Fixed one URL

Fixed two

`modelsum`

test errors that were a result of rounding on macos.

- Fixed two URLs

Possible breaking change:

`tableby()`

,`modelsum()`

, and`freqlist()`

now use the`caption=`

argument in`knitr::kable()`

to generate captions (`comparedf()`

already does). (#310)Changes to

`DESCRIPTION`

file:Changed

`broom`

requirement to >= 0.7.1, in which a bug with`geepack::geeglm`

was fixed. This affected one test in the test suite.Added

`geepack`

package to “Suggests” (#279).Removed

`gam`

from the “Suggests”, in favor of`splines`

, which the`modelsum()`

vignette actually uses.Changed

`survival`

requirement to`>= 2.43-1`

.

Other changes:

Added code to error informatively when “Suggests” aren’t available. (#317)

`tableby()`

:Added

`selectall()`

.Added “label” option to

`cat.simplify=`

and`ord.simplify=`

for`tableby()`

/`paired()`

. (#288)Fixed a bug in

`tableby()`

/`paired()`

where`stats.labels=`

specification would remove all default labels. (#316)Added

`wt()`

(Wilcoxon test) option for`tableby()`

. (#321)Fixed a bug in

`tableby()`

relating to a weird edge case when a by-level is “Total” and the total label is set to something else.Added a feature to

`tableby.control()`

to allow for the total column to be moved before the other columns. (#320)Added a feature to

`tableby.control()`

to allow for dropping of categorical levels. (#318)Added

`meanse()`

for`tableby()`

. (#315)

`modelsum()`

:Added

`relrisk()`

to`modelsum()`

families (with corresponding addition of`geepack`

package to “Suggests”). (#279)Fixed a bug in

`modelsum()`

with confidence level for survival.Suppressed warnings with new broom version when using

`MASS::glm.nb()`

.

`comparedf()`

:Added option to

`diffs()`

for extracting not-shared observations. (#305)Fixed bug in

`comparedf()`

when things are infinite. (#306)

`write2()`

:- Added note to
`write2()`

vignette about a global option for R Markdown documents in R Studio. (#312)

- Added note to

Change R requirement to >= 3.4.0.

Fixed a bug to conform with new

`broom`

publication, and change`broom`

requirement to >= 0.7.0. (#296)Fixed a bug to conform with new

`knitr`

publication, and change`knitr`

requirement to >= 1.29. (#299, #300, #301)The GitHub repository was moved from https://github.com/eheinzen/arsenal/ to https://github.com/mayoverse/arsenal/. The corresponding

`pkgdown`

site is now at https://mayoverse.github.io/arsenal/`freqlist()`

: Changed the default for`addNA`

to be`TRUE`

in the formula method, so that you only have to specify`na.options`

like in the table method.`modelsum()`

:Added support for conditional logistic regressions. (#275)

Fixed a bug in

`modelsum.control()`

with confidence interval specification.Expanded the statistic list for survival models.

Eliminated call to

`broom::confint_tidy()`

. (#296)

`tableby()`

/`paired()`

:Removed checks for existance of stat functions (the check wasn’t working anyway) and search both the enclosing environment as well as

`parent.frame()`

(for custom stat functions).`tableby()`

: better described`as.tbstat()`

and`as.countpct()`

in the vignette, and make`as.countpct()`

slightly more flexible. (#283)`paired()`

: fixed a bug with detecting stat functions.`tableby()`

: added an error if reserved terms are used in the by-variable. (#277)Added an option for HTML footnotes (and superscripts) in

`summary.tableby()`

. (#298)

Added a

`pkgdown`

site: https://eheinzen.github.io/arsenal/Moved knitr to an import. (#255)

`comparedf()`

: Added support for tolerances by variable. (#167)`tableby()`

/`paired()`

:`tableby()`

:Allowed for changing of “Overall” and “Total” labels. (#253, #261)

Allowed for suppression of N’s in the header. (#256, #36)

Allowed for digits formatting of N’s in the header. (#257)

Escaped

`%`

for`text="latex"`

. (#258)Added to vignette describing

`merge(all=TRUE)`

.Fixed vignette re: outputting to CSV. (#278)

`paired()`

:Allowed for changing of “Difference” label. (#271)

Removed “…” from the documentation for

`paired.internal`

per CRAN’s request (PR#16223 for R-devel).

