Mark-Recapture Distance Sampling (mrds)

Documentation for package ‘mrds’ version 2.0.5

DESCRIPTION file.

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A B C D E F G H I K L M N P Q R S T V

mrds-package

Mark-Recapture Distance Sampling (mrds)

-- A --

adj.check.order	Check order of adjustment terms
adjfct.cos	Detection functions
adjfct.herm	Detection functions
adjfct.poly	Detection functions
apex.gamma	Detection functions
assign.default.values	Assign default values to list elements that have not been already assigned
assign.par	Extraction and assignment of parameters to vector
average.line	Average detection function line for plotting

-- B --

book.tee.data

Golf tee data used in chapter 6 of Advanced Distance Sampling examples

-- C --

calcp.mrds	Average detection probability calculation
cdf.ds	Cumulative distribution function (cdf) for fitted distance sampling detection function
cds	CDS function definition
coef.ds	Extract coefficients
coef.io	Extract coefficients
coef.io.fi	Extract coefficients
coef.rem	Extract coefficients
coef.rem.fi	Extract coefficients
coef.trial	Extract coefficients
coef.trial.fi	Extract coefficients
coefficients	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
covn	Computes empirical variance of encounter rate
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

-- D --

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
DeltaMethod	Numeric Delta Method approximation for the variance-covariance matrix
det.tables	Observation detection tables
detfct	Detection functions
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
ds.function	Distance Sampling Functions

-- E --

errors

Error function

-- F --

flnl	Log-likelihood computation for distance sampling data
flt.lnl	Log-likelihood computation for distance sampling data
flt.var	Hessian computation for fitted distance detection function model parameters
fpt.lnl	Log-likelihood computation for distance sampling data
fr	Detection functions
fx	Detection functions

-- G --

g0	Detection functions
getpar	Extraction and assignment of parameters to vector
gof.ds	Goodness of fit tests for distance sampling models
gof.io	Goodness of fit tests for distance sampling models
gof.io.fi	Goodness of fit tests for distance sampling models
gof.rem	Goodness of fit tests for distance sampling models
gof.rem.fi	Goodness of fit tests for distance sampling models
gof.trial	Goodness of fit tests for distance sampling models
gof.trial.fi	Goodness of fit tests for distance sampling models
gstdint	Integral of standardized (scale=1) detection function

-- H --

hermite.poly	Detection functions
histline	Plot histogram line

-- I --

integratedetfct	Numerically integrate distance detection function over specified range
integratedetfct.logistic	Collection of functions for logistic detection functions
integratelogistic	Collection of functions for logistic detection functions
integratelogistic.analytic	Collection of functions for logistic detection functions
integratelogisticdup	Collection of functions for logistic detection functions
io.glm	Iterative offset GLM/GAM for fitting detection function
is.linear.logistic	Collection of functions for logistic detection functions
is.logistic.constant	Collection of functions for logistic detection functions

-- K --

keyfct.gamma	Detection functions
keyfct.hn	Detection functions
keyfct.hz	Detection functions

-- L --

logisticbyx	Collection of functions for logistic detection functions
logisticbyz	Collection of functions for logistic detection functions
logisticdetfct	Collection of functions for logistic detection functions
logisticdupbyx	Collection of functions for logistic detection functions
logit	Logit function

-- M --

mcds	MCDS function definition
mrds	Mark-Recapture Distance Sampling (mrds)

-- N --

NCovered	Compute estimated abundance in covered (sampled) region
NCovered.ds	Compute estimated abundance in covered (sampled) region
NCovered.io	Compute estimated abundance in covered (sampled) region
NCovered.io.fi	Compute estimated abundance in covered (sampled) region
NCovered.rem	Compute estimated abundance in covered (sampled) region
NCovered.rem.fi	Compute estimated abundance in covered (sampled) region
NCovered.trial	Compute estimated abundance in covered (sampled) region
NCovered.trial.fi	Compute estimated abundance in covered (sampled) region

-- P --

p.det	Double-platform detection probability
pcramer	Q-Q plot, KS and CVM goodness of fit tests for distance detection functions
pdot.dsr.integrate.logistic	Collection of functions for logistic detection functions
pks	Q-Q plot, KS and CVM goodness of fit tests for distance detection functions
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 model
plot.io.fi	Plot fit of detection functions and histograms of data from distance sampling model
plot.rem	Plot fit of detection functions and histograms of data from distance sampling model
plot.rem.fi	Plot fit of detection functions and histograms of data from distance sampling model
plot.trial	Plot fit of detection functions and histograms of data from distance sampling model
plot.trial.fi	Plot fit of detection functions and histograms of data from distance sampling model
plot_cond	Plot conditional detection function from distance sampling model
plot_uncond	Plot unconditional detection function from distance sampling model
predict.ddf	Predictions from distance sampling ds models
predict.ds	Predictions from distance sampling ds models
predict.io	Predictions from distance sampling io models
predict.io.fi	Predictions from distance sampling io.fi models
predict.rem	Predictions from distance sampling rem models
predict.rem.fi	Predictions from distance sampling rem.fi models
predict.trial	Predictions from distance sampling trial models
predict.trial.fi	Predictions from distance sampling trial.fi models
print.ddf.gof	Prints results of goodness of fit tests for detection functions
print.det.tables	Prints results of observer detection tables
print.dht	Prints density and abundance estimates based on Horvitz-Thompson-like estimator
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

-- Q --

qqplot.ddf

Q-Q plot, KS and CVM goodness of fit tests for distance detection functions

-- R --

rem.glm

Iterative offset model fitting of mark-recapture with removal model

-- S --

scalevalue	Detection functions
setbounds	Set parameter bounds
setcov	Creates design matrix for covariates in detection function
sethazard	Set initial values for detection function based on distance sampling
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.
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

-- T --

tablecgf	Spline approximation to scale dependent integration of detection function
test.breaks	Test validity for histogram breaks(cutpoints)

-- V --

varn	Computes empirical variance of encounter rate