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clinDR (version 2.5.3)

Simulation and Analysis Tools for Clinical Dose Response Modeling

Description

Bayesian and ML Emax model fitting, graphics and simulation for clinical dose response. The summary data from the dose response meta-analyses in Thomas, Sweeney, and Somayaji (2014) and Thomas and Roy (2016) Wu, Banerjee, Jin, Menon, Martin, and Heatherington(2017) are included in the package. The prior distributions for the Bayesian analyses default to the posterior predictive distributions derived from these references.

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Version

Install

install.packages('clinDR')

Monthly Downloads

540

Version

2.5.3

License

GPL (>= 2)

Maintainer

Neal Thomas

Last Published

September 21st, 2026

Functions in clinDR (2.5.3)

compileStanModels

Compile rstan Emax models after package clinDR is installed
emaxPrior.control

Set the parameters of the prior distribution for the Emax model implemented in fitEmaxB.
emaxsolve

Solve Emax function for target value
mcmc.control

Settings for restan execution in function fitEmaxB
emaxsim

Simulate Emax maximum likelihood estimation
emaxalt

Fit 4- or 3-parameter Emax model substituting simpler curves if convergence not achieved.
fitEmax

ML fit of hyperbolic or sigmoidal Emax models to continuous/binary dose response data.
emaxsimB

Simulate Emax Bayesian estimation
fitEmaxB

Bayesian fit of hyperbolic or sigmoidal Emax models to continuous/binary dose response data.
emaxfun

Vectorized versions of the hyperbolic and sigmoidal Emax models
plot.emaxsimBobj

Plot dose response from a data set generated by emaxsimB
plot.fitEmax

Plot a Emax model and dose group means.
nllogis

The negative log likelihood function for a 3- or 4- parameter Emax model on the logit scale for binary dose response.
plot.emaxsimB

Plot the output of emaxsimB
metaData

Dose response data from several published meta-analyses
plot.emaxsim

Plot the output of emaxsim
plot.emaxsimobj

Plot dose response from a data set generated by emaxsim
plot.plotB

Plot Bayes dose response curve and dose group means
plot.fitEmaxB

Plot a Emax model and dose group means.
plotB

Plot Bayes dose response curve and dose group means
predict.fitEmaxB

Estimated mean and posterior intervals derived from a Bayesian hyperbolic or sigmiodial Emax model.
predict.emaxsimBobj

Mean response estimates (posterior means) and SE (posterior SD) for specified doses for a simulated emaxsimBobj object
predict.emaxsimB

Mean response and SE for each replicate data set in an emaxsimB object
printemaxPrior

Generate and Save Protocol/SAP Text for Emax Prior Distributions
print.emaxsimBobj

Print a summary of the fitted Emax model
print.emaxsimB

Print simulation output from emaxsimB
print.emaxsim

Print simulation output from emaxsim
print.emaxsimobj

Print a data set generated by emaxsim
predict.emaxsimobj

Mean response and SE for specified doses for a simulated emaxsimobj object
showStanModels

Display STAN model code.
selEstan

Select a pre-compiled rstan Emax model
runSimulations

Shiny app for function emaxsim(B)
summary.fitEmaxB

Print a summary of the fitted Bayesian Emax model
summary.emaxsimBobj

Summarize Emax fit to a data set generated by emaxsimB
summary.emaxsimB

Summary of output of emaxsimB
sigmaEmax

Extract Emax model residual SD estimates
predict.fitEmax

Estimated mean/proportion and confidence intervals derived from the maximum likelihood fit of a 3- or 4- parameter Emax model.
print.fitEmaxB

Print a summary of the fitted Bayesian Emax model
print.fitEmax

Print a summary of the fitted Emax model
predict.emaxalt

Mean response and SE for specified doses for a simulated object output by function emaxalt
predict.emaxsim

Mean response and SE for specified doses for each replicate data set in an emaxsim object
prior.control

Set the parameters of the prior distribution for the Emax model implemented in fitEmaxB.
update.emaxsimobj

Update estimation in a data set generated by emaxsim
summary.emaxsimobj

Summarize Emax fit to a data set generated by emaxsim
targetBeta

Find a scaled Beta distribution matching specified probabilities
randomEmax

Random data constructor function for emaxsim(B) creating random parameters for an Emax model for continuous or binary data.
vcovEmax

Extract Emax model variance-covariance matrix for ML estimates
summary.emaxsim

Summary of output of emaxsim
plotBdensity

Density plot displaying Bayes prior or posterior dose response
summary.fitEmax

Print a summary of the fitted Emax model
targetCI

Compute the dose with confidence interval exceeding a target change from placebo for each simulated example in an emaxsim object.
plotD

Basic plot of dose group means
targetD

Compute the MLE (and its SE) of the dose achieving a specified target improvement from placebo.
startEmax

Compute starting parameter values for the 3- or 4- Emax model.
clinDR-package

Bayesian and maximum likelihood Emax model fitting, graphics and simulation for clinical dose response.
checkMonoEmax

Bayes posterior predictive test for Emax (monotone) model fit
"Extract.emaxsim"

Extract a simulation from the output of emaxsim
bpchkMonoEmax

Bayes posterior predictive test for Emax (monotone) model fit
coefEmax

Extract Emax model parameter estimates
"Extract.emaxsimB"

Extract a simulation from the output of emaxsimB
SeEmax

Asymptotic SE for dose response estimates from a 3- or 4- parameter Emax model
RandEmax

Random data constructor function for emaxsim creating random parameters for an Emax model for continuous or binary data.
FixedMean

Fixed means (proportions) random data constructor for emaxsim for continuous or binary data
DRDensityPlot

Plot Bayes or confidence interval density contours over a grid of points (usually dose or time)