cap_hist_to_n_m_u {Petersen}

Convert capture history data to n, m and u for use in BTSPAS

Description

Convert capture history data to n, m and u for use in BTSPAS

Usage

cap_hist_to_n_m_u(data, sep = "..")

Arguments

data

Data frame containing the variables:

• cap_hist Capture history (see details below)

• freq Number of times this capture history was observed

plus any other covariates (e.g. discrete strata and/or continuous covariates) to be used in the model fitting.

sep

Separator used between strata in cap_hit

Details

The frequency variable (freq in the data argument) is the number of animals with the corresponding capture history.

Capture histories (cap_hist in the data argument) are character values of the format xx..yy is a capture_history where xx and yy are the temporal stratum (e.g., julian week) and '..' separates the two temporal strata. If a fish is released in temporal stratum and never captured again, then yy is set to 0; if a fish is newly captured in temporal stratum yy, then xx is set to zero. For example, a capture history of 23..23 indicates animals released in temporal stratum 23 and recaptured in temporal stratum 23; a capture history of 23..00 indicates animals released in temporal stratum 23 and never seen again; a capture history of 00..23 indicates animals newly captured in temporal stratum 23 at the second sampling event.

. In the diagonal case, fish are only recovered in the same temporal stratum. In the non-diagonal case, fish are allowed to move among temporal strata.

It is not necessary to label the temporal strata starting at 1; BTSPAS will treat the smallest value of the temporal strata seen as the first stratum and will interpolate for temporal strata without any data. Temporal strata labels should be numeric, i.e., do NOT use A, B, C etc.

Value

A list with entries for the stratum index, n (number released), m matrix of recoveries in the current, next, etc stratum, and u (number of unmarked fish) captured in this recovery stratum.

Examples

data(data_btspas_diag1)
cap_hist_to_n_m_u(data_btspas_diag1)

data(data_btspas_nondiag1)
cap_hist_to_n_m_u(data_btspas_nondiag1)