Log message:
(misc/R-Hmisc) Updated 5.1.0 to 5.1.1

Changes in version 5.1-1 (2023-09-11)

   * meltData: generalized to allow melting on either left or right
     side of formula, added ... arguments passed to label(), made
     variable a factor to keep original order
   * formatCons: fixed bug where lang != 'latex' should have been lang
     == 'plain' which made msdsize to be ignored for html output
   * spikecomp: made more reliable by not assuming as much about
     pretty() boundaries
   * redun: added rank and qrank options
   * added print and plot methods for princmp
   * redun: added ability to use numeric matrix instead of formula
   * ggplot.transcan: fixed bug when adata is empty
   * ggplot.transace: new function
   * transace: added trantab result, added as.matrix(x) so can run on
     data frames of all numeric variables; added automatic setting of
     binary, category, etc. if x is a data frame/table;
     non-downward-compatible change: made returned object of class
     transace with different format; remove pr and pl arguments from
     transace.  Changed first argument to a formula and required
     monotone(), categorical(), linear() to wrap variables in the
     formula instead of specifying with separate arguments
   * runParallel: put in NAMESPACE
   * qcrypt: new function for encrypting and decrypting data with a
     safe workflow
   * aregImpute: added constraint argument to allow general
     constraints on values imputed with predictive mean matching

Log message:
(misc/R-Hmisc) Updated 4.8.0 to 5.1.0

Changes in version 5.1-0 (2023-05-04)

   * fit.mult.impute: added robust, cluster, robmethod arguments to
     incorporate rms::robcov to do robust sandwich covariance
     estimation with multiple imputation

   * testCharDateTime: new function
   * added totxt function in markupSpecs$html to convert html to plain text
   * describe.vector: fixed for mChoice variables with plain output, fixed NA \ 
dection for mChoice in general; added shortmChoice option, now defaulting to \ 
printing mChoice summary using numeric codes, and printing levels once up front; \ 
changed back to old behavior of not printing extremes if frequency table is \ 
printed; changed printing of lowest and highest 5 values to 6 significant digits \ 
if numeric; added argument rmhtml to strip html from variable labels
   * mChoice: changed result to NA instead of '' if no choices are made and \ 
add.note=FALSE; fixed label; improved print.summary.mChoice formatting
   * htmlVerbatim: removed blank line before </pre>
   * htmltabv: new function to make simple html table of a series of verbatim \ 
outputs from print() of objects
   * summary.mChoice: added short= argument
   * print.summary.mChoice: if options(prType='html') is in effect, calls \ 
htmltabv to compose output in a space-savings 2-column html table, and renders \ 
entire output in html
   * describe: retrieved format* attribute of variables
   * vlab: fixed bug
   * dotchartp: fixed bug when sort was logical resulting in o=NULL; changes in \ 
R made x[NULL,] quit working
   * vlab, hlab, hlabs: improved logic and also look in global environment
   * spikecomp: added new options that facilitate sparklines
   * html.data.frame: added new argument disableq to disable Quarto table style
   * describe: for html use disableq for html.data.frame
   * added gt, sparkline, jsonlite packages to SUGGESTS
   * added which= argument to print.describe
	 * html_describe_cat, html_describe_con: new internal functions to print gt \ 
tables when which= is given to print.describe
   * describe: for date/time variables use lowest observed value for leftmost \ 
point of first bin, instead of pretty()
   * describe: compute min, max, mean no. of characters (after trimming white \ 
space) for character variables that are not tabulated because of too many \ 
levels; used by html_describe_cat; also added mode and its count for this \ 
situation
   * htmlwidgets: added to SUGGESTS
   * html.describe: changed html to Hmisc::html to avoid conflicts with gt
   * describe: added trans argument to transform x for the purpose of making \ 
spike histograms
   * spikecomp: generalized, describe.vector now calls it, changed how \ 
addggLayers calls it
   * fit.mult.impute: added method= including stacking to facilitate likelihood \ 
ratio tests with rms::processMI
   * histboxp, dhistboxp: fixed bugs where range() should have been diff(range())
   * fit.mult.impute: for stacked ols fits correct residual d.f.

