openCR-internal: Internal Functions

In openCR: Open Population Capture-Recapture

Internal Functions

Description

Functions called by openCR.fit when details$R == TRUE, and some others

Usage

prwi (type, n, x, jj, cumss, nmix, w, fi, li, openval, PIA, PIAJ, intervals, CJSp1)

prwisecr (type, n, x, nc, jj, kk, mm, nmix, cumss, w, fi, li, gk, openval, 
    PIA, PIAJ, binomN, Tsk, intervals, h, hindex, CJSp1, moveargsi, 
    movementcode, sparsekernel, edgecode, usermodel, kernel = NULL, 
    mqarray = NULL, cellsize = NULL, r0)

PCH1 (type, x, nc, cumss, nmix, openval0, PIA0, PIAJ, intervals)

PCH1secr (type, individual, x, nc, jj, cumss, kk, mm, openval0, PIA0, PIAJ, gk0,
    binomN, Tsk, intervals,  moveargsi, movementcode, sparsekernel, edgecode, 
    usermodel, kernel, mqarray, cellsize, r0) 

pradelloglik (type, w, openval, PIAJ, intervals)

cyclic.fit (..., maxcycle = 10, tol = 1e-5, trace = FALSE) 

Arguments

type	character
n	integer index of capture history
x	integer index of latent class
jj	integer number of primary sessions
cumss	integer vector cumulative number of secondary sessions at start of each primary session
nmix	integer number of latent classes
w	array of capture histories
fi	integer first primary session
li	integer last primary session
openval	dataframe of real parameter values (one unique combination per row)
PIA	parameter index array (secondary sessions)
PIAJ	parameter index array (primary sessions)
intervals	integer vector
h	numeric 3-D array of hazard (mixture, mask position, hindex)
hindex	integer n x s matrix indexing h for each individual, secondary session
CJSp1	logical; should CJS likelihood include first primary session?
moveargsi	integer 2-vector for index of move.a, move.b (negative if unused)
movementcode	integer 0 static, 1 uncorrelated etc.
sparsekernel	logical; if TRUE then only cardinal and intercardinal axes are included
edgecode	integer 0 none, 1 wrap, 2 truncate
usermodel	function to fill kernel
kernel	dataframe with columns x,y relative coordinates of kernel cell centres
mqarray	integer matrix
cellsize	numeric length of side of kernel cell
r0	numeric; effective radius of zero cell for movement models (usually 0.5)
gk	real array
Tsk	array detector usage
openval0	openval for naive animals
PIA0	PIA for naive animals
individual	logical; TRUE if model uses individual covariates
gk0	gk for naive animals
nc	number of capture histories
kk	number of detectors
mm	number of points on habitat mask
binomN	code for distribution of counts (see secr.fit)
...	named arguments passed to openCR.fit or predict (see extractFocal)
maxcycle	integer maximum number of cycles (maximizations of a given parameter)
tol	absolute tolerance for improvement in log likelihood
trace	logical; if TRUE a status message is given at each maximization

Details

cyclic.fit implements cyclic fixing more or less as described by Schwarz and Arnason (1996) and used by Pledger et al. (2010). The intention is to speed up maximization when there are many (beta) parameters. However, fitting is slower than with a single call to openCR.fit, and the function is here only as a curiosity (it is not exported in 1.2.0).

Value

cyclic.fit returns a fitted model object of class ‘openCR’.

Other functions return numeric components of the log likelihood.

References

Pledger, S., Pollock, K. H. and Norris, J. L. (2010) Open capture–recapture models with heterogeneity: II. Jolly-Seber model. Biometrics 66, 883–890.

Schwarz, C. J. and Arnason, A. N. (1996) A general methodology for the analysis of capture-recapture experiments in open populations. Biometrics 52, 860–873.

See Also

openCR.fit

Examples

## Not run: 

openCR:::cyclic.fit(capthist = dipperCH, model = list(p~t, phi~t), tol = 1e-5, trace = TRUE)


## End(Not run)

openCR documentation built on Sept. 25, 2022, 5:06 p.m.