Received: by mail.netbsd.org (Postfix, from userid 605) id D928D84D8C; Mon, 25 Apr 2022 13:29:19 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id 1D17984D23 for ; Mon, 25 Apr 2022 13:29:19 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([127.0.0.1]) by localhost (mail.netbsd.org [127.0.0.1]) (amavisd-new, port 10025) with ESMTP id Ez8-qPqn1pDz for ; Mon, 25 Apr 2022 13:29:18 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.NetBSD.org [IPv6:2001:470:a085:999:28c:faff:fe03:5984]) by mail.netbsd.org (Postfix) with ESMTP id E097084CEF for ; Mon, 25 Apr 2022 13:29:17 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id CCE84FB1A; Mon, 25 Apr 2022 13:29:17 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1650893357110110" MIME-Version: 1.0 Date: Mon, 25 Apr 2022 13:29:17 +0000 From: "Makoto Fujiwara" Subject: CVS commit: pkgsrc/misc/R-Hmisc To: pkgsrc-changes@NetBSD.org Reply-To: mef@netbsd.org X-Mailer: log_accum Message-Id: <20220425132917.CCE84FB1A@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_1650893357110110 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: mef Date: Mon Apr 25 13:29:17 UTC 2022 Modified Files: pkgsrc/misc/R-Hmisc: Makefile distinfo 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 * 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 * 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 To generate a diff of this commit: cvs rdiff -u -r1.3 -r1.4 pkgsrc/misc/R-Hmisc/Makefile \ pkgsrc/misc/R-Hmisc/distinfo Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1650893357110110 Content-Disposition: inline Content-Length: 1459 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/misc/R-Hmisc/Makefile diff -u pkgsrc/misc/R-Hmisc/Makefile:1.3 pkgsrc/misc/R-Hmisc/Makefile:1.4 --- pkgsrc/misc/R-Hmisc/Makefile:1.3 Thu Sep 26 22:14:05 2019 +++ pkgsrc/misc/R-Hmisc/Makefile Mon Apr 25 13:29:17 2022 @@ -1,7 +1,7 @@ -# $NetBSD: Makefile,v 1.3 2019/09/26 22:14:05 brook Exp $ +# $NetBSD: Makefile,v 1.4 2022/04/25 13:29:17 mef Exp $ R_PKGNAME= Hmisc -R_PKGVER= 4.2-0 +R_PKGVER= 4.7-0 CATEGORIES= misc MAINTAINER= pkgsrc-users@NetBSD.org Index: pkgsrc/misc/R-Hmisc/distinfo diff -u pkgsrc/misc/R-Hmisc/distinfo:1.3 pkgsrc/misc/R-Hmisc/distinfo:1.4 --- pkgsrc/misc/R-Hmisc/distinfo:1.3 Tue Oct 26 10:58:56 2021 +++ pkgsrc/misc/R-Hmisc/distinfo Mon Apr 25 13:29:17 2022 @@ -1,5 +1,5 @@ -$NetBSD: distinfo,v 1.3 2021/10/26 10:58:56 nia Exp $ +$NetBSD: distinfo,v 1.4 2022/04/25 13:29:17 mef Exp $ -BLAKE2s (R/Hmisc_4.2-0.tar.gz) = 62e637c02306ff3c779ee64998a60e28abb8b26f75820688806fad9776b04f6d -SHA512 (R/Hmisc_4.2-0.tar.gz) = 370cabd67c8c2016ecfd57e096f8de31a5cea5bbced9cf19d470214eb55e8979d34e7433361c3ceeaed26ea78aa6c0288c5a3d0104732ff80d77b4e5f8d0fd72 -Size (R/Hmisc_4.2-0.tar.gz) = 732731 bytes +BLAKE2s (R/Hmisc_4.7-0.tar.gz) = 5e12932f1a38f4cf50ab92d1ade6c04790317c8bd08a14600c0c90733b8e2381 +SHA512 (R/Hmisc_4.7-0.tar.gz) = cf6dd96f21536fac5b64090f2e88b426fae513fba02ef1fc2ad08286d3061a99c9a58b1280091ddc27810210135daf7ba5c64fca26d3cdb850fe951dff48b4d1 +Size (R/Hmisc_4.7-0.tar.gz) = 790794 bytes --_----------=_1650893357110110--