NEWS

Hmisc 5.2-0 (2024-10-28)

added requireNamespace for safer in qcrypt
require R 4.2.0 or later, to handle pipes
new function pMedian for pseudomedian (Hodges-Lehmann one-sample estimator)
added pMedian to describe function
Converted all Ratfor code to Fortran 2018

Hmisc 5.1-3 (2024-05-28)

areg.boot: intercepted use of xlim when y is categorical; need to improve logic on xout=
redun: stored scores matrix in returned object, suitable for r2describe
r2describe: new function to list strongest predictors of each variable in a matrix, from all the other columns
movStats: added lrm_args argument
logrank (in spower.s): removed non-working non-executed code for stratified log rank, change hazard ratio estimate to Pike's estimator. Previous hazard ratio calculation was incorrect.
qcrypt: added service=NA to bypass keyring
runParallel: changed progress directory explicitly to /tmp for Mac
printL: new function
redun: got around model.frame problem so that negated variables are omitted from analysis; also fixed printing of missing values

Hmisc 5.1-2 (2024-03-11)

dotchartpl: remove length(ugroup) criterion (unsure what this was doing and made lower and upper be not plotted)
dotchartpl: got around new bug in plotly when numeric vectors were given to axis ticktext; changed to character via format()
cut2: fixed to handle large g values (Thanks Cole Beck https://github.com/harrelfe/Hmisc/pull/170)
Added dependency on R 4.1.0 or later because of use of new pipe operator in describe etc.
GiniMd: got around bug in sum(empty vector) = 0 by returning NA if na.rm=FALSE and there were any NAs
testCharDateTime: correctly handle case where all values are NA or ” and convert=TRUE
hdquantile: allowed for scalar probs (see https://github.com/harrelfe/Hmisc/pull/180; thanks Cole Beck)
movStats: added nignore argument, defaults to 10 (the previous behavior)
history.data.frame, ecdf: fixed dev issue https://github.com/harrelfe/Hmisc/issues/181
spikecomp: for tresult='segments' removed attributes from vectors to make data.table compliant
xless: adapted for MacOS using open system command

Hmisc 5.1-1 (2023-09-12)

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

Hmisc 5.1-0 (2023-05-08)

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.

Hmisc 5.0-1 (2023-03-08)

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

Hmisc 4.8-0 (2023-02-09)

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
addggLayers: new function to add extended box plot and/or spike histograms as layers to a 'ggplot2' plot
seqFreq: new function to find sequential counts of exclusions to do NAs in multiple variables, arranging so that the variable with the highest number of NAs is examined first, the subsequent variables' NAs are examined in observations that were not NA from previous variables' exclusions

Hmisc 4.7-2 (2022-11-18)

grType: changed to use find.package() instead of the slow installed.packages() (thanks: Uwe Ligges)
latex.default: changed to by default omit the LaTeX comment; specify options(omitlatexcom=FALSE) to get original behavior
ggplot.transcan: corrected color/color assignments; thanks: David Norris
restoreHattrib: fixed to ignore attributes for variables that are not in obj
popower: fixed URL for Live Free or Dichotomize
getRs: improved to use rstudioapi to load the file into a script editor window
mChoice: added ignoreNA argument and made new default behavior ignoreNA=TRUE unlike the prior versions; made value (appearing with semicolons) null instead of 0 when no choice was selected, which makes option add.none finally work
mChoice: added condition argument to intersect all values instead of unioning them
mChoicelike: new function like inmChoice but allowing matching on pieces of labels and optionally ignoring the case
nmChoice: new function to compute the number of choices that were made per observation
describe: fixed length > 1 problem with check for timeDate class
Merge: better error message if unexpected variable from non-id-variable overlap
all.is.numeric: corrected to return TRUE is the only non-NA values after converting to numeric were originally NA, addedd what='nonnum' argument

