tidy.lm() and
tidy.glm() for full-rank fits (#1112 by
@capnrefsmmat).tidy.sparseMatrix(),
tidy.dgCMatrix(), and tidy.dgTMatrix(). Note
that tidy.confusionMatrix(), for relevant objects outputted
from the caret package, is unaffected (#1113).tidy.anova() works again with anova
objects from the lme4 package (broken by addition of the
terms column in the previous release)broom 1.0.0 is the first “production” release of the broom package, and includes a number of notable changes to both functionality and governance.
As of this release, the broom team will be following a set of guidelines that clarify the scope of further development on the package. Given the package’s wide use and long history, these guidelines prioritize backward compatibility over internal consistency and completeness. You can read those guidelines here!
We’ve also made notable changes to error handling in this release:
tidy() methods will now warn when supplied an
exponentiate argument if it will be ignored.augment() methods will now warn when supplied a
newdata argument if it will be ignored.lm and glm is now displayed only once per
session, per unique dispatch. That is, if a class_a object
is tidied using a (g)lm method, broom will not warn when
tidying class_a objects for the rest of the session, but if
a class_b object is tidied using a (g)lm
method in the same session, broom will warn again (#1101).Other fixes and improvements:
exponentiate argument to tidy.boot()
(#1039).tidy.htest() converting matrix-columns to
vector-columns (#1081).tidy.glht() with
conf.int = TRUE (#1103).tidy.zoo() when input data does not
have colnames (#1080).tidy.svyolr() when
p.values = TRUE. Instead of aliasing
tidy.polr() directly, tidy.svyolr() lightly
wraps that method and warns if p.values is supplied
(#1107).term column and introduces support for
car::lht() output in tidy.anova() (#1106 by
@grantmcdermott).glance.anova method (which previously
dispatched to theglance.data.frame() tidier, #1106 by
@grantmcdermott).This update makes significant improvements to documentation, fixes a number of bugs, and brings the development flow of the package up to date with other packages in the tidymodels.
In the big picture, this release:
\dontrun or
\donttest have been workshopped to run reliably.glance.fixest error when model includes only fixed
effects and no regressors (#1018 by @arcruz0,
#1088 by @vincentarelbundock).tidy.speedlm
(#1084 by @cgoo4, #1087 by
@vincentarelbundock).nobs column to the output of
glance.svyglm (#1085 by
@fschaffner, #1086 by
@vincentarelbundock).tidy.prcomp description entries use consistent
punctuation (#1072 by
@PursuitOfDataScience).glance.fixest and
tidy.btergm.MASS::polr output in the
corresponding tidy and augment methods.Nearly identical source to broom 0.7.11—updates the maintainer email address to an address listed in other CRAN packages maintained by the same person.
augment.rqs. Now function preserves the original
data.frame names also when the input
data.frame only has one column (#1052 by
@ilapros).tidy.rma when x$ddf
has length greater than 1 (#1064 by
@wviechtb).glance.lavaan in anticipation of upcoming
tidyr release (#1067 by
@DavisVaughan).tidy.crr(). The
tidy.crr(conf.level=) argument was previously ignored
(#1068 by @ddsjoberg).pysch::mediate output is
dispatched to tidy.mediate (#1037 by
@LukasWallrich).tidy.rma
(#1041 by @TarenSanders)augment_columns(); most package users should use
augment() in favor of augment_columns(). See
?augment_columns for more details.emmeans by fixing non-standard
column names in case of asymptotically derived inferential statistics.
