CensusToCaptHist {BaSTA}

Constructs a capture-history matrix from repeated individual observations to be used in Bayesian Survival Trajectory Analysis (BaSTA).

Description

This function takes a table of repeated observations per individual (e.g., discrete interval census), consisting of a pair of vectors with ID and observation date (e.g., year), and converts it into a capture-history matrix to be used as part of a BaSTA CMR data input.

Usage

CensusToCaptHist(ID, d, dformat = "%Y", timeInt = "Y")

Arguments

ID

A vector with individual IDs.

d

A vector of dates when each individual was observed (see details).

dformat

Defines the date format for d when d is of class character (see details).

timeInt

A one character string specifying which time interval should be used between capture occasions. Arguments are “Y” for years, “M” for months, “W” for weeks and “D” for days (see details)..

Details

The d argument can be specified as an object of class POSIXct or POSIXlt, as a vector of integer time intervals or as a character string indicating the day, month and year. (e.g. dd/mm/yyyy, mmddyyyy, mm-dd-yyyy etc.). When d is of class character then argument dformat needs to be specified using the same conventions as in function format.POSIXct for objects of class POSIXct or POSIXlt.

Value

Creates an object of class “data.frame” with the reconstructed capture recapture matrix.

Author(s)

Owen R. Jones [e-mail].

See Also

DataCheck for running a data check on the input data for function basta.FixCMRdata to fix potential issues for capture-mark-recapture data. bastaCMRdat for an example of input CMR datasets.

Examples

## Create a simulated vector of repeated IDs:
IDvec <- sort(sample(1:5, size = 15, replace = TRUE))

## Simulate dates (e.g., years) of observation per individual:
dVec <- rep(0, length(IDvec))
for(i in unique(IDvec)) {
  svec <- which(IDvec == i)
  dVec[svec] <- sort(sample(1990:1995, length(svec)))
}

## Construct the capture-recapture matrix:
Y <- CensusToCaptHist(ID = IDvec,  d = dVec)