2013-04-16 Bjoern Bornkamp (version 0.9-6) * optDesign Re-named "fmodels" argument to "models". * optDesign for solnp if lowbnd and uppbnd are specified now use a feasible starting value (otherwise solnp might get into problems). * plot.DRMod, plot.MCPMod now use lattice graphics * powMCT removed bug in case of placAdj = TRUE (thanks to Tobias Mielke for reporting this) * ess.mcmc minor change to avoid occasional NA's * Mods removed class c("Mods", "standMod"), now there is only a class "Mods", this changes the API of MCTtest, optContr and MCPMod function (direction argument no longer needed, as this info is now contained in the "Mods" object). * neurodeg added the simulated longitudinal dose-finding data set neurodeg * targN catch incorrect matrix dimension, when in case of only one alternative model * fitModel.bndnls old version used narrowed bnds for 1-dim model, when a starting value was supplied manually (instead of calculated via optGrid); fixed. * MCTtest re-name of p-value column to "adj-p". 2013-03-06 Bjoern Bornkamp (version 0.9-5) * targN, powN added function targN to evaluate a target function (e.g. power) for different sample sizes (similar to the old powerMM function). powN is a convenience function for multiple contrast tests using the power. * sampSizeMCT added convenience function for sample size calculation for multiple contrast tests using the power. * optContr Re-named "weights" argument to "w" 2013-02-12 Bjoern Bornkamp (version 0.9-4) * TD, ED Fixed bug for model = linInt and placAdj = TRUE * powMCT Fixed bug for nr(altModels)=1 in case placAdj=TRUE * Mods Add requirement that placebo dose needs to be included * print.bFitMod Do not show n.eff for bootstrap samples * ess.mcmc return NA, if there is just one unique value in chain * fitMod, MCTtest catch situations, where type = "normal" and placAdj = TRUE * bFitMod fixed bug for column names of linear model in case of placAdj = TRUE * MCPMod: Fixed sign error in model selection, when critV was specified 2013-01-29 Bjoern Bornkamp (version 0.9-3) * fitMod Improvements of efficiency (removed calls to do.call in optLoc) * MCPMod passes direction argument now also to TD * optDesign solnp is now the default optimizer * calcCrit default for arg designCrit in calcCrit changed (to harmonize calcCrit and optDesign) * bFitMod use fitMod.raw in bFitMod.bootstrap (for efficiency) * critVal Remove contMat argument (was unused) * powMCT Allow power calculation for placebo adjusted data 2013-01-09 Bjoern Bornkamp (version 0.9-1) * Complete re-structuring and tidying up of the package. Main ideas: (i) smoother integration of g-functions (ii) focus on core functionality (iii) more general code/easier extensibility. * New features: Bayesian dose-response fitting, nicer plots, optimal designs for non-normal responses, ... * Special Thanks to Tobias Mielke for testing of the package and numerous bug reports. * Previous versions of the source are available under http://cran.r-project.org/package=DoseFinding under "Old sources", a Windows binary of the last version before the changes is available under http://goo.gl/p1UZ7. 2012-08-22 Bjoern Bornkamp (version 0.6-3) * Added PACKAGE = "DoseFinding" to ".C" calls 2012-04-04 Bjoern Bornkamp (version 0.6-2) * calcOptDesign partial rewrite of optDes.c and optDesign.R to fix segfault bug. 2012-02-20 Bjoern Bornkamp (version 0.6-1) * vcov.gDRMod is now functional, predict.gDRMod now allows calculation of confidence intervals * gFitDRModel minor changes in underlying optimizer * explicitly export the gradients of the model functions now 2012-01-24 Bjoern Bornkamp (version 0.5-7) * gFitDRModel now always returns an estimate (either the best value from nlminb or from the grid search if nlminb fails) * gMCPtest: use sigma = corMat instead of corr = corMat in p/qmvnorm calls (mvtnorm complained in 1-dimensional case) * gFitDRModel: Introduced default for bnds argument. * plot.MCPMod: Plot clinRel in the right place, when direction is equal to "decreasing" (thanks to Jan Rekowski) * planMM, critVal: When vCov is specified now right correlation matrix is calculated * calcOptDesign: Additional argument (standDopt) to allow for optional standardization (division of the log determinant by the number of parameters) of the D-optimal design criterion. 2011-10-19 Bjoern Bornkamp (version 0.5-6) * getGrid corrected bug for Ngrd > 75025 * calcOptDesign: For method = "exact" and n2 > 0 the function did not return the optimal incremental design but the overall optimal design 2011-08-31 Bjoern Bornkamp (version 0.5-5) * gFitDRModel can now fit dose-response models without intercept * gMCPtest minor changes to allow for user defined contrast matrix 2011-08-09 Bjoern Bornkamp (version 0.5-4) * MCPtest now uses correct degrees of freedom if addCovars != ~1 * Feedback from Andreas Krause led to a number smaller changes in the package (e.g., plot.(g)DRMod or fitDRModel). Thanks Andreas! * Print lattice plots explicitly to increase compability with Sweave. 