Package: unmarked 1.4.3.9005
Ken Kellner
unmarked: Models for Data from Unmarked Animals
Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Authors:
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unmarked.pdf |unmarked.html✨
unmarked/json (API)
NEWS
| # Install 'unmarked' in R: |
| install.packages('unmarked', repos = c('https://biodiverse.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/biodiverse/unmarked/issues
Uses libs:
Datasets:
- MesoCarnivores - Occupancy data for coyote, red fox, and bobcat
- Switzerland - Swiss landscape data
- catbird - BBS Point Count and Occurrence Data from 2 Bird Species
- catbird.bin - BBS Point Count and Occurrence Data from 2 Bird Species
- crossbill - Detection/non-detection data on the European crossbill
- cruz - Landscape data for Santa Cruz Island
- gf.data - Green frog count index data
- gf.obs - Green frog count index data
- issj - Distance-sampling data for the Island Scrub Jay
- jay - European Jay data from the Swiss Breeding Bird Survey 2002
- linetran - Simulated line transect data
- mallard.obs - Mallard count data
- mallard.site - Mallard count data
- mallard.y - Mallard count data
- masspcru - Massachusetts North American Amphibian Monitoring Program Data
- ovendata.list - Removal data for the Ovenbird
- pcru.bin - 2001 Delaware North American Amphibian Monitoring Program Data
- pcru.data - 2001 Delaware North American Amphibian Monitoring Program Data
- pcru.y - 2001 Delaware North American Amphibian Monitoring Program Data
- pfer.bin - 2001 Delaware North American Amphibian Monitoring Program Data
- pfer.data - 2001 Delaware North American Amphibian Monitoring Program Data
- pfer.y - 2001 Delaware North American Amphibian Monitoring Program Data
- pointtran - Simulated point-transect data
- woodthrush - BBS Point Count and Occurrence Data from 2 Bird Species
- woodthrush.bin - BBS Point Count and Occurrence Data from 2 Bird Species
Last updated 27 days agofrom:d6c2f1ae00. Checks:OK: 3 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 25 2024 |
| R-4.5-win-x86_64 | OK | Oct 25 2024 |
| R-4.5-linux-x86_64 | OK | Oct 25 2024 |
| R-4.4-win-x86_64 | NOTE | Oct 25 2024 |
| R-4.4-mac-x86_64 | NOTE | Oct 25 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 25 2024 |
| R-4.3-win-x86_64 | NOTE | Oct 25 2024 |
| R-4.3-mac-x86_64 | NOTE | Oct 25 2024 |
| R-4.3-mac-aarch64 | NOTE | Oct 25 2024 |
Exports:backTransformbupcoefcolextcomputeMPLElambdaconfintcrossValcsvToUMFdistsampdistsampOpendoublePiFundrexpdrhazdrhndxexpdxhazdxhnfitListfittedformatDistDataformatLongformatMultformatWidegdistremovalgdistsampgetBgetDatagetFPgetLgetPgetYgmultmixgoccugpcountgrexpgrhazgrhngxexpgxhazgxhnheadhistIDSimputeMissinglambda2psilinearComblogLikLRTmakeCrPiFunmakeCrPiFunMbmakeCrPiFunMhmakeRemPiFunmodSelmultinomPoismultmixOpennmixTTDnonparbootnumSitesnumYobsCovsobsCovs<-obsNumobsToYobsToY<-occuoccuCOPoccuFPoccuMSoccuMultioccuPENoccuPEN_CVoccuRNoccuTTDoptimizePenaltyparbootpcountpcount.spHDSpcountOpenplotplotEffectsplotEffectsDataposteriorSamplespowerAnalysispredictprofileprojectedrandomTermsranefremovalPiFunresidualssampleSizeSEshinyPowersight2perpdistsigmasimulatesiteCovssiteCovs<-smoothedSSEsummaryunmarkedFrameDSunmarkedFrameDSOunmarkedFrameGDRunmarkedFrameGDSunmarkedFrameGMMunmarkedFrameGOccuunmarkedFrameGPCunmarkedFrameMMOunmarkedFrameMPoisunmarkedFrameOccuunmarkedFrameOccuCOPunmarkedFrameOccuFPunmarkedFrameOccuMSunmarkedFrameOccuMultiunmarkedFrameOccuTTDunmarkedFramePCOunmarkedFramePCountunmarkedMultFrameunmarkedPowerListupdatevcovvifyearlySiteCovsyearlySiteCovs<-
Dependencies:latticeMASSMatrixrbibutilsRcppRcppArmadilloRcppEigenRdpackreformulasTMB
Modeling variation in abundance using capture-recapture data
Rendered fromcap-recap.Rmdusingknitr::rmarkdownon Oct 25 2024.Last update: 2022-05-09
Started: 2022-05-09
