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.

Author | Mike Meredith |

Date of publication | 2016-10-05 09:30:05 |

Maintainer | Mike Meredith <mmeredith@wcs.org> |

License | GPL-3 |

Version | 0.1.0 |

**AICc:** Akaike's Information Criterion with small-sample correction -...

**AICtable:** Make a table for AIC or other criterion

**allCombinations:** Create formulae for all combinations of covariates

**as_Bwiqid:** Conversion to class Bwiqid

**Bbinomial:** Bayesian analysis of binomial data

**biodIndices:** Biodiversity indices

**Bnormal:** Bayesian modelling of a normal (Gaussian) distribution

**BoccSS:** Bayesian single-season occupancy modelling

**Bsecr:** Spatially explicit capture-recapture (secr) density...

**closedCaptures:** Analysis of mark-recapture data for closed populations

**dippers:** Capture-recapture data for European dippers

**distance_measures:** Plug-in distance-measure functions for 'distShell'.

**distShell:** Distance Matrix Computation

**distTestData:** An artificial data set to test distance/dissimilarity...

**GrandSkinks:** Multi-season detection data for grand skinks

**KanhaTigers:** Capture history matrix for camera-trapped tigers

**KillarneyBirds:** Abundance of woodland birds

**linkFunctions:** Logit and probit links for generalised linear modelling

**MeadowVoles:** Robust design mark-recapture data for meadow voles

**occ2sps:** Single-season two-species occupancy estimation

**occMS:** Multi-season occupancy estimation

**occSS:** Single-season occupancy estimation

**occSSrn:** Royle-Nichols model for single-season occupancy estimation

**plot_Bwiqid:** Plot method for objects of class 'Bwiqid'

**plotComb:** Display a posterior probability distribution from the comb...

**plotDiagnostics:** Diagnostic graphics for MCMC output

**plotPost:** Graphic display of a posterior probability distribution

**postPriorOverlap:** Overlap between posterior and prior probability...

**print_Bwiqid:** Print method for objects of class 'Bwiqid'

**railSims:** Simulated detection/non-detection data for two species of...

**richCurve:** Species richness estimates based on accumulation curves

**richEstimators:** Species richness estimators

**richRarefy:** Sample-based rarefaction curves

**salamanders:** Occupancy data for blue ridge salamanders

**seedbank:** Seed abundances in soil samples

**showShinyApp:** Display a 'shiny' application

**stdPriors:** Standardisation and priors

**survivalCJS:** Survival from recapture data with Cormack-Jolly-Seber (CJS)...

**survivaRD:** Survival from mark-recapture data with robust design

**TDist:** The Student t Distribution

**Temburong:** Tree species count data

**WAIC:** Extract the Watanabe-Akaike Information Criterion (WAIC)

**weta:** Detection data for weta in gorse bushes

**window_Bwiqid:** Time windows for 'Bwiqid' objects

**wiqid-package:** Fast, simple estimation functions for wildlife population...

wiqid

wiqid/inst

wiqid/inst/tests

wiqid/inst/tests/testthat

wiqid/inst/tests/testthat/test-occMS.R

wiqid/inst/tests/testthat/test-occSS0.R

wiqid/inst/tests/testthat/test-occSS.R

wiqid/inst/tests/testthat/test-occSStime.R

wiqid/inst/tests/testthat/test-dist.R

wiqid/inst/tests/testthat/test-occSScovSite.R

wiqid/inst/tests/testthat/test-survCJS.R

wiqid/inst/tests/testthat/test-occ2sps.R

wiqid/inst/tests/testthat/test-0JAGS.R

wiqid/inst/tests/testthat/test-closedCap2.R

wiqid/inst/tests/testthat/test-biod.R