Hmisc 4.7-1 (2022-08-15)

plot.describe: added bvspace argument to control spacing between categorical variables
getRs: changed default put argument to 'source', changed RStudio code
html.contents.data.frame: changed long space to &emsp; to render in more browser
.q: new quoting function, extends Cs
html.contents.data.frame, html.describe: added title to html
plot.curveRep: added method='data' so can set up for ggplot2
combplotp, dotchart3, dotchartpl, plot.describe, plotlyM, scat1d: look at options(plotlyauto=TRUE) and if set override height and width to NULL to that plotly will use auto sizing
dataframeReduce: return information about dropped variables as attribute 'info'
plotCorrM: added hjust=1 if xangle is not zero
Merge: changed to rely on merge.data.table in addition to merge.data.frame
formatCons used by summaryM and summary.formula: respect outer.size for html
options(localHfiles=TRUE) makes 'getRs' and 'getHdata' read from local file directories instead of from github or our web server
various .Rd files: got rid of \var{} to pass new CRAN checks
fit.mult.impute: fixed bug when using mice. Thanks: Michał Krassowski https://github.com/harrelfe/Hmisc/issues/152
fit.mult.impute: fixed bug with deparse(substitute(fitter)) when fitter is an anonymous function. Thanks Thanks: Michał Krassowski https://github.com/harrelfe/Hmisc/issues/157
plot.summaryM: fixed bug not fetching group label from correct place. Thanks: Thomas [email protected]
bpplt: fixed par(mai). Thanks: [email protected]
plot.summaryM: similar correction

Hmisc 4.7-0 (2022-04-19)

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
na.pattern: greatly simplified, and added data.table support

Hmisc 4.6-0 (2021-10-07)

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
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

Hmisc 4.5-0 (2021-02-28)

approxExtrap: changed x and y to as.numeric. Thanks: [email protected]
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

Hmisc 4.4-2 (2020-11-29)

rcorr: captured loss of precision leading to square root of a negative number. Thanks: Ann Voss <[email protected]>
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

Hmisc 4.4-1 (2020-08-10)

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

Hmisc 4.4-0 (2020-03-23)

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

Hmisc 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

Hmisc 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

Hmisc 4.2-0 (2019-01-26)

putHcap: new function
inst/tests/example.Rmd: changed to html document, replaced putHfig calls with new putHcap
knitrSet: new lang='blogdown' option
fit.mult.impute: suppressed warning for orm if there were no missing Ys (thanks: Lucy D'Agostino McGowan)
knitrSet: made more functional for blogdown
knitrSet: removed duplicate setting of out.width
fit.mult.impute: added step-by-step instructions for imputing missing baseline variables when analyzing serial data
histboxp: changed to display quantiles using line segments, and centered segments vertically. added connect argument with default set to connect quantiles with a line
wtd.quantile: removed observations with missing weights
print.summaryM, latex.summaryM: if no statistical results, do nothing and return
naclus: checking missings in character variables to also use is.na
dotchartpl: backsolve from Wilson confidence interval when prop=0 or 1; added nobigtracename argument; fixed trace names
putHfig: added file=FALSE to return character vector instead of writing
histboxp: added showlegend so that can be called in a loop
histboxpM: new function to call histboxp for multiple variables in a data frame
htmlSN: re-wrote for speed, and added argument pretty=
plot.summaryS: added plotly method when options(grType='plotly')
plotp: moved generic from rms to Hmisc
plotlyM: new function to make it easy to use plotly to produce multiple graphics of certain types, with specifications coming from a data frame
plotp.summaryS: new plotly method for summaryS
mbarclpl, medvpl: new auxiliary functions for plotp.summaryS
dhistboxp: new function
markupSpecs$httml: added new function mdchunk to intersperse markdown with R object output
markupSpecs$html$varlabel: if html is TRUE run label and units through htmlTranslate
dotchartpl: removed stratified by groupname from hover text
plot.summaryS: removed transhtml argument
markupSpecs$html cap-type functions: called htmlTranslate(...,greek=TRUE) on long and short captions
formatTestStats: ran P-values with < through latexTranslate to make latex.summary.formula.reverse and latex.summaryM work correctly
hidingTOC: new function by Thomas Dupont for various features for floating table of contents with RMarkdown html reports
histbackback: use pretty() to label breaks
cut2: added formatfun argument, by github.com/harrelfe/Hmisc/commit/c8816d589b2e95eed15b96a886558a92bb143abd
latex.default: fixed midfules for booktabs with ctable: https://github.com/harrelfe/Hmisc/pull/100
formatTestStats: trapped logical length mismatch
latex.default: checks options(omitlatexcom) and if TRUE suppresses emitting LaTeX comments; keeps Rmarkdown/pandoc from trying to escape LaTeX comment characters, putting the comments in the final output

