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unmarked (version 1.4.3)

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) .

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Install

install.packages('unmarked')

Monthly Downloads

7,038

Version

1.4.3

License

GPL (>= 3)

Homepage

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

Maintainer

Last Published

September 1st, 2024

Functions in unmarked (1.4.3)

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

Cross-validation methods for fitted unmarked models and fit lists

constructor of unmarkedFitList objects

confint-methods

Methods for Function confint in Package `unmarked'

Methods for bracket extraction [ in Package `unmarked'

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

Landscape data for Santa Cruz Island

Open population model for distance sampling data

Distance-sampling detection functions and associated density functions

Bin distance data

Methods for Function fitted in Package `unmarked'

2001 Delaware North American Amphibian Monitoring Program Data

Convert .CSV File to an unmarkedFrame

Convert between wide and long data formats.

Create unmarkedMultFrame from Long Format Data Frame

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

linearComb-methods

Methods for Function linearComb in Package `unmarked'

Simulated line transect data

A function to impute missing entries in continuous obsCovs

Green frog count index data

Generalized multinomial N-mixture model

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

European Jay data from the Swiss Breeding Bird Survey 2002

Fit multi-scale occupancy models

Generalized binomial N-mixture model for repeated count data

Massachusetts North American Amphibian Monitoring Program Data

Create functions to compute multinomial cell probabilities

Methods for Function getFP in Package `unmarked'

Methods for Function getP in Package `unmarked'

Model selection results from an unmarkedFitList

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

Fit N-mixture Time-to-detection Models

Methods for Function getB in Package `unmarked'

Fit the occupancy model using count dta

nonparboot-methods

Nonparametric bootstrapping in unmarked

Fit the MacKenzie et al. (2002) Occupancy Model

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

Multinomial-Poisson Mixtures Model

Open population multinomial N-mixture model

Mallard count data

optimizePenalty-methods

Identify Optimal Penalty Parameter Value

Removal data for the Ovenbird

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) using cross-validation

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

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

Parametric bootstrap method for fitted models inheriting class.

Fit the occupancy model of Royle and Nichols (2003)

Fit Single-Season and Dynamic Multi-State Occupancy Models

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

Fit spatial hierarchical distance sampling model.

Plot marginal effects of covariates in unmarked models

Fit the N-mixture model of Royle (2004)

Extract estimates of random effect terms

Conduct a power analysis for an unmarked model

posteriorSamples

Draw samples from the posterior predictive distribution

Compute multinomial cell probabilities

predict-methods

Methods for Function predict in Package `unmarked'

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

simulate-methods

Methods for Function simulate in Package `unmarked'

Methods for Function ranef in Package unmarked

unmarkedEstimate-class

Class "unmarkedEstimate"

Simulated point-transect data

unmarkedEstimateList-class

Class "unmarkedEstimateList"

Launch a Shiny app to help with power analysis

unmarked-package

Models for Data from Unmarked Animals

Convert sight distance and sight angle to perpendicular distance.

unmarkedFit-class

Class "unmarkedFit"

Extract estimates of random effect standard deviations

unmarkedFitList-class

Class "unmarkedFitList"

unmarkedFrameGDR

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

unmarkedFrameMMO

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

unmarkedFrameOccu

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

unmarkedFrameMPois

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

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.

unmarkedFramePCO

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

Create an unmarkedFrame, or one of its child classes.

unmarkedPowerList

Summarize a series of unmarked power analyses

unmarkedPower-methods

Methods for unmarkedPower objects

unmarkedFrame-class

Class "unmarkedFrame"

unmarkedFrameOccuTTD

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

unmarkedFrameOccuCOP

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

unmarkedFrameOccuFP

Organize data for the single season occupancy models fit by occuFP

unmarkedFrameOccuMS

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

unmarkedFramePCount

Organize data for the N-mixture model fit by pcount

Compute Variance Inflation Factors for an unmarkedFit Object.

unmarkedFrameOccuMulti

Organize data for the multispecies occupancy model fit by occuMulti

unmarkedMultFrame

Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS, or unmarkedFrameGPC object

Methods for Function vcov in Package `unmarked'

unmarkedRanef-class

Class "unmarkedRanef"

Methods for Function SE in Package `unmarked'

Fit the integrated distance sampling model of Kery et al. (2022).

Compute Sum of Squared Residuals for a Model Fit.

Methods for Function coef in Package `unmarked'

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

backTransform-methods

Methods for Function backTransform in Package `unmarked'

computeMPLElambda

Compute the penalty weight for the MPLE penalized likelihood method

BBS Point Count and Occurrence Data from 2 Bird Species

Swiss landscape data

Occupancy data for coyote, red fox, and bobcat