hist_tad: Time-at-Depth histogram
In RchivalTag: Analyzing and Interactive Visualization of Archival Tagging Data

hist_tad

R Documentation

Time-at-Depth histogram

Description

generates daily or back-to-back (e.g. Day-vs-Night-) Time-at-Depth histograms from binned depth or depth time series data

Usage

hist_tad(df, 
            bin_breaks=NULL, bin_prefix="Bin", 
            select_id, select_from='Ptt', aggregate_by='Ptt',
            date, min_perc,
            main, xlab='Time at Depth (%)', ylab="Depth (m)", labeling=TRUE,
            xlim=c(0, 100), adaptive.xlim=FALSE, 
            split_by=NULL, split_levels, xlab2=split_levels, 
            ylab.side=2, ylab.line, ylab.font=1,
            xlab.side=3, xlab.line=2.5, xlab.font=1,
            xlab2.side=1, xlab2.line=1, xlab2.font=2,
            main.side=3, main.line=3.8, main.font=1,
            col=c("darkgrey", "white"),
            xticks, ylabels,
            do_mid.ticks=TRUE, yaxis.pos=0, 
            mars, space=0,
            plot_sd=TRUE, plot_se, plot_nrec=TRUE, plot_ntags=TRUE,
            cex=1.2, cex.main=cex, cex.lab=cex, cex.inf=cex.axis,cex.axis=1, 
            return.sm=FALSE, 
            subplot=FALSE, inside=FALSE,Type="TAD")

Arguments

`df`	dataframe that either contains depth time series data (as a vector "Depth") or several vectors of Time-at-Depth frequencies. In the latter case, column names composed of a common `bin_prefix` (default is "Bin.") hold the pre-binned Time-at-Depth frequencies whose depth limits are defined in `bin_breaks`.
`bin_breaks, bin_prefix`	`bin_breaks` is a numeric vector of depth bin breaks for the histogram data. In case of binned data (e.g. from standard wildlife computer histogram files), column names with a `bin_prefix` are expected to contain the preprossesed data (by default: Bin1, Bin2, Bin3, etc.). Alternatively, depth time series data will be directly converted using function ts2histos.
`select_id, select_from`	these arguments allow to take a direct subset of the input dataframe. `select_from` defines the vector whereas `select_id` defines the identification key(s) that should be selected.
`aggregate_by`	character vector defining the columns by which the tagging data should be aggregated. Should contain columns that identify tags (e.g. Serial, Ptt, DeployID) the date and/or day time period (to seperate records from night, day, dawn and dusk see classify_DayTime). Default values are: date, Day and Ptt.
`date`	An optional vector to select depth data of a specified date/-range.
`min_perc`	optional number, defining the minimum data coverage (in percent) of histogram entries obtained from depth time series data.
`main, xlab, ylab, labeling`	The titles for the plot, x- and y-axes to be plotted if `labeling` is set `TRUE` (default).
`xlim, adaptive.xlim`	a vector defining the limits (x1,x2) of the x-axis, by default c(0,100). However, if `adaptive.xlim` is set `TRUE`, these limits will be overwritten, and the maximum value (xlim[2]) will be chosen from the histogram data.
`split_by`	Name of the logical vector by which TaD data should be splitted (e.g. daytime; see classify_DayTime).
`split_levels, xlab2`	Character vector defining the name and order of the levels of the split_by vector (e.g. c("Night", "Day") for split_by vector 'day.time'. The same groups are plotted as a second x-axis label if not defined otherwise (`xlab2`=`split_levels`).
`ylab.side, ylab.line, ylab.font`	side, line and font of second y-axis label.
`xlab.side, xlab.line, xlab.font`	side, line and font of first x-axis label.
`xlab2.side, xlab2.line, xlab2.font`	side, line and font of second x-axis labels.
`main.side, main.line, main.font`	side, line and font of plot title.
`col`	colours to be used for the TaD-histogram, by default 'grey' and 'white' (corresponding to the values of split_by/split_levels).
`xticks, ylabels`	tick labels of the x-axis and ylabels of the y-axis to show in the plot.
`do_mid.ticks`	whether centered tick-labels, indicating the depth range of histogram cells, shall be plotted (by default `FALSE`). Alternatively, tick labels will be indicated at the breakpoints of the histrogram cells.
`yaxis.pos`	x-axis coordinate at which the y-axis should be plotted (by default xlim[1], and thus 0).
`mars`	a numerical vector of the form `c(bottom, left, top, right)`, decribing the number of margin lines to be specified on the each side of the plot. The default is `c(2.1, 4.1, 6.1, 2.1)`. In case that `do_mid.ticks` is `TRUE` margins are: `c(2.1, 8, 6.1, 2.1)`.
`space`	the space between the histogram bars.
`plot_sd, plot_se, plot_nrec , plot_ntags`	whether standard deviation or standard error bars, the number of records and tags shall be plotted (default is `TRUE`) inside the TaD/TaT histogram. (if plot_se is `TRUE`, plot_sd will be overwritten!).
`cex, cex.main, cex.lab, cex.inf, cex.axis`	font size of the title (`cex.main`), x- and y-axes labels (`cex.lab`), other labels, like the number of records (`cex.inf`) as well as of the tick marks.
`return.sm`	whether summary information of the TaD histograms, including the number of records per summary period, the relative frequencies per bin and corresponding standard deviation, should be plotted (default is `TRUE`).
`subplot, inside`	whether the TaD histogram is a subplot or an inner plot of a figure (default is `FALSE`). If `subplot` or `inside` are set `TRUE`, graphic margins will not be set by `hist_tad`. In case that `inside` is `TRUE`, no axis-labels and titels wil be plotted.
`Type`	The Type of data to be plotted (`TAD`: Time-at-Depth histograms; `TAT`: Time-at-Temperature histograms)