(#1046 by @crsh)augment.mlogit and adds
.resid column to output. (#1045,
#1053, #1055, and #1056 by
@jamesrrae and @gregmacfarlane)glance.survfit().tidy.crr(), which were
previously exponentiated when exponentiate = FALSE
(#1023 by @leejasme)Rchoice tidiers, as the newest 0.3-3 release
requires R 4.0+ and does not re-export needed generics.ergm tidiers in anticipation of changes in
later releases. (#1034 by @krivit)glance.ergm related to handling of MCMC
details.tidy.epi.2by2 that resulted in errors with
new version of epiR (#1028 by
@nt-williams)exponentiate argument to tidy.gam()
tidier applicable for parametric terms (#1013 by
@ddsjoberg)exponentiate argument to
tidy.negbin() tidier (#1011 by
@ddsjoberg)spdep tidiers following breaking
changes in the most recent releaseaugment tidiers resulting in
.fitted and .se.fit array columns.y non-numeric after
tidy_xyz (#973 by @jiho)MASS:glm.nb (#998 by
@joshyam-k)tidy.fixest that sometimes prevented
arguments like se from being used (#1001 by
@karldw)tidy.fixest that resulted in errors when
columns with name x are present (#1007 by
@grantmcdermott)gamlss
tidiers in favor of those provided in broom.mixednnet::multinom tidier in the case that
the response variable has only two levels (#993 by
@vincentarelbundock and @hughjonesd)broom 0.7.4 introduces tidier support for a number of new model objects and improves functionality of many existing tidiers!
Rchoice objects (#961 by
@vincentarelbundock and @Nateme16)car::leveneTest
(#968 by @vincentarelbundock and
@mkirzon)cmprsk::crr
(#971 and #552 by
@vincentarelbundock and @margarethannum)augment() method for gam objects
(#975 and #645 by
@vincentarelbundock)vars objects (#979 and
#161 by @vincentarelbundock and
@Diego-MX)This release also restores tidiers for felm objects from
the lfe package, which was recently unarchived from
CRAN.
tidy.emmGrid can now return std.error and
conf.* columns at the same time. (#962 by
@vincentarelbundock and @jmbarbone)tidy.garch can now produce confidence intervals
(#964 by @vincentarelbundock and
@IndrajeetPatil)tidy.coxph can now report confidence intervals on
models utilizing penalized/clustering terms (#966 by
@vincentarelbundock and @matthieu-faron)augment.lm now works when some regression weights are
equal to zero (#965 by @vincentarelbundock and
@vnijs)tidy.coxph can now handle models utilizing
penalized/clustering terms (#966 and #969 by
@vincentarelbundock, @matthieu-faron, and
@KZARCA)tidy.speedglm on R 4.0.0+ (#974
by @uqzwang)#977 and
#666 by @vincentarelbundock and
@atyre2)In broom 0.7.0, we introduced an error for model objects
that subclassed lm and relied on tidy.lm(), or
similarly for tidy.glm(). Tidiers for these objects were
supported unintentionally, and we worried that tidiers for these objects
would silently report inaccurate results.
In hindsight, this change was unnecessarily abrupt. We’ve decided to
roll back this change, instead providing the following warning before
allowing such objects to fall back to the
lm/glm tidier methods:
Tidiers for objects of class {subclass} are not maintained by the broom team, and are only supported through the {dispatched_method} tidier method. Please be cautious in interpreting and reporting broom output.”
In addition,
summary.lm objects
(#953 by @grantmcdermott)lfe package, which was
archived from CRAN.While broom 0.7.1 is a minor release, it includes a number of exciting new features and bug fixes!
margins objects. (#700 by
@grantmcdermott)mlogit objects
(#887 by @gregmacfarlane)glance.coeftest() method (#932 by
@grantmcdermott)One of the more major improvements in this release is the addition of
the interval argument to some augment methods
for confidence, prediction, and credible intervals. These columns will
be consistently labeled .lower and .upper!
(#908 by @grantmcdermott, #925 by
@bwiernik)
In addition…
glance.aov() method to include an
r.squared column!glance.survfit() now passes ... to
summary.survfit() to allow for adjustment of RMST and other
measures (#880 by @vincentarelbundock)glm and
lm now error more informatively.newdata warning message in
augment.*() output when the newdata didn’t
contain the response variable—augment methods no longer expect the
response variable in the supplied newdata argument.
