Frank Harrell
2014-Apr-17 00:01 UTC
[R] [R-pkgs] Updates to Hmisc, rms, and greport packages
The Hmisc package has had a number of updates/fixes:
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
The rms package has also had some changes, and the survfit.formula
function has been REMOVED, replaced by the npsurv function:
Changes in version 4.2-0 (2014-04-13)
* Deprecated survfit.formula so would not overlap with function in
survival
* Added function npsurv, survplot.npsurv
* REMOVED survfit.formula
* Used new type argument to label.Surv for fitting functions
* cph: added weights argument to residuals.coxph (Thanks: Thomas Lumley)
* survfit.cph: fixed bug in using wrong type variable. Thanks:
Zhiyuan Sun
* cph: added weighted=TRUE in call to residuals.coxph (Thanks: T Lumley)
* orm.fit: improved ormfit to not try to deal with NaN in V,
assuming that step-halving will happen
Some improvements have been made in the greport package:
Changes in version 0.5-1 (2014-04-15)
* survReport: changed to use npsurv instead of survfit.formula
* exReport: changed order of output so that analysis of randomized
patients marked for exclusions appears last; use LaTeX chngpage package
to allow detailed table to go into left margin so as to be centered on page
* exReport: added adjustwidth argument
* accrualReport: allowed enrollment target N to be omitted
* exReport: fine tuning
* nriskReport: new report to show number of subjects still being
followed at each day
* Merge: added support for data.table
* nriskReport: added id() variable
* exReport: fixed bug when there is an exclusion with 0 frequency
* accrualReport: improved graphics formatting, added minrand argument
* accrualReport: added enrollmax argument, clarified notation
* exReport: added ignoreExcl, ignoreRand arguments
* all: added greportOption texwhere; default is 'gentex'; can
specify texwhere='' to write non-appendix LaTeX code to console as for
knitr
* dReport: for byx for discrete Y, sense when Y is binary and use
Wilson interval instead of bootstrap; adjust SE using confidence
interval if proportion is 0 or 1
* dReport: changed discreteness non-binary classification to use
maximum number of unique values or Y instead of minimum
* add globalVariables call to nriskReport
--
Frank E Harrell Jr Professor and Chairman School of Medicine
Department of Biostatistics Vanderbilt University
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