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unmarked (version 0.11-0)

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

8,578

Version

0.11-0

License

GPL (>= 3)

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Repository

http://github.com/ianfiske/unmarked

Homepage

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

Maintainer

Andy Royle

Last Published

September 3rd, 2015

Functions in unmarked (0.11-0)

unmarked-package

Models for Data from Unmarked Animals

Create an unmarkedFrame, or one of its child classes.

constructor of unmarkedFitList objects

computeMPLElambda

Compute the penalty weight for the MPLE penalized likelihood method

Methods for Function ranef in Package unmarked

confint-methods

Methods for Function confint in Package `unmarked'

Mallard count data

Swiss landscape data

Fit the occupancy model of Royle and Nichols (2003)

Massachusetts North American Amphibian Monitoring Program Data

BBS Point Count and Occurrence Data from 2 Bird Species

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

Fit the N-mixture model of Royle (2004)

Bin distance data

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

simulate-methods

Methods for Function simulate in Package `unmarked'

Methods for Function SE in Package `unmarked'

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

unmarkedMultFrame

Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object

Compute Sum of Squared Residuals for a Model Fit.

Multinomial-Poisson Mixtures Model

2001 Delaware North American Amphibian Monitoring Program Data

A function to impute missing entries in continuous obsCovs

unmarkedEstimate-class

Class "unmarkedEstimate"

Landscape data for Santa Cruz Island

unmarkedFrameMPois

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

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

Distance-sampling detection functions and associated density functions

Parametric bootstrap method for fitted models inheriting class.

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

Methods for Function coef in Package `unmarked'

Model selection results from an unmarkedFitList

Convert .CSV File to an unmarkedFrame

Methods for bracket extraction [ in Package `unmarked'

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

Methods for Function getFP in Package `unmarked'

Convert between wide and long data formats.

Methods for Function vcov in Package `unmarked'

unmarkedRanef-class

Class "unmarkedRanef"

Methods for Function getP in Package `unmarked'

Simulated point-transect data

unmarkedFrameDS

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

Convert sight distance and sight angle to perpendicular distance.

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

Generalized binomial N-mixture model for repeated count data

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

predict-methods

Methods for Function predict in Package `unmarked'

MHB European Jay data set

unmarkedFrameOccu

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

Methods for Function fitted in Package `unmarked'

Removal data for the Ovenbird

Simulated line transect data

Compute multinomial cell probabilities

linearComb-methods

Methods for Function linearComb in Package `unmarked'

unmarkedFit-class

Class "unmarkedFit"

Create unmarkedMultFrame from Long Format Data Frame

unmarkedFramePCO

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

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

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

nonparboot-methods

Nonparametric bootstrapping in unmarked

unmarkedFrame-class

Class "unmarkedFrame"

unmarkedEstimateList-class

Class "unmarkedEstimateList"

unmarkedFramePCount

Organize data for the N-mixture model fit by pcount

Methods for Function getB in Package `unmarked'

Generalized multinomial N-mixture model

Green frog count index data

unmarkedFrameOccuFP

Organize data for the single season occupancy models fit by occuFP