| Internal {secrdesign} | R Documentation |
Internal Functions
Description
Functions that are called internally by secrdesign. These are exported and may be called separately for testing etc.
Usage
compactSample (traps, n)
GApenfn(traps, sigma)
'outputtype<-'(object, value)
Arguments
traps |
secr trapsobject |
n |
integer number in sample ( |
sigma |
numeric sparial scale parameter |
object |
object output from |
value |
replacement value for outputtype of object |
Details
compactSample selects a detector at random and returns the a compact subset of surrounding detectors.
GApenfn is the default pen_fn used by GAoptim When called with a non-null penalty argument.
Values of outputtype map to class of the run.scenarios output as follows
| Output type | Class |
| secrfit | c("fittedmodels", "secrdesign", "list") |
| ipsecrfit | c("fittedmodels", "secrdesign", "list") |
| predicted | c("estimatetables", "secrdesign", "list") |
| derived | c("estimatetables", "secrdesign", "list") |
| regionN | c("estimatetables", "secrdesign", "list") |
| coef | c("estimatetables", "secrdesign", "list") |
| user | c("estimatetables", "secrdesign", "list") |
| secrsummary | c("summary", "secrdesign", "list") |
| capthist | c("rawdata", "secrdesign", "list") |
| selectedstatistics | c("selectedstatistics", "secrdesign", "list") |
Calling the replacement function automatically changes the class of the output object as appropriate. This determines how the output is handled by downstream functions such as summary. Using a custom extractfn or post-processing the output sometimes requires the outputtype to be set manually (see example in the Multi-model section of secrdesign-vignette.pdf).
Value
GApenfn – a numeric vector with the number of trap pairs separated by 2.5-3.5 sigma and 3.5-4.5 sigma.
compactSample – an object like traps, but with only n rows.
References
Durbach, I., Borchers, D., Sutherland, C. and Sharma, K. (2021) Fast, flexible alternatives to regular grid designs for spatial capture–recapture. Methods in Ecology and Evolution 12, 298–310. DOI 10.1111/2041-210X.13517
See Also
Examples
CStraps <- compactSample(traps(captdata), n = 20)
plot(traps(captdata))
plot(CStraps, add = TRUE, detpar = list(fg = 'blue',pch = 16))
GApenfn(CStraps, sigma = 25)