#' Plot histogram of single-species activity
#'
#' The function generates a histogram of species diel activity in 1-hour
#' intervals.
#'
#' Activity is calculated from the time of day of records. The date is ignored.
#'
#' \code{recordDateTimeFormat} defaults to the "YYYY-MM-DD HH:MM:SS"
#' convention, e.g. "2014-09-30 22:59:59". \code{recordDateTimeFormat} can be
#' interpreted either by base-R via \code{\link[base]{strptime}} or in
#' \pkg{lubridate} via \code{\link[lubridate]{parse_date_time}} (argument
#' "orders"). \pkg{lubridate} will be used if there are no "\%" characters in
#' \code{recordDateTimeFormat}.
#'
#' For "YYYY-MM-DD HH:MM:SS", \code{recordDateTimeFormat} would be either
#' "\%Y-\%m-\%d \%H:\%M:\%S" or "ymd HMS". For details on how to specify date
#' and time formats in R see \code{\link[base]{strptime}} or
#' \code{\link[lubridate]{parse_date_time}}.
#'
#' @param recordTable data.frame. the record table created by
#' \code{\link{recordTable}}
#' @param species Name of the single species for which to create a histogram of
#' activity
#' @param allSpecies logical. Create plots for all species in \code{speciesCol}
#' of \code{recordTable}? Overrides argument \code{species}
#' @param speciesCol character. name of the column specifying species names in
#' \code{recordTable}
#' @param recordDateTimeCol character. name of the column specifying date and
#' time in \code{recordTable}
#' @param recordDateTimeFormat character. format of column
#' \code{recordDateTimeCol} in \code{recordTable}
#' @param plotR logical. Show plots in R graphics device?
#' @param writePNG logical. Create pngs of the plots?
#' @param plotDirectory character. Directory in which to create png plots if
#' \code{writePNG = TRUE}
#' @param createDir logical. Create \code{plotDirectory}?
#' @param pngMaxPix integer. image size of png (pixels along x-axis)
#' @param \dots additional arguments to be passed to function
#' \code{\link[graphics]{hist}}
#' @return It returns invisibly a vector of species record date and time in
#' \code{POSIXlt} format. If \code{allSpecies == TRUE}, all species' vectors
#' are returned in an invisible named list.
#'
#' @note If you have a sufficiently large number of records you may wish to
#' consider using \code{\link{activityDensity}} instead. Please be aware that
#' this function (like the other activity... function of this package) use
#' clock time. If your survey was long enough to see changes in sunrise and
#' sunset times, this may result in biased representations of species activity.
#'
#' @author Juergen Niedballa
#'
#' @seealso \code{\link{activityDensity}}, \code{\link{activityRadial}},
#' \code{\link{activityOverlap}}
#'
#' @examples
#'
#'
#' # load record table
#' data(recordTableSample)
#'
#' # generate activity histogram
#' species4activity <- "VTA" # = Viverra tangalunga, Malay Civet
#'
#' activityHistogram (recordTable = recordTableSample,
#' species = species4activity,
#' allSpecies = FALSE)
#'
#' @export activityHistogram
#'
activityHistogram <- function(recordTable,
species,
allSpecies = FALSE,
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "ymd HMS",
plotR = TRUE,
writePNG = FALSE,
plotDirectory,
createDir = FALSE,
pngMaxPix = 1000,
...){
wd0 <- getwd()
mar0 <- par()$mar
on.exit(setwd(wd0))
on.exit(par(mar = mar0), add = TRUE)
checkForSpacesInColumnNames(speciesCol = speciesCol, recordDateTimeCol = recordDateTimeCol)
