wiqid: 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.

AuthorMike Meredith
Date of publication2016-10-05 09:30:05
MaintainerMike Meredith <mmeredith@wcs.org>
LicenseGPL-3
Version0.1.0

View on CRAN

Man pages

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...

Files in this package

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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