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 now contains only the following columns: logLik, AIC, BIC, deviance, df.residual, 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](https://github.com/atyre2), [@batpigandme](https://github.com/batpigandme), [@bfgray3](https://github.com/bfgray3), [@bmannakee](https://github.com/bmannakee), [@briatte](https://github.com/briatte), [@cawoodjm](https://github.com/cawoodjm), [@cimentadaj](https://github.com/cimentadaj), [@dan87134](https://github.com/dan87134), [@dgrtwo](https://github.com/dgrtwo), [@dmenne](https://github.com/dmenne), [@ekatko1](https://github.com/ekatko1), [@ellessenne](https://github.com/ellessenne), [@erleholgersen](https://github.com/erleholgersen), [@ethchr](https://github.com/ethchr), [@Hong-Revo](https://github.com/Hong-Revo), [@huftis](https://github.com/huftis), [@IndrajeetPatil](https://github.com/IndrajeetPatil), [@jacob-long](https://github.com/jacob-long), [@jarvisc1](https://github.com/jarvisc1), [@jenzopr](https://github.com/jenzopr), [@jgabry](https://github.com/jgabry), [@jimhester](https://github.com/jimhester), [@josue-rodriguez](https://github.com/josue-rodriguez), [@karldw](https://github.com/karldw), [@kfeilich](https://github.com/kfeilich), [@larmarange](https://github.com/larmarange), [@lboller](https://github.com/lboller), [@mariusbarth](https://github.com/mariusbarth), [@michaelweylandt](https://github.com/michaelweylandt), [@mine-cetinkaya-rundel](https://github.com/mine-cetinkaya-rundel), [@mkuehn10](https://github.com/mkuehn10), [@mvevans89](https://github.com/mvevans89), [@nutterb](https://github.com/nutterb), [@ShreyasSingh](https://github.com/ShreyasSingh), [@stephlocke](https://github.com/stephlocke), [@strengejacke](https://github.com/strengejacke), [@topepo](https://github.com/topepo), [@willbowditch](https://github.com/willbowditch), [@WillemSleegers](https://github.com/WillemSleegers), [@wilsonfreitas](https://github.com/wilsonfreitas), and [@MatthieuStigler](https://github.com/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.