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CVS commit: pkgsrc/misc/R-Hmisc
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 <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@localhost
* 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@localhost>
* 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.
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@localhost
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
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