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occu()
|
Fit the MacKenzie et al. (2002) Occupancy Model |
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goccu()
|
Fit multi-scale occupancy models |
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colext()
|
Fit the dynamic occupancy model of MacKenzie et. al (2003) |
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occuFP()
|
Fit occupancy models when false positive detections occur (e.g., Royle and Link [2006] and Miller et al. [2011]) |
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occuMS()
|
Fit Single-Season and Dynamic Multi-State Occupancy Models |
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occuMulti()
|
Fit the Rota et al. (2016) Multi-species Occupancy Model |
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occuPEN()
|
Fit the MacKenzie et al. (2002) Occupancy Model with the penalized likelihood methods of Hutchinson et al. (2015) |
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occuTTD()
|
Fit Single-Season and Dynamic Time-to-detection Occupancy Models |
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occuCOP()
|
Fit the occupancy model using count dta |
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occuRN()
|
Fit the occupancy model of Royle and Nichols (2003) |
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pcount()
|
Fit the N-mixture model of Royle (2004) |
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distsamp()
|
Fit the hierarchical distance sampling model of Royle et al. (2004) |
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IDS()
|
Fit the integrated distance sampling model of Kery et al. (2022). |
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multinomPois()
|
Multinomial-Poisson Mixtures Model |
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pcount.spHDS()
|
Fit spatial hierarchical distance sampling model. |
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gpcount()
|
Generalized binomial N-mixture model for repeated count data |
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gmultmix()
|
Generalized multinomial N-mixture model |
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gdistsamp()
|
Fit the generalized distance sampling model of Chandler et al. (2011). |
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gdistremoval()
|
Fit the combined distance and removal model of Amundson et al. (2014). |
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pcountOpen()
|
Fit the open N-mixture models of Dail and Madsen and extensions |
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distsampOpen()
|
Open population model for distance sampling data |
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multmixOpen()
|
Open population multinomial N-mixture model |
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nmixTTD()
|
Fit N-mixture Time-to-detection Models |
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unmarkedFrame()
|
Create an unmarkedFrame, or one of its child classes. |
|
unmarkedFrame-class coordinates,unmarkedFrame-method coordinates coords getY getY,unmarkedFrame-method head,unmarkedFrame-method hist,unmarkedFrameDS-method mapInfo numSites numSites,unmarkedFrame-method numY numY,unmarkedFrame-method obsCovs,unmarkedFrame-method obsCovs obsCovs obsCovs obsNum,unmarkedFrame-method obsNum obsToY,unmarkedFrame-method obsToY obsToY obsToY plot,unmarkedFrame,missing-method plot,unmarkedFrameOccuMulti,missing-method plot,unmarkedFrameOccuTTD,missing-method projection,unmarkedFrame-method projection siteCovs,unmarkedFrame-method siteCovs siteCovs siteCovs unmarkedFrameOccu-class unmarkedFrameOccuMulti-class unmarkedFrameOccuMS-class unmarkedFrameOccuTTD-class unmarkedFrameMPois-class unmarkedFramePCount-class unmarkedFrameDS-class unmarkedMultFrame-class unmarkedFramePCO-class unmarkedFrameGMM-class unmarkedFrameGDS-class unmarkedFrameGPC-class unmarkedFrameDSO-class unmarkedFrameMMO-class show,unmarkedFrame-method show,unmarkedFrameOccuMulti-method show,unmarkedFrameOccuTTD-method show,unmarkedMultFrame-method show,unmarkedFrameOccuCOP-method summary,unmarkedFrame-method summary,unmarkedFrameDS-method summary,unmarkedMultFrame-method summary,unmarkedFrameOccuMulti-method summary,unmarkedFrameOccuTTD-method summary,unmarkedFrameOccuCOP-method [,unmarkedFrameOccuMulti,missing,numeric,missing-method [,unmarkedFrameOccuTTD,missing,numeric,missing-method [,unmarkedFrameGDR,missing,numeric,missing-method [,unmarkedFrameOccuMS,numeric,missing,missing-method [,unmarkedFrameOccuTTD,numeric,missing,missing-method [,unmarkedFrameOccuMulti,numeric,missing,missing-method [,unmarkedFrameDSO,numeric,missing,missing-method [,unmarkedFrameGDR,numeric,missing,missing-method [,unmarkedFrameGDR,logical,missing,missing-method [,unmarkedFrameOccuCOP,missing,numeric,missing-method [,unmarkedFrameOccuCOP,numeric,missing,missing-method [,unmarkedFrameOccuCOP,numeric,numeric,missing-method