wiqid/inst/tests/testthat/test-occSSrn.R

wiqid/inst/tests/testthat/test-closedCap.R

wiqid/inst/tests/testthat/test-Bnormal.R

wiqid/inst/tests/testthat/test-rich.R

wiqid/inst/tests/testthat/test-BoccSS.R

wiqid/inst/shiny

wiqid/inst/shiny/Quadratic

wiqid/inst/shiny/Quadratic/ui.R

wiqid/inst/shiny/Quadratic/server.R

wiqid/inst/shiny/Quadratic/helper_visQuad.R

wiqid/inst/shiny/Beta

wiqid/inst/shiny/Beta/ui.R

wiqid/inst/shiny/Beta/server.R

wiqid/inst/shiny/Beta/helper_visBeta.R

wiqid/inst/shiny/Gamma

wiqid/inst/shiny/Gamma/ui.R

wiqid/inst/shiny/Gamma/server.R

wiqid/inst/shiny/Gamma/helper_visGamma.R

wiqid/NAMESPACE

wiqid/data

wiqid/data/GrandSkinks.rda

wiqid/data/distTestData.rda

wiqid/data/MeadowVoles.rda

wiqid/data/railSims.rda

wiqid/data/KanhaTigers.rda

wiqid/data/salamanders.rda

wiqid/data/dippers.rda

wiqid/data/Temburong.rda

wiqid/data/KillarneyBirds.rda

wiqid/data/weta.rda

wiqid/data/seedbank.rda

wiqid/R

wiqid/R/closedCapMtcov.R
wiqid/R/AllCombinations.R
wiqid/R/WAIC.R
wiqid/R/survRDah.R
wiqid/R/occSS0.R
wiqid/R/converters.R
wiqid/R/checkPriors.R
wiqid/R/AICc.R
wiqid/R/Bwiqid_methods.R
wiqid/R/Bbinomial.R
wiqid/R/occSSrn.R
wiqid/R/richEstimators.R
wiqid/R/onAttach.R
wiqid/R/distShell.R
wiqid/R/closedCapMt.R
wiqid/R/survRD.R
wiqid/R/closedCapM0.R
wiqid/R/Bsecr.R
wiqid/R/richEstimatorsMore.R
wiqid/R/Bnormal_2.R
wiqid/R/BoccSS0.R
wiqid/R/Misc.R
wiqid/R/postPriorOverlap.R
wiqid/R/TDist.R
wiqid/R/Bwiqid_plots.R
wiqid/R/Bnormal.R
wiqid/R/BoccSS.R
wiqid/R/showShinyApp.R
wiqid/R/occSScovSite.R
wiqid/R/as_Bwiqid.R
wiqid/R/occSS.R
wiqid/R/richRarefy.R
wiqid/R/wiqid_methods.R
wiqid/R/occSStime.R
wiqid/R/occMStime.R
wiqid/R/occMS.R
wiqid/R/occSSrnSite.R
wiqid/R/verify.R
wiqid/R/plotComb.R
wiqid/R/closedCapMhJK.R
wiqid/R/closedCapMb.R
wiqid/R/survCJS.R
wiqid/R/survCJSaj.R
wiqid/R/plotPost.R
wiqid/R/richCurve.R
wiqid/R/ch2mArray.R
wiqid/R/occMS0.R
wiqid/R/occ2sps0.R
wiqid/R/occMScovSite.R
wiqid/R/biodIndices.R
wiqid/R/extraMethods.R
wiqid/R/distMeasures.R
wiqid/R/closedCapMh2.R
wiqid/R/justRunJags.R
wiqid/R/BsurvCJS.R
wiqid/R/occ2sps.R
wiqid/MD5

wiqid/README

wiqid/DESCRIPTION

wiqid/man

wiqid/man/distShell.Rd
wiqid/man/richEstimators.Rd
wiqid/man/figures

wiqid/man/figures/plotPost1.jpg

wiqid/man/figures/HDIskew.jpg

wiqid/man/figures/plotPost2.jpg

wiqid/man/figures/HDIbimodal.jpg

wiqid/man/figures/linkFunctions.jpg

wiqid/man/weta.Rd
wiqid/man/postPriorOverlap.Rd
wiqid/man/linkFunctions.Rd
wiqid/man/occSSrn.Rd
wiqid/man/allCombinations.Rd
wiqid/man/closedCaptures.Rd
wiqid/man/richCurve.Rd
wiqid/man/GrandSkinks.Rd
wiqid/man/distTestData.Rd
wiqid/man/salamanders.Rd
wiqid/man/KanhaTigers.Rd
wiqid/man/occ2sps.Rd
wiqid/man/railSims.Rd
wiqid/man/Bbinomial.Rd
wiqid/man/as_Bwiqid.Rd
wiqid/man/AICc.Rd
wiqid/man/survivalCJS.Rd
wiqid/man/richRarefy.Rd
wiqid/man/TDist.Rd
wiqid/man/print_Bwiqid.Rd
wiqid/man/occSS.Rd
wiqid/man/dippers.Rd
wiqid/man/WAIC.Rd
wiqid/man/Bsecr.Rd
wiqid/man/MeadowVoles.Rd
wiqid/man/plot_Bwiqid.Rd
wiqid/man/occMS.Rd
wiqid/man/plotPost.Rd
wiqid/man/BoccSS.Rd
wiqid/man/seedbank.Rd
wiqid/man/KillarneyBirds.Rd
wiqid/man/stdPriors.Rd
wiqid/man/window_Bwiqid.Rd
wiqid/man/distance_measures.Rd
wiqid/man/plotComb.Rd
wiqid/man/wiqid-package.Rd
wiqid/man/Temburong.Rd
wiqid/man/Bnormal.Rd
wiqid/man/showShinyApp.Rd
wiqid/man/biodIndices.Rd
wiqid/man/survivaRD.Rd
wiqid/man/AICtable.Rd
wiqid/man/plotDiagnostics.Rd
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