(#897 by @rudeboybert)tidy.geeglm() not being
sensitive to the exponentiate argument
(#867)augment.fixest() returning residuals in the
.fitted column. The method also now takes a
type.residuals argument and defaults to the same
type.predict argument as the fixest
predict() method. (#877 by
@karldw)tidy.felm confidence interval bug. Replaces
“robust” argument with “se.type”. (#919 by
@grantmcdermott; supersedes #818 by
@kuriwaki)tidy.drc() where some term labels would
result in the overwriting of entries in the curve column
(#914)tidy.zoo() (#916 by
@WillemVervoort)tidy.prcomp() assigning the
wrong PC labels from “loadings” and “scores” matrices (#910
by @tavareshugo)tidy.polr() bug where p-values could only be
returned if exponentiate = FALSE.We followed through with the planned deprecation of character vector tidiers in this release. Other vector tidiers that were soft-deprecated in 0.7.0 will be fully deprecated in a later release.
broom 0.7.0 is a major release with a large number of
new tidiers, soft-deprecations, and planned hard-deprecations of
functions and arguments.
We have changed how we report degrees of freedom for
lm objects (#212, #273). This is especially important for
instructors in statistics courses. Previously the df column
in glance.lm() reported the rank of the design matrix. Now
it reports degrees of freedom of the numerator for the overall
F-statistic. This is equal to the rank of the model matrix minus one
(unless you omit an intercept column), so the new df should
be the old df minus one.
We are moving away from supporting summary.*()
objects. In particular, we have removed tidy.summary.lm()
as part of a major overhaul of internals. Instead of calling
tidy() on summary-like objects, please call
tidy() directly on model objects moving forward.
We have removed all support for the quick argument
in tidy() methods. This is to simplify internals and is for
maintainability purposes. We anticipate this will not influence many
users as few people seemed to use it. If this majorly cramps your style,
let us know, as we are considering a new verb to return only model
parameters. In the meantime, stats::coef() together with
tibble::enframe() provides most of the functionality of
tidy(..., quick = TRUE).
All conf.int arguments now default to
FALSE, and all conf.level arguments now
default to 0.95. This should primarily affect
tidy.survreg(), which previously always returned confidence
intervals, although there are some others.
Tidiers for emmeans-objects use the arguments
conf.int and conf.level instead of relying on
the argument names native to the emmeans::summary()-methods
(i.e., infer and level). Similarly,
multcomp-tidiers now include a call to
summary() as previous behavior was akin to setting the now
removed argument quick = TRUE. Both families of tidiers now
use the adj.p.value column name when appropriate. Finally,
emmeans-, multcomp-, and
TukeyHSD-tidiers now consistently use the column names
contrast and null.value instead of
comparison, level1 and level2, or
lhs and rhs (see #692).
This release of broom soft-deprecates the following
functions and tidier methods:
bootstrap()confint_tidy()fix_data_frame()finish_glance()augment.glmRob()tidy.table() and tidy.ftable() have been
deprecated in favor of tibble::as_tibble()tidy.summaryDefault() and
glance.summaryDefault() have been deprecated in favor of
skimr::skim()We have also gone forward with our planned mixed model deprecations,
and have removed the following methods, which now live in
broom.mixed:
tidy.brmsfit()tidy.merMod(), glance.merMod(),
augment.merMod()tidy.lme(), glance.lme(),
augment.lme()tidy.stanreg(), glance.stanreg()tidyMCMC(), tidy.rjags(),
tidy.stanfit()augment.factanal() now returns a tibble with columns
names .fs1, .fs2, …, instead of
factor1, factor2, … (#650)
We have renamed the output of augment.htest(). In
particular, we have renamed the .residuals column to
.resid and the .stdres to
.std.resid for consistency. These changes will only affect
chi-squared tests.
tidy.ridgelm() now always return a GCV
column and never returns an xm column. (#533 by @jmuhlenkamp)
tidy.dist() no longer supports the
upper argument.
augment() methodsThe internals of augment.*() methods have largely been
overhauled.
