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unmarked (version 1.0.1)

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

7,038

Version

1.0.1

License

GPL (>= 3)

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Repository

http://github.com/ianfiske/unmarked

Homepage

http://groups.google.com/group/unmarked

Maintainer

Last Published

July 2nd, 2020

Functions in unmarked (1.0.1)

backTransform-methods

Methods for Function backTransform in Package `unmarked'

Compute Sum of Squared Residuals for a Model Fit.

Cross-validation methods for fitted unmarked models and fit lists

computeMPLElambda

Compute the penalty weight for the MPLE penalized likelihood method

Methods for Function coef in Package `unmarked'

confint-methods

Methods for Function confint in Package `unmarked'

Methods for Function SE in Package `unmarked'

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

constructor of unmarkedFitList objects

Swiss landscape data

BBS Point Count and Occurrence Data from 2 Bird Species

Methods for bracket extraction [ in Package `unmarked'

Distance-sampling detection functions and associated density functions

Convert .CSV File to an unmarkedFrame

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

Open population model for distance sampling data

Create unmarkedMultFrame from Long Format Data Frame

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

linearComb-methods

Methods for Function linearComb in Package `unmarked'

Simulated line transect data

Methods for Function getP in Package `unmarked'

Bin distance data

Generalized binomial N-mixture model for repeated count data

A function to impute missing entries in continuous obsCovs

Green frog count index data

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

Convert between wide and long data formats.

Generalized multinomial N-mixture model

Landscape data for Santa Cruz Island

Methods for Function fitted in Package `unmarked'

European Jay data from the Swiss Breeding Bird Survey 2002

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

Open population multinomial N-mixture model

Multinomial-Poisson Mixtures Model

Parametric bootstrap method for fitted models inheriting class.

Methods for Function getB in Package `unmarked'

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

Fit the occupancy model of Royle and Nichols (2003)

Methods for Function getFP in Package `unmarked'

nonparboot-methods

Nonparametric bootstrapping in unmarked

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) using cross-validation

Fit the N-mixture model of Royle (2004)

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

posteriorSamples

Draw samples from the posterior predictive distribution

Fit spatial hierarchical distance sampling model.

unmarkedFit-class

Class "unmarkedFit"

Removal data for the Ovenbird

unmarkedFitList-class

Class "unmarkedFitList"

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

Model selection results from an unmarkedFitList

simulate-methods

Methods for Function simulate in Package `unmarked'

Massachusetts North American Amphibian Monitoring Program Data

Fit the MacKenzie et al. (2002) Occupancy Model

unmarked-package

Models for Data from Unmarked Animals

unmarkedFrameOccuMS

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

2001 Delaware North American Amphibian Monitoring Program Data

unmarkedFrameOccuMulti

Organize data for the multispecies occupancy model fit by occuMulti

unmarkedRanef-class

Class "unmarkedRanef"

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

unmarkedFrameMMO

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

Methods for Function vcov in Package `unmarked'

unmarkedFramePCount

Organize data for the N-mixture model fit by pcount

unmarkedFrameMPois

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

unmarkedMultFrame

Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object

Methods for Function ranef in Package unmarked

unmarkedFrameDS

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

unmarkedFrameDSO

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

Convert sight distance and sight angle to perpendicular distance.

Fit Single-Season and Dynamic Multi-State Occupancy Models

unmarkedFrameOccu

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

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

predict-methods

Methods for Function predict in Package `unmarked'

unmarkedFrameOccuFP

Organize data for the single season occupancy models fit by occuFP

unmarkedEstimateList-class

Class "unmarkedEstimateList"

Create functions to compute multinomial cell probabilities

unmarkedEstimate-class

Class "unmarkedEstimate"

Compute multinomial cell probabilities

Mallard count data

unmarkedFrameOccuTTD

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

Create an unmarkedFrame, or one of its child classes.

unmarkedFramePCO

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

Compute Variance Inflation Factors for an unmarkedFit Object.

Simulated point-transect data

unmarkedFrame-class

Class "unmarkedFrame"