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...

Functions

acfPlot Man page
AICc Man page
AICtable Man page
allCombinations Man page
as.Bwiqid Man page
as.Bwiqid.bugs Man page
as.Bwiqid.default Man page
as.Bwiqid.mcmc.list Man page
as.Bwiqid.rjags Man page
as.Bwiqid.runjags Man page
Bbinom Man page
biodBerger Man page
biodBrillouin Man page
biodShannon Man page
biodSimpson Man page
Bnormal Man page
Bnormal2 Man page
BoccSS Man page
BoccSS0 Man page
Bsecr0 Man page
BsurvCJS Man page
Bwiqid-class Man page
closedCapM0 Man page
closedCapMb Man page
closedCapMh2 Man page
closedCapMhJK Man page
closedCapMt Man page
closedCapMtcov Man page
densityPlot Man page
diagnostic plots Man page
dippers Man page
Distance Measures Man page
distBrayCurtis Man page
distChaoJaccCorr Man page
distChaoJaccNaive Man page
distChaoSorCorr Man page
distChaoSorNaive Man page
distChord Man page
distJaccard Man page
distMatching Man page
distMorisitaHorn Man page
distOchiai Man page
distPreston Man page
distRogersTanimoto Man page
distShell Man page
distSimRatio Man page
distSorensen Man page
distTestData Man page
distWhittaker Man page
Diversity indices Man page
dt2 Man page
GrandSkinks Man page
KanhaTigers Man page
KillarneyBirds Man page
links Man page
links Man page
Links Man page
MeadowVoles Man page
occ2sps Man page
occMS Man page
occMS0 Man page
occMScovSite Man page
occMStime Man page
occSS Man page
occSS0 Man page
occSScovSite Man page
occSSrn Man page
occSSrn0 Man page
occSSrnSite Man page
occSStime Man page
plot.Bwiqid Man page
plotComb Man page
plotPost Man page
postPriorOverlap Man page
print.Bwiqid Man page
Priors Man page
pt2 Man page
qt2 Man page
railSims Man page
richACE Man page
richBoot Man page
richChao1 Man page
richChao2 Man page
richCurve Man page
richDouble Man page
richDuplicate Man page
richICE Man page
richJack1 Man page
richJack2 Man page
richJackA1 Man page
richJackA2 Man page
richMM Man page
richRarefy Man page
richRenLau Man page
richSingle Man page
richSobs Man page
richUnique Man page
rt2 Man page
salamanders Man page
seedbank Man page
showShinyApp Man page
Species richness estimators Man page
Standardisation Man page
Standardization Man page
survCJS Man page
survCJSaj Man page
survRD Man page
survRDah Man page
TDist Man page
Temburong Man page
TemburongBA Man page
tracePlot Man page
WAIC Man page
weta Man page
window.Bwiqid Man page
wiqid Man page
wiqid-package Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.