If you pass a dataset to augment() via the
data or newdata arguments, you are now
guaranteed that the augmented dataset will have exactly the same number
of rows as the original dataset. This differs from previous behavior
primarily when there are missing values. Previously
augment() would drop rows containing NA. This
should no longer be the case.
augment.*() methods no longer accept an
na.action argument.
In previous versions, several augment.*() methods
inherited the augment.lm() method, but required additions
to the augment.lm() method itself. We have shifted away
from this approach in favor of re-implementing many
augment.*() methods as standalone methods making use of
internal helper functions. As a result, augment.lm() and
some related methods have deprecated (previously unused)
arguments.
augment() tries to give an informative error when
data isn’t the original training data.
The .resid column in the output of
augment().* methods is now consistently defined as
y - y_hat
anova objects from the car package
(#754)pam objects from the cluster package (#637
by @abbylsmith)drm objects from the drc package (#574 by
@edild)summary_emm objects from the emmeans
package (#691 by @crsh)epi.2by2 objects from the epiR package
(#711)fixest objects from the fixest package
(#785 by @karldw)regsubsets objects from the leaps package
(#535)lm.beta objects from the lm.beta package
(#545 by @mattle24)rma objects from the metafor package (#674
by @malcolmbarrett, @softloud)mfx, logitmfx, negbinmfx,
poissonmfx, probitmfx, and
betamfx objects from themfx package (#700 by
@grantmcdermott)lmrob and glmrob objects from the
robustbase package (#205, #505)sarlm objects from the spatialreg package
(#847 by @gregmacfarlane and @petrhrobar)speedglm objects from the speedglm package
(#685)svyglm objects from the survey package
(#611)systemfit objects from the systemfit
package (by @jaspercooper)glance.aov(),
which used to inherit from the glance.lm() method and now
contains only the following columns: logLik,
AIC, BIC, deviance, df.residual,
and nobs (see #212). Note that tidy.aov()
gives more complete information about degrees of freedom in an
aov object.tidy.felm() now has a
robust = TRUE/FALSE option that supports robust and cluster
standard errors. (#781 by @kuriwaki)
Make .fitted values respect
type.predict argument of augment.clm().
(#617)
Return factor rather than numeric class predictions in
.fitted of augment.polr(). (#619) Add an
option to return p.values in tidy.polr().
(#833 by @LukasWallrich)
tidy.kmeans() now uses the names of the input
variables in the output by default. Set col.names = NULL to
recover the old behavior.
Previously, F-statistics for weak instruments were returned
through glance.ivreg(). F-statistics are now returned
through tidy.ivreg(instruments = TRUE). Default is
tidy.ivreg(instruments = FALSE).
glance.ivreg() still returns Wu-Hausman and Sargan test
statistics.
glance.biglm() now returns a
df.residual column.
tidy.prcomp() argument matrix gained
new options "scores", "loadings", and
"eigenvalues". (#557 by @GegznaV)
tidy_optim() now provides the standard error if the
Hessian is present. (#529 by @billdenney)
tidy.htest() column names are now run through
make.names() to ensure syntactic correctness. (#549 by
@karissawhiting)
tidy.lmodel2() now returns a p.value
column. (#570)
tidy.lsmobj() gained a conf.int
argument for consistency with other tidiers.
tidy.polr() now returns p-values if
p.values is set to TRUE and the model does not contain
factors with more than two levels.
tidy.zoo() now doesn’t change column names that have
spaces or other special characters (previously they were converted to
data.frame friendly column names by
make.names.)
glance.lavaan() now uses lavaan extractor functions
instead of subsetting the fit object manually. (#835)
glance.lm() no longer errors when only an intercept
is provided as an explanatory variable. (#865)
tidy.survreg() when robust is
set to TRUE in model fitting (#842, #728)glance.lavaan(): address confidence
interval error (#577) and correct reported nobs and
norig (#835)tibble (#824)glance.*() methods have been refactored in
order to return a one-row tibble even when the model matrix is
rank-deficient (#823)tidy.drc() (#798)glm and
lm in order to error more informatively. (#749, #736, #708,
#186)augment.kmeans() to work with masked
data (#609)augment.Mclust() to work on univariate
data (#490)tidy.htest() to supports equal
variances (#608)tidy.boot() to support
confidence intervals (#581)tidy.polr() when passed
conf.int = TRUE (#498)Many glance() methods now return a nobs
column, which contains the number of data points used to fit the model!