Added support for “min”, “max”, “sd”, “mean”, and “var” (#259) and “gmean”, “gsd”, “gmeansd”, “gmeanCI” (#260) and “Npct” (#263) and “sum” (#281).

Added a more informative error message when no summary statistic is computed. (#273)

`modelsum()`

:Fixed “statistic.F” for family=“gaussian”. (#262)

Fixed “Nevents” for family=“survival”. (#266)

Fixed vignette re: outputting to CSV. (#278)

`freqlist()`

: Updated`head.summary.freqlist()`

and`tail.summary.freqlist()`

to comply with new R-devel definitions.Updated “labels” vignette. (#267)

Added

`escape =`

argument to`formulize()`

. (#282)

`tableby()`

/`paired()`

:Redid how weights are handled. The only user-visible changes should be that standard deviations on length-1 groups are now reported as

`NA`

instead of`NaN`

.Fixed a bug with

`modpval.tableby()`

when factors are involved. (#239)Added

`meanCI()`

and`medianmad()`

. (#230, #232)Added the units for

`difftime`

statistics when using dates (e.g.,`meansd`

,`medianmad`

,`iqr`

).Fixed Chi-square and Fisher’s Exact test for one-level categorical variables. (#227, #228)

Fixed the n’s in the header when using weights. (#229)

Fixed a bug with confidence levels supplied through the control argument. (#234)

`paired()`

: fixed a bug when using`count()`

with factors. (#235)`tableby.control()`

: added explicit`times=`

argument for survival summaries.Added option to run statistical tests even if one by-group has 0 observations. (#233, #250, #251)

Stopped the formatting of p-values when they’re not numeric (if, say, they’re pre-formatted by the user). (#249)

`modelsum()`

:Added functionality for multiple adjustor sets. (#240)

Fixed “Nmiss” and “N” when used with strata, which now both report the missings for the entire fit. (#241, #242, #243)

Suppressed messages from

`pROC::auc()`

when calculating AUC. (#244)Fixed confidence level for survival models. (#245)

Added an option for the likelihood ratio test for the main effect (but not the adjustors):

`p.value.lrt`

(#238)Blanked out p-values that are NA. (#246)

`code.chunk()`

:Fixed logic checking the length of

`chunk.opts=`

.Allowed for empty code chunks. (#236)

`verbatim()`

: removed named argument in favor of the dots; reworked the object structure to fix edge case printing oddities. (#248)Removed defunct functions.

`comparedf()`

:Fixed a bug when “row.names” was used in combination with other by-variables. (#212)

Allowed for comparison of variables which have any class in common. (#216)

`summary.comparedf()`

:Removed the “comparedf.frame.summary” class from the first element to allow it to print. (#211)

Fixed a bug with reporting blank by-variables. (#213)

Fixed a bug with reporting by-variables as variables in common. (#214)

`modelsum()`

: added Wald confidence intervals to`binom.stats=`

. (#219)`tableby()`

/`paired()`

:Fixed a bug with

`merge.arsenal_table()`

losing control parameters for`tableby()`

objects. (#221)Allowed for variable-name-only

`labelTranslations=`

assignment for terms with inline statistical test specification. Backward compatibility should be maintained here. (#220)Fixed a bug with assigning

`NULL`

labels with inline statistical test specifications. (#222)`summary.tableby()`

: fixed a bug with formatting when strata aren’t in alphabetical order and have different number of elements (e.g., if only one includes missing values). (#215)

`tableby()`

/`paired()`

:Added “Nmiss” to default

`surv.stats=`

in`tableby.control()`

.Fixed a bug when some

`Surv()`

elements are NA. (#208)`tableby.control()`

: fixed a bug with simplifying categorical and numeric output. (#199, #203) This fix also allows for simplification of custom statistics. (#200)`tableby.control()`

: added`date.simplify=`

and`ordered.simplify=`

arguments. (#202) The order of arguments has changed slightly for consistency.`paired.control()`

: took away the arguments that should be the same as`tableby.control()`

, and only included arguments with new defaults or which don’t appear in`tableby.control()`

.Added the functions

`countN()`

and`Nrisk()`

(#201).`Nrisk()`

now outputs what`NriskSurv()`

used to;`NriskSurv()`

now outputs what its name suggests: the number at risk, and the survival. Additionally,`as.countpct()`

gains the`which.pct=`

argument, whose default of`0`

may break the formatting of percents (`digits.pct=`

).

