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 <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

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

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

Files in this package

mrds
mrds/inst
mrds/inst/ONEWS
mrds/NAMESPACE
mrds/NEWS
mrds/data
mrds/data/ptdata.distance.rda
mrds/data/ptdata.single.rda
mrds/data/book.tee.data.rda
mrds/data/stake78.rda
mrds/data/pronghorn.rda
mrds/data/stake77.rda
mrds/data/lfgcwa.rda
mrds/data/ptdata.dual.rda
mrds/data/ptdata.removal.rda
mrds/data/lfbcvi.rda
mrds/R
mrds/R/predict.trial.fi.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/predict.io.fi.R mrds/R/logisticbyz.R mrds/R/logisticdupbyx_fast.R mrds/R/ddf.io.fi.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/coef.trial.fi.R mrds/R/summary.rem.fi.R mrds/R/is.linear.logistic.R mrds/R/plot_cond.R mrds/R/compute.Nht.R mrds/R/summary.io.fi.R mrds/R/gof.trial.fi.R mrds/R/keyfct.th.R mrds/R/create.varstructure.R mrds/R/NCovered.io.fi.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/prob.se.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/calc.se.Np.R mrds/R/gof.io.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/ds.function.r
mrds/R/DeltaMethod.R mrds/R/logisticdetfct.R mrds/R/detfct.R mrds/R/ddf.trial.fi.R mrds/R/mcds.R mrds/R/process.data.R mrds/R/ddf.io.R mrds/R/print.summary.io.fi.R mrds/R/print.summary.trial.fi.R mrds/R/survey.region.dht.R mrds/R/dht.se.R mrds/R/qqplot.ddf.R mrds/R/coef.rem.fi.R mrds/R/NCovered.trial.R mrds/R/flt.var.R mrds/R/setinitial.ds.R mrds/R/plot.trial.fi.R mrds/R/adjfct.herm.R mrds/R/summary.io.R mrds/R/average.line.cond.R mrds/R/ddf.R mrds/R/gof.ds.R mrds/R/NCovered.rem.fi.R mrds/R/NCovered.io.R mrds/R/ddf.rem.R mrds/R/g0.R mrds/R/dht.deriv.R mrds/R/print.summary.rem.fi.R mrds/R/print.ddf.R
mrds/R/integratepdf.r
mrds/R/predict.rem.fi.R mrds/R/NCovered.R mrds/R/detfct.fit.mono.R mrds/R/cdf.ds.R mrds/R/gof.io.fi.R mrds/R/summary.trial.fi.R mrds/R/integratelogistic.R mrds/R/pcramer.R mrds/R/plot.trial.R mrds/R/keyfct.hn.R mrds/R/solvecov.R mrds/R/NCovered.trial.fi.R mrds/R/gof.rem.fi.R mrds/R/rescale_pars.R mrds/R/plot.rem.fi.R mrds/R/ddf.gof.R mrds/R/plot.io.fi.R mrds/R/predict.io.R mrds/R/mrds-package.R mrds/R/det.tables.R mrds/R/assign.default.values.R mrds/R/getpar.R
mrds/R/flpt.lnl.r
mrds/R/detfct.fit.opt.R mrds/R/ddf.rem.fi.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/detfct.fit.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/coef.io.fi.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/print.summary.io.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/plot.io.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/coef.io.R mrds/R/varn.R mrds/R/gof.trial.R
mrds/README.md
mrds/MD5
mrds/DESCRIPTION
mrds/man
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/process.data.Rd mrds/man/logisticdetfct.Rd mrds/man/is.logistic.constant.Rd mrds/man/print.summary.rem.fi.Rd 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/summary.rem.fi.Rd 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/print.summary.io.fi.Rd 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/plot.io.fi.Rd mrds/man/prob.deriv.Rd mrds/man/prob.se.Rd mrds/man/logisticdupbyx.Rd mrds/man/check.mono.Rd mrds/man/calc.se.Np.Rd mrds/man/ddf.gof.Rd mrds/man/ddf.io.fi.Rd mrds/man/assign.par.Rd mrds/man/integratelogistic.analytic.Rd mrds/man/pronghorn.Rd mrds/man/print.summary.ds.Rd mrds/man/summary.trial.fi.Rd 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/ddf.trial.fi.Rd mrds/man/summary.rem.Rd mrds/man/print.summary.io.Rd 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/plot.trial.fi.Rd mrds/man/lfgcwa.Rd mrds/man/plot_cond.Rd mrds/man/plot.layout.Rd mrds/man/test.breaks.Rd mrds/man/plot.rem.fi.Rd mrds/man/det.tables.Rd mrds/man/DeltaMethod.Rd mrds/man/ddf.Rd mrds/man/summary.io.fi.Rd mrds/man/print.summary.rem.Rd mrds/man/logisticdupbyx_fast.Rd mrds/man/keyfct.th2.Rd mrds/man/ddf.rem.fi.Rd mrds/man/print.summary.trial.fi.Rd mrds/man/detfct.fit.Rd mrds/man/dht.se.Rd mrds/man/detfct.fit.opt.Rd 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/summary.io.Rd mrds/man/cds.Rd mrds/man/ddf.io.Rd 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/plot.io.Rd mrds/man/book.tee.data.Rd 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

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