makeJAGSmask-package: Habitat matrices for use with SECR analysis in JAGS or BUGS
In mikemeredith/makeJAGSmask: Construct a Habitat Matrix for Use with SECR Analysis in JAGS or BUGS
Description
Functions to create habitat masks for spatially explicit capture-recapture (SECR) analysis in BUGS or JAGS. Currently this is done by converting a mask prepared by the secr package.
Details
The original code for spatially explicit capture-recapture (SECR) analysis in BUGS or JAGS worked with a rectangular state space assumed to be uniformly good habitat. The JAGS or BUGS model can be modified to allow for part of the rectangle to be designated as unsuitable habitat; proposed activity centre (AC) locations are checked against a matrix to determine if they lie in good or bad habitat, and locations in bad habitat are rejected.
This look-up procedure is repeated for every animal in the augmented data set and for every iteration of the MCMC chain; so if you have 200 animals in the augmented data set and run 100,000 interations, that means 20 million look-ups. It makes sense to minimize the code needed for the look-up and do the complicated stuff before or after the MCMC run.
The JAGS code is written so that truncating the x and y coordinates of the proposed AC produces the indices into the habitat matrix. This matrix has to be configured so that habMat[x, y] returns 1 if the AC is in suitable habitat, 0 otherwise.
The matrix needed for JAGS is constructed by the functions convertRaster or convertMask starting from a raster or a mask produced by the function secr::make.mask.
The estimate of sigma is in units of pixel width. This can be extracted from the mask object with the function pixelWidth.
AC locations in the MCMC output from JAGS will also be in the units used for the habitat matrix, ie, pixel width, with origin at (1, 1); the function convertOutput converts these back to the original coordinate system.
Author(s)
Mike Meredith
Maintainer: Mike Meredith <mike@mmeredith.net>
mikemeredith/makeJAGSmask documentation built on May 19, 2021, 1:10 a.m.
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Description
Functions to create habitat masks for spatially explicit capture-recapture (SECR) analysis in BUGS or JAGS. Currently this is done by converting a mask prepared by the secr package.
Details
The original code for spatially explicit capture-recapture (SECR) analysis in BUGS or JAGS worked with a rectangular state space assumed to be uniformly good habitat. The JAGS or BUGS model can be modified to allow for part of the rectangle to be designated as unsuitable habitat; proposed activity centre (AC) locations are checked against a matrix to determine if they lie in good or bad habitat, and locations in bad habitat are rejected.
This look-up procedure is repeated for every animal in the augmented data set and for every iteration of the MCMC chain; so if you have 200 animals in the augmented data set and run 100,000 interations, that means 20 million look-ups. It makes sense to minimize the code needed for the look-up and do the complicated stuff before or after the MCMC run.
The JAGS code is written so that truncating the x and y coordinates of the proposed AC produces the indices into the habitat matrix. This matrix has to be configured so that habMat[x, y] returns 1 if the AC is in suitable habitat, 0 otherwise.
The matrix needed for JAGS is constructed by the functions convertRaster or convertMask starting from a raster or a mask produced by the function secr::make.mask.
The estimate of sigma is in units of pixel width. This can be extracted from the mask object with the function pixelWidth.
AC locations in the MCMC output from JAGS will also be in the units used for the habitat matrix, ie, pixel width, with origin at (1, 1); the function convertOutput converts these back to the original coordinate system.
Author(s)
Mike Meredith
Maintainer: Mike Meredith <mike@mmeredith.net>
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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