Package: BinaryEPPM 3.0

David M. Smith

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

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) <doi:10.1002/bimj.201100214> and Smith and Faddy (2019) <doi:10.18637/jss.v090.i08>.

Authors:David M. Smith [aut, cre], Malcolm J. Faddy [aut]

BinaryEPPM_3.0.tar.gz
BinaryEPPM_3.0.tar.gz(r-4.5-noble)BinaryEPPM_3.0.tar.gz(r-4.4-noble)
BinaryEPPM_3.0.tgz(r-4.4-emscripten)BinaryEPPM_3.0.tgz(r-4.3-emscripten)
BinaryEPPM.pdf |BinaryEPPM.html✨
BinaryEPPM/json (API)

# Install 'BinaryEPPM' in R:
install.packages('BinaryEPPM', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • Berkshires.litters - The data are of the number of male piglets born in litters of varying sizes for the Berkshire breed of pigs.
  • KupperHaseman.case - Kupper and Haseman example data
  • 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.
  • ropespores.case - Dilution series for the presence of rope spores.
  • ropespores.grouped - Dilution series for the presence of rope spores.
  • wordcount.case - Number of occurences of an article in five-word and ten-word samples from two authors.
  • wordcount.grouped - Number of occurences of an article in five-word and ten-word samples from two authors.

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

29 exports 0.00 score 7 dependencies 35 scripts 254 downloads

Last updated 4 months agofrom:3e932ad744. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 03 2024
R-4.5-linuxNOTESep 03 2024

Exports:BBprobBinaryEPPMCBprobcoef.BinaryEPPMcooks.distance.BinaryEPPMdoubexpdoubrecipEPPMprobfitted.BinaryEPPMGBprobhatvalues.BinaryEPPMLL.gradientLL.Regression.BinarylogLik.BinaryEPPMloglogModel.BCBinProbModel.BinaryModel.GBModel.JMVGBnegcomplogplot.BinaryEPPMpowerlogitpredict.BinaryEPPMprint.BinaryEPPMprint.summaryBinaryEPPMresiduals.BinaryEPPMsummary.BinaryEPPMvcov.BinaryEPPMwaldtest.BinaryEPPM

Dependencies:expmFormulalatticelmtestMatrixnumDerivzoo

Mean and Scale-Factor Modeling of Under- and Overdispersed Grouped Binary Data

Rendered fromVignette_RSP_one.pdf.asisusingR.rsp::asison Sep 03 2024.

Last update: 2024-06-05
Started: 2024-06-05

Readme and manuals

Help Manual

Help pageTopics
Mean and Scale-Factor Modeling of Under- And Over-Dispersed Binary DataBinaryEPPM-package
Calculation of vector of probabilities for the beta binomial distribution.BBprob
The data are of the number of male piglets born in litters of varying sizes for the Berkshire breed of pigs.Berkshires.litters
Fitting of EPPM models to binary data.BinaryEPPM
Calculation of vector of probabilities for the correlated binomial distribution.CBprob
Extraction of model coefficients for BinaryEPPM Objectscoef.BinaryEPPM
Cook's distance for BinaryEPPM Objectscooks.distance.BinaryEPPM
Double exponential Link Functiondoubexp
Double reciprocal Link Functiondoubrecip
Calculation of vector of probabilities for a extended Poisson process model (EPPM).EPPMprob
Extraction of fitted values from BinaryEPPM Objectsfitted.BinaryEPPM
Calculation of vector of probabilities for the EPPM binomial distribution.GBprob
Extraction of hat matrix values from BinaryEPPM Objectshatvalues.BinaryEPPM
Kupper and Haseman example dataKupperHaseman.case
Function used to calculate the first derivatives of the log likelihood with respect to the model parameters.LL.gradient
Function called by optim to calculate the log likelihood from the probabilities and hence perform the fitting of regression models to the binary data.LL.Regression.Binary
Extract Log-LikelihoodlogLik.BinaryEPPM
Log-log Link Functionloglog
Probabilities for beta and correlated binomial distributions given p's and scale-factors.Model.BCBinProb
Function for obtaining output from distributional models.Model.Binary
Probabilities for binomial and EPPM extended binomial distributions given p's and b.Model.GB
Probabilities for EPPM extended binomial distributions given p's and scale-factors.Model.JMVGB
Negative complementary log-log Link Functionnegcomplog
The data are of the number of male piglets born in litters of varying sizes for the Parkes breed of pigs.Parkes.litters
Diagnostic Plots for BinaryEPPM Objectsplot.BinaryEPPM
Power Logit Link Functionpowerlogit
Prediction Method for BinaryEPPM Objectspredict.BinaryEPPM
Printing of BinaryEPPM Objectsprint.BinaryEPPM
Printing of summaryBinaryEPPM Objectsprint.summaryBinaryEPPM
Residuals for BinaryEPPM Objectsresiduals.BinaryEPPM
Dilution series for the presence of rope spores.ropespores.case
Dilution series for the presence of rope spores.ropespores.grouped
Summary of BinaryEPPM Objectssummary.BinaryEPPM
Variance/Covariance Matrix for Coefficientsvcov.BinaryEPPM
Wald Test of Nested Models for BinaryEPPM Objectswaldtest.BinaryEPPM
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.wordcount.grouped
The data are of the number of male piglets born in litters of varying sizes for the Yorkshire breed of pigs.Yorkshires.litters