Details

Time-at-Temperature (Tat) and Time-at-Depth (TaD) fequencies are a standard data product of archival tags (incl. tag models TDR-Mk9, PAT-Mk10 and miniPAT by Wildlife Computers) that allow to assess habitat preferences of tagged animals (see function read_histos). It can be likewise generated from transmitted or recovered time series data sets using function ts2histos.

However, different depth and temperature bin breaks are often used during different deployment programs, which makes a later comparitive analysis of TaT and TaT data difficult. For such cases, the function combine_histos and merge_histos can be applied to merge TaT and TaD frequencies based on common bin breaks of different tags.

The purpose of this function is the visualization of Time-at-Depth (TaD) histograms, whereas hist_tad is the related function for Time-at-Temperature (TaT) data.

Author(s)

Robert K. Bauer

Examples

ts_file <- system.file("example_files/104659-Series.csv",package="RchivalTag")
ts_df <- read_TS(ts_file)
head(ts_df)

tad_breaks <- c(0, 2, 5, 10, 20, 50, 100, 200, 300, 400, 600, 2000)
tat_breaks <- c(10,12,15,17,18,19,20,21,22,23,24,27)

## example 1a) convert only DepthTS data to daily TAD frequencies:
ts2histos(ts_df, tad_breaks = tad_breaks)
hist_tad(ts_df, bin_breaks = tad_breaks)
hist_tad(ts_df, bin_breaks = tad_breaks, do_mid.ticks = FALSE)

## convert 1b) only TemperatureTS data to daily TAT frequencies:
tat <- ts2histos(ts_df, tat_breaks = tat_breaks)
hist_tat(ts_df, bin_breaks = tat_breaks, do_mid.ticks = FALSE)
hist_tat(tat$TAT$merged, do_mid.ticks = FALSE)

## convert 1c) DepthTS & TemperatureTS data to daily TAD & TAT frequencies:
ts2histos(ts_df, tad_breaks = tad_breaks, tat_breaks = tat_breaks)

## convert 1d) back-to-back histogram showing day vs night TAD frequencies:
ts_df$Lat <- 4; ts_df$Lon=42.5 ## required geolocations to estimate daytime
head(ts_df)
ts_df2 <- classify_DayTime(get_DayTimeLimits(ts_df)) # estimate daytime
head(ts_df2)

ts2histos(ts_df2, tad_breaks = tad_breaks,split_by = "daytime")
hist_tad(ts_df2, bin_breaks = tad_breaks,split_by = "daytime", do_mid.ticks = FALSE)


## example 2) rebin daily TAD frequencies:
tad <- ts2histos(ts_df, tad_breaks = tad_breaks)
tad2 <- rebin_histos(hist_list = tad, tad_breaks = tad_breaks[c(1:3,6:12)])
par(mfrow=c(2,2))
hist_tad(tad, do_mid.ticks = FALSE) ## example for multiple individuals
hist_tad(tad$TAD$merged, do_mid.ticks = FALSE)
hist_tad(tad$TAD$merged, bin_breaks = tad_breaks[c(1:3,6:12)]) ## from inside hist_tad


## example 3) read, merge and plot TAD frequency data from several files:
## part I - read histogram data from two files:
hist_dat_1 <- read_histos(system.file("example_files/104659-Histos.csv",package="RchivalTag"))
hist_dat_2 <- read_histos(system.file("example_files/104659b-Histos.csv",package="RchivalTag"))
## note the second list is based on the same data (tag), but on different bin_breaks

## part II - combine TAD/TAT frecuency data from seperate files in one list:
hist_dat_combined <- combine_histos(hist_dat_1, hist_dat_2)
par(mfrow=c(2,1))
hist_tad(hist_dat_combined)
hist_tat(hist_dat_combined)

## part III - force merge TAD/TAT frecuency data from seperate files 
# in one list, by applying common bin_breaks:
hist_dat_merged <- merge_histos(hist_dat_combined,force_merge = TRUE)
hist_tad(hist_dat_merged)
hist_tat(hist_dat_merged)

## part IV - plot merged data:
hist_tad(hist_dat_merged) # of all tags
unique(hist_dat_merged$TAD$merged$df$DeployID) ## list unique tags in merged list
hist_tad(hist_dat_merged, select_id = "15P1019b", select_from = 'DeployID') # of one tag

## part V - unmerge data:
unmerge_histos(hist_dat_merged)

RchivalTag documentation built on Nov. 10, 2023, 5:06 p.m.