Changes in version 5.0-1 (2023-03-06)
   * rendHTML: when knitr is not running and object is not html, assumes it is \ 
RMarkdown and calls rmarkdown::render to render it to html, then displays in \ 
viewer
   * princmp: new function to help in interpreting principal components and \ 
sparse principal components
   * getabd: new function to fetch datasets from The Analysis of Biological Data
   * runParallel: new function to make the parallel package easy to use and to \ 
improve structure of combined final result
   * hashCheck: new function to run digest::digest on a series of argument to \ 
create a hash, fetch an existing result file which contains the hash of the \ 
input objects the last time an analysis was run, and to return the results \ 
stored in the file (an .rds file) if the hashes match, or NULL otherwise
   * runifChanged: new function to re-run code if an input changed, as judged by \ 
hashChech
   * hlab: new function to retrieve plotting-formatted variable label from a \ 
current dataset or from the object created by extractlabs (LabelsUnits, which \ 
takes priority)
   * hlabs: new function to call ggplot2 labs() after running variable names \ 
through hlab()
   * vlab: new function like hlab but returns text string form of label/units
   * extractlabs: new function: for one or more data frames/tables saves a data \ 
table of all variables that had a non-blank label or units attribute.
   * nCoincident: new function to count the number of x,y pairs that are likely \ 
to be coincident, i.e., hidden from view in a scatterplot
   * meltData: new function to take a formula and melt a data frame/table so \ 
that all right-hand-side formula variables are played against the left-hand side \ 
variable
   * ebpcomp: new function to compute coordinates of components of an extended \ 
box plot.  Along with spikecomp these are useful for adding things to ggplot2 \ 
graphs.
   * spikecomp: new function to compute coordinates of components of a spike \ 
histogram
   * movStats: new general function for estimating the relationship between a \ 
continuous variable and a response, possibly stratified by another variable
   * csv.get: changed autodates to autodate and passed to cleanup.import; \ 
implemented text=
   * fImport: new function; front-end for `rio` package for general file import
   * transcan.Rd: added new example for completing a data frame with single \ 
imputations
   * combine.levels: added plevels argument and implemented new capabilities for \ 
ordered variables, for which only consecutive levels are allowed to be combined
   * fit.mult.impute: added fun argument so user can run any function on each \ 
fit from a completed dataset, e.g., a model validation using an rms function
   * errbar: passed argument main to last instance of plot()
   * princmp: fixed sparse PC total variance explained by asking for k PCs where \ 
k is one less than number of columns
   * removed dependencies for Formula (importFrom), ggplot2 (importFrom), \ 
lattice (suggests), survival (suggests)
   * NOTE: users who depended on ggplot2 or survival being loaded by Hmisc need \ 
to require() or library() themselves
   * reformM: improved by Yong Hao Pua to handle variables enclosed in functions
   * dotchartpl: fixed bug - was not sorting if groups omitted
   * completer: new function by Yong-Hao Pua, Singapore General Hospital that \ 
facilitates drawing of multiple imputations to get one or more completed \ 
datasets
   * ecdfSteps: compute coordinates of empirical CDF for a variable, with \ 
possible extension of the domain so that steps at y=0 and 1 will be visable
   * fit.mult.impute: fixed to all data=a data table

Log message:
(misc/R-Hmisc) Updated 4.7.0 to 4.8 0

Changes in version 4.8-0 (2023-02-08)
   * rendHTML: new function to render HTML, sensing if knitr is
     running and if so using knitr::asis_output, otherwise htmltools

   * contents, describe: added the use of rendHTML so that HTML can be
     rendered from the console, and made it so that if
     options(prType='html') is in effect the html method will be
     invoked automatically when printing

Log message:
(misc/R-Hmisc) TEST_DEPENDS x 9 added, more missing

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

Log message:
misc: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes

The following distfiles could not be fetched (possibly fetched
conditionally?):

./misc/libreoffice/distinfo libreoffice/harfbuzz-2.6.4.tar.xz

Log message:
misc: Remove SHA1 hashes for distfiles

Log message:
Add a missing dependency on graphics/R-latticeExtra.

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://mail-index.netbsd.org/tech-pkg/2019/08/02/msg021711.html