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unmarked (version 1.3.2)

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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Install

install.packages('unmarked')

Monthly Downloads

5,867

Version

1.3.2

License

GPL (>= 3)

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Repository

https://github.com/ianfiske/unmarked

Homepage

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

Maintainer

Ken Kellner

Last Published

July 8th, 2023

Functions in unmarked (1.3.2)

Occupancy data for coyote, red fox, and bobcat

BBS Point Count and Occurrence Data from 2 Bird Species

Compute Sum of Squared Residuals for a Model Fit.

Swiss landscape data

Methods for Function getP in Package `unmarked'

Open population model for distance sampling data

Methods for Function SE in Package `unmarked'

Green frog count index data

Create functions to compute multinomial cell probabilities

Distance-sampling detection functions and associated density functions

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

Cross-validation methods for fitted unmarked models and fit lists

confint-methods

Methods for Function confint in Package `unmarked'

linearComb-methods

Methods for Function linearComb in Package `unmarked'

Simulated line transect data

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

Bin distance data

Methods for bracket extraction [ in Package `unmarked'

Mallard count data

Landscape data for Santa Cruz Island

Convert .CSV File to an unmarkedFrame

Methods for Function getB in Package `unmarked'

Create unmarkedMultFrame from Long Format Data Frame

Multinomial-Poisson Mixtures Model

Methods for Function getFP in Package `unmarked'

Generalized multinomial N-mixture model

Fit the occupancy model of Royle and Nichols (2003)

Generalized binomial N-mixture model for repeated count data

Fit the MacKenzie et al. (2002) Occupancy Model

optimizePenalty-methods

Identify Optimal Penalty Parameter Value

Open population multinomial N-mixture model

Removal data for the Ovenbird

Fit N-mixture Time-to-detection Models

Convert between wide and long data formats.

constructor of unmarkedFitList objects

Methods for Function fitted in Package `unmarked'

Extract estimates of random effect terms

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

nonparboot-methods

Nonparametric bootstrapping in unmarked

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

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

European Jay data from the Swiss Breeding Bird Survey 2002

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

Methods for Function ranef in Package unmarked

2001 Delaware North American Amphibian Monitoring Program Data

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

Fit Single-Season and Dynamic Multi-State Occupancy Models

Conduct a power analysis on an unmarked model

A function to impute missing entries in continuous obsCovs

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

Fit the Rota et al. (2016) Multi-species Occupancy Model

Simulated point-transect data

Fit spatial hierarchical distance sampling model.

posteriorSamples

Draw samples from the posterior predictive distribution

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

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

unmarked-package

Models for Data from Unmarked Animals

unmarkedEstimate-class

Class "unmarkedEstimate"

predict-methods

Methods for Function predict in Package `unmarked'

Fit the open N-mixture models of Dail and Madsen and extensions

Plot marginal effects of covariates in unmarked models

Compute multinomial cell probabilities

Extract estimates of random effect standard deviations

Massachusetts North American Amphibian Monitoring Program Data

simulate-methods

Methods for Function simulate in Package `unmarked'

Create an unmarkedFrame, or one of its child classes.

unmarkedFrameDS

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

unmarkedFrameOccuMS

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

unmarkedFrameOccuMulti

Organize data for the multispecies occupancy model fit by occuMulti

unmarkedEstimateList-class

Class "unmarkedEstimateList"

unmarkedFrameMMO

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

unmarkedFrameGDR

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

unmarkedFramePCount

Organize data for the N-mixture model fit by pcount

unmarkedFrameDSO

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

unmarkedMultFrame

Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object

unmarkedFrameMPois

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

Model selection results from an unmarkedFitList

unmarkedFit-class

Class "unmarkedFit"

Parametric bootstrap method for fitted models inheriting class.

unmarkedRanef-class

Class "unmarkedRanef"

Fit the N-mixture model of Royle (2004)

unmarkedFrameOccu

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

unmarkedFrameOccuFP

Organize data for the single season occupancy models fit by occuFP

unmarkedFrameOccuTTD

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

unmarkedFramePCO

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

unmarkedPower-methods

Methods for unmarkedPower objects

Convert sight distance and sight angle to perpendicular distance.

Launch a Shiny app to help with power analysis

unmarkedPowerList

Create or summarize a series of unmarked power analyses

Methods for Function vcov in Package `unmarked'

Compute Variance Inflation Factors for an unmarkedFit Object.

unmarkedFitList-class

Class "unmarkedFitList"

unmarkedFrame-class

Class "unmarkedFrame"

Methods for Function coef in Package `unmarked'

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

backTransform-methods

Methods for Function backTransform in Package `unmarked'

computeMPLElambda

Compute the penalty weight for the MPLE penalized likelihood method