2011-05-06 Bjoern Bornkamp (version 0.5-3) * Ensure in rndDesign that N is recognized as an integer by using N <- round(N), to avoid floating point problems. * Remove naming bug in gFitDRModel (drFit instead of drEst) 2011-04-27 Bjoern Bornkamp (version 0.5-2) * Corrected bug in b-vector for sigEmax model (calcBvec, only affected MED-type optimal designs) * Included INDEX file to order the overview help-page better * predict.DRMod now stops when type = "fullModel" and the argument newdata does not contain values for all variables specified in addCovars (thanks to Mouna). 2011-03-25 Bjoern Bornkamp (version 0.5-1) * Restructured calcOptDesign function to allow for user defined criteria functions. * The MCPMod object now always contains a estDose and fm entry (which is NA in case of non-significance or non-convergence) * Added generalized fitting code, variances and covariances of estimates are not available at the moment. * Added vCov argument to planMM, sampSize, powerMM (so it is possible to take into account covariances when calculating optimal contrasts) * Changed order in trellis plots in plotModels (order as specified in models list instead of alphanumerical order) * Restructured and summarized help pages * Removed dependency on numDeriv package (only suggested now), this is only needed for calculating optimal designs involving the beta model. 2011-02-09 Bjoern Bornkamp (version 0.4-3) * Minor change in Makevars file (so that DoseFinding works on Solaris). 2011-02-09 Bjoern Bornkamp (version 0.4-2) * calcBayesEst, getUpdDesign: Minor changes to make functions more suited for general purpose use. 2010-12-01 Bjoern Bornkamp (version 0.4-1) * Introduced new functions calcBayesEst and getUpdDesign, both were used for simulation purposes in the paper Bornkamp et al. (2011) "Response Adaptive Dose-Finding under Model Uncertainty" (to appear in Annals of Applied Statistics). 2010-11-12 Bjoern Bornkamp (version 0.3-1) * calcOptDesign now has an additional optimizer "exact". This methods calculates all possible designs for a given sample size and then selects the best. * Changed order in MakeVars as requested * calcCrit now checks whether there are not less design points than parameters. * Code now checks for positive sigma in powCalc and powerMM 2010-11-05 Bjoern Bornkamp (version 0.2-3) * MED function now checks for clinRel > 0 (thanks to Georgina). * Changed minor bug in output from print.MCPtest (print one-sided just once) * Code now outputs a warning, when 'models' argument is missing (in MCPMod and fullMod function); in fitDRModel it outputs a warning if 'model' is missing * Introduced a default base = 0 and maxEff = 1 for the plotModels function. * Added a summary method for DRMod objects. * Removed superfluous addCovarVals argument from predict.DRMod * Removed option method = "mult" in calcOptDesign 2010-07-08 Bjoern Bornkamp (version 0.2-2) * calcCrit and calcOptDesign now check for NA, NaN or +-Inf values in the gradient and bvector (and stop execution when these values occur) before passing these values to the C code. * Introduced a logLik method for DRMod objects * Changed mvtnorm.control default argument for "interval" to reflect recent changes in mvtnorm package. 2010-05-27 Bjoern Bornkamp (version 0.2-1) * Made the getGrad function (gradient for dose-response model), including documentation available for end-user (was previously hidden in NAMESPACE) * Changes in the plot.MCPMod function (col argument for panel.superpose was read in different order depending on lattice options, now there is a manual workaround with panel.xyplot calls for each group) 2010-05-20 Bjoern Bornkamp (version 0.1-3) * Smaller changes in calcCrit functions (the parameter p is now calculated by the nPars function as in getOptDesign) * Add further options to powerScenario function (now possible to for user-specified row and column names for output matrix) 2010-05-13 Bjoern Bornkamp (version 0.1-2) * Removed one example from sampSize to reduce check time. * modelSelect: Use first model when two models have exactly the same AIC or BIC value. * predict.DRMod: Return NA as standard deviation if code cannot calculate Cholesky transformation of covariance matrix (thanks to Setia Pramana for the hint). * calcCrit: Code now allows for specifying multiple designs in a matrix. 2010-04-14 Bjoern Bornkamp (version 0.1-1) * fitModel.nls now checks whether nls with plinear option made a positive number of iterations (as additional convergence check). In some cases (eg. when number of parameters = number of doses) plinear does not do any iteration and does *not* put out a warning message that the algorithm failed. * The calcOptDesign function now allows for upper and lower bounds on the allocation weights. * There is no longer the need to specify clinRel, when one wants to calculate a D-optimal design. * Output of bootMCPMod function in case of model averaging now also includes dose estimates under each model & corrected bug in print.bootMCPMod function (thanks to Setia Pramana) 2010-03-08 Bjoern Bornkamp (version 0.1) * 1st Release as version 0.1. Improvements over MCPMod package: - Extended and improved version of MCPMod (allowing for covariates and robustified self-developed optimizer) - Functions for MCP (MCPtest) and Modelling (fitDRModel) part now available to the user - New functions (eg. bootMCPMod, powerScenario) - Functions for calculating optimal designs