`comparedf()`

:Added additional summary table to the

`summary()`

output.Moved the

`max.print...=`

arguments to`comparedf.control()`

.`max.print.diff=`

is now deprecated and is replaced by`max.print.diffs.per.var=`

.`max.print.diffs=`

was also added to control overall number of differences printed.Fixed a bug with numeric percent tolerances when both values being compared are 0. (#206)

Fixed a bug in

`diffs()`

(and hence`summary()`

) when no variables are compared (#207). Note that this change also included a change to the by-variables reported in the`comparedf()`

object when merging over row.names.

**There are a few non-backwards-compatible updates.**

Major changes:

Renamed

`compare()`

->`comparedf()`

and`comparison.control()`

->`comparedf.control()`

. (#179)`modelsum()`

: Fixed bug(s) with interaction terms. (#173, #177)Added a new function

`loosen.labels()`

which removes the classes added by`keep.labels()`

and thereby speeds up subsetting when labels are no longer needed. This is now used in`tableby()`

,`modelsum()`

,`freqlist()`

, and`paired()`

.

Smaller changes:

`tableby()`

/`paired()`

:Fixed two bugs relating to

`modpval.tableby()`

: one which didn’t properly assign the p-value name (#174), and one which broke`as.data.frame()`

when assigning custom p-values for only one strata (#175).These now issue informative error when class isn’t recognized. (#180)

Fixed two bugs in the

`tableby()`

vignette:`modpval.tableby()`

wasn’t working properly (#170), and`pfootnote=TRUE`

was commented out (#169).Fixed a bug with per-variable stats and digit specifications being lost when using the

`subset=`

argument. (#182, #183)Made all-NA summaries prettier. (#190)

This now issues a warning when

`coin`

isn’t available for the trend test. (#193)

`comparedf()`

:This now allows for zero-row data.frames. (#166)

`comparedf.control()`

now allows for named`tol.vars=`

argument to manually match column names. (#165)

`freqlist()`

:Fixed a bug where labels would get dropped when using the

`subset=`

argument. (#184)Fixed a bug where labels were lost when subsetting the table and using strata terms. (#196)

`freqlist()`

: implemented a`sort()`

method to sort tables on frequency. (#187)`summary.freqlist()`

: Implemented`head()`

and`tail()`

. (#188)`summary.freqlist()`

: fixed a bug when all table counts are 0 and`sparse=FALSE`

. (#186, #194)

`keep.labels()`

:This no longer sticks another class on data.frames.

Fixed a bug with replacement for objects of class

`"keep_labels"`

.

`formulize()`

: added the`collapse=`

and`collapse.y=`

arguments. (#197)

There is a new class system (`"arsenal_table"`

) which unifies `tableby()`

, `modelsum()`

, and `freqlist()`

.

`arsenal`

now imports and re-exports`utils::head()`

and`utils::tail()`

.`arsenal`

now has a sticker!`arsenal_table`

:Implemented a new class (without a constructor).

`labels<-.arsenal_table()`

doesn’t support unnamed labels, as it’s unclear how to assign them to multiple by-variables and strata. It also doesn’t give warnings if your labels are not used.`[.arsenal_table()`

has an argument`j=`

to select the by-variables.`merge.arsenal_table()`

has arguments to select which by-variables to keep if not all are in common. It also checks to make sure that strata, weights, and by-variables are all identical.`print.arsenal_table()`

shows y- and x-variables, plus any strata.

