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BinaryEPPM (version 3.0)

Mean and Scale-Factor Modeling of Under- And Over-Dispersed Binary Data

Description

Under- and over-dispersed binary data are modeled using an extended Poisson process model (EPPM) appropriate for binary data. A feature of the model is that the under-dispersion relative to the binomial distribution only needs to be greater than zero, but the over-dispersion is restricted compared to other distributional models such as the beta and correlated binomials. Because of this, the examples focus on under-dispersed data and how, in combination with the beta or correlated distributions, flexible models can be fitted to data displaying both under- and over-dispersion. Using Generalized Linear Model (GLM) terminology, the functions utilize linear predictors for the probability of success and scale-factor with various link functions for p, and log link for scale-factor, to fit a variety of models relevant to areas such as bioassay. Details of the EPPM are in Faddy and Smith (2012) and Smith and Faddy (2019) .

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Version

Install

install.packages('BinaryEPPM')

Monthly Downloads

245

Version

3.0

License

GPL-2

Maintainer

Last Published

June 4th, 2024

Functions in BinaryEPPM (3.0)

Model.JMVGB

Probabilities for EPPM extended binomial distributions given p's and scale-factors.
Model.BCBinProb

Probabilities for beta and correlated binomial distributions given p's and scale-factors.
Model.GB

Probabilities for binomial and EPPM extended binomial distributions given p's and b.
coef.BinaryEPPM

Extraction of model coefficients for BinaryEPPM Objects
cooks.distance.BinaryEPPM

Cook's distance for BinaryEPPM Objects
doubrecip

Double reciprocal Link Function
Parkes.litters

The data are of the number of male piglets born in litters of varying sizes for the Parkes breed of pigs.
Yorkshires.litters

The data are of the number of male piglets born in litters of varying sizes for the Yorkshire breed of pigs.
Model.Binary

Function for obtaining output from distributional models.
powerlogit

Power Logit Link Function
doubexp

Double exponential Link Function
print.BinaryEPPM

Printing of BinaryEPPM Objects
logLik.BinaryEPPM

Extract Log-Likelihood
print.summaryBinaryEPPM

Printing of summaryBinaryEPPM Objects
loglog

Log-log Link Function
fitted.BinaryEPPM

Extraction of fitted values from BinaryEPPM Objects
plot.BinaryEPPM

Diagnostic Plots for BinaryEPPM Objects
negcomplog

Negative complementary log-log Link Function
residuals.BinaryEPPM

Residuals for BinaryEPPM Objects
vcov.BinaryEPPM

Variance/Covariance Matrix for Coefficients
waldtest.BinaryEPPM

Wald Test of Nested Models for BinaryEPPM Objects
wordcount.grouped

Number of occurences of an article in five-word and ten-word samples from two authors.
wordcount.case

Number of occurences of an article in five-word and ten-word samples from two authors.
predict.BinaryEPPM

Prediction Method for BinaryEPPM Objects
hatvalues.BinaryEPPM

Extraction of hat matrix values from BinaryEPPM Objects
summary.BinaryEPPM

Summary of BinaryEPPM Objects
ropespores.grouped

Dilution series for the presence of rope spores.
ropespores.case

Dilution series for the presence of rope spores.
EPPMprob

Calculation of vector of probabilities for a extended Poisson process model (EPPM).
BinaryEPPM

Fitting of EPPM models to binary data.
BBprob

Calculation of vector of probabilities for the beta binomial distribution.
BinaryEPPM-package

tools:::Rd_package_title("BinaryEPPM")
CBprob

Calculation of vector of probabilities for the correlated binomial distribution.
LL.Regression.Binary

Function called by optim to calculate the log likelihood from the probabilities and hence perform the fitting of regression models to the binary data.
Berkshires.litters

The data are of the number of male piglets born in litters of varying sizes for the Berkshire breed of pigs.
GBprob

Calculation of vector of probabilities for the EPPM binomial distribution.
LL.gradient

Function used to calculate the first derivatives of the log likelihood with respect to the model parameters.
KupperHaseman.case

Kupper and Haseman example data