|
Class "unmarkedFrame" |
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unmarkedMultFrame() unmarkedFrameGMM() unmarkedFrameGDS() unmarkedFrameGPC()
|
Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object |
|
unmarkedFrameDS()
|
Organize data for the distance sampling model of Royle et al. (2004) fit by distsamp |
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unmarkedFrameOccu()
|
Organize data for the single season occupancy models fit by occu and occuRN |
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unmarkedFrameOccuFP()
|
Organize data for the single season occupancy models fit by occuFP |
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unmarkedFrameOccuMulti()
|
Organize data for the multispecies occupancy model fit by occuMulti |
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unmarkedFramePCount()
|
Organize data for the N-mixture model fit by pcount |
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unmarkedFrameMPois()
|
Organize data for the multinomial-Poisson mixture model of Royle (2004) fit by multinomPois |
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unmarkedFrameOccuCOP()
|
Organize data for the occupancy model using count data fit by occuCOP |
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unmarkedFrameOccuMS()
|
Organize data for the multi-state occupancy model fit by occuMS |
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unmarkedFrameOccuTTD()
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Create an unmarkedFrameOccuTTD object for the time-to-detection model fit by occuTTD |
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unmarkedFramePCO()
|
Create an object of class unmarkedFramePCO that contains data used by pcountOpen. |
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unmarkedFrameGDR()
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Organize data for the combined distance and removal point-count model of Amundson et al. (2014) fit by gdistremoval |
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unmarkedFrameMMO()
|
Create an object of class unmarkedFrameMMO that contains data used by multmixOpen. |
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unmarkedFrameDSO()
|
Create an object of class unmarkedFrameDSO that contains data used by distsampOpen. |
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coef(<unmarkedFit>) coef(<unmarkedEstimate>) coef(<linCombOrBackTrans>)
|
Methods for Function coef in Package `unmarked' |
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predict predict-methods predict,ANY-method predict,unmarkedFit-method predict,unmarkedFitOccuFP-method predict,unmarkedFitOccuMulti-method predict,unmarkedFitOccuMS-method predict,unmarkedFitOccuTTD-method predict,unmarkedFitNmixTTD-method predict,unmarkedFitPCount-method predict,unmarkedFitColExt-method predict,unmarkedFitGMM-method predict,unmarkedFitGDS-method predict,unmarkedFitPCO-method predict,unmarkedFitDSO-method predict,unmarkedFitGDR-method predict,unmarkedFitIDS-method predict,unmarkedFitList-method predict,unmarkedRanef-method
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Methods for Function predict in Package `unmarked' |
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linearComb linearComb-methods linearComb,unmarkedEstimate,matrixOrVector-method linearComb,unmarkedFit,matrixOrVector-method show,unmarkedLinComb-method
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Methods for Function linearComb in Package `unmarked' |
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backTransform(<unmarkedFit>) backTransform(<unmarkedEstimate>)
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Methods for Function backTransform in Package `unmarked' |
