Simulation and Analysis Tools for Clinical Dose Response Modeling

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Documentation for package ‘clinDR’ version 2.4.1

• DESCRIPTION file.
• Package NEWS.

Help Pages

clinDR-package	Bayesian and maximum likelihood Emax model fitting, graphics and simulation for clinical dose response.
bpchkMonoEmax	Bayes posterior predictive test for Emax (monotone) model fit
checkMonoEmax	Bayes posterior predictive test for Emax (monotone) model fit
coef.emaxsim	Extract Emax model parameter estimates
coef.emaxsimB	Extract Emax model parameter estimates
coef.fitEmax	Extract Emax model parameter estimates
coef.fitEmaxB	Extract Emax model parameter estimates
compileStanModels	Compile 'rstan' Emax models after package 'clinDR' is installed
DRDensityPlot	Plot Bayes or confidence interval density contours over a grid of points (usually dose or time)
emaxalt	Fit 4- or 3-parameter Emax model substituting simpler curves if convergence not achieved.
emaxfun	Vectorized versions of the hyperbolic and sigmoidal Emax models
emaxPrior.control	Set the parameters of the prior distribution for the Emax model implemented in 'fitEmaxB'.
emaxsim	Simulate Emax maximum likelihood estimation
emaxsimB	Simulate Emax Bayesian estimation
fitEmax	ML fit of hyperbolic or sigmoidal Emax models to continuous/binary dose response data.
fitEmaxB	Bayesian fit of hyperbolic or sigmoidal Emax models to continuous/binary dose response data.
FixedMean	Fixed means (proportions) random data constructor for emaxsim for continuous or binary data
mcmc.control	Settings for 'restan' execution in function 'fitEmaxB'
metaData	Dose response data from several published meta-analyses
nllogis	The negative log likelihood function for a 3- or 4- parameter Emax model on the logit scale for binary dose response.
plot.emaxsim	Plot the output of emaxsim
plot.emaxsimB	Plot the output of emaxsimB
plot.emaxsimBobj	Plot dose response from a data set generated by emaxsimB
plot.emaxsimobj	Plot dose response from a data set generated by emaxsim
plot.fitEmax	Plot a Emax model and dose group means.
plot.fitEmaxB	Plot a Emax model and dose group means.
plot.plotB	Plot Bayes dose response curve and dose group means
plotB	Plot Bayes dose response curve and dose group means
plotBdensity	Density plot displaying Bayes prior or posterior dose response
plotD	Basic plot of dose group means
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
predict.emaxsimB	Mean response and SE for each replicate data set in an emaxsimB object
predict.emaxsimBobj	Mean response estimates (posterior means) and SE (posterior SD) for specified doses for a simulated emaxsimBobj object
predict.emaxsimobj	Mean response and SE for specified doses for a simulated emaxsimobj object
predict.fitEmax	Estimated mean/proportion and confidence intervals derived from the maximum likelihood fit of a 3- or 4- parameter Emax model.
predict.fitEmaxB	Estimated mean and posterior intervals derived from a Bayesian hyperbolic or sigmiodial Emax model.
print.emaxPrior	Print protocol or sap text describing the prior distribution for the model parameters of the input emaxPrior object
print.emaxsim	Print simulation output from emaxsim
print.emaxsimB	Print simulation output from emaxsimB
print.emaxsimBobj	Print a summary of the fitted Emax model
print.emaxsimobj	Print a data set generated by emaxsim
print.fitEmax	Print a summary of the fitted Emax model
print.fitEmaxB	Print a summary of the fitted Bayesian Emax model
prior.control	Set the parameters of the prior distribution for the Emax model implemented in 'fitEmaxB'.
RandEmax	Random data constructor function for emaxsim creating random parameters for an Emax model for continuous or binary data.
randomEmax	Random data constructor function for emaxsim(B) creating random parameters for an Emax model for continuous or binary data.
runSimulations	Shiny app for function 'emaxsim(B)'
SeEmax	Asymptotic SE for dose response estimates from a 3- or 4- parameter Emax model
selEstan	Select a pre-compiled 'rstan' Emax model
showStanModels	Display 'STAN' model code.
sigma.emaxsim	Extract Emax model residual SD estimates
sigma.emaxsimB	Extract Emax model residual SD estimates
sigma.fitEmax	Extract Emax model residual SD estimates
sigma.fitEmaxB	Extract Emax model residual SD estimates
solveDose	Solve Emax function for target value
solveEmax	Solve Emax function for target value
startEmax	Compute starting parameter values for the 3- or 4- Emax model.
summary.emaxsim	Summary of output of emaxsim
summary.emaxsimB	Summary of output of emaxsimB
summary.emaxsimBobj	Summarize Emax fit to a data set generated by emaxsimB
summary.emaxsimobj	Summarize Emax fit to a data set generated by emaxsim
summary.fitEmax	Print a summary of the fitted Emax model
summary.fitEmaxB	Print a summary of the fitted Bayesian Emax model
targetBeta	Find a scaled Beta distribution matching specified probabilities
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.
update.emaxsimobj	Update estimation in a data set generated by emaxsim
vcov.emaxsim	Extract Emax model variance-covariance matrix for ML estimates
vcov.fitEmax	Extract Emax model variance-covariance matrix for ML estimates
[.emaxsim	Extract a simulation from the output of emaxsim
[.emaxsimB	Extract a simulation from the output of emaxsimB