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Fix partial argument warnings - #128

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billdenney:partial-arg
Aug 29, 2021
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Fix partial argument warnings#128
harrelfe merged 2 commits into
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billdenney:partial-arg

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@billdenney

@billdenney billdenney commented Apr 18, 2020 •
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I recently started enabling more strict warnings to show partial argument matching and other warnings.

I found the following warning when using Hmisc, and so I searched for all length= arguments for rep() or seq() and made them length.out=.

1: In rep(to, length = length(from)) :
  partial argument match of 'length' to 'length.out'

@harrelfe
harrelfe merged commit a6284ea into harrelfe:master Aug 29, 2021
netbsd-srcmastr pushed a commit to NetBSD/pkgsrc that referenced this pull request Apr 25, 2022
mef
(misc/R-Hmisc) Updated 4.2.0 to 4.7.0, fix build against R-4.2.0
02e62d3 
Changes in version 4.7-0 (2022-04-18)
   * 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


Changes in version 4.6-0 (2021-10-05)
   * 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
nnn   * 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;
     harrelfe/Hmisc#144)

   * many: tests for presence of suggested packages using
     requireNamespace (thanks for major editing work by Duncan Murdoch
     at harrelfe/Hmisc#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
     harrelfe/Hmisc#135)

   * summaryM: fixed error with prN=TRUE with latex (thanks Matt
	 * Shotwell in harrelfe/Hmisc#109)
	 * many: fix partial argument matching warnings length ->
	 * length.out in rep (thanks Bill Denney in
	 * harrelfe/Hmisc#128)

   * rcspline.restate: was dropping + for exactly zero coefficients
     (thanks harrelfe/Hmisc#118)

   * mdb.get: remove brackets from table names (thanks
     harrelfe/Hmisc#123)

   * latex: added new argument comment so that the generated comment
     can be suppressed (thanks Giuseppe Ragusa
     harrelfe/Hmisc#33)

   * sas.get: added new argument for variable case (thanks Tyler Hunt
     harrelfe/Hmisc#8)

   * format.df: changed to use system option OutDec when cdot is not
     specified (thanks harrelfe/Hmisc#142)

   * C code: changed calls to warning/error routines

   * formatdescribeSingle: changed for character value to make 'NA' work

Changes in version 4.5-0 (2021-02-27)
   * approxExtrap: changed x and y to as.numeric.  Thanks: juha.heikkinen@luke.fi
   * 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

Changes in version 4.4-2 (2020-11-25)

   * rcorr: captured loss of precision leading to square root of a
     negative number.  Thanks: Ann Voss <avoss@novanthealth.org>

   * 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

Changes in version 4.4-1 (2020-08-07)
   * 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

Changes in version 4.4-0 (2020-03-22)
   * 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

Changes in version 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

Changes in version 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
msk pushed a commit to msk/pkgsrc that referenced this pull request May 11, 2026
mef
(misc/R-Hmisc) Updated 4.2.0 to 4.7.0, fix build against R-4.2.0
76af49d 
Changes in version 4.7-0 (2022-04-18)
   * 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


Changes in version 4.6-0 (2021-10-05)
   * 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
nnn   * 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;
     harrelfe/Hmisc#144)

   * many: tests for presence of suggested packages using
     requireNamespace (thanks for major editing work by Duncan Murdoch
     at harrelfe/Hmisc#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
     harrelfe/Hmisc#135)

   * summaryM: fixed error with prN=TRUE with latex (thanks Matt
	 * Shotwell in harrelfe/Hmisc#109)
	 * many: fix partial argument matching warnings length ->
	 * length.out in rep (thanks Bill Denney in
	 * harrelfe/Hmisc#128)

   * rcspline.restate: was dropping + for exactly zero coefficients
     (thanks harrelfe/Hmisc#118)

   * mdb.get: remove brackets from table names (thanks
     harrelfe/Hmisc#123)

   * latex: added new argument comment so that the generated comment
     can be suppressed (thanks Giuseppe Ragusa
     harrelfe/Hmisc#33)

   * sas.get: added new argument for variable case (thanks Tyler Hunt
     harrelfe/Hmisc#8)

   * format.df: changed to use system option OutDec when cdot is not
     specified (thanks harrelfe/Hmisc#142)

   * C code: changed calls to warning/error routines

   * formatdescribeSingle: changed for character value to make 'NA' work

Changes in version 4.5-0 (2021-02-27)
   * approxExtrap: changed x and y to as.numeric.  Thanks: juha.heikkinen@luke.fi
   * 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

Changes in version 4.4-2 (2020-11-25)

   * rcorr: captured loss of precision leading to square root of a
     negative number.  Thanks: Ann Voss <avoss@novanthealth.org>

   * 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

Changes in version 4.4-1 (2020-08-07)
   * 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

Changes in version 4.4-0 (2020-03-22)
   * 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

Changes in version 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

Changes in version 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
jperkin pushed a commit to TritonDataCenter/pkgsrc that referenced this pull request May 14, 2026
mef
(misc/R-Hmisc) Updated 4.2.0 to 4.7.0, fix build against R-4.2.0
2307845 
Changes in version 4.7-0 (2022-04-18)
   * 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


Changes in version 4.6-0 (2021-10-05)
   * 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
nnn   * 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;
     harrelfe/Hmisc#144)

   * many: tests for presence of suggested packages using
     requireNamespace (thanks for major editing work by Duncan Murdoch
     at harrelfe/Hmisc#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
     harrelfe/Hmisc#135)

   * summaryM: fixed error with prN=TRUE with latex (thanks Matt
	 * Shotwell in harrelfe/Hmisc#109)
	 * many: fix partial argument matching warnings length ->
	 * length.out in rep (thanks Bill Denney in
	 * harrelfe/Hmisc#128)

   * rcspline.restate: was dropping + for exactly zero coefficients
     (thanks harrelfe/Hmisc#118)

   * mdb.get: remove brackets from table names (thanks
     harrelfe/Hmisc#123)

   * latex: added new argument comment so that the generated comment
     can be suppressed (thanks Giuseppe Ragusa
     harrelfe/Hmisc#33)

   * sas.get: added new argument for variable case (thanks Tyler Hunt
     harrelfe/Hmisc#8)

   * format.df: changed to use system option OutDec when cdot is not
     specified (thanks harrelfe/Hmisc#142)

   * C code: changed calls to warning/error routines

   * formatdescribeSingle: changed for character value to make 'NA' work

Changes in version 4.5-0 (2021-02-27)
   * approxExtrap: changed x and y to as.numeric.  Thanks: juha.heikkinen@luke.fi
   * 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

Changes in version 4.4-2 (2020-11-25)

   * rcorr: captured loss of precision leading to square root of a
     negative number.  Thanks: Ann Voss <avoss@novanthealth.org>

   * 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

Changes in version 4.4-1 (2020-08-07)
   * 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

Changes in version 4.4-0 (2020-03-22)
   * 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

Changes in version 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

Changes in version 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
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2 participants

@billdenney @harrelfe