Various improvements to infrastructure and testing:
tidy.coeftest now returns non-NA values for conf.low and conf.high for
a model fitted with only a constant term and cluster robust std errors
computed using vcovCL from sandwich (#1227).
Corrected nobs entries in glance.coxph() output: the package used to
return length(object$linear.predictors) (equal to n rather than nevent)
and now uses survival's method (#1224).
Corrected confidence interval values in tidy.boot() and addressed errors
when bootstrapping confidence intervals for multiple terms (#1212).
Reverted deprecation of tidiers for objects from the margins package now that the package is back on CRAN (#1220).
Addressed failure in tidy.anova() ahead of upcoming car
release (#1215).
Clarified documentation for a number of cases where dots were documented as unused but actually passed to internal functions (#1214).
Addressed error in augment.betareg() and augment.betamfx()
with data = NULL and non-null newdata (#1216, #1218).
glance.lm() now returns non-NA values for statistic, p.value, and df
for models fitted with a single predictor and no intercept (@jrob95, #1209).
Added support for conf.level in augment.lm() (#1191 by @zietzm).
Added support for columns adj.r.squared and npar in glance() method for objects outputted from mgcv::gam() (#1172).
Soft-deprecated tidiers for margins objects, as the package was archived from CRAN in April 2024. In the case that the package is back on CRAN before the next package release, broom will once again Suggest and test support for the package (#1200).
Moved forward with deprecation of tidiers for objects from the sp package. See resources linked in tidymodels/broom#1142 for more information on migration from retiring spatial packages.
While this broom release contains no changes to the tidy.survfit() method for objects from the survival package, the package has bumped the minimum required version for survival. Before survival 3.6-4, tidy.survfit() propagated "inconsistent" n.censor values from survival for multi-state models (#1195).
Corrected confidence interval values for precision components in tidy.betareg() output (#1169).
Fixed bug in tidier for car::linearHypothesis() output with long formulas (#1171).
Corrected coefficient values in tidy.varest() output (#1174).
tidy.coxph() will now pass its ellipses ... to summary() internally (#1151 by @ste-tuf).
Transitioned the deprecation of the region argument to tidy.SpatialPolygonsDataFrame from a warn- to a hard-deprecation (#1142).
Removed maptools and rgeos as Suggested packages ahead of their retirement. sp tidiers will be removed from a future release of the package (#1142).
Addressed bug in mlogit tidiers where augment.mlogit() would fail if supplied a model fitted with a non-default dfidx() (#1156 by @gregmacfarlane).
Addressed bug in ANOVA tidiers where tidy.anova() would fail if passed a model with many predictors (#1159 by @jwilliman).
Addressed warnings in ANOVA tidiers for unrecognized column names Resid..Df, Resid..Dev, and Deviance; those columns will be renamed df.residual, residual.deviance, and deviance, respectively (#1159 by @jwilliman).
intercept argument to tidy.aov(), a logical indicating whether to include information on the intercept as the first row of results (#1144 by @victor-vscn).augment.glm() where the .std.resid column always contained standardized deviance residuals regardless of the value passed to the type.residuals argument (#1147).tidy.multinom() where the conf.level argument would be ignored.data argument for augment.coxph() and augment.survreg() has been transitioned from NULL to model.frame(x) (#1126 by @capnrefsmmat).Imports to Suggests.augment() results would not include residuals when the response term included a function call (#1121, #946, #937, #124).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 list
This 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
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)
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)
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)
Improved error messages (#303 by @michaelweylandt)
Compatibility with new rstanarm and loo packages (#298 by @jgabry)
Support for tidying lists return by irlba::irlba
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.