mrds: Mark-Recapture Distance Sampling
Version 2.1.17

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 <jeff.laake@noaa.gov>, David Borchers <dlb@st-and.ac.uk>, Len Thomas <len.thomas@st-and.ac.uk>, David Miller <dave@ninepointeightone.net> and Jon Bishop
Date of publication2016-10-03 22:59:36
MaintainerLaura Marshall <lhm@st-andrews.ac.uk>
LicenseGPL (>= 2)
Version2.1.17
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("mrds")

Getting started

Package overview
README.md

Popular man pages

book.tee.data: Golf tee data used in chapter 6 of Advanced Distance Sampling...
coef.ds: Extract coefficients
ddf.gof: Goodness of fit tests for distance sampling models
ddf.rem.fi: Mark-Recapture Distance Sampling (MRDS) Removal - FI
dht: Density and abundance estimates and variances
histline: Plot histogram line
lfbcvi: Black-capped vireo mark-recapture distance sampling analysis
See all...

All man pages Function index File listing

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
book.tee.data: Golf tee data used in chapter 6 of Advanced Distance Sampling...
calc.se.Np: 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
ddf.io: Mark-Recapture Distance Sampling (MRDS) IO - PI
ddf.io.fi: Mark-Recapture Distance Sampling (MRDS) IO - FI
ddf.rem: Mark-Recapture Distance Sampling (MRDS) Removal - PI
ddf.rem.fi: Mark-Recapture Distance Sampling (MRDS) Removal - FI
ddf.trial: Mark-Recapture Distance Sampling (MRDS) Trial Configuration -...
ddf.trial.fi: Mark-Recapture Analysis of Trial Configuration - FI
DeltaMethod: Numeric Delta Method approximation for the...
detfct.fit: Fit detection function using key-adjustment functions
detfct.fit.opt: 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...
dht.se: 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.io: Plot fit of detection functions and histograms of data from...
plot.io.fi: 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.rem.fi: Plot fit of detection functions and histograms of data from...
plot.trial: Plot fit of detection functions and histograms of data from...
plot.trial.fi: 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.io: Print summary of distance detection function model object
print.summary.io.fi: Print summary of distance detection function model object
print.summary.rem: Print summary of distance detection function model object
print.summary.rem.fi: Print summary of distance detection function model object
print.summary.trial: Print summary of distance detection function model object
print.summary.trial.fi: Print summary of distance detection function model object
prob.deriv: Derivatives for variance of average p and average p(0)...
prob.se: Average p and average p(0) variance
process.data: 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.io: Summary of distance detection function model object
summary.io.fi: Summary of distance detection function model object
summary.rem: Summary of distance detection function model object
summary.rem.fi: Summary of distance detection function model object
summary.trial: Summary of distance detection function model object
summary.trial.fi: 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

