Quick and Dirty Estimates for Wildlife Populations

Provides simple, fast functions for maximum likelihood and Bayesian estimates of wildlife population parameters, suitable for use with simulated data or bootstraps. Early versions were indeed quick and dirty, but optional error-checking routines and meaningful error messages have been added. Includes single and multi-season occupancy, closed capture population estimation, survival, species richness and distance measures.


News

TODO

  • deprecate Bbinom

  • scrap improper default priors for Bnormal, maybe do as original version of BEST

  • Improve Bsecr0...

  • should as.Bwiqid.Bwiqid recalculate diagnostics?

CHANGES in 0.2.1

  • 'diagPlot' no longer uses its own colour palette.

  • window.Bwiqid now adds new diagnostics for Rhat and n.eff.

  • Rhat calculated with 'simpleRhat', n.eff with 'safeNeff' everywhere.

CHANGES in 0.2.0

  • Continuous covariates now standardised to mean=0, SD=1 (instead of SD=0.5). Default priors for 'BoccSS' and 'BsurvCJS' changed to match this.

  • Added 'standardize' and 'standardize2match' functions.

  • Added 'simpleRhat' and 'getMCerror' functions; used by 'as.Bwiqid'.

  • 'diagPlot' gains a 'howMany' argument to plot less than the whole chain.

  • 'as.Bwiqid.data.frame' gains arguments 'n.chains', 'Rhat' and 'n.eff' and is included in the help page.

  • If the variance-covariance matrix cannot be calculated, MLE functions now return the log(likelihood) but number of parameters, df = NA.

  • 'AICc' gains a 'df' argument which overrides the df value in the model object, so an AICc value can be got even if the covariance matrix cannot be calculated.

  • Added *beta2 and *gamma2, wrappers for *beta and *gamma with mean and sd parameters, and *beta3 with mode and concentration.

  • Added getBetaPar and getGammaPar to convert mean/sd parameters to shape/rate.

CHANGES in 0.1.5 (2018-04-20)

  • Fixed check for installation of package shiny in showShinyApp.

CHANGES in 0.1.4 (2018-04-20)

  • new function densityFolded, used in plotPost and plot.Bwiqid when showCurve=TRUE.

  • summary.Bwiqid method added, prints background and returns values invisibly.

  • diagPlot now displays n.eff

  • fix: in as.Bwiqid.mcmc.list, call to gelman.diag wrapped in try.

  • fix: histogram breaks in plotPost are equidistant (as always intended).

  • fix: the first argument to BoccSS0 can be a matrix or data frame with a detection history.

  • fix: occSSrn0 now accepts scalar n, as documented.

CHANGES in 0.1.3 (2017-11-18)

  • Calculation of SEs of fitted values now uses less memory, works for large data sets.

  • Functions more robust to underflow/overflow: closedCap*, occ2sps, occSS*

  • Changed parameterization in Bsecr0 from lam0 to g0; better default priors.

  • Bug fix in BoccSS0: burnin iterations are now discarded.

CHANGES in 0.1.2 (2017-09-10)

  • Added diagPlot function and improved other diagnostic plots.

  • Added function Bpoisson; Bbinom renamed Bbinomial

CHANGES in 0.1.1 (2017-06-09)

  • Added 'coef', 'vcov' and 'predict' methods for 'wiqid' objects.

  • 'survCJS' gains an 'interval' argument to deal with time intervals of unequal length.

  • dots argument added to MLE functions to pass parameters to 'nlm'.

  • Improved coding of several functions to prevent under/overflow issues.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("wiqid")

0.2.1 by Mike Meredith, 6 months ago


Browse source code at https://github.com/cran/wiqid


Authors: Mike Meredith


Documentation:   PDF Manual  


GPL-3 license


Imports stats, truncnorm, MASS, coda

Depends on HDInterval

Suggests secr, shiny, rjags


See at CRAN