details {ipsecr}

Detail Specification for ipsecr.fit

Description

The function ipsecr.fit allows many options. Some of these are used infrequently and have been bundled as a single argument details to simplify the documentation. They are described here in two groups: tuning parameters are listed in the following table, and more exotic options follow, listed alphabetically.

Tuning parameters

Parameter	Default	Description
boxsize1	0.2	scalar or vector of length np for size of design
boxsize2	0.05	as for boxsize1; used from second box onwards
centre	3	number of centre points in simulation design
min.nsim	20	minimum number of simulations per point
max.nsim	200	maximum number of simulations per point
dev.max	0.002	tolerance for precision of points in proxy space (see below)
var.nsim	2000	number of additional simulations to estimate variance-covariance matrix
min.nbox	2	minimum number of attempts to `frame' solution
max.nbox	5	maximum number of attempts to `frame' solution
max.ntries	2	maximum number of attempts at each simulation

dev.max defines a stopping rule: simulations are added in blocks of details$min.nsim until a measure of precision is less than dev.max for all proxies. If a vector of length 2, the first element applies to the first box and the second to all later boxes. The measure of precision may be the standard error on the link scale (details$boxtype = "absolute") or the coefficient of variation (details$boxtype = "relative").

Other ‘details’ components

binomN (default 0 = Poisson) integer code for distribution of counts.

boxtype (default "absolute") switches between specifying box size as additive on the transformed parameter scale ("absolute") and relative on the transformed parameter scale ("relative").

CHmethod (default "internal") chooses between internal C++ code, the secr function sim.capthist, and a user-provided R function with arguments "traps", "popn", "detectfn", "detectpar", and "noccasions". See also popmethod.

contrasts (default NULL) bmay be used to specify the coding of factor predictors. The value should be suitable for the 'contrasts.arg' argument of model.matrix. See ‘Trend across sessions’ in secr-multisession.pdf for an example.

debug (default FALSE) is used only for debugging. In ordinary use it should not be changed from the default.

distribution (default "poisson") specifies the distribution of the number of individuals detected n; this may be conditional on the number in the masked area ("binomial") or unconditional ("poisson"). distribution affects the sampling variance of the estimated density. The component ‘distribution’ may also take a numeric value larger than nrow(capthist), rather than "binomial" or "poisson".

extraparam is a list of starting values for extra 'real' parameters that may be needed for some user-specified models. See the vignette for explanation and an example.

factorial (default "full") chooses between "full" or "fractional" design. Fractional requires the package **FrF2** (Groemping 2014).

forkonunix (default TRUE) switches the cluster type generated by makeCluster between FORK and PSOCK.

FrF2args (default NULL) provides a list of arguments defining a fractional design.

ignorenontarget (default FALSE) may be used to ignore non-target information (the capthist attribute 'nontarget'). The default is to model non-target information if it is present.

ignoreusage (default FALSE) may be used to ignore usage (varying effort) information in the traps component. The default is to include usage in the model.

keep.sim (default FALSE) when TRUE causes ipsecr.fit to save additional output, specifically lists (one component per box) of the simulations and parameters for each box, and the final variance simulations.

newdetector (default NULL) may be used to override the detector type of the traps object embedded in the capthist passed to ipsecr.fit.

Nmax (default 1e4) maximum allowed population size for simulations.

nontargettype (default "exclusive") chooses among options "exclusive", "truncated", "erased, "independent", and "dependent". See vignette.

popmethod (default "internal") chooses between internal C++ code, the secr function sim.popn, and a user-provided R function with arguments 'mask', 'D' (density per cell of mask) and 'N' (number of individuals to simulate). See also CHmethod.

savecall (default TRUE) determines whether the function call is included in the output.

YonX (default TRUE) switches between regression of simulated proxy values Y on controlled parameter values X, or the reverse (which is not fully implemented).

References

Groemping, U. (2014). R Package FrF2 for Creating and Analyzing Fractional Factorial 2-Level Designs. Journal of Statistical Software, 56, 1–56. https://www.jstatsoft.org/article/view/v056i01.

See Also

ipsecr.fit