HRSummary: Calculate metrics of activity space using passive telemetry...

In RossDwyer/VTrack: A Collection of Tools for the Analysis of Passive Acoustic Telemetry Data

Calculate metrics of activity space using passive telemetry data

Description

Produce standard metrics of activity space. Metrics can include Minimum convex polygon area (MCP), fixed Kernel Utilisation Distribution (fKUD) area and Brownian Bridge KUDs (BBKUD). Activity space metrics are calculated for full period of tag life and user defined subset (currently monthly or weekly only). Cumulative activity spaces can also be estimated at set temporal subsets.

Usage

HRSummary(
  COAdata,
  projCRS,
  type = "MCP",
  cont = c(50, 95),
  sub = "%Y-%m",
  cumulative = FALSE,
  storepoly = FALSE,
  h = 500,
  ext = 2,
  grid = 200,
  div = 4
)

Arguments

COAdata	a 'COA' object with estimated center of activity positions (using COA)
projCRS	a coordinate reference system in meters used to accurately estimate area (see CRS)
type	type of activity space metric to calculate. Currently "MCP" for minimum convex polygons, "fKUD" for fixed KUD and "BBKUD" for Brownian bridge KUD. Defaults to "MCP" when no value provided.
cont	contours of activity space models to estimate areas. Defaults to 50% and 95% contours
sub	temporal subset used to calculate subsetted activity space metrics. Currently supports monthly ("%Y-%m") or weekly ("%Y-%W"). Defaults to monthly.
cumulative	TRUE/FALSE, should the operation calculate cumulative activity space areas. Caution this may take a long time depending on size of dataset.
storepoly	TRUE/FALSE, should activity space metrics be saved as spatial objects (polygons or rasters)
h	smoothing factor (in m) associated with error associated with reciever range of passive telemetry system. Defaults to 200 m if none provided.
ext	spatial extent used to calculate probability density metrics of activity space ("fKUD", "BBKUD")
grid	grid size used to calculate probability density metrics of activity space ("fKUD", "BBKUD")
div	sig1 divisor used to correct BBKUD estimates.

Value

Produces a list of 2 tibbles containing Overall (full tag life) and Subsetted (user-defined temporal subsets) metrics of activity space. If storepoly=TRUE additional object within list containing spatial objects (MCP polygons or KUD rasters). Temporal subsets are currently restricted to monthly ("%Y-%m") or weekly ("%Y-%W"). Cumulative measures across temporal subsets included if cumulative=TRUE.

See Also

Input data needs to be setup using setupData, and COAs calculated using COA.

Examples

## Import example datasets
data(IMOSdata)
data(taginfo)
data(statinfo)

## Setup data
ATTdata<- setupData(Tag.Detections = IMOSdata, 
                    Tag.Metadata = taginfo, 
                    Station.Information = statinfo, 
                    source="IMOS")

## Estimate Short-term center of activities
COAdata<-COA(ATTdata)

## Define coordinate system for projection of detection data (in m)
proj<-sp::CRS("+init=epsg:3577")

## Estimate 100% MCP areas
mcp_est<-HRSummary(COAdata,
                   projCRS=proj, 
                   type="MCP", 
                   cont=100)

## Estimate 50% and 95% fKUD areas with cumulative metrics calculated
kud_est<-HRSummary(COAdata, 
                   projCRS=proj, 
                   type="fKUD", 
                   cumulative=TRUE)

## Estimate 20%, 50% and 95% BBKUD contour areas and store polygons
kud_est<-HRSummary(COAdata, 
                   projCRS=proj, 
                   type="BBKUD", 
                   cont=c(20,50,95), 
                   storepoly=TRUE)

RossDwyer/VTrack documentation built on Feb. 23, 2024, 10:40 p.m.