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unmarked (version 1.3.1)

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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install.packages('unmarked')

Monthly Downloads

9,243

Version

1.3.1

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

June 29th, 2023

Functions in unmarked (1.3.1)

computeMPLElambda

Compute the penalty weight for the MPLE penalized likelihood method

backTransform-methods

Methods for Function backTransform in Package `unmarked'

BBS Point Count and Occurrence Data from 2 Bird Species

Occupancy data for coyote, red fox, and bobcat

Landscape data for Santa Cruz Island

Methods for Function SE in Package `unmarked'

Open population model for distance sampling data

confint-methods

Methods for Function confint in Package `unmarked'

Convert .CSV File to an unmarkedFrame

Methods for Function coef in Package `unmarked'

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

constructor of unmarkedFitList objects

Methods for bracket extraction [ in Package `unmarked'

Generalized multinomial N-mixture model

Methods for Function fitted in Package `unmarked'

Bin distance data

Create functions to compute multinomial cell probabilities

Create unmarkedMultFrame from Long Format Data Frame

Green frog count index data

A function to impute missing entries in continuous obsCovs

Open population multinomial N-mixture model

Distance-sampling detection functions and associated density functions

Mallard count data

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

Compute Sum of Squared Residuals for a Model Fit.

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

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

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

predict-methods

Methods for Function predict in Package `unmarked'

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

Massachusetts North American Amphibian Monitoring Program Data

Methods for Function getP in Package `unmarked'

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

unmarkedFrameDSO

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

Swiss landscape data

unmarkedFramePCount

Organize data for the N-mixture model fit by pcount

linearComb-methods

Methods for Function linearComb in Package `unmarked'

Fit Single-Season and Dynamic Multi-State Occupancy Models

Multinomial-Poisson Mixtures Model

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

unmarkedFrameOccuMulti

Organize data for the multispecies occupancy model fit by occuMulti

Create an unmarkedFrame, or one of its child classes.

Model selection results from an unmarkedFitList

Conduct a power analysis on an unmarked model

Parametric bootstrap method for fitted models inheriting class.

Fit the MacKenzie et al. (2002) Occupancy Model

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

Extract estimates of random effect standard deviations

Methods for Function vcov in Package `unmarked'

Simulated line transect data

Convert between wide and long data formats.

Fit the occupancy model of Royle and Nichols (2003)

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

Generalized binomial N-mixture model for repeated count data

unmarkedFitList-class

Class "unmarkedFitList"

unmarkedFrameDS

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

Fit the N-mixture model of Royle (2004)

unmarkedFrameOccuMS

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

2001 Delaware North American Amphibian Monitoring Program Data

unmarkedFrame-class

Class "unmarkedFrame"

unmarkedPowerList

Create or summarize a series of unmarked power analyses

simulate-methods

Methods for Function simulate in Package `unmarked'

optimizePenalty-methods

Identify Optimal Penalty Parameter Value

unmarkedFrameOccuFP

Organize data for the single season occupancy models fit by occuFP

unmarkedFrameOccu

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

Compute multinomial cell probabilities

unmarked-package

Models for Data from Unmarked Animals

Launch a Shiny app to help with power analysis

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

Removal data for the Ovenbird

Simulated point-transect data

Cross-validation methods for fitted unmarked models and fit lists

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

Convert sight distance and sight angle to perpendicular distance.

Plot marginal effects of covariates in unmarked models

unmarkedPower-methods

Methods for unmarkedPower objects

Methods for Function getFP in Package `unmarked'

posteriorSamples

Draw samples from the posterior predictive distribution

unmarkedFrameGDR

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

unmarkedEstimate-class

Class "unmarkedEstimate"

unmarkedFramePCO

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

unmarkedFrameOccuTTD

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

Methods for Function getB in Package `unmarked'

Fit spatial hierarchical distance sampling model.

Extract estimates of random effect terms

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

European Jay data from the Swiss Breeding Bird Survey 2002

unmarkedMultFrame

Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object

Fit N-mixture Time-to-detection Models

unmarkedRanef-class

Class "unmarkedRanef"

nonparboot-methods

Nonparametric bootstrapping in unmarked

Methods for Function ranef in Package unmarked

unmarkedEstimateList-class

Class "unmarkedEstimateList"

unmarkedFrameMMO

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

unmarkedFit-class

Class "unmarkedFit"

unmarkedFrameMPois

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

Compute Variance Inflation Factors for an unmarkedFit Object.