secr: par.secr.fit – R documentation

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par.secr.fit

Fit Multiple SECR Models

Description

These functions are wrappers for secr.fit, region.N and derived that allow multiple models to be fitted simultaneously on multi-core machines (but see Warning).

Usage

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, ...)

Arguments

`arglist`	list of argument lists for `secr.fit` or a character vector naming such lists
`ncores`	integer number of cores to be used for parallel processing
`seed`	integer pseudorandom number seed
`trace`	logical; if TRUE intermediate output may be logged
`logfile`	character name of file to log progress reports
`prefix`	character prefix for names of output
`LB`	logical; if TRUE then use load balancing
`save.intermediate`	logical; if TRUE then each fit is saved to an external file
`...`	other arguments passed to `derived` or `region.N`
`secrlist`	secrlist object

Details

From version 4.0, an arglist may specify ncores for a particular secr fit (previously ncores was ignored in arglist).

trace overrides any settings in arglist. Reporting of intermediate results is unreliable on Windows when ncores > 1.

It is convenient to provide the names of the capthist and mask arguments in each component of arglist as character values (i.e. in quotes); objects thus named are exported from the workspace to each worker process (see Examples).

Setting LB = TRUE when ncores > 1 causes the function to call clusterApplyLB instead of clusterApply. Load balancing in clusterApplyLB is likely to result in faster completion than the default if fits differ in their in execution time and ncores < length(arglist), but this cannot be guaranteed owing to the additional communication required with the worker processes. Results with LB = TRUE for a given seed may not be reproducible.

save.intermediate causes each fit to be saved to a file with extension .RData.

Value

For par.secr.fit - secrlist of model fits (see secr.fit). Names are created by prefixing prefix to the names of argslist. If trace is TRUE then the total execution time and finish time are displayed.

For par.derived - a list of dataframes output from derived, applied to each model in turn.

For par.region.N - a list of dataframes output from region.N, applied to each model in turn.

Warning

With the introduction of multi-threading in secr 4.0, par.secr.fit has lost its speed advantage.

Examples

## Not run: 

fit0 <- list(capthist = 'captdata', model = g0~1) 
fitb <- list(capthist = 'captdata', model = g0~b)
fits <- par.secr.fit (c('fit0','fitb'))
AIC(fits)

par.derived(fits, se.esa = FALSE)

par.region.N(fits)


## End(Not run)

secr

Spatially Explicit Capture-Recapture

v4.4.1

GPL (>= 2)

Authors

Murray Efford

Initial release

2021-05-01