CVS commit: pkgsrc/misc/R-Hmisc

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Thu Jun 15 12:13:14 UTC 2023

Modified Files:
        pkgsrc/misc/R-Hmisc: Makefile distinfo

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


To generate a diff of this commit:
cvs rdiff -u -r1.6 -r1.7 pkgsrc/misc/R-Hmisc/Makefile
cvs rdiff -u -r1.5 -r1.6 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:1.6 pkgsrc/misc/R-Hmisc/Makefile:1.7
--- pkgsrc/misc/R-Hmisc/Makefile:1.6    Sat Feb 18 09:26:08 2023
+++ pkgsrc/misc/R-Hmisc/Makefile        Thu Jun 15 12:13:14 2023
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.6 2023/02/18 09:26:08 mef Exp $
+# $NetBSD: Makefile,v 1.7 2023/06/15 12:13:14 mef Exp $
 
 R_PKGNAME=     Hmisc
-R_PKGVER=      4.8-0
+R_PKGVER=      5.1-0
 CATEGORIES=    misc
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost

Index: pkgsrc/misc/R-Hmisc/distinfo
diff -u pkgsrc/misc/R-Hmisc/distinfo:1.5 pkgsrc/misc/R-Hmisc/distinfo:1.6
--- pkgsrc/misc/R-Hmisc/distinfo:1.5    Sat Feb 18 09:26:08 2023
+++ pkgsrc/misc/R-Hmisc/distinfo        Thu Jun 15 12:13:14 2023
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.5 2023/02/18 09:26:08 mef Exp $
+$NetBSD: distinfo,v 1.6 2023/06/15 12:13:14 mef Exp $
 
-BLAKE2s (R/Hmisc_4.8-0.tar.gz) = fa4deeb908c41272e58ebfb5caf7f49a6fb6f0f62096049d470d16da8e287a14
-SHA512 (R/Hmisc_4.8-0.tar.gz) = 48e774a1cb4d3d31fcc33b3f598ba1490d8206581bdc0ca06301e221fa3040f9dcb4ef253f3726175c693f19f7b6009d7236923727271700b9d312d5cbd9a2b4
-Size (R/Hmisc_4.8-0.tar.gz) = 794994 bytes
+BLAKE2s (R/Hmisc_5.1-0.tar.gz) = 72fc7f2fff9913978f5f39c207d978fdf4b31c506b7709fc73b25eeb6ea7cd76
+SHA512 (R/Hmisc_5.1-0.tar.gz) = 5bd4bc4f1739be73cbe5980389973d4cf266101707ab3ddf3491fa1cdb20fe60dfce4bc5cede780c4d243130a075884d449b50dcbbfb85281a18b34992732d7c
+Size (R/Hmisc_5.1-0.tar.gz) = 863573 bytes