @param .drop should extra dimensions of length 1 be dropped, simplifying the output.  Defaults to \code{TRUE}
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 #' @examples
 #' raply(100, mean(runif(100)))
 #' raply(100, each(mean, var)(runif(100)))
@@ -121,6 +130,9 @@ raply <- function(.n, .expr, .progress = "none", .drop = TRUE) {
 #' @param .progress name of the progress bar to use, see \code{\link{create_progress_bar}}
 #' @param .print automatically print each result? (default: \code{FALSE})
 #' @export
+#' @references Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+#'   Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+#'   \url{http://www.jstatsoft.org/v40/i01/}.
 #' @examples
 #' r_ply(10, plot(runif(50)))
 #' r_ply(25, hist(runif(1000)))

man/a_ply.Rd

@@ -21,6 +21,9 @@
   display plots and saving output.
 }
 \keyword{manip}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{matrix, array or data frame to be processed}
   \item{.margins}{a vector giving the subscripts to split up \code{data} by.  1 splits up by rows, 2 by columns and c(1,2) by rows and columns, and so on for higher dimensions}

man/aaply.Rd

@@ -30,6 +30,9 @@
 }
 \keyword{manip}
 \value{if results are atomic with same type and dimensionality, a vector, matrix or array; otherwise, a list-array (a list with dimensions)}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{matrix, array or data frame to be processed}
   \item{.margins}{a vector giving the subscripts to split up \code{data} by.  1 splits up by rows, 2 by columns and c(1,2) by rows and columns, and so on for higher dimensions}

man/adply.Rd

@@ -22,6 +22,9 @@
 }
 \keyword{manip}
 \value{a data frame}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{matrix, array or data frame to be processed}
   \item{.margins}{a vector giving the subscripts to split up \code{data} by.  1 splits up by rows, 2 by columns and c(1,2) by rows and columns, and so on for higher dimensions}

man/alply.Rd

@@ -24,6 +24,9 @@
   for cases where the results are not atomic.
 }
 \keyword{manip}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \value{list of results}
 \arguments{
   \item{.data}{matrix, array or data frame to be processed}

man/d_ply.Rd

@@ -20,6 +20,9 @@
   their side effects like display plots and saving output.
 }
 \keyword{manip}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{data frame to be processed}
   \item{.variables}{variables to split data frame by, as quoted variables, a formula or character vector}

man/daply.Rd

@@ -24,6 +24,9 @@
 }
 \keyword{manip}
 \value{if results are atomic with same type and dimensionality, a vector, matrix or array; otherwise, a list-array (a list with dimensions)}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{data frame to be processed}
   \item{.variables}{variables to split data frame by, as quoted variables, a formula or character vector}

man/ddply.Rd

@@ -29,6 +29,9 @@
 }
 \keyword{manip}
 \value{a data frame}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{data frame to be processed}
   \item{.variables}{variables to split data frame by, as quoted variables, a formula or character vector}

man/dlply.Rd

@@ -24,6 +24,9 @@
 }
 \keyword{manip}
 \value{if results are atomic with same type and dimensionality, a vector, matrix or array; otherwise, a list-array (a list with dimensions)}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{data frame to be processed}
   \item{.variables}{variables to split data frame by, as quoted variables, a formula or character vector}

man/l_ply.Rd

@@ -18,6 +18,9 @@
   effects like display plots and saving output.
 }
 \keyword{manip}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{list to be processed}
   \item{.fun}{function to apply to each piece}

man/laply.Rd

@@ -27,6 +27,9 @@
 }
 \keyword{manip}
 \value{if results are atomic with same type and dimensionality, a vector, matrix or array; otherwise, a list-array (a list with dimensions)}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{input list}
   \item{.fun}{function to apply to each piece}

man/ldply.Rd

@@ -28,6 +28,9 @@
 }
 \keyword{manip}
 \value{a data frame}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{list to be processed}
   \item{.fun}{function to apply to each piece}

man/llply.Rd

@@ -25,6 +25,9 @@
 }
 \keyword{manip}
 \value{list of results}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{list to be processed}
   \item{.fun}{function to apply to each piece}

man/m_ply.Rd

@@ -22,6 +22,9 @@
   length 0 (\code{list()}).
 }
 \keyword{manip}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{matrix or data frame to use as source of arguments}
   \item{.fun}{function to be called with varying arguments}

man/maply.Rd

@@ -24,6 +24,9 @@
 }
 \keyword{manip}
 \value{if results are atomic with same type and dimensionality, a vector, matrix or array; otherwise, a list-array (a list with dimensions)}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{matrix or data frame to use as source of arguments}
   \item{.fun}{function to be called with varying arguments}

man/mdply.Rd

@@ -27,6 +27,9 @@
 }
 \keyword{manip}
 \value{a data frame}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{matrix or data frame to use as source of arguments}
   \item{.fun}{function to be called with varying arguments}

man/mlply.Rd

@@ -24,6 +24,9 @@
 }
 \keyword{manip}
 \value{list of results}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.data}{matrix or data frame to use as source of arguments}
   \item{.fun}{function to be called with varying arguments}

man/r_ply.Rd

@@ -14,6 +14,9 @@
   \code{\link{replicate}}, but never returns anything
 }
 \keyword{manip}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.n}{number of times to evaluate the expression}
   \item{.expr}{expression to evaluate}

man/raply.Rd

@@ -19,6 +19,9 @@
 }
 \keyword{manip}
 \value{if results are atomic with same type and dimensionality, a vector, matrix or array; otherwise, a list-array (a list with dimensions)}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.n}{number of times to evaluate the expression}
   \item{.expr}{expression to evaluate}

man/rdply.Rd

@@ -19,6 +19,9 @@
 }
 \keyword{manip}
 \value{a data frame}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.n}{number of times to evaluate the expression}
   \item{.expr}{expression to evaluate}

man/rlply.Rd

@@ -19,6 +19,9 @@
 }
 \keyword{manip}
 \value{list of results}
+\references{Hadley Wickham (2011). The Split-Apply-Combine Strategy for
+Data Analysis. Journal of Statistical Software, 40(1), 1-29. 
+\url{http://www.jstatsoft.org/v40/i01/}.}
 \arguments{
   \item{.n}{number of times to evaluate the expression}
   \item{.expr}{expression to evaluate}