Functions called by openCR.fit when details$R == TRUE, and some others
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)
cyclic.fit returns a fitted model object of class `openCR'.
Other functions return numeric components of the log likelihood.
character
integer index of capture history
integer index of latent class
integer number of primary sessions
integer vector cumulative number of secondary sessions at start of each primary session
integer number of latent classes
array of capture histories
integer first primary session
integer last primary session
dataframe of real parameter values (one unique combination per row)
parameter index array (secondary sessions)
parameter index array (primary sessions)
integer vector
numeric 3-D array of hazard (mixture, mask position, hindex)
integer n x s matrix indexing h for each individual, secondary session
logical; should CJS likelihood include first primary session?
integer 2-vector for index of move.a, move.b (negative if unused)
integer 0 static, 1 uncorrelated etc.
logical; if TRUE then only cardinal and intercardinal axes are included
integer 0 none, 1 wrap, 2 truncate
function to fill kernel
dataframe with columns x,y relative coordinates of kernel cell centres
integer matrix
numeric length of side of kernel cell
numeric; effective radius of zero cell for movement models (usually 0.5)
real array
array detector usage
openval for naive animals
PIA for naive animals
logical; TRUE if model uses individual covariates
gk for naive animals
number of capture histories
number of detectors
number of points on habitat mask
code for distribution of counts (see secr.fit)
named arguments passed to openCR.fit or predict (see extractFocal)
integer maximum number of cycles (maximizations of a given parameter)
absolute tolerance for improvement in log likelihood
logical; if TRUE a status message is given at each maximization
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).
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.
openCR.fit
if (FALSE) {
openCR:::cyclic.fit(capthist = dipperCH, model = list(p~t, phi~t), tol = 1e-5, trace = TRUE)
}
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