# Simulation and Analysis Tools for Clinical Dose Response Modeling

## Documentation for package ‘clinDR’ version 1.9

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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
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
emaxsim | Simulate Emax maximum likelihood estimation
emaxsimB | Simulate Emax Bayesian estimation
examples14 | Data from 2014 dose response meta-analysis
examples16 | Data from 2016 dose response meta-analysis
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'
meta14 | Data from 2014 dose response meta-analysis
meta16 | Data from 2016 dose response meta-analysis
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.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.
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
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