mrds

Akaike's An Information Criterion for detection functions

Numeric Delta Method approximation for the variance-covariance matrix

Compute estimated abundance in covered (sampled) region

Add covariate levels detection function plots

Check order of adjustment terms

Get the apex for a gamma detection function

Assign default values to list elements that have not been already assigned

Extraction and assignment of parameters to vector

Average detection function line for plotting

Average conditional detection function line for plotting

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

Find se of average p and N

Cumulative distribution function (cdf) for fitted distance sampling detection function

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 estimator

Create bins from a set of binned distances and a set of cutpoints.

Create detection function object

Create a model frame for ddf fitting

Creates structures needed to compute abundance and variance

Distance Detection Function Fitting

CDS/MCDS Distance Detection Function Fitting

Goodness of fit tests for distance sampling models

Mark-Recapture Distance Sampling (MRDS) IO - PI

Mark-Recapture Distance Sampling (MRDS) IO - FI

Mark-Recapture Distance Sampling (MRDS) Removal - PI

Mark-Recapture Distance Sampling (MRDS) Removal - FI

Mark-Recapture Distance Sampling (MRDS) Trial Configuration - PI

Mark-Recapture Analysis of Trial Configuration - FI

Observation detection tables

Fit detection function using key-adjustment functions

Fit detection function using key-adjustment functions

Density and abundance estimates and variances

Computes abundance estimates at specified parameter values using Horvitz-Thompson-like estimator

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 parameters

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

Black-capped vireo mark-recapture distance sampling analysis

Golden-cheeked warbler mark-recapture distance sampling analysis

log-likelihood value for a fitted detection 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

MCDS function definition

Tips on optimisation issues in mrds models

Mark-Recapture Distance Sampling (mrds)

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 observer

Observation detection tables

Plot fit of detection functions and histograms of data from distance sampling model

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 distance sampling independent observer model with full independence (io.fi)

Layout for plot methods in mrds

Plot fit of detection functions and histograms of data from removal distance sampling 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 trial observer model

Plot fit of detection functions and histograms of data from distance sampling trial observer model

Plot conditional detection function from distance sampling model

Plot unconditional detection function from distance sampling model

Predictions from mrds models

Simple pretty printer for distance sampling analyses

Prints results of goodness of fit tests for detection functions

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

Pronghorn aerial survey data from Wyoming

Single observer point count data example from Distance

Simulated dual observer point count data

Simulated removal observer point count data

Simulated single observer point count data

Quantile-quantile plot and goodness of fit tests for detection functions

Iterative offset model fitting of mark-recapture with removal model

Calculate the parameter rescaling for parameters associated with covariates

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 simulate line transect distance sampling data using a mixture of half-normal detection functions.

Invert of covariance matrices

Wooden stake data from 1977 survey

Wooden stake data from 1978 survey

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

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 region

Test validity for histogram breaks(cutpoints)

Compute empirical variance of encounter rate