Numeric Delta Method approximation for the variance-covariance matrix
Akaike's An Information Criterion for detection functions
Average detection function line for plotting
Average conditional detection function line for plotting
Add covariate levels detection function plots
Compute estimated abundance in covered (sampled) region
Assign default values to list elements that have not been already assigned
Horvitz-Thompson estimates 1/p_i or s_i/p_i
Extract coefficients
Check parameters bounds during optimisations
Extraction and assignment of parameters to vector
Cumulative distribution function (cdf) for fitted distance sampling detection function
Mark-Recapture Distance Sampling (MRDS) IO - PI
Golf tee data used in chapter 6 of Advanced Distance Sampling examples
Check that a detection function is monotone
Creates structures needed to compute abundance and variance
Mark-Recapture Distance Sampling (MRDS) IO - FI
Get the apex for a gamma detection function
Create bins from a set of binned distances and a set of cutpoints.
Goodness of fit tests for distance sampling models
Check order of adjustment terms
Covered region estimate of abundance from Horvitz-Thompson-like estimator
Fit detection function using key-adjustment functions
CDS/MCDS Distance Detection Function Fitting
CDS function definition
Computes abundance estimates at specified parameter values using
Horvitz-Thompson-like estimator
Mark-Recapture Distance Sampling (MRDS) Removal - PI
Mark-Recapture Distance Sampling (MRDS) Removal - FI
Distance Detection Function Fitting
Logistic as a function of covariates
Log-likelihood computation for distance sampling data
Mark-Recapture Distance Sampling (MRDS) Trial Configuration - PI
Observation detection tables
Mark-Recapture Analysis of Trial Configuration - FI
Fit detection function using key-adjustment functions
Hessian computation for fitted distance detection function model parameters
Variance and confidence intervals for density and abundance estimates
Density and abundance estimates and variances
Golden-cheeked warbler mark-recapture distance sampling analysis
Find se of average p and N
Create a model frame for ddf fitting
Create detection function object
Logistic as a function of distance
Parse optimx results and present a nice object
log-likelihood value for a fitted detection function
Layout for plot methods in mrds
Plot fit of detection functions and histograms of data from removal distance
sampling model
Tips on optimisation issues in mrds
models
Plot histogram line
MCDS function definition
Integrate a logistic detection function
Distribution of probabilities of detection
Double-platform detection probability
Compute value of p(0) using a logit formulation
Plot unconditional detection function from distance sampling model
Distance Sampling Functions
Detection functions
Predictions from mrds
models
integratelogistic.analytic
Analytically integrate logistic detection function
pdot.dsr.integrate.logistic
Compute probability that a object was detected by at least one observer
Plot conditional detection function from distance sampling model
Derivatives for variance of average p and average p(0) variance
Set initial values for detection function based on distance sampling
Average p and average p(0) variance
Print summary of distance detection function model object
Plot fit of detection functions and histograms of data from distance
sampling trial observer model
Compute chi-square goodness-of-fit test for ds models
Simulated removal observer point count data
Print summary of distance detection function model object
Integral of pdf of distances
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.
Is a logit model constant for all observations?
Extraction and assignment of parameters to vector
Print distribution of probabilities of detection
Summary of distance detection function model object
Summary of distance detection function model object
Threshold key function
Threshold key function
Iterative offset GLM/GAM for fitting detection function
Logistic for duplicates as a function of covariates (fast)
Numerically integrate pdf of observed distances over specified ranges
Logistic for duplicates as a function of covariates
Logistic detection function
Observation detection tables
Print summary of distance detection function model object
Process data for fitting distance sampling detection function
Black-capped vireo mark-recapture distance sampling analysis
Collection of functions for logistic detection functions
Mark-Recapture Distance Sampling (mrds)
Simulated single observer point count data
Logit function
Wrapper around nlminb
Plot fit of detection functions and histograms of data from distance
sampling trial observer model
Set parameter bounds
Prints density and abundance estimates
Print results of observer detection tables
Plot fit of detection functions and histograms of data from removal distance
sampling model
Plot fit of detection functions and histograms of data from distance sampling model
Print summary of distance detection function model object
Creates design matrix for covariates in detection function
Plot fit of detection functions and histograms of data from distance
sampling independent observer (io
) model
Print summary of distance detection function model object
Invert of covariance matrices
Calculate the parameter rescaling for parameters associated with covariates
Plot fit of detection functions and histograms of data from distance
sampling independent observer model with full independence (io.fi
)
Wooden stake data from 1977 survey
Simple pretty printer for distance sampling analyses
Summary of distance detection function model object
Generate data from a fitted detection function and refit the model
Quantile-quantile plot and goodness of fit tests for detection functions
Pronghorn aerial survey data from Wyoming
Wooden stake data from 1978 survey
Iterative offset model fitting of mark-recapture with removal model
Summary of distance detection function model object
Summary of distance detection function model object
Extrapolate Horvitz-Thompson abundance estimates to entire surveyed region
Prints results of goodness of fit tests for detection functions
Print summary of distance detection function model object
Test validity for histogram breaks(cutpoints)
Simulated dual observer point count data
Single observer point count data example from Distance
Summary of distance detection function model object
Print summary of distance detection function model object
Summary of distance detection function model object
Compute empirical variance of encounter rate