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ranef ranef-methods ranef,unmarkedFitOccu-method ranef,unmarkedFitOccuFP-method ranef,unmarkedFitOccuRN-method ranef,unmarkedFitOccuMulti-method ranef,unmarkedFitOccuMS-method ranef,unmarkedFitPCount-method ranef,unmarkedFitMPois-method ranef,unmarkedFitDS-method ranef,unmarkedFitGMM-method ranef,unmarkedFitGDS-method ranef,unmarkedFitGPC-method ranef,unmarkedFitGMMorGDS-method ranef,unmarkedFitColExt-method ranef,unmarkedFitPCO-method ranef,unmarkedFitOccuTTD-method ranef,unmarkedFitNmixTTD-method ranef,unmarkedFitGDR-method ranef,unmarkedFitDailMadsen-method ranef,unmarkedFitGOccu-method ranef,unmarkedFitOccuCOP-method ranef,unmarkedFitIDS-method
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Methods for Function ranef in Package unmarked |
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unmarkedRanef-class bup bup,unmarkedRanef-method confint,unmarkedRanef-method plot,unmarkedRanef,missing-method show,unmarkedRanef-method
|
Class "unmarkedRanef" |
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posteriorSamples(<unmarkedRanef>) posteriorSamples(<unmarkedFit>)
|
Draw samples from the posterior predictive distribution |
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unmarkedFit unmarkedFit-class getData getData,unmarkedFit-method hessian hessian,unmarkedFit-method hist,unmarkedFitDS-method mle mle,unmarkedFit-method names,unmarkedFit-method nllFun nllFun,unmarkedFit-method parboot,unmarkedFit-method parboot,unmarkedFitOccuMulti-method plot,unmarkedFit,missing-method plot,unmarkedFitOccuMulti,missing-method plot,unmarkedFitGDR,missing-method plot,unmarkedFitIDS,missing-method plot,unmarkedFitOccuCOP,missing-method profile,unmarkedFit-method residuals,unmarkedFit-method residuals,unmarkedFitOccu-method residuals,unmarkedFitOccuFP-method residuals,unmarkedFitOccuRN-method residuals,unmarkedFitOccuMulti-method residuals,unmarkedFitOccuTTD-method residuals,unmarkedFitGDR-method residuals,unmarkedFitIDS-method residuals,unmarkedFitOccuCOP-method update,unmarkedFit-method update,unmarkedFitColExt-method update,unmarkedFitGMM-method update,unmarkedFitOccuMulti-method update,unmarkedFitOccuMS-method update,unmarkedFitOccuTTD-method update,unmarkedFitNmixTTD-method update,unmarkedFitGDR-method update,unmarkedFitIDS-method update,unmarkedFitDailMadsen-method update,unmarkedFitGOccu-method sampleSize sampleSize,unmarkedFit-method unmarkedFitOccu-class unmarkedFitOccuPEN-class unmarkedFitOccuPEN_CV-class unmarkedFitOccuFP-class unmarkedFitPCount-class unmarkedFitDS-class unmarkedFitMPois-class unmarkedFitPCO-class unmarkedFitGMM-class unmarkedFitOccuMulti-class unmarkedFitOccuMS-class unmarkedFitOccuTTD-class unmarkedFitNmixTTD-class unmarkedFitDSO-class unmarkedFitMMO-class unmarkedFitIDS-class plot,profile,missing-method show,unmarkedFit-method summary,unmarkedFit-method summary,unmarkedFitDS-method summary,unmarkedFitIDS-method smoothed smoothed,unmarkedFitColExt-method projected projected,unmarkedFitColExt-method logLik logLik,unmarkedFit-method LRT LRT,unmarkedFit,unmarkedFit-method getY,unmarkedFit-method getY,unmarkedFitOccu-method getY,unmarkedFitColExt-method getY,unmarkedFitOccuRN-method getY,unmarkedFitOccuMulti-method
|
Class "unmarkedFit" |
|
plotEffects(<unmarkedFit>) plotEffectsData(<unmarkedFit>)
|
Plot marginal effects of covariates in unmarked models |
|
randomTerms(<unmarkedEstimate>) randomTerms(<unmarkedFit>)
|
Extract estimates of random effect terms |
|
sigma(<unmarkedEstimate>) sigma(<unmarkedFit>)
|
Extract estimates of random effect standard deviations |
|
birds
|
BBS Point Count and Occurrence Data from 2 Bird Species |
|
crossbill
|
Detection/non-detection data on the European crossbill (Loxia curvirostra) |
|
cruz
|
Landscape data for Santa Cruz Island |
|
frogs
|
2001 Delaware North American Amphibian Monitoring Program Data |
|
gf
|
Green frog count index data |
|
issj
|
Distance-sampling data for the Island Scrub Jay (Aphelocoma insularis) |
|
jay
|
European Jay data from the Swiss Breeding Bird Survey 2002 |
|
linetran
|
Simulated line transect data |
|
mallard
|
Mallard count data |
|
masspcru
|
Massachusetts North American Amphibian Monitoring Program Data |
|
MesoCarnivores
|
Occupancy data for coyote, red fox, and bobcat |
|
ovendata
|
Removal data for the Ovenbird |
|
pointtran
|
Simulated point-transect data |
|
Switzerland
|
Swiss landscape data |