(#597 by @vincentarelbundock)
tidy() no longer checks for a log or logit link when
exponentiate = TRUE, and we have refactored to remove
extraneous exponentiate arguments. If you set
exponentiate = TRUE, we assume you know what you are doing
and that you want exponentiated coefficients (and confidence intervals
if conf.int = TRUE) regardless of link function.
We now use rlang::arg_match() when possible instead
of arg.match() to give more informative errors on argument
mismatches.
The package’s site has moved from https://broom.tidyverse.org/ to https://broom.tidymodels.org/.
Revised several vignettes and moved them to the tidymodels.org website. The existing vignettes will now simply link to the revised versions.
Many improvements to consistency and clarity of documentation.
Various warnings resulting from changes to the tidyr API in v1.0.0 have been fixed. (#870)
Removed dependencies on reshape2 and superseded functions in dplyr.
All documentation now links to help files rather than topics.
Moved core tests to the modeltests package.
Generally, after this release, the broom dev team will first ask that attempts to add tidier methods supporting a model object are first directed to the model-owning package. An article describing best practices in doing so can be found on the {tidymodels} website at https://www.tidymodels.org/learn/develop/broom/, and we will continue adding additional resources to that article as we develop them. In the case that the maintainer is uninterested in taking on the tidier methods, please note this in your issue or PR.
Added a new vignette discussing how to implement new tidier methods in non-broom packages.
tibble 3.0.0 release.
Removed xergm dependency.Fixes failing CRAN checks
Changes to accommodate ergm 3.10 release.
tidy.ergm() no longer has a quick argument.
The old default of quick = FALSE is now the only
option.
tidy(), glance() and
augment() are now re-exported from the generics package.Tidiers now return tibble::tibble()s. This release also
includes several new tidiers, new vignettes and a large number of bug
fixes. We’ve also begun to more rigorously define tidier specifications:
we’ve laid part of the groundwork for stricter and more consistent
tidying, but the new tidier specifications are not yet complete. These
will appear in the next release.
Additionally, users should note that we are in the process of
migrating tidying methods for mixed models and Bayesian models to
broom.mixed. broom.mixed is not on CRAN yet,
but all mixed model and Bayesian tidiers will be deprecated once
broom.mixed is on CRAN. No further development of mixed
model tidiers will take place in broom.
Almost all tidiers should now return tibbles rather than
data.frames. Deprecated tidying methods, Bayesian and mixed
model tidiers still return data.frames.
Users are mostly to experience issues when using
augment in situations where tibbles are stricter than data
frames. For example, specifying model covariates as a matrix object will
now error:
library(broom)
library(quantreg)
fit <- rq(stack.loss ~ stack.x, tau = .5)
broom::augment(fit)
#> Error: Column `stack.x` must be a 1d atomic vector or a listThis is because the default data argument
data = model.frame(fit) cannot be coerced to
tibble.
Another consequence of this is that augment.survreg and
augment.coxph from the survival package now
require that the user explicitly passes data to either the
data or newdata arguments.
These restrictions will be relaxed in an upcoming release of
broom pending support for matrix-columns in tibbles.
Developers are likely to experience issues:
subsetting tibbles with [, which returns a tibble
rather than a vector.
setting rownames on tibbles, which is deprecated.
using matrix and vector tidiers, now deprecated.
handling the additional tibble classes tbl_df and
tbl beyond the data.frame class
linking to defunct documentation files – broom recently moved all
tidiers to a roxygen2 template based documentation
system.