`tableby()`

and`paired()`

:Added functionality for multiple by-variables and strata terms. This required completely reworking the innards of the

`tableby`

object.Removed

`length.tableby()`

(because it was messing up`str()`

and R Studio) and replaced with`head.tableby()`

and`tail.tableby()`

(the original purpose to having`length()`

defined).Implemented

`sort.tableby()`

, which errors out if the object has strata or multiple by-variables, and then runs the default method.`modpval.tableby()`

now requires the first column to be the by-variable, and if the object has a strata, the second column is required to be the corresponding strata value.`tests.tableby()`

now returns a data.frame with a by-variable column and (if applicable) a strata column.`na.tableby()`

now generates functions. The “lhs=” argument determines whether to remove NAs from the first column of the data. If`tableby()`

detects a one-sided formula, it sets this to FALSE. Both versions now remove rows with NAs in the strata column (when applicable).`na.paired()`

now removes rows with NAs in the strata column (when applicable).`padjust.tableby()`

and`padjust.summary.tableby()`

will error if fed an object with strata or multiple by-variables.`as.data.frame.tableby()`

and`as.data.frame.summary.tableby()`

gain the`list.ok=`

argument, for when there are multiple left-hand-sides.Added logic to statistical tests to detect missing levels of the by-variable.

Fixed a bug with LaTeX formatting involving the

`align=`

argument to`knitr::kable()`

.Passing

`term.name=TRUE`

to`summary.tableby()`

or`as.data.frame.summary.tableby()`

will now put the term name in the top left corner of each table.

`modelsum()`

:Added functionality for multiple by-variables and strata terms. This required completely reworking the innards of the

`modelsum`

object.`na.modelsum()`

now removes rows with NAs in the strata column (when applicable).`as.data.frame.modelsum()`

and`as.data.frame.summary.modelsum()`

gain the`list.ok=`

argument, for when there are multiple left-hand-sides.Passing

`term.name=TRUE`

to`summary.modelsum()`

or`as.data.frame.summary.modelsum()`

will now put the term name in the top left corner of each table.

`freqlist()`

:Added functionality for multiple by-variables. This required completely reworking the innards of the

`freqlist`

object.Changed the argument

`groupBy=`

to`strata=`

to match`tableby()`

and`modelsum()`

.Added

`merge.freqlist()`

and`as.data.frame.summary.freqlist()`

. Note that`[.arsenal_table()`

now allows you to remove the cumulative and percent columns.Note that

`labels<-.arsenal_table()`

no longer supports unnamed labels, but now accepts labels for the frequency, cumulative, and percent columns for`freqlist`

objects.Removed the

`digits=`

,`sparse=`

,`single=`

, and`dupLabels=`

arguments from`freqlist()`

and`summary.freqlist()`

. These are now arguments to the new`freq.control()`

, and are passed through the dots (for backwards compatibility).`freqlist()`

also gained the`control=`

argument for objects from`freq.control()`

.`as.data.frame.freqlist()`

no longer rounds its digits, nor does it label its columns. Use`as.data.frame.summary.freqlist()`

for that instead. It also gained the`list.ok=`

argument, for when there are multiple left-hand-sides.

`includeNA()`

: removed the “character” and “numeric” methods, replacing them with a default. In particular, this changes the default label of what used to be`includeNA.numeric()`

.`write2()`

:Changed the output to an

`.Rmd`

file instead of a`.md`

. This shouldn’t break anything, unless you’re relying on the intermediate file.Replaced the

`keep.md=`

argument with`keep.rmd=`

(since we’re not using`.md`

files directly anymore).Added the function

`code.chunk()`

to write executable code chunks to the`.Rmd`

.

`tableby()`

and`paired()`

:fixed a bug with specifying individual statistics for character and logical vectors. (#142)

`tableby()`

and`paired()`

: added a function (`notest()`

) to prevent performing a test on an individual variable. (#144)`summary.tableby()`

: changed NA p-values to blanks. (#145)`summary.tableby()`

: added documentation on`bookdown`

. (#147)Wrote

`padjust()`

, an S3 wrapper for`p.adjust()`

, which can also adjust`tableby()`

(and hence`paired()`

) objects. (#146)`print.summary.tableby()`

,`as.data.frame.summary.tableby()`

: added`width=`

and`min.split=`

as formal arguments.Fixed

`medSurv()`

which was calculating the median survival incorrectly, and removed`rangeTime()`

, an ambiguous survival statistic. (#32)

`modelsum()`

:`summary.modelsum()`

: added documentation on`bookdown`

. (#147)`print.summary.modelsum()`

,`as.data.frame.summary.modelsum()`

: added`width=`

and`min.split=`

as formal arguments.

