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#' Function that summarises a data frame containing stable isotope values (d13C
#' and d15N) grouping by Species and FG columns
#'
#' A wrapper of plyr:ddply to summarise a data frame.
#'
#' @param df a data frame that contains the isotope values. It needs to have the
#' following columns: d13C, d15N, Species and FG. Species stands for the
#' scientific name (or common name), and FG stands for the functional group
#' for each species. If the data frame does not have Species and FG columns,
#' it will raise an error. If the columns change their names, they need to be
#' stated as well in the grouping variable.
#' @param grouping a vector with the name of the columns (variables) that will
#' be used to summarize, and plot the data frame.
#' @param printSummary logical value indicating whether the summary is printed.
#' @param ... optional arguments that are passed to the function for later use.
#'
#' @return a data frame with the summary of the data frame.
#'
#' @export
#'
#' @examples
#' data('Bilagay')
#' subset_CHI <- Bilagay[Bilagay[,'Location'] %in% 'CHI',]
#' summariseIsotopeData(subset_CHI, grouping = c('Spp', 'FG'))
summariseIsotopeData <- function(df = NULL,
grouping = c("Species", "FG"),
printSummary = FALSE,
...) {
# Stupid CRAN fix for variables - see here http://stackoverflow.com/questions/
# 9439256/how-can-i-handle-r-cmd-check-no-visible-binding-for-global-variable-
# notes-when As
# seen in https://github.com/andrewcparnell/simmr/blob/master/R/plot.simmr_
# output.R
d13C <- d15N <- NULL
if (is.null(checkNames(df, c("d13C", "d15N", grouping))))
stop("Check the grouping variable or the names in your dataframe")
summary <- plyr::ddply(df,
grouping,
plyr::summarise,
nC = length(d13C),
meanC = mean(d13C),
sdC = stats::sd(d13C),
seC = stats::sd(d13C)/sqrt(base::length(d13C)),
nN = length(d15N),
meanN = mean(d15N),
sdN = stats::sd(d15N),
seN = stats::sd(d15N)/sqrt(base::length(d15N)))
if (printSummary)
print(summary)
summary
}
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