Package: Rdistance 4.4.4

Rdistance: Density and Abundance from Distance-Sampling Surveys

Distance-sampling (<doi:10.1007/978-3-319-19219-2>) is a field survey and analytical method that estimates density and abundance of survey targets (e.g., animals) when detection probability declines with observation distance. Distance-sampling is popular in 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. Analysis involves fitting smooth (parametric) curves to histograms of observation distances and using those functions to adjust density estimates for missed targets. Routines included here fit curves to observation distance histograms, estimate effective sampling area, density of targets in surveyed areas, and the abundance of targets in a surrounding study area. Confidence interval estimation uses built-in bootstrap resampling. Help files are extensive and have been vetted by multiple authors. Many tutorials are available on the package's website (URL below).

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_4.4.4.tar.gz
Rdistance_4.4.4.zip(r-4.7)Rdistance_4.4.4.zip(r-4.6)Rdistance_4.4.4.zip(r-4.5)
Rdistance_4.4.4.tgz(r-4.6-any)Rdistance_4.4.4.tgz(r-4.5-any)
Rdistance_4.4.4.tar.gz(r-4.7-any)Rdistance_4.4.4.tar.gz(r-4.6-any)
Rdistance_4.4.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
Rdistance/json (API)
NEWS

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

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

Datasets:

On CRAN:

Conda:

6.30 score 11 stars 40 scripts 702 downloads 1 mentions 92 exports 36 dependencies

Last updated from:ee15622074. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK140
source / vignettesOK245
linux-release-x86_64OK141
macos-release-arm64OK212
macos-oldrel-arm64OK147
windows-develOK107
windows-releaseOK150
windows-oldrelOK92
wasm-releaseOK105

Exports:%#%%acre%%cm%%ft%%ha%%inches%%km%%km^2%%m%%m^2%%mi%%mi^2%%yd%abundEstimautoDistSampbcCIbootstrapbspline.expansioncheckUnitscosine.expansiondE.multidE.singledfuncEstimdifferentiableLikelihoodsdistancesdropUnitsEDReffectiveDistanceeffortestimateNESWexpandWexpansionTermsGamma.likeGamma.start.limitsGammaModesGammaReparamgroupSizesgxEstimhalfnorm.likehalfnorm.start.limitshazrate.likehazrate.start.limitshermite.expansionhuber.cumFunchuber.likehuber.start.limitsintegrateDfuncsintegrateGammaLinesintegrateHalfnormLinesintegrateHalfnormPointsintegrateHazrateLinesintegrateHuberLinesintegrateNegexpLinesintegrateNegexpPointsintegrateNumericintegrateOneStepLinesintegrateOneStepNumericintegrateOneStepPointsintegrateTriangleLinesis.pointsis.RdistDfis.smoothedis.UnitlesslikeParamNamesmaximize.gmlEstimatesnegexp.likenegexp.start.limitsnLLobservationTypeoneBsIteroneStep.likeoneStep.start.limitsparseModelperpDistspredDensitypredDfuncspredLikelihoodRdistDfsecondDerivsetOptimizersetUnitssimple.expansionsimpsonCoefssine.expansionstartLimitstransectTypetriangle.liketriangle.start.limitsunnestvarcovarEstim