`summary.freqlist()`

: added documentation on`bookdown`

. (#147)`formulize()`

: added support for names and calls. (#152, #153)

**There are a few non-backwards-compatible updates.**

Major changes:

`modelsum()`

:Added

`family="ordinal"`

to do ordinal logistic regression using`MASS::polr()`

. (#130)Added

`family="negbin"`

to do negative binomial regression using`MASS::glm.nb()`

. (#15)Added support for ordinal regressors and adjustment terms (by adding support for their associated contrasts). (#133)

Allowed for LaTeX formatting. NOTE: this changes (hence possibly breaking old code) the formatting behavior when specifying

`text="html"`

. (#123)

`summary.compare.data.frame()`

: Added a small summary of the input data.frames as the first table. (#126) NOTE: this changes the structure and printed output of`summary()`

!`tableby()`

:Allowed for LaTeX formatting. NOTE: this changes (hence possibly breaking old code) the formatting behavior when specifying

`text="html"`

. (#123)Added functionality to in-formula functions to allow the specification of

`digits=`

(etc.),`numeric.simplify=`

, and`cat.simplify=`

for a single variable. (#107, #134, #139) NB: this has the following breaking changes:There is no longer a “name” element in the “tableby” object’s x-specifications; instead it’s now called “term”

An element for “variable”, containing the variable name, was added to the “tableby” object’s x-specifications.

An element for “control.list”, recording format specifications, was added to the “tableby” object’s x-specifications.

The output of

`as.data.frame.tableby()`

now reports only the variable name in the “variable” column when using internal statistical functions (like`anova()`

and`chisq()`

–it used to include the function call as well).The output of

`as.data.frame.tableby()`

no longer includes category levels in the “term” column; instead, it contains the statistical function used (like`countpct()`

and`count()`

).

Smaller changes:

`modelsum()`

:Added support for

*calls*to the family functions, in case a different link function (for example) is required.Properly propogated “term.name” to the

`as.data.frame()`

method. (#128)Fixed formatting of error about unsupported families.

Removed “concordance” from the list of supported statistics for Poisson regression. This shouldn’t break much code, as specifying “concordance” wouldn’t have shown anything anyway.

Fixed a bug with formatting one-per-model p-values. (#140)

`tableby()`

:Added a warning for when by-variable contains empty string. (#121)

Properly propogated “term.name” to the

`as.data.frame()`

method. (#127)Fixed an error that sometimes occured when using categorical statistics on numeric variables. (#137)

Added an argument to

`tableby.control()`

to simplify one-line numeric output. (#139)

`paired()`

:Added a warning for when by-variable contains empty string. (#121)

Added error to

`na.paired("in.both")`

when there are more than two time points.

`compare.data.frame()`

:Implemented

`n.diff.obs()`

. (#124)Added an argument to

`summary()`

to allow for the display of attributes. (#125)Fixed

`summary()`

to now return the object passed it. (#141)

Updated documentation where appropriate.

**This is a mostly backwards-compatible update.**

Major changes:

Implemented the function

`paired()`

for paired data, based on`tableby()`

. This comes with a very light vignette.`tableby()`

: Change default for chi-square tests to`correct=FALSE`

. Note that this only affects the 2 x 2 case.

Smaller changes:

Added the a default method for label assignment (

`labels<-`

). (#118)Update

`formulize()`

to handle non-syntactic names in the`data=`

argument. (#105)`tableby()`

:Implemented

`is.tableby()`

and`is.summary.tableby()`

. (#112)Changed how arguments are passed to stat tests.

