R: Density and Abundance from Distance-Sampling Surveys

# Density and Abundance from Distance-Sampling Surveys

## Documentation for package ‘Rdistance’ version 4.4.3

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E G H I L M N O P R S T U V misc

Rdistance-package | Rdistance - Distance Sampling Analyses for Abundance Estimation

## -- A --

abundEstim | Distance Sampling Abundance Estimates
AIC.dfunc | AIC-related fit statistics for detection functions
autoDistSamp | Automated classical distance analysis

## -- B --

bcCI | Bias corrected bootstraps
bootstrap | Perform bootstrap iterations
bspline.expansion | B-spline expansion terms

## -- C --

checkNEvalPts | Check number of numeric integration intervals
checkUnits | Check for the presence of units
coef.dfunc | Coefficients of an estimated detection function
colorize | Add color to result if terminal accepts it
control | Rdistance optimization control parameters.
controls | Rdistance optimization control parameters.
cosine.expansion | Cosine expansion terms

## -- D --

dE.multi | Estimate multiple-observer line-transect distance functions
dE.single | Estimate single-observer line-transect distance function
dfuncEstim | Estimate a distance-based detection function
dfuncEstimErrMessage | dfuncEstim error messages
differentiableLikelihoods | Differentiable likelihoods in Rdistance
distance | Rdistance - Distance Sampling Analyses for Abundance Estimation
distances | Observation distances
dropUnits | Unit assignment helpers

## -- E --

EDR | Effective Detection Radius (EDR) for point transects
effectiveDistance | Effective sampling distances
effort | Effort information
errDataUnk | Unknown error message
estimateN | Abundance point estimates
ESW | Effective Strip Width (ESW) for line transects
expandW | Domain of expansion factors
expansionTerms | Distance function expansion terms

## -- G --

Gamma.like | Gamma distance function
Gamma.start.limits | Gamma.start.limits - Start and limit values for Gamma distance function
GammaModes | Modes of the Gamma distribution
GammaReparam | Reparameterize Gamma parameters for use in dgamma
getNCores | Set number of cores
groupSizes | Group Sizes
gxEstim | Estimate g(0) or g(x)

## -- H --

halfnorm.like | Half-normal distance function
halfnorm.start.limits | Start and limit values for halfnorm distance function
hazrate.like | Hazard rate likelihood
hazrate.start.limits | Start and limit values for hazrate distance function
hermite.expansion | Hermite expansion factors
HookeJeeves | 'nlminb' optimizer
huber.cumFunc | Huber Cumulative Function
huber.like | Huber distance function
huber.start.limits | Start and limit values for the Huber distance function

## -- I --

insertOneStepBreaks | Insert oneStep Likelihood breaks
integrateDfuncs | Integration of distance functions
integrateGammaLines | Integrate Gamma line surveys
integrateHalfnormLines | Integrate Half-normal line surveys
integrateHalfnormPoints | Integrate Half-normal Point transects
integrateHazrateLines | Integrate Hazard-rate line survey distance functions
integrateHuberLines | Integrate Line-transect Huber function
integrateKey | Compute and print distance function integration
integrateNegexpLines | Integrate Negative exponential
integrateNegexpPoints | Integrate Negative exponential point surveys
integrateNumeric | Numeric Integration
integrateOneStepLines | Integrate Line-transect One-step function
integrateOneStepNumeric | Numeric Integration of One-step Function
integrateOneStepPoints | Integrate Point-survey One-step function
integrateTriangleLines | Integrate Line-transect Triangle function
intercept.only | Detect intercept-only distance function
is.points | Tests for point surveys
is.RdistDf | Check RdistDf data frames
is.smoothed | Tests for smoothed distance functions
is.Unitless | Test whether object is unitless

## -- L --

likeParamNames | Likelihood parameter names
line-transect | Rdistance - Distance Sampling Analyses for Abundance Estimation
lines.dfunc | lines.dfunc - Line plotting method for distance functions

## -- M --

maximize.g | Find coordinate of function maximum
mlEstimates | Distance function maximum likelihood estimates
model.matrix.dfunc | Rdistance model matrix

## -- N --

nCovars | Number of covariates
negexp.like | Negative exponential likelihood
negexp.start.limits | Start and limit values for negexp distance function
nLL | Negative log likelihood of distances
Nlminb | 'nlminb' optimizer

## -- O --

observationType | Type of observations
oneBsIter | Calculations for one bootstrap iteration
oneStep.like | Mixture of two uniforms likelihood
oneStep.start.limits | oneStep likelihood start and limit values
Optim | 'optim' optimizer

## -- P --

parseModel | Parse Rdistance model
perpDists | Compute off-transect distances from sighting distances and angles
plot.dfunc | Plot method for distance (detection) functions
plot.dfunc.para | Plot parametric distance functions
point-transect | Rdistance - Distance Sampling Analyses for Abundance Estimation
predDensity | Density on transects
predDfuncs | Predict distance functions
predict.dfunc | Predict distance functions
predLikelihood | Distance function values at observations
print.abund | Print abundance estimates
print.dfunc | Print method for distance function object

## -- R --

Rdistance | Rdistance - Distance Sampling Analyses for Abundance Estimation
RdistanceControls | Rdistance optimization control parameters.
RdistDf | Construct Rdistance nested data frames

## -- S --

secondDeriv | Numeric second derivatives
setOptimizer | Set optimizing routine
setUnits | Unit assignment helpers
simple.expansion | Simple polynomial expansion factors
simpsonCoefs | Simpson numerical integration coefficients
sine.expansion | Sine expansion terms
sparrowDetectionData | Brewer's Sparrow detection data
sparrowDf | Brewer's Sparrow detection data frame in Rdistance >4.0.0 format.
sparrowDfuncObserver | Brewer's Sparrow detection function
sparrowSiteData | Brewer's Sparrow site data
startLimits | Distance function starting values and limits
summary.abund | Summarize abundance estimates
summary.dfunc | Summarize a distance function object
summary.rowwise_df | Summary method for Rdistance data frames

## -- T --

thrasherDetectionData | Sage Thrasher detection data
thrasherDf | Sage Thrasher detection data frame in Rdistance >4.0.0 format
thrasherSiteData | Sage Thrasher site data.
transectType | Type of transects
triangle.like | Mixture of triangle and uniform likelihood
triangle.start.limits | triangle likelihood start and limit values

## -- U --

unitHelpers | Unit assignment helpers
unnest | Unnest an RdistDf data frame

## -- V --

varcovarEstim | Estimate variance-covariance

## -- misc --

%#% | Unit assignment helpers
%acre% | Unit assignment helpers
%cm% | Unit assignment helpers
%ft% | Unit assignment helpers
%ha% | Unit assignment helpers
%inches% | Unit assignment helpers
%km% | Unit assignment helpers
%km^2% | Unit assignment helpers
%m% | Unit assignment helpers
%mi% | Unit assignment helpers
%mi^2% | Unit assignment helpers
%m^2% | Unit assignment helpers
%yd% | Unit assignment helpers