broom 0.5.0.9000 Unreleased

To be released as 0.7.0

Changes to augment()

  • 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.

  • Similarly: augment no longer accepts an na.action argument (TODO: figure out why this wasn’t in the function signature in the first place)

Other changes

  • All conf.int arguments now default to FALSE.
  • All conf.level arguments now default to TRUE.
  • Moved core tests to the modeltests package
  • Import tidy(), glance() and augment() generics from modelgenerics
  • Added new vignette detailing use of modelgenerics and modeltests packages
  • Added data argument to augment() generic

Deprecations

Mixed model deprecations

The following have all been deprecated in favor of broom.mixed:

broom 0.5.0 2018-07-17

Tidiers now return tibble::tibble()s. This release also includes several new tidiers, new vignettes and a large number of bugfixes. 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.

Breaking changes

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.

New vignettes

This version of broom includes several new vignettes:

Several old vignettes have also been updated:

Deprecations

  • 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

Other changes

Contributors

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 insighftul and I look forward to working you all again!

@atyre2, @batpigandme, @bfgray3, @bmannakee, @briatte, @cawoodjm, @cimentadaj, @dan87134, @dgrtwo, @dmenne, @ekatko1, @ellessenne, @erleholgersen, @Hong-Revo, @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, and @wilsonfreitas

broom 0.4.4 2018-03-29

  • 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)

broom 0.4.3 2017-11-20

  • 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 (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)

broom 0.4.2 2017-02-13

  • 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)

broom 0.4.1 2016-06-24

  • 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

broom 0.4.0 2015-11-30

  • 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

broom 0.3.7 2015-05-06

  • 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.

broom 0.3.6 2015-02-18

  • 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

broom 0.3.5 2015-01-05

  • 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

broom 0.3.4 2014-11-23

  • 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.

broom 0.3 Unreleased

  • 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.

broom 0.2 Unreleased

  • 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.