Contributing to unmarked: guide to adding a new model to unmarked
Rendered fromcontributing_to_unmarked.Rmdusingknitr::rmarkdownon Oct 25 2024.Last update: 2024-10-03
Started: 2023-12-13
Distance sampling analysis in unmarked
Rendered fromdistsamp.Rmdusingknitr::rmarkdownon Oct 25 2024.Last update: 2022-05-09
Started: 2022-05-09
Dynamic occupancy models in unmarked
Rendered fromcolext.Rmdusingknitr::rmarkdownon Oct 25 2024.Last update: 2024-08-02
Started: 2022-05-09
Multispecies occupancy models with occuMulti
Rendered fromoccuMulti.Rmdusingknitr::rmarkdownon Oct 25 2024.Last update: 2023-04-05
Started: 2022-05-09
Overview of unmarked: an R Package for the Analysis of Data from Unmarked Animals
Rendered fromunmarked.Rmdusingknitr::rmarkdownon Oct 25 2024.Last update: 2024-08-02
Started: 2022-05-09
Power Analysis in unmarked
Rendered frompowerAnalysis.Rmdusingknitr::rmarkdownon Oct 25 2024.Last update: 2024-07-10
Started: 2022-05-09
Simulating datasets
Rendered fromsimulate.Rmdusingknitr::rmarkdownon Oct 25 2024.Last update: 2024-09-04
Started: 2022-05-09
Modeling and mapping species distributions
Rendered fromspp-dist.Rmdusingknitr::rmarkdownon Oct 25 2024.Last update: 2022-05-09
Started: 2022-05-09
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Models for Data from Unmarked Animals | unmarked-package unmarked |
| Methods for bracket extraction [ in Package `unmarked' | [,unmarkedEstimateList,ANY,ANY,ANY-method [,unmarkedFit,ANY,ANY,ANY-method [,unmarkedFrame,list,missing,missing-method [,unmarkedFrame,missing,numeric,missing-method [,unmarkedFrame,numeric,missing,missing-method [,unmarkedFrame,numeric,numeric,missing-method [,unmarkedFrameGDS,numeric,missing,missing-method [,unmarkedFrameGMM,numeric,missing,missing-method [,unmarkedFrameGPC,missing,numeric,missing-method [,unmarkedFrameGPC,numeric,missing,missing-method [,unmarkedFramePCO,missing,numeric,missing-method [,unmarkedFramePCO,numeric,missing,missing-method [,unmarkedMultFrame,missing,numeric,missing-method [,unmarkedMultFrame,numeric,missing,missing-method [-methods |
| Methods for Function backTransform in Package `unmarked' | backTransform backTransform,unmarkedEstimate-method backTransform,unmarkedFit-method backTransform,unmarkedLinComb-method backTransform-methods show,unmarkedBackTrans-method |
| BBS Point Count and Occurrence Data from 2 Bird Species | birds catbird catbird.bin woodthrush woodthrush.bin |
| Methods for Function coef in Package `unmarked' | coef,linCombOrBackTrans-method coef,unmarkedEstimate-method coef,unmarkedFit-method coef-methods |
| Fit the dynamic occupancy model of MacKenzie et. al (2003) | colext |
| Compute the penalty weight for the MPLE penalized likelihood method | computeMPLElambda |
| Methods for Function confint in Package `unmarked' | confint,unmarkedBackTrans-method confint,unmarkedEstimate-method confint,unmarkedFit-method confint,unmarkedLinComb-method confint-methods |
| Detection/non-detection data on the European crossbill (_Loxia curvirostra_) | crossbill |
| Cross-validation methods for fitted unmarked models and fit lists | crossVal crossVal,unmarkedFit-method crossVal,unmarkedFitList-method crossVal-methods show,unmarkedCrossVal-method show,unmarkedCrossValList-method unmarkedCrossVal-class unmarkedCrossValList-class |
| Landscape data for Santa Cruz Island | cruz |
| Convert .CSV File to an unmarkedFrame | csvToUMF |
| Distance-sampling detection functions and associated density functions | detFuns drexp drhaz drhn dxexp dxhaz dxhn grexp grhaz grhn gxexp gxhaz gxhn |
| Fit the hierarchical distance sampling model of Royle et al. (2004) | distsamp |
| Open population model for distance sampling data | distsampOpen |
| constructor of unmarkedFitList objects | fitList |
| Calculate fitted (expected) values from a model | fitted fitted,unmarkedFit-method |
