Package: Rdistance 3.1.2

Rdistance: Distance-Sampling Analyses for Density and Abundance Estimation

Distance-sampling analyses (Buckland et al., (2015) <doi:10.1007/978-3-319-19219-2>) 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.

Authors:Trent McDonald [cre, aut], Jason Carlisle [aut], Aidan McDonald [aut], Ryan Nielson [ctb], Ben Augustine [ctb], James Griswald [ctb], Patrick McKann [ctb], Lacey Jeroue [ctb], Hoffman Abigail [ctb], Kleinsausser Michael [ctb], Joel Reynolds [ctb], Pham Quang [ctb], Earl Becker [ctb], Aaron Christ [ctb], Brook Russelland [ctb], Stefan Emmons [ctb], Will McDonald [ctb], Reid Olson [ctb]

Rdistance_3.1.2.tar.gz
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Rdistance.pdf |Rdistance.html
Rdistance/json (API)
NEWS

# Install 'Rdistance' in R:
install.packages('Rdistance', repos = c('https://tmcd82070.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/tmcd82070/rdistance/issues

Datasets:

On CRAN:

32 exports 8 stars 1.92 score 3 dependencies 1 mentions 39 scripts 253 downloads

Last updated 5 months agofrom:8b75358911. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 05 2024
R-4.5-winERRORSep 05 2024
R-4.5-linuxERRORSep 05 2024
R-4.4-winERRORSep 05 2024
R-4.4-macERRORSep 05 2024
R-4.3-winERRORSep 05 2024
R-4.3-macERRORSep 05 2024

Exports:abundEstimautoDistSampcosine.expansiondfuncEstimdfuncSmuEDReffectiveDistanceestimateNESWF.double.obs.probF.gx.estimF.maximize.gF.nLLF.start.limitsGamma.likeGamma.start.limitshalfnorm.likehazrate.likehermite.expansionintegration.constantisUnitlesslikeParamNameslogistic.likelogistic.start.limitsnegexp.likeperpDistsRdistanceControlssecondDerivsimple.expansionsmu.likeuniform.likeuniform.start.limits

Dependencies:crayonRcppunits

Beginner's Guide to Rdistance Line-Transect Analysis

Rendered fromRdistance_BeginnerLineTransect.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2023-06-12
Started: 2023-03-27

Extended dfuncEstim examples

Rendered fromExtended_dfuncEstim_Examples.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2023-06-13
Started: 2023-05-19

Readme and manuals

Help Manual

Help pageTopics
Rdistance - Distance Sampling Analyses for Abundance EstimationRdistance-package distance line-transect point-transect Rdistance
Estimate abundance from distance-sampling dataabundEstim
AICc and related fit statistics for detection function objectsAIC.dfunc
Automated classical distance analysisautoDistSamp
Coefficients of an estimated detection functioncoef.dfunc
colorize - Add color to result if terminal accepts itcolorize
calculation of cosine expansion for detection function likelihoodscosine.expansion
Estimate a detection function from distance-sampling datadfuncEstim
Estimate a non-parametric smooth detection function from distance-sampling datadfuncSmu
Effective Detection Radius (EDR) for estimated detection functions with point transectsEDR
Calculates the effective sampling distance for estimated detection functionseffectiveDistance
Abundance point estimatesestimateN
Line transect Effective Strip Width (ESW)ESW
Compute double observer probability of detection (No external covariates allowed)F.double.obs.prob
F.gx.estim - Estimate g(0) or g(x)F.gx.estim
Find the coordinate of the maximum of a distance functionF.maximize.g
Return the negative log likelihood for a set of distance valuesF.nLL
Set starting values and limits for parameters of Rdistance functionsF.start.limits
Gamma.like - Gamma distance functionGamma.like
Gamma.start.limits - Start and limit values for Gamma parameters.Gamma.start.limits
Return model frame for dfuncgetDfuncModelFrame
Half-normal likelihood function for distance analyseshalfnorm.like
hazrate.like - Hazard rate likelihoodhazrate.like
Calculation of Hermite expansion for detection function likelihoodshermite.expansion
Compute the integration constant for distance density functionsintegration.constant
isUnitless - Test whether object is unitlessisUnitless
Likelihood parameter nameslikeParamNames
lines.dfunc - Lines method for distance (detection) functionslines.dfunc
logistic.like - Logistic distance function likelihoodlogistic.like
logistic.start.limits - Start and limit values for logistic distance functionlogistic.start.limits
negexp.like - Negative exponential distance functionnegexp.like
Compute off-transect distances from sighting distances and anglesperpDists
plot.dfunc - Plot method for distance (detection) functionsplot.dfunc
Predict method for dfunc objectspredict.dfunc
Print abundance estimatesprint.abund
Print a distance function objectprint.dfunc
Control parameters for 'Rdistance' optimization.RdistanceControls
Numeric second derivativessecondDeriv
Calculate simple polynomial expansion for detection function likelihoodssimple.expansion
Smoothed likelihood function for distance analysessmu.like
Brewer's Sparrow detection datasparrowDetectionData
Brewer's Sparrow site datasparrowSiteData
Summarize abundance estimatessummary.abund
Summarize a distance function objectsummary.dfunc
Sage Thrasher detection datathrasherDetectionData
thrasherSiteData - Sage Thrasher site data.thrasherSiteData
uniform.like - Uniform distance likelihooduniform.like
uniform.start.limits - Start and limit values for uniform distance functionuniform.start.limits