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unmarked (version 1.5.1)

Models for Data from Unmarked Animals

Description

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) , Fiske and Chandler (2011) .

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Version

Install

install.packages('unmarked')

Monthly Downloads

20,371

Version

1.5.1

License

GPL (>= 3)

Homepage

https://groups.google.com/d/forum/unmarked

Maintainer

Ken Kellner

Last Published

September 26th, 2025

Functions in unmarked (1.5.1)

Fit the hierarchical distance sampling model of Royle et al. (2004)

Cross-validation methods for fitted unmarked models and fit lists

Methods for bracket extraction [ in Package `unmarked'

confint-methods

Methods for Function confint in Package `unmarked'

Open population model for distance sampling data

computeMPLElambda

Compute the penalty weight for the MPLE penalized likelihood method

Distance-sampling detection functions and associated density functions

Convert .CSV File to an unmarkedFrame

Landscape data for Santa Cruz Island

Detection/non-detection data on the European crossbill (Loxia curvirostra)

Fit the generalized distance sampling model of Chandler et al. (2011).

Methods for Function getFP in Package `unmarked'

Convert between wide and long data formats.

Create unmarkedMultFrame from Long Format Data Frame

Bin distance data

Create a list of fitted unmarked models

Calculate fitted (expected) values from a model

Fit the combined distance and removal model of Amundson et al. (2014).

Methods for Function getB in Package `unmarked'

2001 Delaware North American Amphibian Monitoring Program Data

Convert Poisson mean (lambda) to probability of occurrence (psi).

Generalized multinomial N-mixture model

Fit the multi-scale occupancy model of Nichols et al. (2008)

Generalized binomial N-mixture model for repeated count data

Get detection probability matrix from a fitted model

Distance-sampling data for the Island Scrub Jay (Aphelocoma insularis)

Simulated line transect data

Green frog count index data

linearComb-methods

Methods for Function linearComb in Package `unmarked'

European Jay data from the Swiss Breeding Bird Survey 2002

Create functions to compute multinomial cell probabilities

Mallard count data

Model selection on a list of unmarked model fits

Massachusetts North American Amphibian Monitoring Program Data

Fit the N-mixture Time-to-detection Model of Strebel et al. (2021)

Fit the MacKenzie et al. (2002) Occupancy Model

Multinomial-Poisson Mixtures Model

Get non-parametric bootstrap samples from an unmarked model

Open population multinomial N-mixture model

Fit the occupancy model using count data

Fit the MacKenzie et al. (2002) Occupancy Model with the penalized likelihood methods of Hutchinson et al. (2015)

optimizePenalty-methods

Identify Optimal Penalty Parameter Value

Fit a community occupancy model with species-level random effects

Removal data for the Ovenbird

Fit the MacKenzie et al. (2002) Occupancy Model with the penalized likelihood methods of Hutchinson et al. (2015) using cross-validation

Fit occupancy models when false positive detections occur (e.g., Royle and Link [2006] and Miller et al. [2011])

Fit the multi-species occupancy model of Rota et al. (2016)

Fit Multi-State Occupancy Models (Nichols et al. 2007, MacKenzie et al. 2009)

Fit Single-Season and Dynamic Time-to-detection Occupancy Models

Fit the occupancy model of Royle and Nichols (2003)

Conduct a power analysis for an unmarked model

posteriorSamples

Draw samples from the posterior predictive distribution

Plot marginal effects of covariates in unmarked models

Compute multinomial cell probabilities

Predict from fitted models and other unmarked objects

Fit the open N-mixture models of Dail and Madsen (2011) and Hostetler and Chandler (2015)

Fit spatial hierarchical distance sampling model.

Parametric bootstrap for unmarked models

Fit the N-mixture model of Royle (2004)

Simulated point-transect data

Extract estimates of random effect standard deviations

unmarkedEstimateList-class

Class "unmarkedEstimateList"

Calculate residuals from a model

Simulate datasets from any unmarked model type

Estimate posterior distributions of latent occupancy or abundance

Estimate posterior distributions of site richness

Extract estimates of random effect terms

Launch a Shiny app to help with power analysis

unmarked-package

Models for Data from Unmarked Animals

unmarkedEstimate-class

Class "unmarkedEstimate"

unmarkedFrameDSO

Create an object of class unmarkedFrameDSO that contains data used by distsampOpen.

unmarkedFitList-class

Class "unmarkedFitList"

unmarkedFrameGDR

Organize data for the combined distance and removal point-count model of Amundson et al. (2014) fit by gdistremoval

Create an unmarkedFrame, or one of its child classes.

unmarkedFrameOccu

Organize data for the single season occupancy models fit by occu and occuRN

unmarkedFrameDS

Organize data for the distance sampling model of Royle et al. (2004) fit by distsamp

unmarkedFrameMPois

Organize data for the multinomial-Poisson mixture model of Royle (2004) fit by multinomPois

unmarkedFrameMMO

Create an object of class unmarkedFrameMMO that contains data used by multmixOpen.

unmarkedFit-class

Class "unmarkedFit"

unmarkedFrame-class

Class "unmarkedFrame"

unmarkedFrameOccuMulti

Organize data for the multispecies occupancy model fit by occuMulti

unmarkedFrameOccuTTD

Create an unmarkedFrameOccuTTD object for the time-to-detection model fit by occuTTD

unmarkedFramePCount

Organize data for the N-mixture model fit by pcount

unmarkedFrameOccuCOP

Organize data for the occupancy model using count data fit by occuCOP

unmarkedFrameOccuComm

Organize data for the community occupancy model fit by occuComm

unmarkedFrameOccuFP

Organize data for the single season occupancy models fit by occuFP

unmarkedModSel-class

unmarkedModSel class and methods

unmarkedMultFrame

Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object

unmarkedFramePCO

Create an object of class unmarkedFramePCO that contains data used by pcountOpen.

unmarkedFrameOccuMS

Organize data for the multi-state occupancy model fit by occuMS

unmarkedPower-methods

Methods for unmarkedPower objects

Compute Variance Inflation Factors for an unmarkedFit Object.

unmarkedPowerList

Summarize a series of unmarked power analyses

Methods for Function vcov in Package `unmarked'

unmarkedRanef-class

Class "unmarkedRanef"

Methods for Function coef in Package `unmarked'

Compute Sum of Squared Residuals for a Model Fit.

Fit the integrated distance sampling model of Kery et al. (2022).

Extract Best Unbiased Predictors (BUPs) of latent variables from ranef output

Occupancy data for coyote, red fox, and bobcat

backTransform-methods

Methods for Function backTransform in Package `unmarked'

Methods for Function SE in Package `unmarked'

BBS Point Count and Occurrence Data from 2 Bird Species

Fit the dynamic occupancy model of MacKenzie et. al (2003)

Swiss landscape data