js.accumulate function

Accumulates common capture history values

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.

js.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.

Returns

modified model_data list that is accumulated

Author(s)

Jeff Laake