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Rdistance (version 2.1.2)

Analyses for Distance-Sampling and Abundance Estimation

Description

Distance-sampling is a popular method for abundance estimation in ecology. This package contains functions and associated routines to analyze distance-sampling data collected on point or line transects. It accommodates line and point transect analyses in one routine that accepts a regression-like formula object. Abundance routines perform automated bootstrapping and automated detection-function selection. Overall (study area) and site-level (transect or point) abundance estimates are available. A large suite of classical, parametric detection functions are included. Some uncommon (e.g., Gamma, negative exponential) detection functions are also included and users can define their own custom detection functions if needed. One form of non-parametric smoothed distance function is included. The help files and vignettes have been vetted by multiple authors and tested in multiple workshop settings.

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install.packages('Rdistance')

Monthly Downloads

498

Version

2.1.2

License

GNU General Public License

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Maintainer

Trent McDonald

Last Published

August 23rd, 2018

Functions in Rdistance (2.1.2)

AIC.dfunc

AICc and related fit statistics for detection function objects
ESW

Effective Strip Width for line transect data
F.maximize.g

Find the coordinate of the maximum of a distance function
RdistanceControls

Control parameters for Rdistance optimization.
abundEstim

Estimate abundance from distance-sampling data
autoDistSamp

Automated classical distance analysis
F.double.obs.prob

Compute double observer probability of detection (No external covariates allowed)
coef.dfunc

Coefficients of an estimated detection function
predict.dfunc

Predict method for dfunc objects
sparrowDetectionData

Brewer's Sparrow detection data (line-transect survey)
sparrowSiteData

Brewer's Sparrow site data (line-transect survey)
print.abund

Print abundance estimates
hermite.expansion

Calculation of Hermite expansion for detection function likelihoods
thrasherDetectionData

Sage Thrasher detection data (point-transect survey)
halfnorm.like

Half-normal likelihood function for distance analyses
dfuncEstim

Estimate a detection function from distance-sampling data
thrasherSiteData

Sage Thrasher site data (point-transect survey)
cosine.expansion

calculation of cosine expansion for detection function likelihoods
integration.constant

Compute the integration constant for distance density functions
hazrate.like

Hazard rate likelihood function for distance analyses
F.nLL

Return the negative log likelihood for a set of distance values
F.start.limits

Set starting values and limits for parameters of Rdistance functions
simple.expansion

Calculate simple polynomial expansion for detection function likelihoods
smu.like

Smoothed likelihood function for distance analyses
estimateN

Abundance point estimates
getDfuncModelFrame

Return model frame for dfunc
Gamma.like

Gamma distance function for distance analyses
Rdistance-package

Rdistance - Distance Sampling Analyses for Abundance Estimation
likeParamNames

Likelihood parameter names
nexexp.like

Negative exponential distance function for distance analyses
perpDists

Compute off-transect distances from sighting distances and angles
uniform.like

Uniform likelihood function for distance analyses
plot.dfunc

Plot a distance (detection) function
print.dfunc

Print a distance function object
secondDeriv

Numeric second derivatives
dfuncSmu

Estimate a non-parametric smooth detection function from distance-sampling data
EDR

Effective Detection Radius (EDR) for estimated detection functions with point transects
effectiveDistance

Calculates the effective sampling distance for estimated detection functions
F.gx.estim

Estimate g(0) or g(x)