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unmarked (version 1.1.0)

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

8,959

Version

1.1.0

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 6th, 2021

Functions in unmarked (1.1.0)

Compute Sum of Squared Residuals for a Model Fit.

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

Swiss landscape data

BBS Point Count and Occurrence Data from 2 Bird Species

backTransform-methods

Methods for Function backTransform in Package `unmarked'

confint-methods

Methods for Function confint in Package `unmarked'

Methods for Function SE in Package `unmarked'

computeMPLElambda

Compute the penalty weight for the MPLE penalized likelihood method

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

Methods for Function coef in Package `unmarked'

Landscape data for Santa Cruz Island

Convert .CSV File to an unmarkedFrame

Methods for Function fitted in Package `unmarked'

Generalized binomial N-mixture model for repeated count data

Generalized multinomial N-mixture model

Distance-sampling detection functions and associated density functions

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

Create functions to compute multinomial cell probabilities

2001 Delaware North American Amphibian Monitoring Program Data

Mallard count data

Bin distance data

Green frog count index data

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

A function to impute missing entries in continuous obsCovs

Methods for Function getP in Package `unmarked'

Methods for Function getB in Package `unmarked'

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

constructor of unmarkedFitList objects

Methods for bracket extraction [ in Package `unmarked'

Methods for Function getFP in Package `unmarked'

European Jay data from the Swiss Breeding Bird Survey 2002

Open population model for distance sampling data

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

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

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

Fit N-mixture Time-to-detection Models

linearComb-methods

Methods for Function linearComb in Package `unmarked'

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

Fit the N-mixture model of Royle (2004)

nonparboot-methods

Nonparametric bootstrapping in unmarked

Fit the occupancy model of Royle and Nichols (2003)

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

Fit the MacKenzie et al. (2002) Occupancy Model

Fit spatial hierarchical distance sampling model.

predict-methods

Methods for Function predict in Package `unmarked'

unmarkedFrameMPois

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

Simulated line transect data

Simulated point-transect data

unmarked-package

Models for Data from Unmarked Animals

unmarkedFrameDSO

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

Removal data for the Ovenbird

Create unmarkedMultFrame from Long Format Data Frame

Convert between wide and long data formats.

unmarkedMultFrame

Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object

unmarkedRanef-class

Class "unmarkedRanef"

unmarkedFitList-class

Class "unmarkedFitList"

unmarkedEstimate-class

Class "unmarkedEstimate"

unmarkedFrame-class

Class "unmarkedFrame"

Model selection results from an unmarkedFitList

Massachusetts North American Amphibian Monitoring Program Data

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

unmarkedEstimateList-class

Class "unmarkedEstimateList"

Extract estimates of random effect standard deviations

posteriorSamples

Draw samples from the posterior predictive distribution

Extract estimates of random effect terms

Create an unmarkedFrame, or one of its child classes.

unmarkedFramePCount

Organize data for the N-mixture model fit by pcount

simulate-methods

Methods for Function simulate in Package `unmarked'

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

Fit Single-Season and Dynamic Multi-State Occupancy Models

unmarkedFrameOccuMS

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

unmarkedFrameOccuFP

Organize data for the single season occupancy models fit by occuFP

Multinomial-Poisson Mixtures Model

unmarkedFrameDS

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

unmarkedFrameOccuMulti

Organize data for the multispecies occupancy model fit by occuMulti

Open population multinomial N-mixture model

Convert sight distance and sight angle to perpendicular distance.

Compute multinomial cell probabilities

unmarkedFrameMMO

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

unmarkedFit-class

Class "unmarkedFit"

Compute Variance Inflation Factors for an unmarkedFit Object.

Methods for Function vcov in Package `unmarked'

unmarkedFrameOccuTTD

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

Parametric bootstrap method for fitted models inheriting class.

Methods for Function ranef in Package unmarked

unmarkedFramePCO

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

unmarkedFrameOccu

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

Cross-validation methods for fitted unmarked models and fit lists