Man pages for DistanceDevelopment/mrds
Mark-Recapture Distance Sampling

adj.check.orderCheck order of adjustment terms
apex.gammaGet the apex for a gamma detection function
assign.default.valuesAssign default values to list elements that have not been...
assign.parExtraction and assignment of parameters to vector
average.lineAverage detection function line for plotting
average.line.condAverage conditional detection function line for plotting
book.tee.dataGolf tee data used in chapter 6 of Advanced Distance Sampling...
calc.se.NpFind se of average p and N
cdf.dsCumulative distribution function (cdf) for fitted distance...
cdsCDS function definition
check.boundsCheck parameters bounds during optimsations
check.monoCheck that a detection function is monotone
coef.dsExtract coefficients
compute.NhtHorvitz-Thompson estimates 1/p_i or s_i/p_i
covered.region.dhtCovered region estimate of abundance from...
create.binsCreate bins from a set of binned distances and a set of...
create.ddfobjCreate detection function object
create.model.frameCreate a model frame for ddf fitting
create.varstructureCreates structures needed to compute abundance and variance
ddfDistance Detection Function Fitting
ddf.dsCDS/MCDS Distance Detection Function Fitting
ddf.gofGoodness of fit tests for distance sampling models
ddf.ioMark-Recapture Distance Sampling (MRDS) IO - PI
ddf.io.fiMark-Recapture Distance Sampling (MRDS) IO - FI
ddf.remMark-Recapture Distance Sampling (MRDS) Removal - PI
ddf.rem.fiMark-Recapture Distance Sampling (MRDS) Removal - FI
ddf.trialMark-Recapture Distance Sampling (MRDS) Trial Configuration -...
ddf.trial.fiMark-Recapture Analysis of Trial Configuration - FI
DeltaMethodNumeric Delta Method approximation for the...
detfct.fitFit detection function using key-adjustment functions
detfct.fit.optFit detection function using key-adjustment functions
det.tablesObservation detection tables
dhtDensity and abundance estimates and variances
dht.derivComputes abundance estimates at specified parameter values...
dht.seVariance and confidence intervals for density and abundance...
distpdfDetection functions
ds.functionDistance Sampling Functions
flnlLog-likelihood computation for distance sampling data
flt.varHessian computation for fitted distance detection function...
g0Compute value of p(0) using a logit formulation
getparExtraction and assignment of parameters to vector
gof.dsCompute chi-square goodness-of-fit test for ds models
gstdintIntegral of pdf of distances
histlinePlot histogram line
integratedetfct.logisticIntegrate a logistic detection function
integratelogistic.analyticAnalytically integrate logistic detection function
integratepdfNumerically integrate pdf of observed distances over...
io.glmIterative offset GLM/GAM for fitting detection function
is.linear.logisticCollection of functions for logistic detection functions
is.logistic.constantIs a logit model constant for all observations?
keyfct.th1Threshold key function
keyfct.th2Threshold key function
lfbcviBlack-capped vireo mark-recapture distance sampling analysis
lfgcwaGolden-cheeked warbler mark-recapture distance sampling...
logisticbyxLogistic as a function of covariates
logisticbyzLogistic as a function of distance
logisticdetfctLogistic detection function
logisticdupbyxLogistic for duplicates as a function of covariates
logisticdupbyx_fastLogistic for duplicates as a function of covariates (fast)
logitLogit function
mcdsMCDS function definition
mrds-optTips on optimisation issues in 'mrds' models
mrds-packageMark-Recapture Distance Sampling (mrds)
NCoveredCompute estimated abundance in covered (sampled) region
nlminb_wrapperWrapper around 'nlminb'
parse.optimxParse optimx results and present a nice object
p.detDouble-platform detection probability
pdot.dsr.integrate.logisticCompute probability that a object was detected by at least...
plot_condPlot conditional detection function from distance sampling...
plot.det.tablesObservation detection tables
plot.dsPlot fit of detection functions and histograms of data from...
plot.ioPlot fit of detection functions and histograms of data from...
plot.io.fiPlot fit of detection functions and histograms of data from...
plot.layoutLayout for plot methods in mrds
plot.remPlot fit of detection functions and histograms of data from...
plot.rem.fiPlot fit of detection functions and histograms of data from...
plot.trialPlot fit of detection functions and histograms of data from...
plot.trial.fiPlot fit of detection functions and histograms of data from...
plot_uncondPlot unconditional detection function from distance sampling...
predict.dsPredictions from 'mrds' models
print.ddfSimple pretty printer for distance sampling analyses
print.ddf.gofPrints results of goodness of fit tests for detection...
print.det.tablesPrint results of observer detection tables
print.dhtPrints density and abundance estimates
print.summary.dsPrint summary of distance detection function model object
print.summary.ioPrint summary of distance detection function model object
print.summary.io.fiPrint summary of distance detection function model object
print.summary.remPrint summary of distance detection function model object
print.summary.rem.fiPrint summary of distance detection function model object
print.summary.trialPrint summary of distance detection function model object
print.summary.trial.fiPrint summary of distance detection function model object
prob.derivDerivatives for variance of average p and average p(0)...
prob.seAverage p and average p(0) variance
process.dataProcess data for fitting distance sampling detection function
pronghornPronghorn aerial survey data from Wyoming
ptdata.distanceSingle observer point count data example from Distance
ptdata.dualSimulated dual observer point count data
ptdata.removalSimulated removal observer point count data
ptdata.singleSimulated single observer point count data
qqplot.ddfQuantile-quantile plot and goodness of fit tests for...
rem.glmIterative offset model fitting of mark-recapture with removal...
rescale_parsCalculate the parameter rescaling for parameters associated...
sample_ddfGenerate data from a fitted detection function and refit the...
setboundsSet parameter bounds
setcovCreates design matrix for covariates in detection function
setinitial.dsSet initial values for detection function based on distance...
sim.mixSimulation of distance sampling data via mixture models...
stake77Wooden stake data from 1977 survey
stake78Wooden stake data from 1978 survey
summary.dsSummary of distance detection function model object
summary.ioSummary of distance detection function model object
summary.io.fiSummary of distance detection function model object
summary.remSummary of distance detection function model object
summary.rem.fiSummary of distance detection function model object
summary.trialSummary of distance detection function model object
summary.trial.fiSummary of distance detection function model object
survey.region.dhtExtrapolate Horvitz-Thompson abundance estimates to entire...
test.breaksTest validity for histogram breaks(cutpoints)
varnCompute empirical variance of encounter rate
DistanceDevelopment/mrds documentation built on Nov. 20, 2017, 2:51 a.m.