activityDensity <- function(recordTable,
species,
allSpecies = FALSE,
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "%Y-%m-%d %H:%M:%S",
plotR = TRUE,
writePNG = FALSE,
plotDirectory,
createDir = FALSE,
pngMaxPix = 1000,
add.rug = TRUE,
...
){
wd0 <- getwd()
mar0 <- par()$mar
on.exit(setwd(wd0))
on.exit(par(mar = mar0), add = TRUE)
tz <- "UTC"
checkForSpacesInColumnNames(speciesCol = speciesCol, recordDateTimeCol = recordDateTimeCol)
if(!is.data.frame(recordTable)) stop("recordTable must be a data frame", call. = FALSE)
if(!speciesCol %in% colnames(recordTable)) stop(paste('speciesCol = "', speciesCol, '" is not a column name in recordTable', sep = ''), call. = FALSE)
if(!recordDateTimeCol %in% colnames(recordTable)) stop(paste('recordDateTimeCol = "', recordDateTimeCol, '" is not a column name in recordTable', sep = ''), call. = FALSE)
stopifnot(is.logical(c(allSpecies, writePNG, plotR, createDir)))
if(allSpecies == FALSE) {
stopifnot(species %in% recordTable[,speciesCol])
stopifnot(hasArg(species))
}
recordTable$DateTime2 <- strptime(as.character(recordTable[,recordDateTimeCol]), format = recordDateTimeFormat, tz = tz)
if("POSIXlt" %in% class(recordTable$DateTime2) == FALSE) stop("couldn't interpret recordDateTimeCol of recordTable using specified recordDateTimeFormat")
if(any(is.na(recordTable$DateTime2))) stop(paste("at least 1 entry in recordDateTimeCol of recordTable could not be interpreted using recordDateTimeFormat. row",
paste(which(is.na(recordTable$DateTime2)), collapse = ", ")))
recordTable$Time2 <- format(recordTable$DateTime2, format = "%H:%M:%S", usetz = FALSE)
# radians time
recordTable$Time.rad <- (as.numeric(as.POSIXct(strptime(recordTable$Time2, format = "%H:%M:%S", tz = tz))) -
as.numeric(as.POSIXct(strptime("0", format = "%S", tz = tz)))) / 3600 * (pi/12)
if(isTRUE(writePNG)){
if(hasArg(plotDirectory)){
if(isTRUE(createDir)){
dir.create(plotDirectory, recursive = TRUE, showWarnings = FALSE)
setwd(plotDirectory)
} else {
stopifnot(file.exists(plotDirectory))
setwd(plotDirectory)
}
} else {
stop("writePNG is TRUE. Please set plotDirectory", call. = FALSE)}
}
pngWidth <- pngMaxPix
pngHeight <- round(pngMaxPix * 0.8)
if(allSpecies == FALSE){
subset_species <- subset(recordTable, recordTable[,speciesCol] == species)
if(nrow(subset_species) == 1) stop(paste(species, "had only 1 record. Cannot estimate density."), call. = FALSE)
try_error_tmp <- try({
if(isTRUE(writePNG)) png(filename = paste("activity_density_", species, "_", Sys.Date(), ".png", sep = ""),
width = pngWidth, height = pngHeight, units = "px", res = 96, type = "cairo")
if(isTRUE(writePNG) | isTRUE(plotR)){ densityPlot(subset_species$Time.rad,
main = paste("Activity of", species),
rug = add.rug,
...)
mtext(paste("number of records:", nrow(subset_species)), side = 3, line = 0)}
if(isTRUE(writePNG)) dev.off()
}, silent = TRUE)
if(class(try_error_tmp) == "try-error") warning(paste(toupper(species), ": ", try_error_tmp[1], " - SKIPPED", sep = ""), call. = FALSE)
} 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)
plot_main_title <- paste("Activity of", spec.tmp)
if(nrow(subset_species) == 1){
warning(paste(toupper(spec.tmp), ": It had only 1 record. Cannot estimate density. - SKIPPED", sep = ""), call. = FALSE)
next
} else {
try_error_tmp <- try({
if(isTRUE(writePNG)) png(filename = paste("activity_density_", spec.tmp, "_", Sys.Date(), ".png", sep = ""),
width = pngWidth, height = pngHeight, units = "px", res = 96, type = "cairo")
if(isTRUE(writePNG) | isTRUE(plotR)){ densityPlot(subset_species$Time.rad,
main = plot_main_title,
rug = add.rug,
...)
mtext(paste("number of records:", nrow(subset_species)), side = 3, line = 0)
}
if(isTRUE(writePNG)) dev.off()
}, silent = TRUE)
if(class(try_error_tmp) == "try-error") warning(paste(toupper(spec.tmp), ": ", try_error_tmp[1], " - SKIPPED", sep = ""), call. = FALSE)
}
subset_species_list[[i]] <- subset_species$Time.rad
names(subset_species_list)[i] <- spec.tmp
}
}
if(allSpecies == FALSE){
return(invisible(subset_species$Time.rad))
} else {
return(invisible(subset_species_list))
}
}
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