Hmisc 4.1-1 (2018-01-03)

describe: quit rounding values when <= 20 distinct values no matter how far apart any two values are spaced. https://stackoverflow.com/questions/47679551
summaryM: fixed to handle character variables properly, by converting them to factors. Thanks: Matt Shotwell
Fortran/ratfor routines hoeffd, jacklins, largrec, rcorr, wclosest: fixed errors where some scalars were single precision, got rid of some warnings

Hmisc 4.1-0 (2017-12-19)

latex.default: insert spaces between multiple entries in bottom index in latex tables (thanks: ecortens https://github.com/harrelfe/Hmisc/pull/73)
latex.summary.formula.reverse,latex.summaryM: fix double replacement of ampersand (Thanks: Evan Cortens https://github.com/harrelfe/Hmisc/pull/72)
fit.mult.impute: verified dfmi formula, added comment
dotchartpl: added refgroup, sortdiff, conf.int arguments to allow inclusion of difference in two proportions across levels of the group variable
plot.summaryP: for plotly, added refgroup to pass to dotchartpl so that differences in proportions can be handled; also passed ... arguments
dotchartpl: added minkeep argument (used by hreport eReport)
markupSpecs$html: added function uncover for hiding chunks; fixed typo in definiton of larger function
knitrSet: when lang='markdown' sets up hook option uncover
knitrSet: added aliases ho for out.height, wo for out.width, added knitrSet arguments ho, wo
wtd.var: replaced with fixed verion by Benjamin Tyner <[email protected]>
inst/tests/example.Rmd: added example with simple caption and font size change for caption
pomodm: new function to work with popower/posamsize to assist translating odds ratios to means and medians for proportional odds model
histboxp: added wmax, mult arguments to tweak margin set-aside
describe: fixed bug in html.describe when there is only one variable
simRegOrd: new function to simulate covariate-adjusted ordinal model two-sample test power
html: use htmlSpecialType for functions calling htmlSpecial, htmlGreek
htmlSpecialType: new function to check options('htmlSpecialType') and use as a default '&' for special symbols
htmlSpecial: added new characters, cleaned up code
impute.transcan: if original variable was logical, convert 0/1 imputations to FALSE/TRUE; design matrix column names were problematic with fit.mult.impute in this case
impute.transcan: converted character variables on input dataset to factor so can replace NAs with imputed codes
htmlTranslate: fixed bug when unicode was in effect: characters were shifted;fixed &# code for pound sign
errbar: properly passed arguments main and sub to plot
html markupSpecs: added sectionNumberDepth function
wtd.quantile: remove zero weight observations early
latexCheckOptions: new function from Richard Heiberger
htmlSN: used new HTML specials mechanism for times symbol
summaryM: added escape.html=FALSE to htmlTable calls
combine, combine<-: removed (were deprecated long time ago)
removed inc-dec.s which defined unused inc<- and dec<- for increment and decrement
NAMESPACE: removed exportPattern("^([^.]|\\..+\\.)") and explicitly exported everything, stopping export of methods
round.POSIXt,trunc.POSIXt: changed to roundPOSIXt, truncPOSIXt to avoid conflicts with R base
asNumericMatrix, matrix2dataFrame: changed to respect original storage.mode. Thanks: Andre Mikulec

Hmisc 4.0-3 (2017-05-02)

bpplot: added plotopts argument
describe, histboxp: improved logic to still slighty round numeric variables with fewer than 100 distinct values, in case some values are really close, when computing frequency distribution (for spike histograms in plot.describe)
all.is.numeric: fixed to handle case where all values are " "; makes describe work
latex.describe.single: changed to always issue vbox, to improve vertical spacing
histboxp: removed zero line so wouldn't collide with data
ggfreqScatter: added smoother to example
latex.summaryM: more transparent naming of quantiles preserving full precision
cut2,describe,dotchart3,ecdf,latex,list.tree,bpplt,panel.plsmo,pstamp,summary.formula,summaryM,transace,t.test.cluster,wtd.Ecdf,Dotplot,zoom: fixed on.exit to properly restore options() to original state
[.pBLock: fixed old behavior of only rataining the pBlock class if the result is a matrix (thanks: Michael Lawrence - lawremi)
addMarginal: added nested argument
putHfig: now throw error if lcap is given with expcoll because of interaction with divs in markdown sub-subheading
plotmathTranslate: improved to put any non-legal expression inside paste()
wtd.var: was returning Inf for fractional weights with method='unbiased'; chaged to use stats:cov.wt for both methods - https://github.com/harrelfe/Hmisc/issues/69
plsmo, summaryS: new example in help files
plot.summaryS: separated xlim and ylim to fix bug where xlim was ignored
plsmo: stop on error if no. observations not large enough for m with method='intervals'
Fortran calls: registered all Fortran functions, removed package name and quotes in first argument in .Fortran(), added F_ to entry point name in those calls, changed useDynLib call in NAMESPACE, added \alias{} for all F_ entries