This version of broom includes several new
vignettes:
vignette("available-methods", package = "broom")
contains a table detailing which tidying methods are available
vignette("adding-tidiers", package = "broom") is an
in-progress guide for contributors on how to add new tidiers to
broom
vignette("glossary", package = "broom") contains
tables describing acceptable argument names and column names for the
in-progress new specification.
Several old vignettes have also been updated:
vignette("bootstrapping", package = "broom") now relies
on the rsample package and a
tidyr::nest-purrr::map-tidyr::unnest
workflow. This is now the recommended workflow for working with multiple
models, as opposed to the old
dplyr::rowwise-dplyr::do based workflow.Matrix and vector tidiers have been deprecated in favor of
tibble::as_tibble and tibble::enframe
Dataframe tidiers and rowwise dataframe tidiers have been deprecated
bootstrap() has been deprecated in favor of the rsample
inflate has been removed from
broom
The alpha argument has been removed from
quantreg tidy methods
The separate.levels argument has been removed from
tidy.TukeyHSD. To obtain the effect of
separate.levels = TRUE, users may
tidyr::separate after tidying. This is consistent with the
multcomp tidier behavior.
The fe.error argument was removed from
tidy.felm. When fixed effects are tidier, their standard
errors are now always included.
The diag argument in tidy.dist has been
renamed diagonal
Advice to help beginners make PRs (#397 by @karldw)
glance support for arima objects fit
with method = "CSS" (#396 by @josue-rodriguez)
A bug fix to re-enable tidying glmnet objects with
family = multinomial (#395 by @erleholgersen)
A bug fix to allow tidying quantreg intercept only
models (#378 by @erleholgersen)
A bug fix for aovlist objects (#377 by @mvevans89)
Support for glmnetUtils objects (#352 by @Hong-Revo)
A bug fix to allow tidy_emmeans to handle column
names with dashes (#351 by @bmannakee)
augment.felm no longer returns .fe_ and
.comp columns
Support saved formulas in augment.felm (#347 by
@ShreyasSingh)
confint_tidy now drops rows of all NA
(#345 by @atyre2)
A new tidier for caret::confusionMatrix objects
(#344 by @mkuehn10)
Tidiers for Kendall::Kendall objects (#343 by @cimentadaj)
A new tidying method for car::durbinWatsonTest
objects (#341 by @mkuehn10)
glance throws an informative error for
quantreg:rq models fit with multiple tau
values (#338 by @bfgray3)
tidy.glmnet gains the ability to retain zero-valued
coefficients with a return_zeros argument that defaults to
FALSE (#337 by @bfgray3)
tidy.manova now retains a Residuals row
(#334 by @jarvisc1)
Tidiers for ordinal::clm,
ordinal::clmm, survey::svyolr and
MASS::polr ordinal model objects (#332 by @larmarange)
Support for anova objects from
car::Anova (#325 by @mariusbarth)
Tidiers for tseries::garch models (#323 by @wilsonfreitas)
Removed dependency on psych package (#313 by @nutterb)
Improved error messages (#303 by @michaelweylandt)
Compatibility with new rstanarm and loo
packages (#298 by @jgabry)
Support for tidying lists return by
irlba::irlba
A truly huge increase in unit tests (#267 by @dchiu911)
Bug fix for tidy.prcomp when missing labels (#265 by
@corybrunson)
Added a pkgdown site at https://broom.tidyverse.org/
(#260 by @jayhesselberth)
Added tidiers for AER::ivreg models (#247 by @hughjonesd)
Added tidiers for the lavaan package (#233 by @puterleat)
Added conf.int argument to tidy.coxph
(#220 by @larmarange)
Added augment method for chi-squared tests (#138 by
@larmarange)
changed default se.type for tidy.rq to match that of
quantreg::summary.rq() (#404 by @ethchr)
Added argument quick for tidy.plm and
tidy.felm (#502 and #509 by @MatthieuStigler)
Many small improvements throughout
Many many thanks to all the following for their thoughtful comments on design, bug reports and PRs! The community of broom contributors has been kind, supportive and insightful and I look forward to working you all again!
