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