Package: wiqid 0.3.3

Ngumbang Juat

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.

Authors:Ngumbang Juat [cre], Mike Meredith [aut], Jason Bryer [ctb], John Kruschke [ctb], Brian Neelon [ctb], Michael Schaub [ctb], R Core Team [ctb]

wiqid_0.3.3.tar.gz
wiqid_0.3.3.zip(r-4.5)wiqid_0.3.3.zip(r-4.4)wiqid_0.3.3.zip(r-4.3)
wiqid_0.3.3.tgz(r-4.4-any)wiqid_0.3.3.tgz(r-4.3-any)
wiqid_0.3.3.tar.gz(r-4.5-noble)wiqid_0.3.3.tar.gz(r-4.4-noble)
wiqid_0.3.3.tgz(r-4.4-emscripten)wiqid_0.3.3.tgz(r-4.3-emscripten)
wiqid.pdf |wiqid.html✨
wiqid/json (API)
NEWS

# Install 'wiqid' in R:
install.packages('wiqid', repos = c('https://mikemeredith.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mikemeredith/wiqid/issues

Datasets:
  • GrandSkinks - Multi-season detection data for grand skinks
  • KanhaTigers - Capture history matrix for camera-trapped tigers
  • KillarneyBirds - Abundance of woodland birds
  • MeadowVoles - Robust design mark-recapture data for meadow voles
  • Temburong - Tree species count data
  • TemburongBA - Tree species count data
  • dippers - Capture-recapture data for European dippers
  • distTestData - An artificial data set to test distance/dissimilarity measures
  • railSims - Simulated detection/non-detection data for two species of rails
  • salamanders - Occupancy data for blue ridge salamanders
  • seedbank - Seed abundances in soil samples
  • toves - Simulated detection/non-detection data for a fictitious species
  • weta - Detection data for weta in gorse bushes

On CRAN:

107 exports 2 stars 1.54 score 7 dependencies 1 dependents 2 mentions 108 scripts 481 downloads

Last updated 2 years agofrom:1bc6d72500. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 06 2024
R-4.5-winNOTESep 06 2024
R-4.5-linuxNOTESep 06 2024
R-4.4-winOKSep 06 2024
R-4.4-macNOTESep 06 2024
R-4.3-winOKSep 06 2024
R-4.3-macNOTESep 06 2024

Exports:AICcAICtableallCombinationsas.BwiqidBbinomBbinomialbiodBergerbiodBrillouinbiodShannonbiodSimpsonBnormalBnormal2BoccSSBoccSS0BpoissonBsecr0BsurvCJSclosedCapM0closedCapMbclosedCapMh2closedCapMhJKclosedCapMtclosedCapMtcovdbeta2dbeta3dgamma2distBrayCurtisdistChaoJaccCorrdistChaoJaccNaivedistChaoSorCorrdistChaoSorNaivedistChorddistJaccarddistMatchingdistMorisitaHorndistOchiaidistPrestondistRogersTanimotodistShelldistSimRatiodistSorensendistWhittakerdt2dt3getBeta2PargetBeta3PargetGammaPargetMCerrorocc2spsoccMSoccMS0occMScovSiteoccMStimeoccSSoccSS0occSScovSiteoccSSrnoccSSrn0occSSrnSiteoccSStimepbeta2pbeta3pgamma2plotACsplotCombplotPostpredictAvgpt2pt3qbeta2qbeta3qgamma2qt2qt3rbeta2rbeta3rgamma2richACErichBootrichChao1richChao2richCurverichDoublerichDuplicaterichICErichJack1richJack2richJackA1richJackA2richMMrichRarefyrichRenLaurichSinglerichSobsrichUniquert2rt3secrFitshowShinyAppsimpleRhatstandardizestandardize2matchsurvCJSsurvCJSajsurvRDsurvRDahWAIC