@atyre2, @batpigandme, @bfgray3, @bmannakee, @briatte, @cawoodjm, @cimentadaj, @dan87134, @dgrtwo, @dmenne, @ekatko1, @ellessenne, @erleholgersen, @ethchr, @huftis, @IndrajeetPatil, @jacob-long, @jarvisc1, @jenzopr, @jgabry, @jimhester, @josue-rodriguez, @karldw, @kfeilich, @larmarange, @lboller, @mariusbarth, @michaelweylandt, @mine-cetinkaya-rundel, @mkuehn10, @mvevans89, @nutterb, @ShreyasSingh, @stephlocke, @strengejacke, @topepo, @willbowditch, @WillemSleegers, @wilsonfreitas, and @MatthieuStigler
Fixed gam tidiers to work with “Gam” objects, due to an update in gam 1.15. This fixes failing CRAN tests
Improved test coverage (thanks to #267 from Derek Chiu)
Changed the deprecated dplyr::failwith to
purrr::possibly
augment and glance on NULLs now return
an empty data frame
Deprecated the inflate() function in favor of
tidyr::crossing
Fixed confidence intervals in the gmm tidier (thanks to #242 from David Hugh-Jones)
Fixed a bug in bootstrap tidiers (thanks to #167 from Jeremy Biesanz)
Fixed tidy.lm with quick = TRUE to return terms as
character rather than factor (thanks to #191 from Matteo
Sostero)
Added tidiers for ivreg objects from the AER package
(thanks to #245 from David Hugh-Jones)
Added tidiers for survdiff objects from the survival
package (thanks to #147 from Michał Bojanowski)
Added tidiers for emmeans from the emmeans package
(thanks to #252 from Matthew Kay)
Added tidiers for speedlm and speedglm
from the speedglm package (#685, thanks to #248 from David
Hugh-Jones)
Added tidiers for muhaz objects from the muhaz
package (thanks to #251 from Andreas Bender)
Added tidiers for decompose and stl
objects from stats (thanks to #165 from Aaron Jacobs)
Added tidiers for lsmobj and ref.grid
objects from the lsmeans package
Added tidiers for betareg objects from the betareg
package
Added tidiers for lmRob and glmRob
objects from the robust package
Added tidiers for brms objects from the brms package
(thanks to #149 from Paul Buerkner)
Fixed tidiers for orcutt 2.0
Changed tidy.glmnet to filter out rows where
estimate == 0.
Updates to rstanarm tidiers (thanks to #177 from
Jonah Gabry)
Fixed issue with survival package 2.40-1 (thanks to #180 from Marcus Walz)
Added AppVeyor, codecov.io, and code of conduct
Changed name of “NA’s” column in summaryDefault output to “na”
Fixed tidy.TukeyHSD to include term
column. Also added separate.levels argument, with option to
separate comparison into level1 and
level2
Fixed tidy.manova to use correct column name for
test (previously, always pillai)
Added kde_tidiers to tidy kernel density
estimates
Added orcutt_tidiers to tidy the results of
cochrane.orcutt orcutt package
Added tidy.dist to tidy the distance matrix output
of dist from the stats package
Added tidy and glance for
lmodel2 objects from the lmodel2 package
Added tidiers for poLCA objects from the poLCA
package
Added tidiers for sparse matrices from the Matrix package
Added tidiers for prcomp objects
Added tidiers for Mclust objects from the Mclust
package
Added tidiers for acf objects
Fixed to be compatible with dplyr 0.5, which is being submitted to CRAN
Added tidiers for geeglm, nlrq, roc, boot, bgterm, kappa, binWidth, binDesign, rcorr, stanfit, rjags, gamlss, and mle2 objects.
