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Rdistance (version 3.0.0)

Distance-Sampling Analyses for Density and Abundance Estimation

Description

Distance-sampling analyses estimate density and abundance of organisms in ecology when detection probability declines with increasing distance from the observers. Distance-sampling is popular in most branches of ecology and especially when organisms are observed from aerial platforms (e.g., airplane or drone), surface vessels (e.g., boat or truck), or along walking transects. Rdistance analyzes data collected on both point and line transects, estimates overall (study area) and site-level (transect or point) density, and allows users to specify regression-like formula (similar to lm or glm) for covariates. A large suite of classical, parametric detection functions are included along with some uncommon parametric functions (e.g., Gamma, negative exponential) and non-parametric smoothed distance functions. Custom (user-defined) detection functions can be implemented (see vignette). Measurement unit integrity is enforced with internal unit conversion when necessary. The help files and vignettes have been vetted by multiple authors and tested in workshop settings.

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install.packages('Rdistance')

Monthly Downloads

483

Version

3.0.0

License

GNU General Public License

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Maintainer

Trent McDonald

Last Published

June 13th, 2023

Functions in Rdistance (3.0.0)

F.double.obs.prob

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

Line transect Effective Strip Width (ESW)
Gamma.like

Gamma.like - Gamma distance function
AIC.dfunc

AICc and related fit statistics for detection function objects
EDR

Effective Detection Radius (EDR) for estimated detection functions with point transects
F.gx.estim

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

Gamma.start.limits - Start and limit values for Gamma parameters.
F.maximize.g

Find the coordinate of the maximum of a distance function
dfuncSmu

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

Estimate abundance from distance-sampling data
colorize

colorize - Add color to result if terminal accepts it
autoDistSamp

Automated classical distance analysis
coef.dfunc

Coefficients of an estimated detection function
effectiveDistance

Calculates the effective sampling distance for estimated detection functions
cosine.expansion

calculation of cosine expansion for detection function likelihoods
dfuncEstim

Estimate a detection function from distance-sampling data
RdistanceControls

Control parameters for Rdistance optimization.
Rdistance-package

Rdistance - Distance Sampling Analyses for Abundance Estimation
hermite.expansion

Calculation of Hermite expansion for detection function likelihoods
estimateN

Abundance point estimates
isUnitless

isUnitless - Test whether object is unitless
likeParamNames

Likelihood parameter names
integration.constant

Compute the integration constant for distance density functions
lines.dfunc

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

logistic.like - Logistic distance function likelihood
getDfuncModelFrame

Return model frame for dfunc
print.dfunc

Print a distance function object
logistic.start.limits

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

negexp.like - Negative exponential distance function
secondDeriv

Numeric second derivatives
thrasherDetectionData

Sage Thrasher detection data
thrasherSiteData

thrasherSiteData - Sage Thrasher site data.
uniform.like

uniform.like - Uniform distance likelihood
plot.dfunc

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

Compute off-transect distances from sighting distances and angles
sparrowDetectionData

Brewer's Sparrow detection data
uniform.start.limits

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

Brewer's Sparrow site data
halfnorm.like

Half-normal likelihood function for distance analyses
hazrate.like

hazrate.like - Hazard rate likelihood
predict.dfunc

Predict method for dfunc objects
print.abund

Print abundance estimates
simple.expansion

Calculate simple polynomial expansion for detection function likelihoods
smu.like

Smoothed 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