recordTable <- dataFrameTibbleCheck(df = recordTable)
if(!speciesCol %in% colnames(recordTable)) stop(paste('speciesCol = "', speciesCol, '" is not a column name in recordTable', sep = ''), call. = FALSE)
if(!recordDateTimeCol %in% colnames(recordTable)) stop(paste('recordDateTimeCol = "', recordDateTimeCol, '" is not a column name in recordTable', sep = ''), call. = FALSE)
stopifnot(is.logical(c(allSpecies, writePNG, plotR, createDir)))
if(allSpecies == FALSE){
stopifnot(hasArg(species))
stopifnot(species %in% recordTable[,speciesCol])
}
timeZone <- "UTC"
recordTable$DateTime2 <- parseDateTimeObject(inputColumn = recordTable[,recordDateTimeCol],
dateTimeFormat = recordDateTimeFormat,
timeZone = timeZone)
recordTable$Hour <- as.POSIXlt(recordTable$DateTime2)$hour
# set graphics parameters and out directory
col_bars <- "gray"
hist_breaks <- seq(0,24,1) # 24
xlab.tmp = "Time of Day [h]"
pngWidth <- pngMaxPix
pngHeight <- round(pngMaxPix * 0.8)
if(isTRUE(writePNG)){
if(hasArg(plotDirectory)){
if(isTRUE(createDir)){
dir.create(plotDirectory, recursive = TRUE, showWarnings = FALSE)
setwd(plotDirectory)
} else {
stopifnot(file.exists(plotDirectory))
setwd(plotDirectory)
}
} else {stop("writePNG is TRUE. Please set plotDirectory")}
}
if(allSpecies == FALSE){
subset_species <- recordTable[recordTable[,speciesCol] == species,]
subset_species$Hour <- subset_species$Hour + 0.1 # otherwise both 0 and 1 will be in histogram class 0
if(isTRUE(writePNG)){
png(filename = paste("activity_histogram_", species, "_", Sys.Date(), ".png", sep = ""),
width = pngWidth, height = pngHeight, units = "px", res = 96, type = "cairo")
hist(subset_species$Hour, breaks = hist_breaks,
col = col_bars,
main = paste("Activity of", species),
xlab = xlab.tmp,
axes = FALSE,
...)
axis(1, at = seq(0,24, by = 3))
axis(2)
box()
mtext(paste("number of records:", length(subset_species$Hour)), side = 3, line = 0)
dev.off()
}
if(isTRUE(plotR)){
hist(subset_species$Hour,
breaks = hist_breaks,
col = col_bars,
freq = TRUE,
main = paste("Activity of", species),
xlab = xlab.tmp,
axes = FALSE,
...)
axis(1, at = seq(0,24, by = 3))
axis(2)
box()
mtext(paste("number of records:", length(subset_species$Hour)), side = 3, line = 0)
}
} else {
subset_species_list <- list()
for(i in 1:length(unique(recordTable[,speciesCol]))){
spec.tmp <- unique(recordTable[,speciesCol])[i]
subset_species <- subset(recordTable, recordTable[,speciesCol] == spec.tmp)
if(isTRUE(writePNG)){
png(filename = paste("activity_histogram_", spec.tmp, "_", Sys.Date(), ".png", sep = ""),
width = pngWidth, height = pngHeight, units = "px", res = 96, type = "cairo")
hist(subset_species$Hour,
breaks = hist_breaks,
col = col_bars,
main = paste("Activity of", spec.tmp),
xlab = xlab.tmp,
axes = FALSE,
...)
axis(1, at = seq(0,24, by = 3))
axis(2)
box()
mtext(paste("number of records:", length(subset_species$Hour)), side = 3, line = 0)
dev.off()
}
if(isTRUE(plotR)){
hist(subset_species$Hour,
breaks = hist_breaks,
col = col_bars,
main = paste("Activity of", spec.tmp),
xlab = xlab.tmp,
axes = FALSE,
...)
axis(1, at = seq(0,24, by = 3))
axis(2)
box()
mtext(paste("number of records:", length(subset_species$Hour)), side = 3, line = 0)
}
subset_species_list[[i]] <- subset_species$DateTime2
names(subset_species_list)[i] <- spec.tmp
}
}
if(allSpecies == FALSE){
return(invisible(subset_species$DateTime2))
} else {
return(invisible(subset_species_list))
}
}
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