Dependencies:callrclicpp11crayondfoptimdplyrexpintgenericsgluehmslifecyclemagrittrmultidplyrotelpillarpkgconfigprettyunitsprocessxprogresspspurrrqs2R6RcppRcppParallelrlangstringfishstringistringrtibbletidyrtidyselectunitsutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
Rdistance - Distance Sampling Analyses for Abundance EstimationRdistance-package distance line-transect point-transect Rdistance
Unit assignment helpers%#% %acre% %cm% %ft% %ha% %inches% %km% %km^2% %m% %mi% %mi^2% %m^2% %yd% dropUnits setUnits unitHelpers
Distance Sampling Abundance EstimatesabundEstim
AIC-related fit statistics for detection functionsAIC.dfunc
Automated classical distance analysisautoDistSamp
Bias corrected bootstrapsbcCI
Perform bootstrap iterationsbootstrap
B-spline expansion termsbspline.expansion
Check number of numeric integration intervalscheckNEvalPts
Check for the presence of unitscheckUnits
Coefficients of an estimated detection functioncoef.dfunc
Add color to result if terminal accepts itcolorize
Cosine expansion termscosine.expansion
Estimate multiple-observer line-transect distance functionsdE.multi
Estimate single-observer line-transect distance functiondE.single
Estimate a distance-based detection functiondfuncEstim
dfuncEstim error messagesdfuncEstimErrMessage
Differentiable likelihoods in RdistancedifferentiableLikelihoods
Observation distancesdistances
Effective Detection Radius (EDR) for point transectsEDR
Effective sampling distanceseffectiveDistance
Effort informationeffort
Unknown error messageerrDataUnk
Abundance point estimatesestimateN
Effective Strip Width (ESW) for line transectsESW
Domain of expansion factorsexpandW
Distance function expansion termsexpansionTerms
Gamma distance functionGamma.like
Gamma.start.limits - Start and limit values for Gamma distance functionGamma.start.limits
Modes of the Gamma distributionGammaModes
Reparameterize Gamma parameters for use in dgammaGammaReparam
Set number of coresgetNCores
Group SizesgroupSizes
Estimate g(0) or g(x)gxEstim
Half-normal distance functionhalfnorm.like
Start and limit values for halfnorm distance functionhalfnorm.start.limits
Hazard rate likelihoodhazrate.like
Start and limit values for hazrate distance functionhazrate.start.limits
Hermite expansion factorshermite.expansion
'nlminb' optimizerHookeJeeves
Huber Cumulative Functionhuber.cumFunc
Huber distance functionhuber.like
Start and limit values for the Huber distance functionhuber.start.limits
Insert oneStep Likelihood breaksinsertOneStepBreaks
Integration of distance functionsintegrateDfuncs
Integrate Gamma line surveysintegrateGammaLines
Integrate Half-normal line surveysintegrateHalfnormLines
Integrate Half-normal Point transectsintegrateHalfnormPoints
Integrate Hazard-rate line survey distance functionsintegrateHazrateLines
Integrate Line-transect Huber functionintegrateHuberLines
Compute and print distance function integrationintegrateKey
Integrate Negative exponentialintegrateNegexpLines
Integrate Negative exponential point surveysintegrateNegexpPoints
Numeric IntegrationintegrateNumeric
Integrate Line-transect One-step functionintegrateOneStepLines
Numeric Integration of One-step FunctionintegrateOneStepNumeric
Integrate Point-survey One-step functionintegrateOneStepPoints
Integrate Line-transect Triangle functionintegrateTriangleLines
Detect intercept-only distance functionintercept.only
Tests for point surveysis.points
Check RdistDf data framesis.RdistDf
Tests for smoothed distance functionsis.smoothed
Test whether object is unitlessis.Unitless
Likelihood parameter nameslikeParamNames
lines.dfunc - Line plotting method for distance functionslines.dfunc
Find coordinate of function maximummaximize.g
Distance function maximum likelihood estimatesmlEstimates
Rdistance model matrixmodel.matrix.dfunc
Number of covariatesnCovars
Negative exponential likelihoodnegexp.like
Start and limit values for negexp distance functionnegexp.start.limits
Negative log likelihood of distancesnLL
'nlminb' optimizerNlminb
Type of observationsobservationType
Calculations for one bootstrap iterationoneBsIter
Mixture of two uniforms likelihoodoneStep.like
oneStep likelihood start and limit valuesoneStep.start.limits
'optim' optimizerOptim
Parse Rdistance modelparseModel
Compute off-transect distances from sighting distances and anglesperpDists
Plot method for distance (detection) functionsplot.dfunc
Plot parametric distance functionsplot.dfunc.para
Density on transectspredDensity
Predict distance functionspredDfuncs
Predict distance functionspredict.dfunc
Distance function values at observationspredLikelihood
Print abundance estimatesprint.abund
Print method for distance function objectprint.dfunc
Rdistance optimization control parameters.control controls RdistanceControls
Construct Rdistance nested data framesRdistDf
Numeric second derivativessecondDeriv
Set optimizing routinesetOptimizer
Simple polynomial expansion factorssimple.expansion
Simpson numerical integration coefficientssimpsonCoefs
Sine expansion termssine.expansion
Brewer's Sparrow detection datasparrowDetectionData
Brewer's Sparrow detection data frame in Rdistance >4.0.0 format.sparrowDf
Brewer's Sparrow detection functionsparrowDfuncObserver
Brewer's Sparrow site datasparrowSiteData
Distance function starting values and limitsstartLimits
Summarize abundance estimatessummary.abund
Summarize a distance function objectsummary.dfunc
Summary method for Rdistance data framessummary.rowwise_df
Sage Thrasher detection datathrasherDetectionData
Sage Thrasher detection data frame in Rdistance >4.0.0 formatthrasherDf
Sage Thrasher site data.thrasherSiteData
Type of transectstransectType
Mixture of triangle and uniform likelihoodtriangle.like
triangle likelihood start and limit valuestriangle.start.limits
Unnest an RdistDf data frameunnest
Estimate variance-covariancevarcovarEstim