Functions

Files

inst
inst/ONEWS
NAMESPACE
NEWS
data
data/ptdata.distance.rda
data/ptdata.single.rda
data/book.tee.data.rda
data/stake78.rda
data/pronghorn.rda
data/stake77.rda
data/lfgcwa.rda
data/ptdata.dual.rda
data/ptdata.removal.rda
data/lfbcvi.rda
R
R/predict.trial.fi.R
R/NCovered.rem.R
R/integratelogisticdup.R
R/adjfct.cos.R
R/gstdint.R
R/check.mono.R
R/predict.io.fi.R
R/logisticbyz.R
R/logisticdupbyx_fast.R
R/ddf.io.fi.R
R/print.ddf.gof.R
R/adjfct.poly.R
R/create.model.frame.R
R/coef.rem.R
R/summary.rem.R
R/gof.rem.R
R/coef.trial.fi.R
R/summary.rem.fi.R
R/is.linear.logistic.R
R/plot_cond.R
R/compute.Nht.R
R/summary.io.fi.R
R/gof.trial.fi.R
R/keyfct.th.R
R/create.varstructure.R
R/NCovered.io.fi.R
R/keyfct.gamma.R
R/dht.R
R/logit.R
R/sethazard.R
R/predict.ds.R
R/scalecheck.R
R/prob.se.R
R/pks.R
R/scalevalue.R
R/keyfct.hz.R
R/print.summary.trial.R
R/predict.trial.R
R/io.glm.R
R/calc.se.Np.R
R/gof.io.R
R/integratedetfct.logistic.R
R/assign.par.R
R/is.logistic.constant.R
R/pdot.dsr.integrate.logistic.R
R/logisticbyx.R
R/print.summary.rem.R
R/integratelogistic.analytic.R
R/ds.function.r
R/DeltaMethod.R
R/logisticdetfct.R
R/detfct.R
R/ddf.trial.fi.R
R/mcds.R
R/process.data.R
R/ddf.io.R
R/print.summary.io.fi.R
R/print.summary.trial.fi.R
R/survey.region.dht.R
R/dht.se.R
R/qqplot.ddf.R
R/coef.rem.fi.R
R/NCovered.trial.R
R/flt.var.R
R/setinitial.ds.R
R/plot.trial.fi.R
R/adjfct.herm.R
R/summary.io.R
R/average.line.cond.R
R/ddf.R
R/gof.ds.R
R/NCovered.rem.fi.R
R/NCovered.io.R
R/ddf.rem.R
R/g0.R
R/dht.deriv.R
R/print.summary.rem.fi.R
R/print.ddf.R
R/integratepdf.r
R/predict.rem.fi.R
R/NCovered.R
R/detfct.fit.mono.R
R/cdf.ds.R
R/gof.io.fi.R
R/summary.trial.fi.R
R/integratelogistic.R
R/pcramer.R
R/plot.trial.R
R/keyfct.hn.R
R/solvecov.R
R/NCovered.trial.fi.R
R/gof.rem.fi.R
R/rescale_pars.R
R/plot.rem.fi.R
R/ddf.gof.R
R/plot.io.fi.R
R/predict.io.R
R/mrds-package.R
R/det.tables.R
R/assign.default.values.R
R/getpar.R
R/flpt.lnl.r
R/detfct.fit.opt.R
R/ddf.rem.fi.R
R/coef.ds.R
R/logisticdupbyx.R
R/nlminb_wrapper.R
R/plot.layout.R
R/check.bounds.R
R/plot.rem.R
R/rem.glm.R
R/ddf.ds.R
R/detfct.fit.R
R/adj.check.order.R
R/print.dht.R
R/parse.optimx.R
R/summary.ds.R
R/create.ddfobj.R
R/optimx.setup.R
R/coef.io.fi.R
R/plot_uncond.R
R/ddf.trial.R
R/print.det.tables.R
R/plot.det.tables.R
R/apex.gamma.R
R/sim.mix.R
R/histline.R
R/print.summary.io.R
R/test.breaks.R
R/p.det.R
R/cds.R
R/summary.trial.R
R/coef.trial.R
R/setcov.R
R/hermite.poly.R
R/plot.io.R
R/prob.deriv.R
R/average.line.R
R/model.description.R
R/NCovered.ds.R
R/setbounds.R
R/predict.rem.R
R/flnl.R
R/plot.ds.R
R/zzz.R
R/covered.region.dht.R
R/print.summary.ds.R
R/coef.io.R
R/varn.R
R/gof.trial.R
README.md
MD5
DESCRIPTION
man
man/gof.ds.Rd
man/stake77.Rd
man/dht.Rd
man/setinitial.ds.Rd
man/is.linear.logistic.Rd
man/mrds-opt.Rd
man/adj.check.order.Rd
man/process.data.Rd
man/logisticdetfct.Rd
man/is.logistic.constant.Rd
man/print.summary.rem.fi.Rd
man/print.ddf.gof.Rd
man/lfbcvi.Rd
man/assign.default.values.Rd
man/create.varstructure.Rd
man/ptdata.dual.Rd
man/parse.optimx.Rd
man/check.bounds.Rd
man/compute.Nht.Rd
man/plot.det.tables.Rd
man/summary.rem.fi.Rd
man/plot.rem.Rd
man/mrds-package.Rd
man/flt.var.Rd
man/print.dht.Rd
man/integratedetfct.logistic.Rd
man/predict.ds.Rd
man/mcds.Rd
man/varn.Rd
man/ptdata.distance.Rd
man/distpdf.Rd
man/ddf.rem.Rd
man/print.summary.io.fi.Rd
man/create.ddfobj.Rd
man/summary.trial.Rd
man/ddf.ds.Rd
man/histline.Rd
man/setbounds.Rd
man/flnl.Rd
man/sim.mix.Rd
man/keyfct.th1.Rd
man/plot.io.fi.Rd
man/prob.deriv.Rd
man/prob.se.Rd
man/logisticdupbyx.Rd
man/check.mono.Rd
man/calc.se.Np.Rd
man/ddf.gof.Rd
man/ddf.io.fi.Rd
man/assign.par.Rd
man/integratelogistic.analytic.Rd
man/pronghorn.Rd
man/print.summary.ds.Rd
man/summary.trial.fi.Rd
man/average.line.Rd
man/getpar.Rd
man/plot.trial.Rd
man/NCovered.Rd
man/cdf.ds.Rd
man/stake78.Rd
man/nlminb_wrapper.Rd
man/print.summary.trial.Rd
man/setcov.Rd
man/ddf.trial.fi.Rd
man/summary.rem.Rd
man/print.summary.io.Rd
man/gstdint.Rd
man/logit.Rd
man/plot.ds.Rd
man/logisticbyx.Rd
man/coef.ds.Rd
man/survey.region.dht.Rd
man/plot.trial.fi.Rd
man/lfgcwa.Rd
man/plot_cond.Rd
man/plot.layout.Rd
man/test.breaks.Rd
man/plot.rem.fi.Rd
man/det.tables.Rd
man/DeltaMethod.Rd
man/ddf.Rd
man/summary.io.fi.Rd
man/print.summary.rem.Rd
man/logisticdupbyx_fast.Rd
man/keyfct.th2.Rd
man/ddf.rem.fi.Rd
man/print.summary.trial.fi.Rd
man/detfct.fit.Rd
man/dht.se.Rd
man/detfct.fit.opt.Rd
man/apex.gamma.Rd
man/logisticbyz.Rd
man/ptdata.single.Rd
man/rem.glm.Rd
man/average.line.cond.Rd
man/integratepdf.Rd
man/summary.io.Rd
man/cds.Rd
man/ddf.io.Rd
man/print.ddf.Rd
man/io.glm.Rd
man/covered.region.dht.Rd
man/g0.Rd
man/p.det.Rd
man/rescale_pars.Rd
man/plot.io.Rd
man/book.tee.data.Rd
man/pdot.dsr.integrate.logistic.Rd
man/print.det.tables.Rd
man/create.model.frame.Rd
man/summary.ds.Rd
man/plot_uncond.Rd
man/ddf.trial.Rd
man/dht.deriv.Rd
man/qqplot.ddf.Rd
man/ds.function.Rd
man/ptdata.removal.Rd
mrds documentation built on May 19, 2017, 5:49 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

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