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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
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