Issue a warning if statistical tests are requested when there are fewer than two by-levels. (#108)

Fixed

`trend()`

and`anova()`

to return an object instead of the object being invisible.Implemented the stat functions

`binomCI()`

and`rowbinomCI()`

for binomial confidence intervals. (#117)`summary.tableby()`

: ignore row.names when printing summary objects.`summary.tableby()`

and`as.data.frame.summary.tableby()`

: added a`term.name=`

argument. (#110)`summary.tableby()`

: pass`text="html"`

to get better formatting in R shiny. (#114)Implemented

`Ops.tableby()`

to compare tableby objects to a number (p-value). (#96)Implemented

`xtfrm.tableby()`

, so that tableby objects can be sorted by p-value. (#96)Implemented

`length.tableby()`

, so that`head()`

and`tail()`

also work. (#97)Implemented

`countcellpct()`

for counts and cell percentages. (#106)

`modelsum()`

:Implemented

`is.modelsum()`

and`is.summary.modelsum()`

. (#111)`summary.modelsum()`

: ignore row.names when printing summary objects.`summary.modelsum()`

and`as.data.frame.summary.modelsum()`

: added a`term.name=`

argument. (#109)Allow for

`weights=`

and`na.action=`

. (#99)Fixed problem with column names which are prefixes of other column names. (#98)

Fixed problem with column labels overwriting categorical levels which also match. (#100)

`summary.modelsum()`

: pass`text="html"`

to get better formatting in R shiny. (#115)

`freqlist()`

:Implemented

`is.freqlist()`

and`is.summary.freqlist()`

. (#113)Fixed a problem with a column named “method”. (#95)

`summary.freqlist()`

: ignore row.names when printing summary objects.

Update documentation.

Implemented

`write2()`

methods for`"summary.tableby"`

,`"summary.modelsum"`

, and`"summary.freqlist"`

objects. (#89, #90, #91)Center-aligned

`tableby()`

grouping columns in the summary output. (#93)

**This is a mostly backwards-compatible update.**

Major changes:

`summary.freqlist()`

now returns an object.`print.summary.freqlist()`

prints the resulting object. (#76)

Smaller changes:

`tableby()`

:Fixed a bug in

`print.summary.tableby()`

involving the lack of wrapping for long labels. (#59)`as.data.frame.summary.tableby()`

has been implemented, and`print.summary.tableby()`

updated accordingly. (#60)Fixed a bug with assigning labels for tableby objects when some value names are unmatched. (#64)

Fixed a bug in

`print.summary.tableby()`

with regards to knitting in R Markdown with plots immediately following. (#65)Fixed a bug in

`print.summary.tableby()`

with regards to PDF output in bookdown. (#69)Changed

`tests.tableby()`

to return a data.frame without factors.Fixed a bug in

`meansd()`

when all inputs are NA. (#80)Fixed a bug with

`kwt()`

,`anova()`

, and`summary.tableby()`

formatting when all inputs are NA. (#81)Fixed a bug with survival statistics when all inputs are NA. (#82)

Fixed a bug with

`logrank()`

when all inputs are NA. (#83)Fixed how arguments get passed to stats functions in

`tableby()`

. In particular, this affected the`times=`

option. (#84)Added

`iqr()`

as a tableby stat option. (#86)Fixed quantile functions

`q1q3()`

and`medianq1q3()`

for dates. (#87)

`modelsum()`

:Fixed a bug in

`print.summary.modelsum()`

involving the lack of wrapping for long labels. (#59)Fixed a bug in

`print.summary.modelsum()`

with regards to knitting in R Markdown with plots immediately following. (#66)Fixed a bug in

`print.summary.modelsum()`

with regards to PDF output in bookdown. (#70)`as.data.frame.summary.modelsum()`

has been implemented, and`print.summary.modelsum()`

updated accordingly. (#74)

`freqlist()`

:Fixed a bug in

`summary.freqlist()`

with regards to knitting in R Markdown with plots immediately following. (#67)Fixed a bug in

`summary.freqlist()`

with regards to PDF output in bookdown. (#71)

Other:

`includeNA()`

now has dots, and the factor method gained a`first=`

argument. (#62)`includeNA()`

also gained a numeric method, especially for use in`freqlist.formula()`

. (#78)Fixed a bug in

`print.summary.compare.data.frame()`

with regards to PDF output in bookdown. (#72)

**This is a non-backwards-compatible update.**

Major changes:

`freqlist()`

:`freqlist()`

is now an S3 generic. (#35)The first argument to

`freqlist()`

has changed from`tab=`

to`object=`

, for S3 consistency. (#35)`freqlist.formula()`

was implemented, piggybacking off of`stats::xtabs()`

. (#35)The

`title=`

argument was added to`summary.freqlist()`

. Passing`caption=`

through the dots to`knitr::kable()`

will now throw an error. (#34)

`tableby()`

:`as.data.frame.tableby()`

has been totally overhauled. It now uses list-columns to give exact values.`summary.tableby()`

has been totally overhauled.Most arguments are no longer named, but passed through the dots.

