wiqid: Quick and Dirty Estimates for Wildlife Populations

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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

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