Installing the wiqid package

Back to home page The wiqid package for R statistical software provides Quick and Dirty functions for the analysis of Wildlife data.

There is an introduction to wiqid here. The package is still getting major changes, meaning that your old scripts may not work with new versions of wiqid.

Some of the simpler Bayesian MCMC functions in wiqid are coded in R, others use JAGS and the rjags package.

Installing wiqid

wiqid is now on CRAN !

You can now install wiqid and the packages it requires from within R with the command install.packages("wiqid"). You can also go to the Packages > Install package(s)... menu item and select wiqid from the pop-up list, but with more than 9,000 packages on the list, I find typing easier.

After installing wiqid

For full functionality, you will need to have JAGS installed, as well as the rjags, secr and shiny packages.

1. JAGS: If you are using Mac or Ubuntu, check out the notes here or here. Go to the JAGS download page. A link at the top of the page gives you the latest installer; on Windows, this takes you to an HTML page with a choice of installers, depending on the version of R you are using. Install in the default directory.

JAGS 4 was released in October 2015; to use JAGS 4 you need version of rjags_4-4 or later. Or you can continue to use the old rjags_3-x version with JAGS 3.

2. rjags: Once you have installed JAGS, you can install the rjags package in R with

install.packages("rjags")

Check that it has been installed correctly and can link to JAGS by doing

library(rjags)

3. secr and shiny: You can install these in R with

install.packages(c("secr", "shiny"))

Both these packages depend on a number of other packages, and they will also be downloaded automatically.
 

Main recent changes

In 0.1.0: On CRAN. New functions dt2, pt2, qt2 and rt2, wrappers for the dt family which allow specification of mean and SD. Optional checking of capture history in occ* functions with verify argument.

In 0.0.404: A technical update: testthat files changed to work with R 3.3.x. wiqid_0.0.404.zip (384 KB); wiqid_0.0.404.tar.gz (197 KB)

In 0.0.403: The hdi function removed, use HDInterval::hdi instead (it's faster for large objects). wiqid_0.0.403.zip (384 KB); wiqid_0.0.403.tar.gz (197 KB)

In 0.0.402: No longer Depends on rjags and JAGS, though those are needed for full functionality. wiqid_0.0.402.zip (392 KB); wiqid_0.0.402.tar.gz (200 KB)

In 0.0.401: Functions using MCMCpack scrapped; added function showShinyApp to display beta and gamma distributions. wiqid_0.0.401.zip (386 KB), wiqid_0.0.401.tar.gz (200 KB)

In 0.0.399: Function plotComb added to use with the comb method of calculating posterior probabilities. wiqid_0.0.399.zip (381 KB), wiqid_0.0.399.tar.gz (196 KB)

In 0.0.397: Bayesian survival function, BsurvCJS, gains a priors argument. wiqid_0.0.397.zip (380 KB), wiqid_0.0.397.tar.gz (195 KB)

In 0.0.396: Bayesian functions speeded up and argument names standardized; dependence on other packages reduced; experimental WAIC added to BoccSS (not fully tested!). wiqid_0.0.396.zip (373 KB), wiqid_0.0.396.tar.gz (194 KB)

In 0.0.391: occ2sps can now take site covariates (method of specifying the model has changed). wiqid_0.0.391.zip (375 KB), wiqid_0.0.391.tar.gz (192 KB)

In 0.0.390: added Bbinom; changed way of calculating variances in MLE methods. wiqid_0.0.390.zip (367 KB), wiqid_0.0.390.tar.gz (189 KB)

In 0.0.388: revamp of Bnormal as two separate functions with different prior options. wiqid_0.0.388.zip (363 KB), wiqid_0.0.388.tar.gz (188 KB)

In 0.0.384: added Bregress and Blogit (wrappers for MCMCpack functions); survCJS and BsurvCJS gain a group argument; probit link option in occSS* functions; BoccSS runs in parallel. wiqid_0.0.384.zip (356 KB), wiqid_0.0.384.tar.gz (185 KB)

In 0.0.382: added Bayesian modelling of a normal distribution. wiqid_0.0.382.zip (300 KB), wiqid_0.0.382.tar.gz (139 KB)

 

Updated 2 Oct 2016 by Mike Meredith