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misc/RHmisc,
Harrell miscellaneous
Branch: CURRENT,
Version: 4.7.0,
Package name: RHmisc4.7.0,
Maintainer: pkgsrcusersContains many functions useful for data analysis, highlevel graphics,
utility operations, functions for computing sample size and power,
importing and annotating datasets, imputing missing values, advanced
table making, variable clustering, character string manipulation,
conversion of R objects to LaTeX and html code, and recoding
variables.
Required to run:[
lang/g95] [
math/R] [
graphics/RlatticeExtra] [
math/Rgtable] [
graphics/Rggplot2] [
textproc/Rhtmltools] [
converters/Rbase64enc] [
math/Racepack] [
math/RFormula] [
graphics/Rviridis] [
textproc/Rdata.table] [
textproc/RhtmlTable]
Required to build:[
pkgtools/cwrappers]
Master sites: (Expand)
Version history: (Expand)
 (20220425) Updated to version: RHmisc4.7.0
 (20190731) Package added to pkgsrc.se, version RHmisc4.2.0 (created)
CVS history: (Expand)
20220505 01:07:00 by Makoto Fujiwara  Files touched by this commit (1) 
Log message:
(misc/RHmisc) TEST_DEPENDS x 9 added, more missing

20220425 15:29:17 by Makoto Fujiwara  Files touched by this commit (2) 
Log message:
(misc/RHmisc) Updated 4.2.0 to 4.7.0, fix build against R4.2.0
Changes in version 4.70 (20220418)
* 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 crossreference
Changes in version 4.60 (20211005)
* 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/rpackagedevel/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 4.50 (20210227)
* 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 4.42 (20201125)
* 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 4.41 (20200807)
* 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 multistate 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 zerolength 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 4.40 (20200322)
* 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 4.31 (20200207)
* Depend on survival >= 3.16
* 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 4.30 (20191107)
* 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 datetimes, for Gmd not format as
datetime
* 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

20211026 12:59:39 by Nia Alarie  Files touched by this commit (378) 
Log message:
misc: Replace RMD160 checksums with BLAKE2s checksums
All checksums have been doublechecked against existing RMD160 and
SHA512 hashes
The following distfiles could not be fetched (possibly fetched
conditionally?):
./misc/libreoffice/distinfo libreoffice/harfbuzz2.6.4.tar.xz

20211007 16:35:55 by Nia Alarie  Files touched by this commit (378) 
Log message:
misc: Remove SHA1 hashes for distfiles

20190927 00:14:06 by Brook Milligan  Files touched by this commit (1) 
Log message:
Add a missing dependency on graphics/RlatticeExtra.

20190808 21:53:58 by Brook Milligan  Files touched by this commit (189)  
Log message:
Update all R packages to canonical form.
The canonical form [1] of an R package Makefile includes the
following:
 The first stanza includes R_PKGNAME, R_PKGVER, PKGREVISION (as
needed), and CATEGORIES.
 HOMEPAGE is not present but defined in math/R/Makefile.extension to
refer to the CRAN web page describing the package. Other relevant
web pages are often linked from there via the URL field.
This updates all current R packages to this form, which will make
regular updates _much_ easier, especially using pkgtools/R2pkg.
[1] http://mailindex.netbsd.org/techpkg/2019/08/02/msg021711.html
