wiqid: Quick and Dirty Estimates for Wildlife Populations
Version 0.1.0

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.

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AuthorMike Meredith
Date of publication2016-10-05 09:30:05
MaintainerMike Meredith <mmeredith@wcs.org>
LicenseGPL-3
Version0.1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("wiqid")

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

AICc Man page Source code
AICc.default Source code
AICtable Man page Source code
Bbinom Man page Source code
Bnormal Man page Source code
Bnormal2 Man page Source code
BoccSS Man page Source code
BoccSS0 Man page Source code
Bsecr0 Man page Source code
BsurvCJS Man page Source code
Bwiqid-class Man page
Distance Measures Man page
Diversity indices Man page
GrandSkinks Man page
KanhaTigers Man page
KillarneyBirds Man page
Links Man page
MeadowVoles Man page
Prh1 Source code
Prh1A Source code
Priors Man page
Species richness estimators Man page
Standardisation Man page
Standardization Man page
TDist Man page
Temburong Man page
TemburongBA Man page
WAIC Man page Source code
acfPlot Man page Source code
allCombinations Man page Source code
as.Bwiqid Man page Source code
as.Bwiqid.Bwiqid Source code
as.Bwiqid.bugs Man page Source code
as.Bwiqid.data.frame Source code
as.Bwiqid.default Man page Source code
as.Bwiqid.jagsUI Source code
as.Bwiqid.mcmc Source code
as.Bwiqid.mcmc.list Man page Source code
as.Bwiqid.rjags Man page Source code
as.Bwiqid.runjags Man page Source code
as.data.frame.runjags Source code
biodBerger Man page Source code
biodBrillouin Man page Source code
biodShannon Man page Source code
biodSimpson Man page Source code
ch2mArray Source code
checkPriors Source code
closedCapM0 Man page Source code
closedCapMb Man page Source code
closedCapMh2 Man page Source code
closedCapMhJK Man page Source code
closedCapMt Man page Source code
closedCapMtcov Man page Source code
densityPlot Man page Source code
diagnostic plots Man page
dippers Man page
distBrayCurtis Man page Source code
distChaoJaccCorr Man page Source code
distChaoJaccNaive Man page Source code
distChaoSorCorr Man page Source code
distChaoSorNaive Man page Source code
distChord Man page Source code
distJaccard Man page Source code
distMatching Man page Source code
distMorisitaHorn Man page Source code
distOchiai Man page Source code
distPreston Man page Source code
distRogersTanimoto Man page Source code
distShell Man page Source code
distSimRatio Man page Source code
distSorensen Man page Source code
distTestData Man page
distWhittaker Man page Source code
dt2 Man page Source code
fixCI Source code
fixNames Source code
gammaShRaFromMeanSD Source code
gammaShRaFromModeSD Source code
getMARKci Source code
head.Bwiqid Source code
justRunJags Source code
justRunJagsSerial Source code
links Man page Man page
loadJagsModules Source code
logLik.wiqid Source code
logSumExp Source code
nobs.wiqid Source code
occ2sps Man page Source code
occ2sps0 Source code
occMS Man page Source code
occMS0 Man page Source code
occMScovSite Man page Source code
occMStime Man page Source code
occSS Man page Source code
occSS0 Man page Source code
occSScovSite Man page Source code
occSSrn Man page Source code
occSSrn0 Man page Source code
occSSrnSite Man page Source code
occSStime Man page Source code
onAttach Source code
plot.Bwiqid Man page Source code
plotComb Man page Source code
plotPost Man page Source code
postPriorOverlap Man page Source code
print.Bwiqid Man page Source code
print.wiqid Source code
pt2 Man page Source code
qArray Source code
qArrayAJ Source code
qt2 Man page Source code
railSims Man page
richACE Man page Source code
richBoot Man page Source code
richChao1 Man page Source code
richChao2 Man page Source code
richCurve Man page Source code
richDouble Man page Source code
richDuplicate Man page Source code
richICE Man page Source code
richJack1 Man page Source code
richJack2 Man page Source code
richJackA1 Man page Source code
richJackA2 Man page Source code
richMM Man page Source code
richRarefy Man page Source code
richRenLau Man page Source code
richSingle Man page Source code
richSobs Man page Source code
richUnique Man page Source code
rt2 Man page Source code
salamanders Man page
seedbank Man page
selectCovars Source code
showShinyApp Man page Source code
signifish Source code
stdModel Source code
stddata Source code
stdform Source code
survCJS Man page Source code
survCJSaj Man page Source code
survRD Man page Source code
survRDah Man page Source code
tail.Bwiqid Source code
tracePlot Man page Source code
unloadJagsModules Source code
verifyDH Source code
weta Man page
window.Bwiqid Man page Source code
wiqid Man page
wiqid-package Man page

