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Added medtest() to tableby() for a
median test. (#327)
Account for NAs in sign.test() in
paired(). (#326)
Add Nsigntest() for paired().
(#326)
Add "Nevents" for binomial GLMs. (#325)
A fix for R devel when digits=0.
Fixed one URL
Fixed two modelsum test errors that were a result of
rounding on macos.
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():
write2() vignette about a global option
for R Markdown documents in R Studio. (#312)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.
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 documentation
Changed format.translations list to
defaultLabelTranslations() function, and removed labels for
sex and age.
Tweaked labels<-.freqlist to allow for list
input.
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.
First release contains major functions tableby(),
modelsum(), freqlist(),
formulize(), and write2....
Vignettes are included for tableby(),
modelsum(), and freqlist().
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.