mrds: Mark-Recapture Distance Sampling

Animal abundance estimation via conventional, multiple covariate and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function fitting is performed via maximum likelihood. Also included are diagnostics and plotting for fitted detection functions. Abundance estimation is via a Horvitz-Thompson-like estimator.

AuthorJeff Laake <>, David Borchers <>, Len Thomas <>, David Miller <> and Jon Bishop
Date of publication2016-10-03 22:59:36
MaintainerLaura Marshall <>
LicenseGPL (>= 2)

View on CRAN

Man pages

adj.check.order: Check order of adjustment terms

apex.gamma: Get the apex for a gamma detection function

assign.default.values: Assign default values to list elements that have not been...

assign.par: Extraction and assignment of parameters to vector

average.line: Average detection function line for plotting

average.line.cond: Average conditional detection function line for plotting Golf tee data used in chapter 6 of Advanced Distance Sampling... Find se of average p and N

cdf.ds: Cumulative distribution function (cdf) for fitted distance...

cds: CDS function definition

check.bounds: Check parameters bounds during optimsations

check.mono: Check that a detection function is monotone

coef.ds: Extract coefficients

compute.Nht: Horvitz-Thompson estimates 1/p_i or s_i/p_i

covered.region.dht: Covered region estimate of abundance from...

create.ddfobj: Create detection function object

create.model.frame: Create a model frame for ddf fitting

create.varstructure: Creates structures needed to compute abundance and variance

ddf: Distance Detection Function Fitting

ddf.ds: CDS/MCDS Distance Detection Function Fitting

ddf.gof: Goodness of fit tests for distance sampling models Mark-Recapture Distance Sampling (MRDS) IO - PI Mark-Recapture Distance Sampling (MRDS) IO - FI

ddf.rem: Mark-Recapture Distance Sampling (MRDS) Removal - PI Mark-Recapture Distance Sampling (MRDS) Removal - FI

ddf.trial: Mark-Recapture Distance Sampling (MRDS) Trial Configuration -... Mark-Recapture Analysis of Trial Configuration - FI

DeltaMethod: Numeric Delta Method approximation for the... Fit detection function using key-adjustment functions Fit detection function using key-adjustment functions

det.tables: Observation detection tables

dht: Density and abundance estimates and variances

dht.deriv: Computes abundance estimates at specified parameter values... Variance and confidence intervals for density and abundance...

distpdf: Detection functions

ds.function: Distance Sampling Functions

flnl: Log-likelihood computation for distance sampling data

flt.var: Hessian computation for fitted distance detection function...

g0: Compute value of p(0) using a logit formulation

getpar: Extraction and assignment of parameters to vector

gof.ds: Compute chi-square goodness-of-fit test for ds models

gstdint: Integral of pdf of distances

histline: Plot histogram line

integratedetfct.logistic: Integrate a logistic detection function

integratelogistic.analytic: Analytically integrate logistic detection function

integratepdf: Numerically integrate pdf of observed distances over...

io.glm: Iterative offset GLM/GAM for fitting detection function

is.linear.logistic: Collection of functions for logistic detection functions

is.logistic.constant: Is a logit model constant for all observations?

keyfct.th1: Threshold key function

keyfct.th2: Threshold key function

lfbcvi: Black-capped vireo mark-recapture distance sampling analysis

lfgcwa: Golden-cheeked warbler mark-recapture distance sampling...

logisticbyx: Logistic as a function of covariates

logisticbyz: Logistic as a function of distance

logisticdetfct: Logistic detection function

logisticdupbyx: Logistic for duplicates as a function of covariates

logisticdupbyx_fast: Logistic for duplicates as a function of covariates (fast)

logit: Logit function

mcds: MCDS function definition

mrds-opt: Tips on optimisation issues in 'mrds' models

mrds-package: Mark-Recapture Distance Sampling (mrds)

NCovered: Compute estimated abundance in covered (sampled) region

nlminb_wrapper: Wrapper around 'nlminb'

parse.optimx: Parse optimx results and present a nice object

p.det: Double-platform detection probability

pdot.dsr.integrate.logistic: Compute probability that a object was detected by at least...

plot_cond: Plot conditional detection function from distance sampling...

plot.det.tables: Observation detection tables

plot.ds: Plot fit of detection functions and histograms of data from... Plot fit of detection functions and histograms of data from... Plot fit of detection functions and histograms of data from...

plot.layout: Layout for plot methods in mrds

plot.rem: Plot fit of detection functions and histograms of data from... Plot fit of detection functions and histograms of data from...

plot.trial: Plot fit of detection functions and histograms of data from... Plot fit of detection functions and histograms of data from...

plot_uncond: Plot unconditional detection function from distance sampling...

predict.ds: Predictions from 'mrds' models

print.ddf: Simple pretty printer for distance sampling analyses

print.ddf.gof: Prints results of goodness of fit tests for detection...