| Bin distance data | formatDistData |
| Create unmarkedMultFrame from Long Format Data Frame | formatMult |
| Convert between wide and long data formats. | formatLong formatWide |
| 2001 Delaware North American Amphibian Monitoring Program Data | frog2001pcru frog2001pfer frogs pcru.bin pcru.data pcru.y pfer.bin pfer.data pfer.y |
| Fit the combined distance and removal model of Amundson et al. (2014). | gdistremoval |
| Fit the generalized distance sampling model of Chandler et al. (2011). | gdistsamp |
| Methods for Function getB in Package `unmarked' | getB getB,unmarkedFitOccuFP-method getB-methods |
| Methods for Function getFP in Package `unmarked' | getFP getFP,unmarkedFitOccuFP-method getFP-methods |
| Get detection probability matrix from a fitted model | getP getP,unmarkedFit-method |
| Green frog count index data | gf gf.data gf.obs |
| Generalized multinomial N-mixture model | gmultmix |
| Fit multi-scale occupancy models | goccu |
| Generalized binomial N-mixture model for repeated count data | gpcount |
| Fit the integrated distance sampling model of Kery et al. (2022). | hist,unmarkedFitIDS-method IDS names,unmarkedFitIDS-method |
| A function to impute missing entries in continuous obsCovs | imputeMissing |
| Distance-sampling data for the Island Scrub Jay (_Aphelocoma insularis_) | issj |
| European Jay data from the Swiss Breeding Bird Survey 2002 | jay |
| Convert Poisson mean (lambda) to probability of occurrence (psi). | lambda2psi |
| Methods for Function linearComb in Package `unmarked' | linearComb linearComb,unmarkedEstimate,matrixOrVector-method linearComb,unmarkedFit,matrixOrVector-method linearComb-methods show,unmarkedLinComb-method |
| Simulated line transect data | linetran |
| Create functions to compute multinomial cell probabilities | makeCrPiFun makeCrPiFunMb makeCrPiFunMh makePiFuns makeRemPiFun |
| Mallard count data | mallard mallard.obs mallard.site mallard.y |
| Massachusetts North American Amphibian Monitoring Program Data | masspcru |
| Occupancy data for coyote, red fox, and bobcat | MesoCarnivores |
| Model selection results from an unmarkedFitList | coef,unmarkedModSel-method modSel modSel-methods SE,unmarkedModSel-method show,unmarkedModSel-method summary,unmarkedModSel-method unmarkedModSel-class |
| Multinomial-Poisson Mixtures Model | multinomPois |
| Open population multinomial N-mixture model | multmixOpen |
| Fit N-mixture Time-to-detection Models | nmixTTD |
| Get non-parametric bootstrap samples from an 'unmarked' model | nonparboot nonparboot,unmarkedFit-method nonparboot-methods |
| Fit the MacKenzie et al. (2002) Occupancy Model | occu |
| Fit the occupancy model using count dta | occuCOP |
| Fit occupancy models when false positive detections occur (e.g., Royle and Link [2006] and Miller et al. [2011]) | occuFP |
| Fit Single-Season and Dynamic Multi-State Occupancy Models | occuMS |
| Fit the Rota et al. (2016) Multi-species Occupancy Model | occuMulti |
| Fit the MacKenzie et al. (2002) Occupancy Model with the penalized likelihood methods of Hutchinson et al. (2015) | occuPEN |
| Fit the MacKenzie et al. (2002) Occupancy Model with the penalized likelihood methods of Hutchinson et al. (2015) using cross-validation | occuPEN_CV |
| Fit the occupancy model of Royle and Nichols (2003) | occuRN |
| Fit Single-Season and Dynamic Time-to-detection Occupancy Models | occuTTD |
| Identify Optimal Penalty Parameter Value | optimizePenalty optimizePenalty,unmarkedFitOccuMulti-method optimizePenalty-methods |
| Removal data for the Ovenbird | ovendata ovendata.list |
| Parametric bootstrap method for 'unmarked' models | parboot parboot,unmarkedFit-method plot,parboot,missing-method show,parboot-method |
| Fit the N-mixture model of Royle (2004) | pcount |
| Fit spatial hierarchical distance sampling model. | pcount.spHDS |
