cjs.accumulate: Accumulates common capture history values

In marked: Mark-Recapture Analysis for Survival and Abundance Estimation

Accumulates common capture history values

Description

To speed up compuation, animals with the same capture history and design matrix are accumulated and represented by a frequency. Computes starting values for Phi and p parameters from the list of design matrices and the summarized data list including ch matrix and first and last vectors. If any values are missing (NA) or abs(par)>5, they are set to 0.

Usage

cjs.accumulate(x, model_data, nocc, freq, chunk_size)

Arguments

x	data
model_data	list of design matrices, fixed parameters and time intervals all which can vary by animal
nocc	number of capture occasions
freq	frequency of each capture history before accumulation
chunk_size	size that determines number of pieces of data/design matrix that are handled. Smaller chunk_size requires more time but less memory. 1e7 is default set in cjs.

Value

modified model_data list that is accumulated

Author(s)

Jeff Laake

marked documentation built on Oct. 19, 2023, 5:06 p.m.