print.det.tables: Print results of observer detection tables

print.dht: Prints density and abundance estimates

print.summary.ds: Print summary of distance detection function model object Print summary of distance detection function model object Print summary of distance detection function model object

print.summary.rem: Print summary of distance detection function model object Print summary of distance detection function model object

print.summary.trial: Print summary of distance detection function model object Print summary of distance detection function model object

prob.deriv: Derivatives for variance of average p and average p(0)... Average p and average p(0) variance Process data for fitting distance sampling detection function

pronghorn: Pronghorn aerial survey data from Wyoming

ptdata.distance: Single observer point count data example from Distance

ptdata.dual: Simulated dual observer point count data

ptdata.removal: Simulated removal observer point count data

ptdata.single: Simulated single observer point count data

qqplot.ddf: Q-Q plot, KS and CVM goodness of fit tests for distance...

rem.glm: Iterative offset model fitting of mark-recapture with removal...

rescale_pars: Calculate the parameter rescaling for parameters associated...

setbounds: Set parameter bounds

setcov: Creates design matrix for covariates in detection function

setinitial.ds: Set initial values for detection function based on distance...

sim.mix: Simulation of distance sampling data via mixture models...

stake77: Wooden stake data from 1977 survey

stake78: Wooden stake data from 1978 survey

summary.ds: Summary of distance detection function model object Summary of distance detection function model object Summary of distance detection function model object

summary.rem: Summary of distance detection function model object Summary of distance detection function model object

summary.trial: Summary of distance detection function model object Summary of distance detection function model object

survey.region.dht: Extrapolate Horvitz-Thompson abundance estimates to entire...

test.breaks: Test validity for histogram breaks(cutpoints)

