AIC.ddf                 Akaike's An Information Criterion for detection
                        functions
DeltaMethod             Numeric Delta Method approximation for the
                        variance-covariance matrix
MCDS.exe                Run MCDS.exe as a backend for mrds
NCovered                Compute estimated abundance in covered
                        (sampled) region
add.df.covar.line       Add covariate levels detection function plots
adj.check.order         Check order of adjustment terms
adj.cos                 Cosine adjustment term, not the series.
adj.herm                Hermite polynomial adjustment term, not the
                        series.
adj.poly                Simple polynomial adjustment term, not the
                        series.
adj.series.grad.cos     Series of the gradient of the cosine adjustment
                        series w.r.t. the scaled distance.
adj.series.grad.herm    Series of the gradient of the Hermite
                        polynomial adjustment series w.r.t. the scaled
                        distance.
adj.series.grad.poly    Series of the gradient of the simple polynomial
                        adjustment series w.r.t. the scaled distance.
apex.gamma              Get the apex for a gamma detection function
assign.default.values   Assign default values to list elements that
                        have not been already assigned
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 examples
calc.se.Np              Find se of average p and N
cdf.ds                  Cumulative distribution function (cdf) for
                        fitted distance sampling detection function
cds                     CDS function definition
check.bounds            Check parameters bounds during optimisations
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
                        Horvitz-Thompson-like estimator
create.bins             Create bins from a set of binned distances and
                        a set of cutpoints.
create.command.file     create.command.file
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 - PI
ddf.trial.fi            Mark-Recapture Analysis of Trial Configuration
                        - FI
det.tables              Observation detection tables
detfct.fit              Fit detection function using key-adjustment
                        functions
detfct.fit.opt          Fit detection function using key-adjustment
                        functions
dht                     Density and abundance estimates and variances
dht.deriv               Computes abundance estimates at specified
                        parameter values using Horvitz-Thompson-like
                        estimator
dht.se                  Variance and confidence intervals for density
                        and abundance estimates
distpdf.grad            Gradient of the non-normalised pdf of distances
                        or the detection function for the distances.
ds.function             Distance Sampling Functions
flnl                    Log-likelihood computation for distance
                        sampling data
flnl.constr.grad.neg    (Negative) gradients of constraint function
flnl.grad               Gradient of the negative log likelihood
                        function
flt.var                 Hessian computation for fitted distance
                        detection function model parameters
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 specified ranges
integratepdf.grad       Numerically integrates the non-normalised pdf
                        or the detection function of observed distances
                        over specified ranges.
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.grad.hn          The gradient of the half-normal key function
keyfct.grad.hz          The gradient of the hazard-rate key function
keyfct.th1              Threshold key function
keyfct.th2              Threshold key function
keyfct.tpn              Two-part normal key function
lfbcvi                  Black-capped vireo mark-recapture distance
                        sampling analysis
lfgcwa                  Golden-cheeked warbler mark-recapture distance
                        sampling analysis
logLik.ddf              log-likelihood value for a fitted detection
                        function
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-package            Mark-Recapture Distance Sampling (mrds)
mrds_opt                Tips on optimisation issues in 'mrds' models
nlminb_wrapper          Wrapper around 'nlminb'
p.det                   Double-platform detection probability
p.dist.table            Distribution of probabilities of detection
parse.optimx            Parse optimx results and present a nice object
pdot.dsr.integrate.logistic
                        Compute probability that a object was detected
                        by at least one observer
plot.det.tables         Observation detection tables
plot.ds                 Plot fit of detection functions and histograms
                        of data from distance sampling model
plot.io                 Plot fit of detection functions and histograms
                        of data from distance sampling independent
                        observer ('io') model
plot.io.fi              Plot fit of detection functions and histograms
                        of data from distance sampling independent
                        observer model with full independence ('io.fi')
plot.rem                Plot fit of detection functions and histograms
                        of data from removal distance sampling model
plot.rem.fi             Plot fit of detection functions and histograms
                        of data from removal distance sampling model
plot.trial              Plot fit of detection functions and histograms
                        of data from distance sampling trial observer
                        model
plot.trial.fi           Plot fit of detection functions and histograms
                        of data from distance sampling trial observer
                        model
plot_cond               Plot conditional detection function from
                        distance sampling model
plot_layout             Layout for plot methods in mrds
plot_uncond             Plot unconditional detection function from
                        distance sampling model
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 functions
print.det.tables        Print results of observer detection tables
print.dht               Prints density and abundance estimates
print.p_dist_table      Print distribution of probabilities of
                        detection
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) variance
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              Quantile-quantile plot and goodness of fit
                        tests for detection functions
rem.glm                 Iterative offset model fitting of
                        mark-recapture with removal model
rescale_pars            Calculate the parameter rescaling for
                        parameters associated with covariates
sample_ddf              Generate data from a fitted detection function
                        and refit the model
setbounds               Set parameter bounds
setcov                  Creates design matrix for covariates in
                        detection function
setinitial.ds           Set initial values for detection function based
                        on distance sampling
sim.mix                 Simulation of distance sampling data via
                        mixture models Allows one to simulate line
                        transect distance sampling data using a mixture
                        of half-normal detection functions.
solvecov                Invert of covariance matrices
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 surveyed region
test.breaks             Test validity for histogram breaks(cutpoints)
varn                    Compute empirical variance of encounter rate