Hmisc 4.0-2 (2016-12-31)

pngNeedle: fixed bug in html.describe under Windows by not specifying /tmp as the temporary file directory - https://github.com/harrelfe/Hmisc/issues/63; used tempdir() instead of tempfile()
html.describe.single: reuse the same temporary file for intermediate png output for spike histograms
htmlGreek, htmlSpecial: new internal functions
htmlTranslate: added unicode argument, default FALSE, use htmlGreek
tobase64image: new internal function. Thanks: Dirk Eddelbuettel
Changed IMPORTS: base64 to base64enc
spss.get, stata.get: made use of foreign package files' ability to use URLs as the file argument
sasxport.get, getZip: allowed for https (thanks: Kurt Hornik)
getRs: removed unused where argument
latex: revert changes that removed fix to column duplication in cellTexCmds
latex: added continued argument
plot.describe: fixed bug in not using formula notation for plotly
histSpikeg: added plotly support, stop curtaining x range when xlim omitted, use approxExtrap to show data density outside of prediction range for x
histSpikep: deleted function
dotchartpl: added lower, upper
describe.vector: changed structure(NULL, ...) to structure(list(), ...)

Hmisc 4.0-1 (2016-12-08)

gbayes: new test file, fixed bug in posterior mean when mix=0,1 in gbayesMixPost
ggfreqScatter: added prfreq and cuts arguments
latex.summary.formula.reverse, latex.summaryM, html.summaryM: fixed bug with backslash added before % for html, improved typesetting language logic
latex.describe: fixed bug that prevented spike histogram from appearing
ggplot.summaryP: moved text out of aes in geom_point, left in main aes
plot.describe, plot.summaryP: put text aes in ggplot(), increased ggplotly height to allow popups for top continuous variables in plot.describe
dotchartp, dotchartpl, plot.describe: moved height and width from plotly::layout to plot_ly because of changes in plotly 4.5.6
bppltp: added data= to plot::add_* because plotly was evaluating using the wrong copy of x,y, etc.
plot.summary.formula.reverse, plot.summaryM: removed subtitles argument since not used
upData: fixed bug when converting existing variable to factor; was not recognizing new storage model and tried to run floor()
latex.summary.formula.reverse: fixed bug where outer quantiles and frequencies were not being rendered
latex.default: put \par in front of insert.bottom if table.env is FALSE, so that text is not put to the side of the table
histboxp: new function for plotly stratified spike histograms with box plot statistics also depicted
format.df, latex.default: added arguments already.math.row.names, already.math.col.names that if TRUE prevent any math mode changes
latex.default: fixed problem with duplication of columns in the cellT...exCmds array (thanks: Thomas Dupont)
tests/summaryM-customtest: new test (see https://github.com/harrelfe/Hmisc/issues/61)
describe: improved logic for deciding when and how to show frequency table, changed condense argument
htmlVerbatim: added propts and omit1b arguments
latexNeedle, pngNeedle: added x argument
latex.describe: allowed for unequally-spaced x in spike histograms
html.describe: added spike histograms
base64: new IMPORTS in DESCRIPTION
sedit, latexTranslate: changed 1 : length(text) to seq_along(text). Thanks: Greg Snow
ggfreqScatter: better formatting of axis tick mark labels
latexVerbatim: implemented file=”

Hmisc 4.0-0 (2016-11-01)

