                 Changes in version 2.5.2 (2025-10-02)                  

    o   Updated code for compatability with newer versions of R and rstan.  
	Several bug fixes included.

                 Changes in version 2.4.1 (2023-08-09)                  

    o   The prior distribution for fitEmaxB and emaxsimB by default now 
	truncate the ED50/P50 distribution to (0.001,1000), and truncate 
	the lambda distribution to (0.3,4.0).  Along with adjustments to 
	the MCMC default control parameters, divergences reported by STAN 
	have been largely eliminated.  These changes, along with some changes 
	to the iternal parameterization of the STAN model, produce
	small numerical changes from past versions of clinDR

                        Changes in version 2.3.7                        

    o   Function fitEmaxB can now be applied to first-stage fitted
	output with correlation between the initial dose group estimates.  
	The function checkMonoEmax is now deprecated and replaced by the
	function bpchkMonoEmax with input now the output object of
	function fitEmaxB.

    o   The shiny app has been renamed runSimulations.  It has been
	extensively updated

                        Changes in version 2.3.6                        

    o   Added print function for prior objects created by 
	emaxPrior.control().  The output is a text file that
	describes the prior distribution.  There is an option ('sap')
	for a more detailed version appropriate for an SAP, and a
	shorter version for protocols.  The RandEmax function is 
	now deprecated and replaced by randomEmax, which generates
	data with Emax model parameters now generated from a 
	distribution described by the object output of 
	emaxPrior.control().

                 Changes in version 2.3.5 (2021-04-12)                  

    o   Added shiny interface for emaxsim(B) initiated with runShiny()

    o   Changed the default prior scale parameter for loglambda from 
	0.85 to 0.425.  This change effects fitEmaxB and emaxsimB

    o   Changed the default sample size in mcmc.control to yield 9999
	samples of the model parameters by default

                  Changes in version 2.3 (2020-07-01)                   

    o   Added percentiles of the posterior distribution of the 
	model parameter to the output object of emaxsimB

    o   Standardized default Emax model to 4-parameter sigmoid.  
	Changes made to fitEmax and emaxsim that may affect
	execution of older code.

    o   Standardized confidence/posterior level to clev=0.9.  
	Changes made to summary.emaxsimB, plotB, plotD, targetCI.

    o   SE calculation adjusted by add 1/2 0/1 to rates in
	emaxsim(B) to avoid NA in pairwise comparisons with
	low response rate data

    o   Several minor bug fixes in emaxsim

                         Changes in version 2.2                         

    o   metaData updated with removal of a duplicate 
	compound-indication.  Meta-prior default values
	also updated in second decimal places.

                         Changes in version 2.1                         

    o   New parameterization of the Emax function has been implemented in
	fitEmaxB and emaxsimB.  The 'emax' parameter has been replaced by
	the difference in response at a targeted dose versus placebo.  Corresponding 
	changes have been made in the supporting methods.  Each parameter nows
	has a prior t-distribution with DF that can be specified.  The default
	values in the prior distributions are based on meta-data updated through
	August 2019.

    o   The proportion of divergent MCMC iterations for each emaxsimB 
	simulated analysis is now returned as part of the output

    o   Plot symbols are printed on top of error bars for better visibility

    o   Several bug fixes for function plotB relating to plots with active
	controls.  xat option added to control axis labeling. The dac option was 
	removed.

    o   Plotting of Bayes estimates in fitEmaxB and plotB is now based (default) on the posterior median
	rather than the mean to avoid problems with occassion extreme values in MCMC output.  Posterior
	medians were added to means in output of predict.fitEmaxB.

    o   Changed log option to logScale option in plotting functions to avoid masking of the log function.

    o   Meta data in examples14 and examples16 has been replaced by the data metaData, which aggregates all
	of the dose response meta data from previous studies through August 2019.  The meta data from all 
	compounds are now in a single file with a common format.

    o   Added functions solveDose and solveEmax.  solveDose returns the dose yielding a target
	response for the input Emax model parameters.  solveEmax returns the Emax parameter 
	yielding a target response at a specified dose

                        Changes in version 1.9.5                        

    o   Additional input error checking

    o   pboAdj in fitEmax can now fit multiple protocols with/without placebo
	adjustment
	= Changed check for centered covariates in fitEmax(B) to accept larger difference with zero

    o   Created new metaData with all dose response studies included in 
	the meta-analyses through Aug 2019.  A new unified data format is used. 
	The older examples14 and examples16 data have been removed (they are 
	part of metaData)

                  Changes in version 1.9 (2019-01-04)                   

    o   Add support for baseline covariates in fitEmax, fitEmaxB and supporting
	functions

    o   Add showStanModels function to display the STAN code for Emax models

    o   Corrected output of popSD naming in emaxsim extraction function

    o   Consolidated Bayesian Emax models into a single STAN model file.  
	Specification of model type (e.g., hyperbolic vs sigmoidal) is no 
	longer required in selEstan and showStanModels functions

    o   The 'logit' parameter in function checkMonoEmax was re-named 'binary'

    o   Return printed matrices as invisible objects in print.emaxsim(B) and
	print.emaxsim(B)obj 

                  Changes in version 1.8 (2018-05-04)                   

    o   Added testMods of class Mods from R package DoseFinding to the
	output object of emaxsim(B).  testMods gives the functions defining the
	contrasts for MCP-MOD testing.  The ED50contr and lambdacontr that
	can also be used to define the contrasts were removed.

