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

Functions

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

Files

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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