summaryP: fixed exclude1 logic - was not excluding enough levels (inconsistent use of variable names vs. labels)
latexTranslate: any NAs in first argument changed to "" before conversion
minor.tick: added arguments to pass through (thanks: vhorvath)
tests/latexpng.r: test conversion of LaTeX table to png
latexTabular: made it properly call latexTranslate separately for each column, convert argument to matrix or data frame if a vector
tests/latexTabular.r: new test
latexDotchart: added call to latexTranslate to escape special characters for LaTeX such as underscore and pound sign
ggfreqScatter: new function
grType: new non-exported service function to sense if plotly is in effect
plot.describe: new function to make plotly graph for describe objects
describe: changed output: 3 decimal places for Info, new format for frequency table, separated logic for 10 extreme values from logic for frequency table, significant changes to print.describe
dotchartp: new version of dotchart3 for plotly charts
summaryD: modified to use dotchartp if options(grType='plotly') is in effect
nFm: added argument html
label.default, label.Surv, labelPlotmath: added html argument to implement HTML markup in place of plotmath (for plotly)
now imports htmlTable, viridis
html.contents.data.frame: return invisibly if file=”
htmlVerbatim: new function
html.contents.data.frame: improved html
html.data.frame: changed column headers from h4 to strong
ggfreqScatter: added html argument
knitrSet: was ignoring default figure h and w
html.summaryM: new function using new version of latex.summaryM
markupSpecs: new list object defining markup elements for latex and html, used by summaryM
show.html, print.html: removed; conflicted with htmltools/rmarkdown
label: required exact match on attribute name "label" to not retrieve the "labels" attribute (thanks: Ivan Puzek)
htmlSN: new function to convert floating point to scientific format usint html
upData, cleanup.import: fix NA becoming new factor levels (thanks: Beau Bruce)
htmlTranslate: new function
plotlySave: new function
histSpikep: new function
upData: new argument html
plot.describe: added ggplot2 graphics, improved continuous display using ggplotly
labelPlotmath: cleaned up by using markupSpecs
capitalize: fixed bug - did not cap. first letter if other letters after it were upper case (thanks: dchiu911)
html.summaryM: added brmsd argument to put mean, SD on separate line
Save: changed default back to use gzip for speed
knitrSet: used new knitr way to set aliases for option names
latexTabular: made translate argument apply to body of table also; implemented multi-line header
html.data.frame: added several arguments
describe: added html method
html markupSpecs object: added bibliographic database utility functions
bppltp: new service function for extended box plots for plotly
plot.summaryM: new plotly method
prType: new service function used to detect user settings for html, latex for print methods
html.contents.data.frame: removed file and append arguments and output an html character vector instead
prList: new function
GiniMd: moved to Hmisc from rms
describe: added GMD (Gini's mean difference) and relabeled unique to distinct
latex.summaryM: added Needspace{2.7in} before 2nd and later strata
ggplot.summaryP: added point labels for use with plotly as hover text
latex.summaryP: fixed bad linebreak at strata boundaries
dotchartpl: new plotly dot chart function especially for summaryP
plot.summaryP: new plotly method using dotchartpl when options(grType='plotly')
putHfig: new function to render graphics with captions in HTML reports
pngNeedle: new function, like latexNeedle but useful with HTML reports
html.data.frame: added width and caption arguments
plotlyParm: list object with plotly helper functions
summaryD, dotchartp: added symbol and col arguments
upData: improved efficiency, added labelled class to variables without it but having labels (e.g., data imported using haven package)
gbayesMixPost: mixed error in posterior odds of the mixing parameter that resulted in incorrect posterior probabilities when the variance of the statistic was appreciable; added option to compute posterior mean

Hmisc 3.17-4 (2016-05-02)

latex.summaryP: correctly ordered rows after running reshape because groups was present
rcspline.plot: took confidence limits into account when computing default ylim
bootkm: new test in tests
[.ynbind: Made it return an unclassed vector if the user was subsetting to a single column. Upcoming R release fails in table() otherwise. Thanks: Michael Lawrence <[email protected]>
Merge: added function (moving from greport package)
data.table: imports

Hmisc 3.17-3 (2016-04-03)

latex.default: added blank lines after textbf with insert.top unless center='center' (was unless 'none')
plot.summaryS: fixed bug were limits were not aligned with columns (thanks: Liping Du)
mgp.axis: respected par('tcl') but only as extreme as -0.4
mgp.axis: added cex.axis, cex.lab arguments
aregImpute: added reformM function for permuting order of variables. Thanks: Yong Hao Pua
latex: fixed rownamesTexCmd error

Hmisc 3.17-2 (2016-02-21)

consolidate: A simpler version of assignment form of consolidate, avoids eval/match.call and works with the byte-compiler (thanks: Tomas Kalibera)
relevel.labelled: new function (thanks: Max Gordon)
fit.mult.impute: remove contrasts attribute for imputations done by mice
formatCons: fixed bug when stats contains one row (thanks: Cole Beck)
Hmisc.h: removed reference to S.h
fit.mult.impute.s: moved source code to separate file, away from transcan.s
fit.mult.impute: added warning if fitter is lm, which does not use imputation variances for sigma or standard errors
spss.get: added reencode argument (Thanks: Andreas Osowski)