Dependencies:codaHDIntervallatticeMASSmcmcOutputplotrixtruncnorm

Readme and manuals

Help Manual

Help pageTopics
Fast, simple estimation functions for wildlife population modelswiqid-package wiqid
Akaike's Information Criterion with small-sample correction - AICcAICc
Make a table for AIC or other criterionAICtable
Create formulae for all combinations of covariatesallCombinations
Bayesian analysis of binomial dataBbinom Bbinomial
Bayesian modelling of a normal (Gaussian) distributionBnormal Bnormal2
Bayesian single-season occupancy modellingBoccSS BoccSS0
Bayesian analysis of count dataBpoisson
Spatially explicit capture-recapture (secr) density estimation using MCMCBsecr0
The Beta DistributionBetaDist dbeta2 dbeta3 getBeta2Par getBeta3Par pbeta2 pbeta3 qbeta2 qbeta3 rbeta2 rbeta3
Conversion to class Bwiqid (deprecated)as.Bwiqid as.Bwiqid.default Bwiqid-class
Analysis of mark-recapture data for closed populationsclosedCapM0 closedCapMb closedCapMh2 closedCapMhJK closedCapMt closedCapMtcov
Deprecated functions in package wiqidplotPost
Capture-recapture data for European dippersdippers
Plug-in distance-measure functions for 'distShell'.Distance Measures distBrayCurtis distChaoJaccCorr distChaoJaccNaive distChaoSorCorr distChaoSorNaive distChord distJaccard distMatching distMorisitaHorn distOchiai distPreston distRogersTanimoto distSimRatio distSorensen distWhittaker
Distance Matrix ComputationdistShell
An artificial data set to test distance/dissimilarity measuresdistTestData
Biodiversity indicesbiodBerger biodBrillouin biodShannon biodSimpson Diversity indices
The Gamma Distributiondgamma2 GammaDist getGammaPar pgamma2 qgamma2 rgamma2
MCMC error using the batch method (deprecated)getMCerror
Multi-season detection data for grand skinksGrandSkinks
Capture history matrix for camera-trapped tigersKanhaTigers
Abundance of woodland birdsKillarneyBirds
Logit and probit links for generalised linear modellingLinks links
Robust design mark-recapture data for meadow volesMeadowVoles
Single-season two-species occupancy estimationocc2sps
Multi-season occupancy estimationoccMS occMS0 occMScovSite occMStime
Single-season occupancy estimationoccSS occSS0 occSScovSite occSStime
Plot method for objects of class 'Bwiqid'plot.Bwiqid
Plot Activity Centres from 'Bsecr0' outputplotACs
Display a posterior probability distribution from the comb methodplotComb
Predict method for objects of class 'wiqid'predict.wiqid
Predict average values from multiple fitted modelspredictAvg
Print and summary methods for objects of class 'Bwiqid'print.Bwiqid summary.Bwiqid
Standardisation and priorsPriors Standardisation Standardization
Simulated detection/non-detection data for two species of railsrailSims
Species richness estimates based on accumulation curvesrichCurve richDouble richDuplicate richSingle richSobs richUnique
Sample-based rarefaction curvesrichRarefy
Royle-Nichols model for single-season occupancy estimationoccSSrn occSSrn0 occSSrnSite
Occupancy data for blue ridge salamanderssalamanders
Spatially Explicit Capture-RecapturesecrFit
Seed abundances in soil samplesseedbank
Display a 'shiny' applicationshowShinyApp
The Brooks-Gelman-Rubin (BGR) convergence diagnostic (deprecated)simpleRhat
Species richness estimatorsrichACE richBoot richChao1 richChao2 richICE richJack1 richJack2 richJackA1 richJackA2 richMM richRenLau Species richness estimators
Scaling and centring of vectors, matrices and arraysstandardize standardize2match
Survival from recapture data with Cormack-Jolly-Seber (CJS) modelBsurvCJS survCJS survCJSaj
Survival from mark-recapture data with robust designsurvRD survRDah
The Generalized Student's t Distributiondt2 dt3 pt2 pt3 qt2 qt3 rt2 rt3 TDist
Tree species count dataTemburong TemburongBA
Simulated detection/non-detection data for a fictitious speciestoves
Extract the Watanabe-Akaike Information Criterion (WAIC)WAIC
Detection data for weta in gorse bushesweta
The 'wiqid' S3 classwiqid-class