Simulation and Analysis Tools for Clinical Dose Response Modeling


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Documentation for package ‘clinDR’ version 2.3.5

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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
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.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.
runShiny 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