r-cran-hmisc 3.17-1-1 / usr / lib / R / site-library / Hmisc / NEWS

Changes in version 3.17-1 (2015-12-17)
   * 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

Changes in version 3.17-0 (2015-09-20)
   * 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

Changes in version 3.16-0 (2015-04-25)
   * 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

Changes in version 3.15-0 (2015-02-15)
   * 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

Changes in version 3.14-6 (2014-11-16)
   * 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"

Changes in version 3.14-5 (2014-09-11)
   * 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

Changes in version 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

Changes in version 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

Changes in version 3.14-2 (2014-02-26)
   * 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

Changes in version 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

Changes in version 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 <szehnder@uni-bonn.de>
   * 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)

Changes in version 3.13-0 (2013-11-18)
   * 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 <sarkarbayazid@gmail.com>
	 * 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 <matthieu.stigler@gmail.com>
   * 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