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Log Message: (misc/R-Hmisc) Updated 4.2.0 to 4.7.0, fix build against R-4.2.0 Changes in version 4.7-0 (2022-04-18) * html.contents.data.frame: properly closed html <a> * simPOcuts: new function to demonstrate variation in odds ratios due to random chance * R2Measures: new function to compute various pseudo R^2 measures * putHcap: added new capabilities around the subsub argument * print.summary.formula.response: added markdown argument * knitrSet: added rudimentary quarto support * knitrSet: sense figure labels of the form fig-... used by Quarto, and generate correct cross-reference Changes in version 4.6-0 (2021-10-05) * package: improved author formatting in DESCRIPTION * html: markupSpecs$html$session: added citations for any Harrell packages that are loaded, respecting current output format in effect with knitr * soprobMarkovOrdm: new function to compute state occupancy probabilities from proportion odds model fits * plotCorrM: new function to graph correlation matrices and gap time relationships using ggplot2 * ggplotlyr: new function to use plotly::ggplotly to render ggplot2 graphs but intercepting hover text to remove extraneous labels * Fixed Heiberger email address * propTrans: removed zero frequency combinations * combplotp: fixed bug in case regarding recognition of positives nnn * propsPO: fixed making y factor * soprobMarkovOrdm: added as.data.frame(generated data) * estSeqMarkovOrd: extended timecriterion function to allow user to return the event/censoring time and indicator, and to allow groupContrast to compute using a variance formula * estSeqMarkovOrd: trapped errors better, returning attribute failures, and added maxest and maxvest argument to declare large parameter or variance estimates as failed iterations; changed from vgam to vglm and sped up computations by using previous coefficient estimates as starting values * session in markupSpecs: added citations for several other packages * soprobMarkovOrdm: extended to work with VGAM package * describe: fix error with . (thanks to Cole Beck; https://github.com/harrelfe/Hmisc/pull/144) * many: tests for presence of suggested packages using requireNamespace (thanks for major editing work by Duncan Murdoch at https://github.com/harrelfe/Hmisc/pull/143 motivated by https://stat.ethz.ch/pipermail/r-package-devel/2021q2/007101.html) * mdb.get: fix for Windows by changing from system to system2 (thanks to Rainer Hurling at https://github.com/harrelfe/Hmisc/pull/135) * summaryM: fixed error with prN=TRUE with latex (thanks Matt * Shotwell in https://github.com/harrelfe/Hmisc/pull/109) * many: fix partial argument matching warnings length -> * length.out in rep (thanks Bill Denney in * https://github.com/harrelfe/Hmisc/pull/128) * rcspline.restate: was dropping + for exactly zero coefficients (thanks https://github.com/harrelfe/Hmisc/pull/118) * mdb.get: remove brackets from table names (thanks https://github.com/harrelfe/Hmisc/pull/123) * latex: added new argument comment so that the generated comment can be suppressed (thanks Giuseppe Ragusa https://github.com/harrelfe/Hmisc/pull/33) * sas.get: added new argument for variable case (thanks Tyler Hunt https://github.com/harrelfe/Hmisc/pull/8) * format.df: changed to use system option OutDec when cdot is not specified (thanks https://github.com/harrelfe/Hmisc/issues/142) * C code: changed calls to warning/error routines * formatdescribeSingle: changed for character value to make 'NA' work Changes in version 4.5-0 (2021-02-27) * approxExtrap: changed x and y to as.numeric. Thanks: juha.heikkinen@luke.fi * upData: fix column subsetting for data.tables * dotchartpl: intercepted missing Diff * simMarkovOrd, soprobMarkovOrd, intMarkovOrd, estSeqMarkovOrd: new functions for Markov proportional odds model simulation and calculation of state occupancy probabilities * ggfreqScatter: added by argument * VGAM package added to Suggests in DESCRIPTION * html markupSpecs mdchunk: added caption argument, allowed for vectors * propsTrans: added labels argument for plotly, added numerators and denominators in tooltips, fixed bug where factor levels were reversed if odds.ratio specified Changes in version 4.4-2 (2020-11-25) * rcorr: captured loss of precision leading to square root of a negative number. Thanks: Ann Voss <avoss@novanthealth.org> * summaryS: sapply was doubling names * pairUpDiff: created for dotchartpl - function to pair up grouped observations for sorting by descending differences and computing approximate confidence intervals for the difference given individual confidence limits * dotchartpl: added new arguments and functionality to handle quantities other than proportions (e.g., hazards) and streamlined code using pairUpDiff * propsPO: added tooltip text for gpplot that will be transmitted to ggplotly; reversed order of categories so lowest category put at bottom of bar * dotchartpl: suppressed confidence intervals when the number of groups is not 2; fixed bug where hover text confidence intervals were repeats of the last computed interval instead of properly using all the intervals; added dec argument * added estSeqSim and gbayesSeqSim functions * ggfreqScatter: stopped varying alpha and just varied color, as alpha collided with the color scheme * histSpike: added minimal=TRUE and bins arguments Changes in version 4.4-1 (2020-08-07) * popower: added approximate S.E. of log(OR) in results * propsPO: new function for exploring proportional odds * propsTrans: new function for showing distributions of successive state transitions * changed acepack to suggests * multEventChart: new function for multi-state event charts based on code written by Lucy D'Agostino McGowan * getHdata: changed to use hbiostat.org/data/repo * markupSpecs$markdown$tof: new function to render a table of figures with short captions * knitrSet: added capfile argument to store figure tags and short captions * getLatestSource: changed to use GitHub and hbiostat.org/R/packagename/dir.txt * histboxpM: added width argument * upData: handled zero-length subsets (Thanks: Will Gray) * upData: made faster for large datasets * ffCompress: removed from package and put in Github Rscripts * Changed maintainer email Changes in version 4.4-0 (2020-03-22) * combplotp: new function for attribute plots with plotly * summaryP: made to work with new default stringsAsFactors=FALSE * plotlyM: fixed bug where need to unlist if only one graph produced * plotlyM: added ECDF support through fitter='ecdf' * keepHattrib, restoreHattrib: new functions for saving Hmisc attributes that can be restored later, e.g., after data.table processes a data frame Changes in version 4.3-1 (2020-02-07) * Depend on survival >= 3.1-6 * pomodm: checked that x is sorted * markupSpecs: added ord function for ordinal representation of integers * mChoice: removed unused argument sort. from help file Changes in version 4.3-0 (2019-11-07) * Corrected typos in aregImpute help file. Thanks: Mark Seeto. * describe: changed to print 5 lowest and highest values even if frequency table printed, added a line of printed output specifying any rounding done for the frequency table * vcov.fit.mult.impute: use vcov.orm if object has orm class. intercepts=mid logic was not working for this * New service function convertPdate to do automatic date conversions and handle partial dates such as YYYY and mm/YYYY with imputation, for cleanup.import * cleanup.import: new arguments autodate, autonum, fracnn * describe: formatted dates if there is only one distinct value; changed to sense date or date-times, for Gmd not format as date-time * plot.describe: treated date/time variables as numeric * cleanup.import: refined autonum considerNA * ggfreqScatter: added stick=TRUE argument * markupSpecs: changed math and similar functions to use ... argument instead of x * summaryDp: new function for plotly dotcharts stratifying separately on a series of variables * dotchartpl: added height argument * html.describe: fixed but where markupSpecs$html utility function last arguments were not named in calls

Revision | Action | file |

1.4 | modify | pkgsrc/misc/R-Hmisc/distinfo |

1.4 | modify | pkgsrc/misc/R-Hmisc/Makefile |