secr-deprecated: Deprecated Functions in Package 'secr'

In secr: Spatially Explicit Capture-Recapture

Deprecated Functions in Package secr

Description

These functions will be removed from future versions of secr or have been renamed.

par.secr.fit (arglist, ncores = 1, seed = NULL, trace = TRUE, logfile = "logfile.txt", prefix = "fit.", LB = FALSE, save.intermediate = FALSE)

par.derived (secrlist, ncores = 1, ...)

par.region.N (secrlist, ncores = 1, ...)

fx.total (object, sessnum = 1, mask = NULL, ncores = NULL, ...)

fxi.secr (object, i = NULL, sessnum = 1, X = NULL, ncores = NULL, ...)

buffer.contour (traps, buffer, nx = 64, convex = FALSE, ntheta = 100, plt = TRUE, add = FALSE, poly = NULL, poly.habitat = TRUE, fill = NULL, ...)

pdot.contour (traps, border = NULL, nx = 64, detectfn = 0, detectpar = list(g0 = 0.2, sigma = 25, z = 1), noccasions = NULL, binomN = NULL, levels = seq(0.1, 0.9, 0.1), poly = NULL, poly.habitat = TRUE, plt = TRUE, add = FALSE, fill = NULL, ...)

esa.plot (object, max.buffer = NULL, spacing = NULL, max.mask = NULL, detectfn, detectpar, noccasions, binomN = NULL, thin = 0.1, poly = NULL, poly.habitat = TRUE, session = 1, plt = TRUE, type = c('density', 'esa', 'meanpdot', 'CVpdot'), n = 1, add = FALSE, overlay = TRUE, conditional = FALSE, ...)

fxi.contour (object, i = 1, sessnum = 1, border = 100, nx = 64, levels = NULL, p = seq(0.1,0.9,0.1), plt = TRUE, add = FALSE, fitmode = FALSE, plotmode = FALSE, fill = NULL, output = c('list','sf','SPDF'), ncores = NULL, ...)

fxi.mode (object, i = 1, sessnum = 1, start = NULL, ncores = NULL, ...)

Details

Since the introduction of multi-threading in secr 4.0 it is no longer efficient to use parallel worker processes.

list.secr.fit replaces par.secr.fit.

Functions par.derived and par.region.N can be replaced by a simple call of lapply (see Examples in list.secr.fit).

Some functions have been renamed to avoid the ambiguous ".":

Old	New
fxi.secr	fxi (S3 generic with method for secr objects)
fxi.contour	fxiContour
fxi.mode	fxiMode
fx.total	fxTotal
esa.plot	esaPlot
pdot.contour	pdotContour
buffer.contour	bufferContour

See Also

secr-defunct, list.secr.fit, secr-version5

secr documentation built on Nov. 4, 2024, 9:06 a.m.