Mark-Recapture Distance Sampling
Summary of distance detection function model object
Summary of distance detection function model object
Summary of distance detection function model object
Summary of distance detection function model object
Extrapolate Horvitz-Thompson abundance estimates to entire surveyed re...
Test validity for histogram breaks(cutpoints)
Summary of distance detection function model object
Add covariate levels detection function plots
Check order of adjustment terms
Akaike's An Information Criterion for detection functions
Get the apex for a gamma detection function
Assign default values to list elements that have not been already assi...
Extraction and assignment of parameters to vector
Average conditional detection function line for plotting
Average detection function line for plotting
Find se of average p and N
Cumulative distribution function (cdf) for fitted distance sampling de...
CDS function definition
Check parameters bounds during optimisations
Check that a detection function is monotone
Extract coefficients
Horvitz-Thompson estimates 1/p_i or s_i/p_i
Covered region estimate of abundance from Horvitz-Thompson-like estima...
Create bins from a set of binned distances and a set of cutpoints.
create.command.file
Create detection function object
Create a model frame for ddf fitting
Creates structures needed to compute abundance and variance
CDS/MCDS Distance Detection Function Fitting
Goodness of fit tests for distance sampling models
Mark-Recapture Distance Sampling (MRDS) IO - FI
Mark-Recapture Distance Sampling (MRDS) IO - PI
Distance Detection Function Fitting
Mark-Recapture Distance Sampling (MRDS) Removal - FI
Mark-Recapture Distance Sampling (MRDS) Removal - PI
Mark-Recapture Analysis of Trial Configuration - FI
Mark-Recapture Distance Sampling (MRDS) Trial Configuration - PI
Numeric Delta Method approximation for the variance-covariance matrix
Observation detection tables
Fit detection function using key-adjustment functions
Fit detection function using key-adjustment functions
Computes abundance estimates at specified parameter values using Horvi...
Density and abundance estimates and variances
Variance and confidence intervals for density and abundance estimates
Detection functions
Distance Sampling Functions
Log-likelihood computation for distance sampling data
Hessian computation for fitted distance detection function model param...
Compute value of p(0) using a logit formulation
Extraction and assignment of parameters to vector
Compute chi-square goodness-of-fit test for ds models
Integral of pdf of distances
Plot histogram line
Integrate a logistic detection function
Analytically integrate logistic detection function
Numerically integrate pdf of observed distances over specified ranges
Iterative offset GLM/GAM for fitting detection function
Collection of functions for logistic detection functions
Is a logit model constant for all observations?
Threshold key function
Threshold key function
Two-part normal key function
Logistic as a function of covariates
Logistic as a function of distance
Logistic detection function
Logistic for duplicates as a function of covariates
Logistic for duplicates as a function of covariates (fast)
Logit function
log-likelihood value for a fitted detection function
MCDS function definition
Run MCDS.exe as a backend for mrds
Mark-Recapture Distance Sampling (mrds)
Tips on optimisation issues in mrds models
Compute estimated abundance in covered (sampled) region
Wrapper around nlminb
Double-platform detection probability
Distribution of probabilities of detection
Parse optimx results and present a nice object
Compute probability that a object was detected by at least one observe...
Observation detection tables
Plot fit of detection functions and histograms of data from distance s...
Plot fit of detection functions and histograms of data from distance s...
Plot fit of detection functions and histograms of data from distance s...
Plot fit of detection functions and histograms of data from removal di...
Plot fit of detection functions and histograms of data from removal di...
Plot fit of detection functions and histograms of data from distance s...
Plot fit of detection functions and histograms of data from distance s...
Plot conditional detection function from distance sampling model
Layout for plot methods in mrds
Plot unconditional detection function from distance sampling model
Predictions from mrds models
Prints results of goodness of fit tests for detection functions
Simple pretty printer for distance sampling analyses
Print results of observer detection tables
Prints density and abundance estimates
Print distribution of probabilities of detection
Print summary of distance detection function model object
Print summary of distance detection function model object
Print summary of distance detection function model object
Print summary of distance detection function model object
Print summary of distance detection function model object
Print summary of distance detection function model object
Print summary of distance detection function model object
Derivatives for variance of average p and average p(0) variance
Average p and average p(0) variance
Process data for fitting distance sampling detection function
Quantile-quantile plot and goodness of fit tests for detection functio...
Iterative offset model fitting of mark-recapture with removal model
Calculate the parameter rescaling for parameters associated with covar...
Generate data from a fitted detection function and refit the model
Set parameter bounds
Creates design matrix for covariates in detection function
Set initial values for detection function based on distance sampling
Simulation of distance sampling data via mixture models Allows one to ...
Invert of covariance matrices
Summary of distance detection function model object
Summary of distance detection function model object
Compute empirical variance of encounter rate
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.
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