It now returns an object, abusing in the process

`as.data.frame.tableby()`

.`print.summary.tableby()`

prints the resulting object. (#8)`print.summary.tableby()`

now uses`knitr::kable()`

to print results, instead of internal functions. As such, non-exported helper functions have all been removed.

The arguments to

`tableby.control()`

have changed. Warnings will be issued for using old arguments.`nsmall=`

has been removed.`digits=`

takes its place.`nsmall.pct=`

and`digits.test=`

have been renamed to`digits.pct=`

and`digits.p=`

, respectively.There’s now an option for count digits (

`digits.count=`

).`format.p=`

has been added, to turn on formatting of p-values.`q1q3`

is no longer a default continuous statistic.

NAs can be included in percents using

`includeNA()`

. (#57)Some additional survival summary functions are now available. (#32)

It is now possible to report row-percents using

`countrowpct()`

. (#9)

`modelsum()`

:`modelsum()`

has been totally overhauled:It now uses

`stats::model.frame()`

and unevaluated calls instead of custom-creating data.frames.It now allows for non-syntactic names (#44, #45).

`as.data.frame.modelsum()`

has been totally overhauled. It now gives exact values instead of formatted values.`summary.modelsum()`

has been totally overhauled.Most arguments are no longer named, but passed through the dots.

It now returns an object, abusing in the process

`as.data.frame.modelsum()`

.`print.summary.modelsum()`

prints the resulting object. (#37)`print.summary.modelsum()`

now uses`knitr::kable()`

to print results, instead of internal functions. As such, non-exported helper functions have all been removed.`print.summary.modelsum()`

now strips leading and trailing whitespace from labels to fix formatting with`text=FALSE`

. (#48)`labelTranslations=`

no longer accepts labels for the statistics columns. Use`modelsum.control(stat.labels=)`

for this instead.

The arguments to

`modelsum.control()`

have changed. Warnings will be issued for using old arguments.`nsmall=`

has been removed.`digits=`

takes its place.`nsmall.ratio=`

and`digits.test=`

have been renamed to`digits.ratio=`

and`digits.p=`

, respectively.`format.p=`

has been added, to turn off formatting of p-values.`stat.labels=`

has been added, to label the statistics columns.

`"[.modelsum"()`

now has a named argument, and accepts character, numeric, and logical subscripts.

Smaller changes:

`freqlist()`

:`freqlist()`

will no longer issue a warning about using the deprecated`varnames=`

argument.`print.freqlist()`

has been made slightly more concise. The only change to the printed output is making “variables” singular (“variable”) when only one variable is present.

`tableby()`

:`tableby()`

has also been made slightly more concise and easier to read.A bug was fixed when trying to specify “stats” attributes for categorical variables. (#39)

A bug was fixed relating to unnamed passing of arguments for

`medianrange()`

. (#49)`as.data.frame.tableby()`

no longer breaks with date ranges. (#10)`as.data.frame.tableby()`

no longer breaks with both`count()`

and`countpct()`

. (#51)`labels<-.tableby()`

no longer breaks for unmatched variables. (#53)`labels<-.tableby()`

now accepts`NULL`

to set all labels to NULL. (#52)The function

`Nmiss2()`

is now exported for`tableby()`

. Note that it is exactly the same as`Nmiss()`

, but is interpreted differently in`tableby()`

.

`modelsum()`

:`modelsum()`

has been made slightly more concise.“Nmiss2” has been added to the

`modelsum()`

object and no longer replaces “Nmiss”.`as.data.frame.modelsum()`

no longer turns “<0.001” into`NA`

. (#31)`as.data.frame.modelsum()`

no longer breaks if there are too many adjustment variables. (#12)`summary.modelsum()`

now has working labels for factors. (#13)`"labels<-.modelsum"()`

has been tweaked slightly. The results shouldn’t change.`print.modelsum()`

has been fixed to show its y-variable. (#33)

Documentation and vignettes have been re-reviewed and updated where appropriate.

