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unmarked (version 1.1.1)

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.

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Install

install.packages('unmarked')

Monthly Downloads

9,243

Version

1.1.1

License

GPL (>= 3)

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Repository

https://github.com/ianfiske/unmarked

Homepage

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

Maintainer

Andy Royle

Last Published

May 27th, 2021

Functions in unmarked (1.1.1)

Methods for Function SE in Package `unmarked'

Compute Sum of Squared Residuals for a Model Fit.

Cross-validation methods for fitted unmarked models and fit lists

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

backTransform-methods

Methods for Function backTransform in Package `unmarked'

confint-methods

Methods for Function confint in Package `unmarked'

Swiss landscape data

Methods for Function coef in Package `unmarked'

BBS Point Count and Occurrence Data from 2 Bird Species

computeMPLElambda

Compute the penalty weight for the MPLE penalized likelihood method

Convert .CSV File to an unmarkedFrame

Open population model for distance sampling data

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

Distance-sampling detection functions and associated density functions

Green frog count index data

Methods for Function getP in Package `unmarked'

2001 Delaware North American Amphibian Monitoring Program Data

constructor of unmarkedFitList objects

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

Methods for bracket extraction [ in Package `unmarked'

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

Create unmarkedMultFrame from Long Format Data Frame

Convert between wide and long data formats.

European Jay data from the Swiss Breeding Bird Survey 2002

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

A function to impute missing entries in continuous obsCovs

Landscape data for Santa Cruz Island

Methods for Function getB in Package `unmarked'

Model selection results from an unmarkedFitList

Create functions to compute multinomial cell probabilities

Massachusetts North American Amphibian Monitoring Program Data

Methods for Function getFP in Package `unmarked'

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

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

Open population multinomial N-mixture model

Mallard count data

Multinomial-Poisson Mixtures Model

Bin distance data

Methods for Function fitted in Package `unmarked'

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

Fit spatial hierarchical distance sampling model.

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

Compute multinomial cell probabilities

Fit the MacKenzie et al. (2002) Occupancy Model

Fit the N-mixture model of Royle (2004)

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

Generalized binomial N-mixture model for repeated count data

linearComb-methods

Methods for Function linearComb in Package `unmarked'

Fit N-mixture Time-to-detection Models

Generalized multinomial N-mixture model

Extract estimates of random effect standard deviations

Fit the occupancy model of Royle and Nichols (2003)

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

unmarkedFit-class

Class "unmarkedFit"

unmarkedEstimateList-class

Class "unmarkedEstimateList"

nonparboot-methods

Nonparametric bootstrapping in unmarked

Extract estimates of random effect terms

predict-methods

Methods for Function predict in Package `unmarked'

Simulated point-transect data

posteriorSamples

Draw samples from the posterior predictive distribution

unmarkedFitList-class

Class "unmarkedFitList"

unmarkedFrame-class

Class "unmarkedFrame"

unmarkedEstimate-class

Class "unmarkedEstimate"

unmarked-package

Models for Data from Unmarked Animals

unmarkedFrameOccu

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

unmarkedFrameOccuMulti

Organize data for the multispecies occupancy model fit by occuMulti

unmarkedFrameMPois

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

simulate-methods

Methods for Function simulate in Package `unmarked'

unmarkedFrameOccuTTD

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

Methods for Function ranef 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

Fit Single-Season and Dynamic Multi-State Occupancy Models

unmarkedFrameDSO

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

Parametric bootstrap method for fitted models inheriting class.

Compute Variance Inflation Factors for an unmarkedFit Object.

Simulated line transect data

Removal data for the Ovenbird

Methods for Function vcov in Package `unmarked'

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

unmarkedFrameMMO

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

unmarkedFramePCO

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

unmarkedFrameOccuFP

Organize data for the single season occupancy models fit by occuFP

unmarkedMultFrame

Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object

unmarkedFrameOccuMS

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

Convert sight distance and sight angle to perpendicular distance.

unmarkedRanef-class

Class "unmarkedRanef"

unmarkedFramePCount

Organize data for the N-mixture model fit by pcount