Subject: CVS commit: pkgsrc/misc/R-Hmisc
From: Makoto Fujiwara
Date: 2023-06-15 14:13:14
Message id: 20230615121314.80DB6FA89@cvs.NetBSD.org

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

Files:
RevisionActionfile
1.7modifypkgsrc/misc/R-Hmisc/Makefile
1.6modifypkgsrc/misc/R-Hmisc/distinfo