Tests have been updated to reflect major changes.

This is a patch to fix an error appearing with R-devel. We anticipate releasing v1.0.0 soon, which will not be backwards-compatible.

- Re-fix trailing whitespace problem in tableby. (#3)

Updated

`freqlist()`

to be more efficient. (#20)`freqlist()`

now allows named labels.Fixed one-sided formula detection in

`tableby()`

when used with`formulize()`

. (#21)Changed environment of formula returned by

`formulize()`

.Added variable-name subsetting to

`[.tableby()`

. One can now subset by logicals, numerics, or character vectors.Fixed a bug in

`tableby()`

related to zero-length factor levels. (#22)Fixed a bug in

`tableby()`

and`modelsum()`

when calling them without loading the package. (#25)Allowed

`nsmall =`

and`digits =`

to be 0, for rounding to integers. (#23)Added

`yaml()`

function to use with`write2()`

. (#28)Added the

`yaml`

package as a suggested package.Added

`write2()`

methods for`compare.data.frame()`

objects. (#27)Updated documentation.

Code all now in GitHub; issues can now be submitted there. Checking is now performed automatically on Travis-CI.

Included documentation for getting a caption with

`write2()`

and`freqlist()`

. (#16)Fixed subsetting in

`modelsum()`

. (#14)Fixed multiple class errors in

`tableby()`

. (#17)Fixed subset dropping labels in

`tableby()`

and`modelsum()`

with new function`keep.labels()`

to make labels “stick”. (#1)Added a vignette discussing labels.

Add

`compare.data.frame()`

, with an accompanying vignette.

Updated

`labelTranslation`

documentationChanged

`format.translations`

list to`defaultLabelTranslations()`

function, and removed labels for sex and age.Tweaked

`labels<-.freqlist`

to allow for list input.

- Updated
`tableby()`

vignette.

Tweaked

`freqlist()`

to behave better with data.frame subsetting and the infamous`drop=TRUE`

.Added

`dupLabels=`

argument to`summary.freqlist()`

. (#6)Added a label for

`medianq1q3()`

in`tableby.control()`

. (#4)Changed the

`...`

vs.`control=`

action in`tableby()`

and`modelsum()`

to fix which arguments are used over which other arguments. (#5)Moved import

`broom`

and`stringr`

to “Suggests”, adding`magrittr`

for piping.Added piping to

`write2*()`

vignette.Several

`tableby()`

fixes for counts and percents.New options in

`tableby.control()`

to modify the statistical tests performed. (#2)Fixed trailing whitespace issue in

`tableby()`

(#3)

The CRAN release of the locally stable 0.2.3. For NEWS on this version, see below.

Tweaked the DESCRIPTION to include

`write2()`

.

Fixed ordered stats in

`tableby()`

.Fixed a problem with

`as.data.frame.modelsum()`

introduced in v0.2.1.

Added

`count()`

function for tableby stats.Two problems with survival models in

`modelsum()`

have been resolved.

`write2.list()`

has been implemented, allowing multiple tables output into a single document.`write2.verbatim()`

has been implemented, allowing monospaced output. The vignette has been updated along with all documentation.The

`summary()`

output for`tableby`

and`modelsum`

objects now prints an extra blank header line, for better use inside R Markdown code chunks.Two bugs in

`tableby()`

were corrected.

Vignettes have been updated.

`write2()`

is now exported and supports all output formats supported by`rmarkdown::render()`

. There is now a vignette for it and the S3 methods have been expanded to handle more inputs, including`knitr::kable()`

,`xtable::xtable()`

, and`pander::pander_return()`

.Fixed a bug in

`summary.modelsum()`

.

`broom`

and`stringr`

have been moved to`imports`

instead of`depends`

.Several minor tweaks to

`freqlist`

for better readability and performance.

- The description and the title are more descriptive now, per request.

First release contains major functions

`tableby()`

,`modelsum()`

,`freqlist()`

,`formulize()`

, and`write2...`

.Vignettes are included for

`tableby()`

,`modelsum()`

, and`freqlist()`

.