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clinDR (version 2.4.1)

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

292

Version

2.4.1

License

GPL (>= 2)

Maintainer

Neal Thomas

Last Published

August 9th, 2023

Functions in clinDR (2.4.1)

DRDensityPlot

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

Extract Emax model parameter estimates
RandEmax

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

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

Bayes posterior predictive test for Emax (monotone) model fit
clinDR-package

Bayesian and maximum likelihood Emax model fitting, graphics and simulation for clinical dose response.
"Extract.emaxsim"

Extract a simulation from the output of emaxsim
"Extract.emaxsimB"

Extract a simulation from the output of emaxsimB
FixedMean

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

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

Simulate Emax maximum likelihood estimation
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
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.
emaxfun

Vectorized versions of the hyperbolic and sigmoidal Emax models
mcmc.control

Settings for restan execution in function fitEmaxB
fitEmaxB

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

Simulate Emax Bayesian estimation
plot.emaxsimobj

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

Plot dose response from a data set generated by emaxsimB
metaData

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

Plot a Emax model and dose group means.
plot.emaxsim

Plot the output of emaxsim
plot.emaxsimB

Plot the output of emaxsimB
plotB

Plot Bayes dose response curve 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.fitEmax

Plot a Emax model and dose group means.
plot.plotB

Plot Bayes dose response curve and dose group means
printemaxPrior

Print protocol or sap text describing the prior distribution for the model parameters of the input emaxPrior object
predict.fitEmaxB

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

Mean response and SE for specified doses for a simulated emaxsimobj object
predict.emaxsim

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

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

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

Basic plot of dose group means
predict.emaxsimB

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

Shiny app for function emaxsim(B)
prior.control

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

Print a summary of the fitted Emax model
print.emaxsimB

Print simulation output from emaxsimB
predict.emaxsimBobj

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

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

Print simulation output from emaxsim
print.fitEmax

Print a summary of the fitted Emax model
print.fitEmaxB

Print a summary of the fitted Bayesian Emax model
selEstan

Select a pre-compiled rstan Emax model
plotBdensity

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

Print a summary of the fitted Emax model
summary.fitEmaxB

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

Summarize Emax fit to a data set generated by emaxsim
print.emaxsimobj

Print a data set generated by emaxsim
targetCI

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

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

Summary of output of emaxsimB
targetBeta

Find a scaled Beta distribution matching specified probabilities
summary.emaxsimBobj

Summarize Emax fit to a data set generated by emaxsimB
showStanModels

Display STAN model code.
sigmaEmax

Extract Emax model residual SD estimates
update.emaxsimobj

Update estimation in a data set generated by emaxsim
startEmax

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

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

Summary of output of emaxsim