Hmisc 3.17-1 (2015-12-18)

sasxport.get: added lowernames argument with default equal to the previous behavior (convert varixcable names to lower case)
biVar, rcorrp.cens, spower, transace: changed 1 - pnorm(z) to pnorm(-z)
latex.summaryM: added arguments prob, prN, and legend.bottom
print.summaryM: added arguments prob and prN
Save: changed to use compress='xz' by default, and added compress argument
drawPlot: fixed bug in defining Points and Curve functions; added col argument to Points and Curve; removed helper functions for Points and Curve from Key.s; returned object invisibly; added type='loess' to Curve()
upFirst: new function
mdb.get: added mdbexportArgs argument which among other things allows -b strip to be omitted
html: for hevea added definition of tabularnewline as \\, changed method to default to hevea
summaryM: fixed calculation of N for mChoice variables
stat-plsmo.r: re-written by Hadley Wickham (thanks!) to work with new ggplot2
ggplot.summaryP, ggplot.transcan: added mapping and environment arguments to satisfy rules about generics

Hmisc 3.17-0 (2015-09-21)

format.df (used by latex.default): added space after textless, textgreater
label: changed default for units to value of plot
getRs: replaced where argument with guser, grepo, gdir, dir to allow easy fetching of updated functions from Hmisc etc.
Separated sas.get source code from other .get functions and from upData/cleanup.import by putting into 3 separate files. Moved stata.get into misc.get.s
upData: for Stat/Transfer exported R workspaces, change variables into factors to incorporate value labels when present; added subset argument and reporting of number of observations pre and post subsetting
latex.default: added comma after botcap directive for ctable. Thanks: Paul Trowbridge
Hmisc-internal.Rd: removed alias{[.terms}
latex.default: for longtable when no caption is given, subtract one from table counter
latex.summaryM: quit ignoring insert.bottom if it is a character string (thanks: JoAnn Alvarez)
minor.tick: revised version by Earl Belllinger that fixes problem reported in https://github.com/harrelfe/Hmisc/issues/28
several functions: used new names when assigning temporary functions
NAMESPACE: add imports to base functions to avoid new R CMD CHECK warnings
ffCompress: new function
knitrSet: changed fig.path default to ” instead of NULL to work with knitr 1.11
html.latex: added argument rmarkdown
htmltools: added to suggests in DESCRIPTION
tests: new test script latex-html.Rmd for latex -> html under Rmarkdown/knitr/Rstudio, new test for cut2
plsmo, panel.plsmo: added method='intervals', mobs, ifun arguments

Hmisc 3.16-0 (2015-04-30)

html.contents.data.frame: corrected html space character to add semicolon
ggplot.summaryP: added size of points according to denominators
colorFacet: new function
labelPlotmath: added chexpr argument (used by rms::ggplot.Predict)
rcsplineFunction: added type='integral'
summaryP: fixed bug with sort=FALSE using mfreq when shouldn't
summaryP: stored levels(val) in original levels order
summaryM: removed observations added by addMarginal when computing N in left column of tables
html.latex: added method for htlatex, added where argument, cleaned up code, implemented file=” for knitr when using html/Rmarkdown
summaryM, summary.formula: changed calls to translate to gsub()
summaryP: corrected but in exclude1 logic, moved exclude1 to methods that operate on summaryP objects and out of summaryP itself
addMarginal: respect original levels, add argument margloc
added latticeExtra:: in front of function calls
numeric.string, all.is.numeric: replaced options(warn=-1) with suppressWarnings() (thanks: Yihui)
arrGrob, print.arrGrob: new functions
wtd.var: added maximum likelihood method, fixed unbiased method, improved documentation (all provided by Benjamin Tyner)
Changed all any(duplicated()) to anyDuplicated(); thanks Benjamin Tyler
getRs: new function to interact with https://github.com/harrelfe/rscripts
knitrSet: new function to setup knitr with nice defaults for books etc.
rcorr: fixed sensing of NAs and diagonal elements of n matrix; thanks: Keith Jewell, Campden BRI Group; similar for hoeffd