| Fit the open N-mixture models of Dail and Madsen and extensions | pcountOpen |
| Compute multinomial cell probabilities | doublePiFun piFuns removalPiFun |
| Plot marginal effects of covariates in unmarked models | plotEffects plotEffects,unmarkedFit-method plotEffects-methods plotEffectsData plotEffectsData,unmarkedFit-method plotEffectsData-methods |
| Simulated point-transect data | pointtran |
| Draw samples from the posterior predictive distribution | posteriorSamples posteriorSamples,unmarkedFit-method posteriorSamples,unmarkedRanef-method posteriorSamples-methods show,unmarkedPostSamples-method unmarkedPostSamples-class [,unmarkedPostSamples,ANY,ANY,ANY-method |
| Conduct a power analysis for an unmarked model | powerAnalysis powerAnalysis,list-method powerAnalysis,unmarkedFit-method powerAnalysis,unmarkedFrame-method |
| Predict from fitted models and other unmarked objects | predict predict,unmarkedFit-method predict,unmarkedFitList-method predict,unmarkedFitOccuMS-method predict,unmarkedFitOccuMulti-method predict,unmarkedRanef-method |
| Extract estimates of random effect terms | randomTerms randomTerms,unmarkedEstimate-method randomTerms,unmarkedFit-method randomTerms-methods |
| Estimate posterior distributions of latent occupancy or abundance | ranef ranef,unmarkedFit-method |
| Calculate residuals from a model | residuals residuals,unmarkedFit-method |
| Methods for Function SE in Package `unmarked' | SE SE,linCombOrBackTrans-method SE,unmarkedEstimate-method SE,unmarkedFit-method SE-methods |
| Launch a Shiny app to help with power analysis | shinyPower |
| Convert sight distance and sight angle to perpendicular distance. | sight2perpdist |
| Extract estimates of random effect standard deviations | sigma sigma,unmarkedEstimate-method sigma,unmarkedFit-method sigma-methods |
| Data simulation in unmarked | simulate simulate,character-method simulate,unmarkedFit-method simulate,unmarkedFrame-method |
| Compute Sum of Squared Residuals for a Model Fit. | SSE SSE,unmarkedFit-method SSE,unmarkedFitGDR-method SSE,unmarkedFitIDS-method SSE,unmarkedFitOccuMulti-method SSE-methods |
| Swiss landscape data | Switzerland |
| Class "unmarkedEstimate" | show,unmarkedEstimate-method summary,unmarkedEstimate-method unmarkedEstimate unmarkedEstimate-class |
| Class "unmarkedEstimateList" | names,unmarkedEstimateList-method show,unmarkedEstimateList-method summary,unmarkedEstimateList-method unmarkedEstimateList-class |
| Class "unmarkedFit" | getData getData,unmarkedFit-method getY,unmarkedFit-method hist,unmarkedFitDS-method logLik logLik,unmarkedFit-method LRT LRT,unmarkedFit,unmarkedFit-method names,unmarkedFit-method plot,profile,missing-method plot,unmarkedFit,missing-method profile,unmarkedFit-method projected projected,unmarkedFitColExt-method sampleSize sampleSize,unmarkedFit-method smoothed smoothed,unmarkedFitColExt-method summary,unmarkedFit-method unmarkedFit unmarkedFit-class update,unmarkedFit-method |
| Class "unmarkedFitList" | coef,unmarkedFitList-method modSel,unmarkedFitList-method SE,unmarkedFitList-method summary,unmarkedFitList-method |
| Create an unmarkedFrame, or one of its child classes. | unmarkedFrame |
| Class "unmarkedFrame" | getY getY,unmarkedFrame-method head,unmarkedFrame-method hist,unmarkedFrameDS-method numSites numSites,unmarkedFrame-method numY numY,unmarkedFrame-method obsCovs obsCovs,unmarkedFrame-method obsCovs<- obsCovs<-,unmarkedFrame-method obsNum obsNum,unmarkedFrame-method obsToY obsToY,unmarkedFrame-method obsToY<- obsToY<-,unmarkedFrame-method plot,unmarkedFrame,missing-method plot,unmarkedFrameOccuMulti,missing-method plot,unmarkedFrameOccuTTD,missing-method show,unmarkedFrame-method show,unmarkedFrameOccuCOP-method show,unmarkedFrameOccuMulti-method show,unmarkedFrameOccuTTD-method show,unmarkedMultFrame-method siteCovs