Files

inst
inst/tests
inst/tests/testthat
inst/tests/testthat/test-occMS.R
inst/tests/testthat/test-occSS0.R
inst/tests/testthat/test-occSS.R
inst/tests/testthat/test-occSStime.R
inst/tests/testthat/test-dist.R
inst/tests/testthat/test-occSScovSite.R
inst/tests/testthat/test-survCJS.R
inst/tests/testthat/test-occ2sps.R
inst/tests/testthat/test-0JAGS.R
inst/tests/testthat/test-closedCap2.R
inst/tests/testthat/test-biod.R
inst/tests/testthat/test-occSSrn.R
inst/tests/testthat/test-closedCap.R
inst/tests/testthat/test-Bnormal.R
inst/tests/testthat/test-rich.R
inst/tests/testthat/test-BoccSS.R
inst/shiny
inst/shiny/Quadratic
inst/shiny/Quadratic/ui.R
inst/shiny/Quadratic/server.R
inst/shiny/Quadratic/helper_visQuad.R
inst/shiny/Beta
inst/shiny/Beta/ui.R
inst/shiny/Beta/server.R
inst/shiny/Beta/helper_visBeta.R
inst/shiny/Gamma
inst/shiny/Gamma/ui.R
inst/shiny/Gamma/server.R
inst/shiny/Gamma/helper_visGamma.R
NAMESPACE
data
data/GrandSkinks.rda
data/distTestData.rda
data/MeadowVoles.rda
data/railSims.rda
data/KanhaTigers.rda
data/salamanders.rda
data/dippers.rda
data/Temburong.rda
data/KillarneyBirds.rda
data/weta.rda
data/seedbank.rda
R
R/closedCapMtcov.R
R/AllCombinations.R
R/WAIC.R
R/survRDah.R
R/occSS0.R
R/converters.R
R/checkPriors.R
R/AICc.R
R/Bwiqid_methods.R
R/Bbinomial.R
R/occSSrn.R
R/richEstimators.R
R/onAttach.R
R/distShell.R
R/closedCapMt.R
R/survRD.R
R/closedCapM0.R
R/Bsecr.R
R/richEstimatorsMore.R
R/Bnormal_2.R
R/BoccSS0.R
R/Misc.R
R/postPriorOverlap.R
R/TDist.R
R/Bwiqid_plots.R
R/Bnormal.R
R/BoccSS.R
R/showShinyApp.R
R/occSScovSite.R
R/as_Bwiqid.R
R/occSS.R
R/richRarefy.R
R/wiqid_methods.R
R/occSStime.R
R/occMStime.R
R/occMS.R
R/occSSrnSite.R
R/verify.R
R/plotComb.R
R/closedCapMhJK.R
R/closedCapMb.R
R/survCJS.R
R/survCJSaj.R
R/plotPost.R
R/richCurve.R
R/ch2mArray.R
R/occMS0.R
R/occ2sps0.R
R/occMScovSite.R
R/biodIndices.R
R/extraMethods.R
R/distMeasures.R
R/closedCapMh2.R
R/justRunJags.R
R/BsurvCJS.R
R/occ2sps.R
MD5
README
DESCRIPTION
man
man/distShell.Rd
man/richEstimators.Rd
man/figures
man/figures/plotPost1.jpg
man/figures/HDIskew.jpg
man/figures/plotPost2.jpg
man/figures/HDIbimodal.jpg
man/figures/linkFunctions.jpg
man/weta.Rd
man/postPriorOverlap.Rd
man/linkFunctions.Rd
man/occSSrn.Rd
man/allCombinations.Rd
man/closedCaptures.Rd
man/richCurve.Rd
man/GrandSkinks.Rd
man/distTestData.Rd
man/salamanders.Rd
man/KanhaTigers.Rd
man/occ2sps.Rd
man/railSims.Rd
man/Bbinomial.Rd
man/as_Bwiqid.Rd
man/AICc.Rd
man/survivalCJS.Rd
man/richRarefy.Rd
man/TDist.Rd
man/print_Bwiqid.Rd
man/occSS.Rd
man/dippers.Rd
man/WAIC.Rd
man/Bsecr.Rd
man/MeadowVoles.Rd
man/plot_Bwiqid.Rd
man/occMS.Rd
man/plotPost.Rd
man/BoccSS.Rd
man/seedbank.Rd
man/KillarneyBirds.Rd
man/stdPriors.Rd
man/window_Bwiqid.Rd
man/distance_measures.Rd
man/plotComb.Rd
man/wiqid-package.Rd
man/Temburong.Rd
man/Bnormal.Rd
man/showShinyApp.Rd
man/biodIndices.Rd
man/survivaRD.Rd
man/AICtable.Rd
man/plotDiagnostics.Rd
wiqid documentation built on May 19, 2017, 11:18 p.m.