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Rdistance (version 3.1.4)

Distance-Sampling Analyses for Density and Abundance Estimation

Description

Distance-sampling analyses () estimate density and abundance of survey targets (e.g., animals) when detection declines with distance. Distance-sampling is popular ecology, especially when survey targets are observed from aerial platforms (e.g., airplane or drone), surface vessels (e.g., boat or truck), or along walking transects. Both point and line transects can be analyzed. Outputs include overall (study area) density and abundance, effective sampling distances, and model fit statistics. A large suite of classical, parametric detection functions (e.g., half-normal, hazard rate) is included along with uncommon parametric functions (e.g., Gamma, negative exponential). Non-parametric smoothed distance functions are included. Measurement unit integrity is enforced via internal unit conversion. The help files and vignettes have been vetted by multiple authors and tested in workshop settings.

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Install

install.packages('Rdistance')

Monthly Downloads

483

Version

3.1.4

License

GNU General Public License

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Maintainer

Trent McDonald

Last Published

March 11th, 2025

Functions in Rdistance (3.1.4)

cosine.expansion

calculation of cosine expansion for detection function likelihoods
autoDistSamp

Automated classical distance analysis
Rdistance-package

Rdistance - Distance Sampling Analyses for Abundance Estimation
abundEstim

Estimate abundance from distance-sampling data
colorize

colorize - Add color to result if terminal accepts it
RdistanceControls

Control parameters for Rdistance optimization.
effectiveDistance

Calculates the effective sampling distance for estimated detection functions
dfuncEstim

Estimate a detection function from distance-sampling data
coef.dfunc

Coefficients of an estimated detection function
dfuncSmu

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

isUnitless - Test whether object is unitless
hazrate.like

hazrate.like - Hazard rate likelihood
logistic.like

logistic.like - Logistic distance function likelihood
getDfuncModelFrame

Return model frame for dfunc
lines.dfunc

lines.dfunc - Lines method for distance (detection) functions
likeParamNames

Likelihood parameter names
hermite.expansion

Calculation of Hermite expansion for detection function likelihoods
halfnorm.like

Half-normal likelihood function for distance analyses
integration.constant

Compute the integration constant for distance density functions
estimateN

Abundance point estimates
perpDists

Compute off-transect distances from sighting distances and angles
secondDeriv

Numeric second derivatives
print.dfunc

Print a distance function object
simple.expansion

Calculate simple polynomial expansion for detection function likelihoods
uniform.like

uniform.like - Uniform distance likelihood
uniform.start.limits

uniform.start.limits - Start and limit values for uniform distance function
plot.dfunc

plot.dfunc - Plot method for distance (detection) functions
smu.like

Smoothed likelihood function for distance analyses
sparrowSiteData

Brewer's Sparrow site data
sparrowDetectionData

Brewer's Sparrow detection data
logistic.start.limits

logistic.start.limits - Start and limit values for logistic distance function
thrasherDetectionData

Sage Thrasher detection data
negexp.like

negexp.like - Negative exponential distance function
summary.abund

Summarize abundance estimates
summary.dfunc

Summarize a distance function object
thrasherSiteData

thrasherSiteData - Sage Thrasher site data.
print.abund

Print abundance estimates
predict.dfunc

Predict method for dfunc objects
EDR

Effective Detection Radius (EDR) for estimated detection functions with point transects
Gamma.start.limits

Gamma.start.limits - Start and limit values for Gamma parameters.
Gamma.like

Gamma.like - Gamma distance function
F.nLL

Return the negative log likelihood for a set of distance values
F.double.obs.prob

Compute double observer probability of detection (No external covariates allowed)
ESW

Line transect Effective Strip Width (ESW)
F.gx.estim

F.gx.estim - Estimate g(0) or g(x)
F.start.limits

Set starting values and limits for parameters of Rdistance functions
AIC.dfunc

AICc and related fit statistics for detection function objects
F.maximize.g

Find the coordinate of the maximum of a distance function