siteCovs,unmarkedFrame-method siteCovs<- siteCovs<-,unmarkedFrame-method summary,unmarkedFrame-method summary,unmarkedFrameDS-method summary,unmarkedFrameOccuCOP-method summary,unmarkedFrameOccuMulti-method summary,unmarkedFrameOccuTTD-method summary,unmarkedMultFrame-method unmarkedFrame-class [,unmarkedFrameDSO,numeric,missing,missing-method [,unmarkedFrameGDR,logical,missing,missing-method [,unmarkedFrameGDR,missing,numeric,missing-method [,unmarkedFrameGDR,numeric,missing,missing-method [,unmarkedFrameMMO,numeric,missing,missing-method [,unmarkedFrameOccuCOP,missing,numeric,missing-method [,unmarkedFrameOccuCOP,numeric,missing,missing-method [,unmarkedFrameOccuCOP,numeric,numeric,missing-method [,unmarkedFrameOccuMS,numeric,missing,missing-method [,unmarkedFrameOccuMulti,missing,numeric,missing-method [,unmarkedFrameOccuMulti,numeric,missing,missing-method [,unmarkedFrameOccuTTD,missing,numeric,missing-method [,unmarkedFrameOccuTTD,numeric,missing,missing-method |
| Organize data for the distance sampling model of Royle et al. (2004) fit by distsamp | unmarkedFrameDS |
| Create an object of class unmarkedFrameDSO that contains data used by distsampOpen. | unmarkedFrameDSO |
| Organize data for the combined distance and removal point-count model of Amundson et al. (2014) fit by 'gdistremoval' | unmarkedFrameGDR unmarkedFrameGDR-class |
| Create an object of class unmarkedFrameMMO that contains data used by multmixOpen. | unmarkedFrameMMO |
| Organize data for the multinomial-Poisson mixture model of Royle (2004) fit by multinomPois | unmarkedFrameMPois |
| Organize data for the single season occupancy models fit by occu and occuRN | unmarkedFrameOccu |
| Organize data for the occupancy model using count data fit by 'occuCOP' | getL getL,unmarkedFrameOccuCOP-method unmarkedFrameOccuCOP |
| Organize data for the single season occupancy models fit by occuFP | unmarkedFrameOccuFP |
| Organize data for the multi-state occupancy model fit by occuMS | unmarkedFrameOccuMS |
| Organize data for the multispecies occupancy model fit by occuMulti | unmarkedFrameOccuMulti |
| Create an unmarkedFrameOccuTTD object for the time-to-detection model fit by occuTTD | unmarkedFrameOccuTTD |
| Create an object of class unmarkedFramePCO that contains data used by pcountOpen. | unmarkedFramePCO |
| Organize data for the N-mixture model fit by pcount | unmarkedFramePCount |
| Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object | unmarkedFrameGDS unmarkedFrameGMM unmarkedFrameGOccu unmarkedFrameGPC unmarkedMultFrame yearlySiteCovs yearlySiteCovs,unmarkedMultFrame-method yearlySiteCovs<- yearlySiteCovs<-,unmarkedMultFrame-method |
| Methods for unmarkedPower objects | plot,unmarkedPower,missing-method show,unmarkedPower-method show,unmarkedPower_old-method summary,unmarkedPower-method summary,unmarkedPower_old-method unmarkedPower-class unmarkedPower-methods unmarkedPower_old-class update,unmarkedPower-method update,unmarkedPower_old-method |
| Summarize a series of unmarked power analyses | plot,unmarkedPowerList,ANY-method plot,unmarkedPowerList_old,ANY-method show,unmarkedPowerList-method show,unmarkedPowerList_old-method summary,unmarkedPowerList-method summary,unmarkedPowerList_old-method unmarkedPowerList unmarkedPowerList,list-method unmarkedPowerList,unmarkedFit-method unmarkedPowerList,unmarkedPower-method unmarkedPowerList-methods unmarkedPowerList_old-class |
| Class '"unmarkedRanef"' | bup bup,unmarkedRanef-method confint,unmarkedRanef-method plot,unmarkedRanef,missing-method show,unmarkedRanef-method unmarkedRanef-class |
| Methods for Function vcov in Package `unmarked' | vcov,linCombOrBackTrans-method vcov,unmarkedEstimate-method vcov,unmarkedFit-method vcov,unmarkedFitOccuMulti-method vcov-methods |
| Compute Variance Inflation Factors for an unmarkedFit Object. | vif |