Hmisc 3.15-0 (2015-02-16)

dvi.latex: For Windows switched from system() to shell() so that cd command works. Thanks: Rich Heiberger
histSpike: added test
histSpikeg: new function for ggplot2
added ggplot2 in DESCRIPTION, NAMESPACE
largest.empty: clarified help file for use with ggplot2, changed how sensed xlim and ylim accordingly
stat_plsmo: new geom for ggplot2
transcan: added ggplot method
transace: removed y-axis labels
residuals.lrm: remove y-axis labels
histSpikeg: added lowess and span arguments
format.df: Andreas Kiermeier: The "..." argument of format.df is no longer ignored, but included in the definition of formt() and passed to format(). The help file has also been updated and the example modified to show an example of big.mark.
getHdata: removed S-Plus specific stuff, updated url to DataSets
summaryP: added ggplot method
NAMESPACE: many additions to register all S3 methods
format.sep: renamed to formatSep

Hmisc 3.14-6 (2014-11-22)

wtd.rank: fixed bug in no weights case (thanks: DPlat)
latex.summaryM, latex.summary.formula.reverse: added npct='slash' to present numerators and denominators horizontally instead of vertically
plsmo: put derivation of ylab earlier so will use original attributes
NAMESPACE: exported more S3 methods for label
contents: added arguments id, range, values
print.contents.data.frame, html.contents.data.frame: added maxlevels argument
curveRep: added option to have the color of frequencies displayed match line colors. Thanks: jstat10
curveRep: changed call to strwidth to use units instead of unit argument
contents.data.frame: corrected omission in help file
wtd.var: corrected denominator. Thanks: Shan Huang
latex.default: changed to use colheads=FALSE to suppress column headings. Thanks: Michael Rose
mdb.get: added system option -b strip to mdb-export to skip binary output
describe help file: added note that correct terminology for "unique" should have been "distinct"

Hmisc 3.14-5 (2014-09-12)

latex.summaryM: fixed bug in caption with test=TRUE. Thanks: Yonghao Pua
csv.get: uses data.table package's fread in place of read.csv if data.table is in effect
combined.levels: sensed all NA vector, now return non-factor numeric instead
dataframeReduce: handle all-NA factor variable
subplot: replaced with latest version from TeachingDemos package by Greg Snow
latexTabular: fixed error in example in help file; result is not a file
latex: another test added in tests/latex.s
summaryP: removed observations with a right-hand-side variable missing
latex.summaryP: fixed bug with wrong column labels due to reshape reordering columns coming from factor levels alphabetically instead of by original levels
format.df: added % & <= >= to list of characters handled, the last two by going into math mode
latex.summaryP: use blank if denominator 0, instead of NaN
summary.formula: fixed problem with deparse formula. Thanks: Andreas Kiermeier
describe: added relative information measure for numeric variables - a measure of how continuous the variable is
wtd.table: detect duplications using duplicated() instead of diff(x) to handle Inf. Thanks: Benjamin Tyner
DESCRIPTION, NAMESPACE: multiple function changes to work in R-devel

Hmisc 3.14-4 (2014-04-13)

rcspline.eval: stop new logic for ignoring outer values when there are many ties when there are also many ties on interior values. Added new logic to use interior unique values of x when the number of unique x is small.
latexBuild: generalized with insert argument
latex.default: modified to use mods of latexBuild, fixed bug with caption.loc='bottom' (thanks: YacineH)
latex.default: fixed bug where comma did not appear after caption={} for ctable (thanks: Johannes Hofrichter)
tests: fit.mult.impute.bootstrap.r: added new example (thanks: Jane Cook)
fit.mult.impute: added call for fit.mult.impute in returned object, replacing call from fitter; makes update work for fit.mult.impute
summary.formula: fixed recognition of multiple left-hand-side variables to trigger call to summaryM (thanks: Kevin Thorpe)
summaryM: changed group label to ” instead of 0 for formulas like age + sex ~ 1
Ecdf: added what argument to all functions
nobsY: return constructed id vector
addMarginal: instead of .marginal. being logical, make it contain names of variables being marginalized over
mChoice.c: fixed some inconsistencies

Hmisc 3.14-3 (2014-03-02)

format.df: clarified in help file that col.just can contain specifications other than l,r,c, e.g., "p{3in}" to get paragraph formatting in a column. Thanks: Ben Bolker
latex.default: added example for the above in tests
label.Surv: got units from inputAttributes in addition, and added type argument