    o   Added coef,sigma, and vcov methods for fitEmax(B), emaxsim(B) objects

    o   The summary.emaxsim and summary.emaxsimB functions now
	return the printed output for extraction.  Summaries for
	the best pairwise comparison were added.

    o   Corrected use of specified starting values in function emaxalt and emaxsim.

    o   Improved error handling in emaxsim(B) to reset random number generator

                  Changes in version 1.7 (2018-02-19)                   

    o   The calling sequence for 'plotPop' in plot.emaxsimobj and
	plot.emaxsimBobj have been changed to ensure a valid value
	is input.

    o   The parameter difPlacebo has been renamed plotDif in
	plot.emaxsim and plot.emaxsimB for consistency with other 
	plotting functions

    o   Corrected bug in MCP-MOD test with negative trends

    o   Corrected bug causing warning messages from DRDensityPlot
	when the quantiles have row or column names

    o   Corrected plotting of population curve at placebo in
	plot.emaxsimB

                  Changes in version 1.6 (2017-12-04)                   

    o   Change package dependencies

    o   Additional documentation for CRAN release

    o   Modify examples for CRAN release

                        Changes in version 1.05                         

    o   Fix bug in parallel processing for emaxsim and emaxsimB

    o   Fix bug in residSD input to customCode in emaxsimB

                        Changes in version 1.04                         

    o   RandEmax can now generate random residual SD from a scaled inverted chi distribution

                        Changes in version 1.03                         

    o   Added prediction interval option to plot.emaxsimobj

    o   Expanded output from emaxsimB when check=TRUE so
	test data for custom code can be generated

                        Changes in version 1.02                         

    o   Improved labeling of output of predict.fitEmax(B) 

    o   Add descriptive label to plot.emaxsim(B) to indicate difference with placebo by default

    o   Corrected bug in emaxsim output of residual SD.  This impacts predictive intervals from several functions.

                        Changes in version 1.01                         

    o   Major update adding Bayesian versions of fitEmax and emaxsim

    o   Supporting methods, e.g., plot, print,... also supplied for
	new Bayesian functions fitEmaxB and emaxsimB

    o   Parallel computing options added for the Bayesian functions

                       Changes in version 0.9.6.5                       

    o   Added log scale option to plot.plotB.R, plotD.R, plot.fitEmax.R, plot.emaxsimobj.R. 
	If plot=plotDif (difference with placebo) and log=TRUE, 
	the plot starts from the lowest nonzero dose.

    o   Improved active control plotting in plot.plotB.R.

    o   Added optional user-specified control over x-axis tick marks.

                       Changes in version 0.9.6.4                       

    o   In checkMonoEmax, included equality in predictive probability calculation.

    o   In plot.fitEmax, if there is no grouping variable, then no panel at the top
	of the plot is created.  The function now returns a list with the ggplot2 
	object and a matrix with the confidence and prediction interval limits.

                       Changes in version 0.9.6.3                       

    o   Added grouped-data option to checkMonoEmax, and test data.

    o   Corrected plotting issue in plotB.

                       Changes in version 0.9.6.2                       

    o   Updated code for fitEmax test statistics.  plot.fitEmax predictive
	 error bars now use the smallest sample size for a dose/strata combination.

    o   plotB now returns the ggplot object so it can be further modified.

    o   fitEmax can now use non-integer prot variable.

                        Changes in version 0.9.6                        

    o   Added binary logistic Emax model fitting to emaxsim and all associated
	 functions

    o   Changed check of the variance-covariance matrix in fitEmax to ensure it
	 is positive definite

    o   Eliminated femax and femaxH

    o   Replaced RandEmax with skewRandEmax and eliminated the name skewRandEmax

                       Changes in version 0.9.5.1                       

    o   Corrected bug in predictive interval for binary data in plot.fitEmax

                        Changes in version 0.9.5                        

    o   Added treatment difference option to plot.fitEmax

    o   Updated implementation of symbol group in plotB

    o   Corrected bugs in prediction intervals in plot.fitEmax

    o   Added treatment difference estimation to predict.fitEmax

    o   Updated emaxsim and its support functions to use fitemax
	 and its support functions

                        Changes in version 0.9.4                        

    o   Added GOF tests to fitEmax output

    o   Fixed symbol bug in plot.fitEmax and plot.logitEmax

    o   Fixed fitEmax and logitEmax to return NULL when convergence fails.

    o   Created fitEmax to unify fitting of Emax models with continuous/binary data

                        Changes in version 0.9.3                        

    o   Updated all graphic output to use ggplot2

    o   Changed order of Emax model parameters to better support fitting 
	 of data from multiple protocols with different placebo response.
	 Order of parameters in logitEmax also changed for consistency across
	 all Emax functions.

    o   Created new function contEmax to fit continuous emax models using
	 ML estimation along with supporting plot and predict functions

    o   Added plot symbol options and residual plots to plot.contEmax and
	 plot.logitEmax

    o   Fixed bug in 4-parameter binary data case for  startEmax

    o   Fixed bug in predictive intervals in plot.logitEmax

    o   Changed default confidence/posterior interval levels to 0.90

                        Changes in version 0.9.2                        

    o   led50 replaces ed50 everywhere.

    o   Changed options for skewRandEmax

    o   Last version before changes to graphics. 

                        Changes in version 0.9.1                        

    o   Numerous changes to DoseResponse package.  The biggest change was to eliminate
	 transformation of the Hill parameter. 
