Internal {openCR}

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)