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unmarked (version 1.2.5)

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. Reference: Fiske and Chandler (2011) .

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install.packages('unmarked')

Monthly Downloads

9,726

Version

1.2.5

License

GPL (>= 3)

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Repository

https://github.com/ianfiske/unmarked

Homepage

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

Maintainer

Last Published

May 13th, 2022

Functions in unmarked (1.2.5)

confint-methods

Methods for Function confint in Package `unmarked'

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

Open population model for distance sampling data

Distance-sampling detection functions and associated density functions

Convert .CSV File to an unmarkedFrame

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

constructor of unmarkedFitList objects

Methods for Function coef in Package `unmarked'

Methods for bracket extraction [ in Package `unmarked'

Methods for Function getB in Package `unmarked'

Bin distance data

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

Methods for Function fitted in Package `unmarked'

Simulated line transect data

European Jay data from the Swiss Breeding Bird Survey 2002

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

2001 Delaware North American Amphibian Monitoring Program Data

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

Create functions to compute multinomial cell probabilities

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

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

Open population multinomial N-mixture model

linearComb-methods

Methods for Function linearComb in Package `unmarked'

Methods for Function getFP in Package `unmarked'

Create unmarkedMultFrame from Long Format Data Frame

Convert between wide and long data formats.

Landscape data for Santa Cruz Island

Massachusetts North American Amphibian Monitoring Program Data

Green frog count index data

Fit N-mixture Time-to-detection Models

Fit Single-Season and Dynamic Multi-State Occupancy Models

Generalized binomial N-mixture model for repeated count data

Mallard count data

Generalized multinomial N-mixture model

unmarkedFrame-class

Class "unmarkedFrame"

Extract estimates of random effect terms

Parametric bootstrap method for fitted models inheriting class.

Removal data for the Ovenbird

Methods for Function getP in Package `unmarked'

Methods for Function ranef in Package unmarked

Compute multinomial cell probabilities

Model selection results from an unmarkedFitList

Simulated point-transect data

Multinomial-Poisson Mixtures Model

nonparboot-methods

Nonparametric bootstrapping in unmarked

Methods for Function vcov in Package `unmarked'

Fit the MacKenzie et al. (2002) Occupancy Model

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

unmarkedFrameOccuMulti

Organize data for the multispecies occupancy model fit by occuMulti

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

Conduct a power analysis on an unmarked model

unmarkedFrameMMO

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

unmarkedFrameGDR

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

unmarkedFrameDS

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

optimizePenalty-methods

Identify Optimal Penalty Parameter Value

predict-methods

Methods for Function predict in Package `unmarked'

posteriorSamples

Draw samples from the posterior predictive distribution

unmarkedRanef-class

Class "unmarkedRanef"

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

unmarkedFrameOccuTTD

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

Compute Variance Inflation Factors for an unmarkedFit Object.

unmarkedFit-class

Class "unmarkedFit"

Convert sight distance and sight angle to perpendicular distance.

simulate-methods

Methods for Function simulate in Package `unmarked'

Fit the occupancy model of Royle and Nichols (2003)

unmarkedEstimate-class

Class "unmarkedEstimate"

unmarked-package

Models for Data from Unmarked Animals

unmarkedFrameOccuMS

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

unmarkedEstimateList-class

Class "unmarkedEstimateList"

Extract estimates of random effect standard deviations

unmarkedFrameOccuFP

Organize data for the single season occupancy models fit by occuFP

unmarkedPowerList

Create or summarize a series of unmarked power analyses

unmarkedFrameMPois

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

unmarkedFitList-class

Class "unmarkedFitList"

unmarkedFrameDSO

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

unmarkedFramePCO

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

unmarkedFramePCount

Organize data for the N-mixture model fit by pcount

Create an unmarkedFrame, or one of its child classes.

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

A function to impute missing entries in continuous obsCovs

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

unmarkedMultFrame

Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object

unmarkedFrameOccu

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

unmarkedPower-methods

Methods for unmarkedPower objects

Fit the N-mixture model of Royle (2004)

Fit spatial hierarchical distance sampling model.

Cross-validation methods for fitted unmarked models and fit lists

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

BBS Point Count and Occurrence Data from 2 Bird Species

backTransform-methods

Methods for Function backTransform in Package `unmarked'

Methods for Function SE in Package `unmarked'

Swiss landscape data

computeMPLElambda

Compute the penalty weight for the MPLE penalized likelihood method

Compute Sum of Squared Residuals for a Model Fit.