Hmisc 3.14-2 (2014-02-28)

latex.default: improved logic using new function in Misc: latexBuild
latex.default: fixed bug with ctable=TRUE with no caption by removing default label
latex.default: improved formatting for insert.top
latex.default: added tests, fixed insert.bottom
latex.summaryM: return stat summary key as legend attribute, use this according to insert.bottom argument
latex.summary.formula.response: fixed bug related to computation of cdec. Thanks: Kevin Thorpe
latex.default: added new argument star: ctables uses this to spread over two columns when the LaTeX document is in \twocolumn mode. Thanks: David Whiting

Hmisc 3.14-1 (2014-02-25)

Added latexNeedle function
Change latexTherm, latexNeedle to use user LaTeX macro \tooltipn to do the pop-up
latex.default: changed line breaks around \end{tabular}
latex.summaryM: put insert.bottom text in minipage so \tooltip will not devote wide space to it
sas.get: added defaultencoding argument and logic (Thanks: Reinhold Koch)
plot.summaryP: omit tick marks for proportion > 1.0
format.df (used by latex): fixed na.blank logic for character var
latex: removed newlines when ending environments, added hyperref argument
latex: added center='centerline', fixed 'centering'
upData, cleanup.import, dataframeReduce: changed argument pr to print
rcspline.eval: added more evasive action in case of extreme ties

Hmisc 3.14-0 (2014-01-22)

Added trans argument to varclus
Removed recode, existsFunction functions, under.unix object, survfitKM, functions used only by S-Plus: comment, mem, mulbar.chart, p.sunflowers
as.category, is.category, untangle.special: removed
Removed reference to .R. from many functions
Remove oldClass, oldUnclass, getFunction
latex.default: changed 'rotate' to 'sideways' for ctable mode. Thanks: Simon Zehnder <[email protected]>
gView: removed
ldBands: removed
summaryP: new function - graphical replacement for tables of proportions
ynbind: new function for combining related yes/no variables into a matrix with a label
added file argument to prn
summaryP: added autoarrange
added addMarginal and nobsY functions
pBlock: new function for blocking variables for summaryP
summaryP: changed text positioning to grid absolutes, added text.at argument
scat1d, histSpike: if grid used and y has grid units, fixed logic for frac
plsmo, panel.plsmo: added scat1d.opts argument
label.Surv, units.Surv: added, removed ::: in survival calls
summarize: added keepcolnames argument
Suppressed startup message unless options(Hverbose=TRUE) is set
summaryS: new function - multi-panel lattice xy and dot plots
summaryD: added ylab argument
dotchart3: quit letting left margin be less than pre-existing one
multLines: new function
Improved nobsY to respect subject IDs when counting number of subjects, and to return an attribute 'formula' without id variable; changed bpplotM, summaryP, summaryS to use this
Removed nobsY calculations from bpplotM, summaryP, summaryS, enhanced nobsY to allow stratification by treatment
panel.bpplot: added violin and violin.opts arguments
summaryS: added medvPanel support during-plot vertical violin plots
plot.summaryP: padded x-axis limits
latexTabular: added translate and hline arguments; moved to its own file and help page
latexTherm: added tooltip using LaTeX ocgtools package
summaryP: stopped reversing order of panels
summaryM: added table.env argument, changed how model.frame built
latex.summaryM: changed to print proportions by default, added round='auto'
character.table: added xpd=NA; thanks: Dale
summaryP: added latex method
latex.default: added insert.top argument
summaryM: added stratification (multiple tables)

Hmisc 3.13-0 (2013-11-21)

Changed n location (nloc argument) in bpplotM
Improved dotchart3 to better compute string widths when there is a mixture of expressions and regular strings for auxdata/auxtitle
Changed rlegend to not take logs if log axes are in effect. Fixes Ecdf(..., log='x', label.curves=list(keys=1:3)). Thanks: Bayazid Sarker <[email protected]>
Extended non-panel (regular) version of plsmo to handle matrix y
Likewise for summaryRc
Added xlim to bpplotM
Added latexTherm function to create LaTeX picture environments to add a series of thermometers to LaTeX text
Fixed deff to handle the case where R^2 = 1. Thanks: Matthieu Stigler <[email protected]>
Added new test file for wtd.mean, wtd.quantile
New test aregImpute3.r for glm Poisson regression
Improved describe.vector to format single unique values
Took away warning about var, s.e., t, p in fit.mult.impute
Switched from subversion to github repository
Changed maintainer from Charles Dupont to Frank Harrell
Changed wtd.loess.noiter to use loess instead of stats:::simpleLoess