Learn R Programming

⚠️There's a newer version (1.5.1) of this package.Take me there.

unmarked (version 1.4.1)

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. References: Kellner et al. (2023) , Fiske and Chandler (2011) .

Copy Link

Version

Install

install.packages('unmarked')

Monthly Downloads

8,284

Version

1.4.1

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/ianfiske/unmarked

Homepage

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

Maintainer

Ken Kellner

Last Published

January 9th, 2024

Functions in unmarked (1.4.1)

Cross-validation methods for fitted unmarked models and fit lists

Distance-sampling detection functions and associated density functions

Convert between wide and long data formats.

Methods for Function getB in Package `unmarked'

constructor of unmarkedFitList objects

Generalized binomial N-mixture model for repeated count data

Bin distance data

Create unmarkedMultFrame from Long Format Data Frame

computeMPLElambda

Compute the penalty weight for the MPLE penalized likelihood method

Methods for Function SE in Package `unmarked'

confint-methods

Methods for Function confint in Package `unmarked'

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

Occupancy data for coyote, red fox, and bobcat

Fit the MacKenzie et al. (2002) Occupancy Model

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

Methods for Function coef in Package `unmarked'

Methods for Function fitted in Package `unmarked'

Methods for bracket extraction [ in Package `unmarked'

Methods for Function getP in Package `unmarked'

Methods for Function getFP in Package `unmarked'

Compute Sum of Squared Residuals for a Model Fit.

BBS Point Count and Occurrence Data from 2 Bird Species

Open population model for distance sampling data

2001 Delaware North American Amphibian Monitoring Program Data

Fit multi-scale occupancy models

A function to impute missing entries in continuous obsCovs

Generalized multinomial N-mixture model

nonparboot-methods

Nonparametric bootstrapping in unmarked

backTransform-methods

Methods for Function backTransform in Package `unmarked'

optimizePenalty-methods

Identify Optimal Penalty Parameter Value

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

Removal data for the Ovenbird

Green frog count index data

Fit Single-Season and Dynamic Multi-State Occupancy Models

European Jay data from the Swiss Breeding Bird Survey 2002

Swiss landscape data

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

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

Multinomial-Poisson Mixtures Model

Fit the occupancy model using count dta

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

posteriorSamples

Draw samples from the posterior predictive distribution

Create functions to compute multinomial cell probabilities

Fit spatial hierarchical distance sampling model.

Extract estimates of random effect terms

linearComb-methods

Methods for Function linearComb in Package `unmarked'

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

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 with the penalized likelihood methods of Hutchinson et al. (2015)

Conduct a power analysis on an unmarked model

Mallard count data

unmarked-package

Models for Data from Unmarked Animals

Methods for Function ranef in Package unmarked

Open population multinomial N-mixture model

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

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

Launch a Shiny app to help with power analysis

Convert sight distance and sight angle to perpendicular distance.

Extract estimates of random effect standard deviations

predict-methods

Methods for Function predict in Package `unmarked'

unmarkedFitList-class

Class "unmarkedFitList"

Landscape data for Santa Cruz Island

Simulated point-transect data

Massachusetts North American Amphibian Monitoring Program Data

Simulated line transect data

unmarkedEstimate-class

Class "unmarkedEstimate"

Fit the occupancy model of Royle and Nichols (2003)

Convert .CSV File to an unmarkedFrame

Model selection results from an unmarkedFitList

unmarkedFrameDS

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

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

simulate-methods

Methods for Function simulate in Package `unmarked'

unmarkedFrame-class

Class "unmarkedFrame"

Create an unmarkedFrame, or one of its child classes.

unmarkedFrameOccuFP

Organize data for the single season occupancy models fit by occuFP

unmarkedFrameOccu

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

unmarkedFrameOccuCOP

Organize data for the occupancy model using count data fit by occuCOP

Parametric bootstrap method for fitted models inheriting class.

Fit the N-mixture model of Royle (2004)

Compute multinomial cell probabilities

unmarkedFrameDSO

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

unmarkedFit-class

Class "unmarkedFit"

unmarkedEstimateList-class

Class "unmarkedEstimateList"

unmarkedFrameMPois

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

unmarkedFrameMMO

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

unmarkedFrameOccuMS

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

unmarkedMultFrame

Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object

unmarkedPower-methods

Methods for unmarkedPower objects

unmarkedFramePCO

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

unmarkedFrameOccuMulti

Organize data for the multispecies occupancy model fit by occuMulti

Plot marginal effects of covariates in unmarked models

unmarkedFrameGDR

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

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

unmarkedFramePCount

Organize data for the N-mixture model fit by pcount

unmarkedPowerList

Create or summarize a series of unmarked power analyses

unmarkedRanef-class

Class "unmarkedRanef"

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