mrds: Mark-Recapture Distance Sampling

Share:

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.

Author
Jeff 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 publication
2016-10-03 22:59:36
Maintainer
Laura Marshall <lhm@st-andrews.ac.uk>
License
GPL (>= 2)
Version
2.1.17

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