varn: Compute empirical variance of encounter rate

Files in this package

mrds/R/ mrds/R/NCovered.rem.R mrds/R/integratelogisticdup.R mrds/R/adjfct.cos.R mrds/R/gstdint.R mrds/R/check.mono.R mrds/R/ mrds/R/logisticbyz.R mrds/R/logisticdupbyx_fast.R mrds/R/ mrds/R/print.ddf.gof.R mrds/R/adjfct.poly.R mrds/R/create.model.frame.R mrds/R/coef.rem.R mrds/R/summary.rem.R mrds/R/gof.rem.R mrds/R/ mrds/R/ mrds/R/is.linear.logistic.R mrds/R/plot_cond.R mrds/R/compute.Nht.R mrds/R/ mrds/R/ mrds/R/ mrds/R/create.varstructure.R mrds/R/ mrds/R/keyfct.gamma.R mrds/R/dht.R mrds/R/logit.R mrds/R/sethazard.R mrds/R/predict.ds.R mrds/R/scalecheck.R mrds/R/ mrds/R/pks.R mrds/R/scalevalue.R mrds/R/keyfct.hz.R mrds/R/print.summary.trial.R mrds/R/predict.trial.R mrds/R/io.glm.R mrds/R/ mrds/R/ mrds/R/integratedetfct.logistic.R mrds/R/assign.par.R mrds/R/is.logistic.constant.R mrds/R/pdot.dsr.integrate.logistic.R mrds/R/logisticbyx.R mrds/R/print.summary.rem.R mrds/R/integratelogistic.analytic.R
mrds/R/DeltaMethod.R mrds/R/logisticdetfct.R mrds/R/detfct.R mrds/R/ mrds/R/mcds.R mrds/R/ mrds/R/ mrds/R/ mrds/R/ mrds/R/survey.region.dht.R mrds/R/ mrds/R/qqplot.ddf.R mrds/R/ mrds/R/NCovered.trial.R mrds/R/flt.var.R mrds/R/setinitial.ds.R mrds/R/ mrds/R/adjfct.herm.R mrds/R/ mrds/R/average.line.cond.R mrds/R/ddf.R mrds/R/gof.ds.R mrds/R/ mrds/R/ mrds/R/ddf.rem.R mrds/R/g0.R mrds/R/dht.deriv.R mrds/R/ mrds/R/print.ddf.R
mrds/R/ mrds/R/NCovered.R mrds/R/ mrds/R/cdf.ds.R mrds/R/ mrds/R/ mrds/R/integratelogistic.R mrds/R/pcramer.R mrds/R/plot.trial.R mrds/R/ mrds/R/solvecov.R mrds/R/ mrds/R/ mrds/R/rescale_pars.R mrds/R/ mrds/R/ddf.gof.R mrds/R/ mrds/R/ mrds/R/mrds-package.R mrds/R/det.tables.R mrds/R/assign.default.values.R mrds/R/getpar.R
mrds/R/ mrds/R/ mrds/R/coef.ds.R mrds/R/logisticdupbyx.R mrds/R/nlminb_wrapper.R mrds/R/plot.layout.R mrds/R/check.bounds.R mrds/R/plot.rem.R mrds/R/rem.glm.R mrds/R/ddf.ds.R mrds/R/ mrds/R/adj.check.order.R mrds/R/print.dht.R mrds/R/parse.optimx.R mrds/R/summary.ds.R mrds/R/create.ddfobj.R mrds/R/optimx.setup.R mrds/R/ mrds/R/plot_uncond.R mrds/R/ddf.trial.R mrds/R/print.det.tables.R mrds/R/plot.det.tables.R mrds/R/apex.gamma.R mrds/R/sim.mix.R mrds/R/histline.R mrds/R/ mrds/R/test.breaks.R mrds/R/p.det.R mrds/R/cds.R mrds/R/summary.trial.R mrds/R/coef.trial.R mrds/R/setcov.R mrds/R/hermite.poly.R mrds/R/ mrds/R/prob.deriv.R mrds/R/average.line.R mrds/R/model.description.R mrds/R/NCovered.ds.R mrds/R/setbounds.R mrds/R/predict.rem.R mrds/R/flnl.R mrds/R/plot.ds.R mrds/R/zzz.R mrds/R/covered.region.dht.R mrds/R/print.summary.ds.R mrds/R/ mrds/R/varn.R mrds/R/gof.trial.R
mrds/man/gof.ds.Rd mrds/man/stake77.Rd mrds/man/dht.Rd mrds/man/setinitial.ds.Rd mrds/man/is.linear.logistic.Rd mrds/man/mrds-opt.Rd mrds/man/adj.check.order.Rd mrds/man/ mrds/man/logisticdetfct.Rd mrds/man/is.logistic.constant.Rd mrds/man/ mrds/man/print.ddf.gof.Rd mrds/man/lfbcvi.Rd mrds/man/assign.default.values.Rd mrds/man/create.varstructure.Rd mrds/man/ptdata.dual.Rd mrds/man/parse.optimx.Rd mrds/man/check.bounds.Rd mrds/man/compute.Nht.Rd mrds/man/plot.det.tables.Rd mrds/man/ mrds/man/plot.rem.Rd mrds/man/mrds-package.Rd mrds/man/flt.var.Rd mrds/man/print.dht.Rd mrds/man/integratedetfct.logistic.Rd mrds/man/predict.ds.Rd mrds/man/mcds.Rd mrds/man/varn.Rd mrds/man/ptdata.distance.Rd mrds/man/distpdf.Rd mrds/man/ddf.rem.Rd mrds/man/ mrds/man/create.ddfobj.Rd mrds/man/summary.trial.Rd mrds/man/ddf.ds.Rd mrds/man/histline.Rd mrds/man/setbounds.Rd mrds/man/flnl.Rd mrds/man/sim.mix.Rd mrds/man/keyfct.th1.Rd mrds/man/ mrds/man/prob.deriv.Rd mrds/man/ mrds/man/logisticdupbyx.Rd mrds/man/check.mono.Rd mrds/man/ mrds/man/ddf.gof.Rd mrds/man/ mrds/man/assign.par.Rd mrds/man/integratelogistic.analytic.Rd mrds/man/pronghorn.Rd mrds/man/print.summary.ds.Rd mrds/man/ mrds/man/average.line.Rd mrds/man/getpar.Rd mrds/man/plot.trial.Rd mrds/man/NCovered.Rd mrds/man/cdf.ds.Rd mrds/man/stake78.Rd mrds/man/nlminb_wrapper.Rd mrds/man/print.summary.trial.Rd mrds/man/setcov.Rd mrds/man/ mrds/man/summary.rem.Rd mrds/man/ mrds/man/gstdint.Rd mrds/man/logit.Rd mrds/man/plot.ds.Rd mrds/man/logisticbyx.Rd mrds/man/coef.ds.Rd mrds/man/survey.region.dht.Rd mrds/man/ mrds/man/lfgcwa.Rd mrds/man/plot_cond.Rd mrds/man/plot.layout.Rd mrds/man/test.breaks.Rd mrds/man/ mrds/man/det.tables.Rd mrds/man/DeltaMethod.Rd mrds/man/ddf.Rd mrds/man/ mrds/man/print.summary.rem.Rd mrds/man/logisticdupbyx_fast.Rd mrds/man/keyfct.th2.Rd mrds/man/ mrds/man/ mrds/man/ mrds/man/ mrds/man/ mrds/man/apex.gamma.Rd mrds/man/logisticbyz.Rd mrds/man/ptdata.single.Rd mrds/man/rem.glm.Rd mrds/man/average.line.cond.Rd mrds/man/integratepdf.Rd mrds/man/ mrds/man/cds.Rd mrds/man/ mrds/man/print.ddf.Rd mrds/man/io.glm.Rd mrds/man/covered.region.dht.Rd mrds/man/g0.Rd mrds/man/p.det.Rd mrds/man/rescale_pars.Rd mrds/man/ mrds/man/ mrds/man/pdot.dsr.integrate.logistic.Rd mrds/man/print.det.tables.Rd mrds/man/create.model.frame.Rd mrds/man/summary.ds.Rd mrds/man/plot_uncond.Rd mrds/man/ddf.trial.Rd mrds/man/dht.deriv.Rd mrds/man/qqplot.ddf.Rd mrds/man/ds.function.Rd mrds/man/ptdata.removal.Rd

Questions? Problems? Suggestions? or email at

All documentation is copyright its authors; we didn't write any of that.