Added tidy methods for lists, including u, d, v
lists from svd, and x, y, z lists used by
image and persp
Added quick argument to tidy.lm,
tidy.nls, and tidy.biglm, to create a smaller
and faster version of the output.
Changed rowwise_df_tidiers to allow the original
data to be saved as a list column, then provided as a column name to
augment. This required removing data from the
augment S3 signature. Also added
tests-rowwise.R
Fixed various issues in ANOVA output
Fixed various issues in lme4 output
Fixed issues in tests caused by dev version of ggplot2
Added tidiers for “plm” (panel linear model) objects from the plm package.
Added tidy.coeftest for coeftest objects from the
lmtest package.
Set up tidy.lm to work with “mlm” (multiple linear
model) objects (those with multiple response columns).
Added tidy and glance for “biglm” and
“bigglm” objects from the biglm package.
Fixed bug in tidy.coxph when one-row matrices are
returned
Added tidy.power.htest
Added tidy and glance for
summaryDefault objects
Added tidiers for “lme” (linear mixed effects models) from the nlme package
Added tidy and glance for
multinom objects from the nnet package.
Fixed bug in tidy.pairwise.htest, which now can
handle cases where the grouping variable is numeric.
Added tidy.aovlist method. This added
stringr package to IMPORTS to trim whitespace from the
beginning and end of the term and stratum
columns. This also required adjusting tidy.aov so that it
could handle strata that are missing p-values.
Set up glance.lm to work with aov
objects along with lm objects.
Added tidy and glance for matrix
objects, with tidy.matrix converting a matrix to a data
frame with rownames included, and glance.matrix returning
the same result as glance.data.frame.
Changed DESCRIPTION Authors@R to new format
Fixed small bug in felm where the
.fitted and .resid columns were matrices
rather than vectors.
Added tidiers for rlm (robust linear model) and
gam (generalized additive model) objects, including
adjustments to “lm” tidiers in order to handle them. See
?rlm_tidiers and ?gam_tidiers for
more.
Removed rownames from tidy.cv.glmnet output
The behavior of augment, particularly with regard to
missing data and the na.exclude argument, has through the
use of the augment_columns function been made consistent
across the following models:
lm
glm
nls
merMod (lme4)
survreg (survival)
coxph (survival)
Unit tests in tests/testthat/test-augment.R were added
to ensure consistency across these models.
tidy, augment and glance
methods were added for rowwise_df objects, and are set up
to apply across their rows. This allows for simple patterns such
as:regressions <- mtcars %>% group_by(cyl) %>% do(mod = lm(mpg ~ wt, .)) regressions %>% tidy(mod) regressions %>% augment(mod)
See ?rowwise_df_tidiers for more.
Added tidy and glance methods for
Arima objects, and tidy for
pairwise.htest objects.
Fixes for CRAN: change package description to title case, removed
NOTES, mostly by adding globals.R to declare global
variables.
This is the original version published on CRAN.
Tidiers have been added for S3 objects from the following packages:
lme4
glmnet
survival
zoo
felm
MASS (ridgelm objects)
tidy and glance methods for data.frames
have also been added, and augment.data.frame produces an
error (rather than returning the same data.frame).
stderror has been changed to std.error
(affects many functions) to be consistent with broom’s naming
conventions for columns.
A function bootstrap has been added based on this example,
to perform the common use case of bootstrapping models.
Added “augment” S3 generic and various implementations. “augment” does something different from tidy: it adds columns to the original dataset, including predictions, residuals, or cluster assignments. This was originally described as “fortify” in ggplot2.
Added “glance” S3 generic and various implementations. “glance” produces a one-row data frame summary, which is necessary for tidy outputs with values like R^2 or F-statistics.
Re-wrote intro broom vignette/README to introduce all three methods.
Wrote a new kmeans vignette.
Added tidying methods for multcomp, sp, and map objects (from fortify-multcomp, fortify-sp, and fortify-map from ggplot2).
Because this integrates substantial amounts of ggplot2 code (with permission), added Hadley Wickham as an author in DESCRIPTION.