NEWS.md
This release was initally intended to be a bugfix release, but enough other things came up to make it a minor release.
broom
update when using export_summs
and plot_coefs
.plot_coefs
arising from the latest update to ggplot2
.export_summs
output for glm
models. [#36]interact_plot
no longer errors if there are missing observations in the original data and quantiles are requested.summ.merMod
, the default p-value calculation is now via the Satterthwaite method if you have lmerTest
installed. The old default, Kenward-Roger, is used by request or when pbkrtest
is installed but not lmerTest
. It now calculates a different degrees of freedom for each predictor and also calculates a variance-covariance matrix for the model, meaning the standard errors are adjusted as well. It is not the default largely because the computation takes too long for too many models.johnson_neyman
now allows you to specify your own critical t value if you are using some alternate method to calculate it.johnson_neyman
now allows you to specify the range of moderator values you want to plot as well as setting a title.sim_slopes
in a way similar to interact_plot
. [#35]interact_plot
(e.g., when modx.values = "plus-minus"
). [#31]plot_coefs
/plot_summs
now supports facetting the coefficients based on user-specified groupings. See ?plot_summs
for details.summ
variants now have pretty output in RMarkdown documents if you have the huxtable
package installed. This can be disabled with the chunk option render = 'normal_print'
.modx.values
, mod2.values
, and pred.values
in place of modxvals
, mod2vals
, and predvals
. Don’t go running to change your code, though; those old argument names will still work, but these new ones are clearer and preferred in new code.plot
method for sim_slopes
objects. Just save your sim_slopes
call to an object and call the plot
function on that object to see what happens. Basically, it’s plot_coefs
for sim_slopes
.huxtable
installed, you can now call as_huxtable
on a sim_slopes
object to get a publication-style table. The interface is comparable to export_summs
.This release has several big changes embedded within, side projects that needed a lot of work to implement and required some user-facing changes. Overall these are improvements, but in some edge cases they could break old code. The following sections are divided by the affected functions. Some of the functions are discussed in more than one section.
interact_plot
, cat_plot
, and effect_plot
These functions no longer re-fit the inputted model to center covariates, impose labels on factors, and so on. This generally has several key positives, including
lm
models, 60% for svyglm
, and 80% for merMod
in my testing). The speed gains increase as the models become more complicated and the source data become larger.log
) in the formula, the function would previously would have a lot of trouble and usually have errors. Now this is supported, provided you input the data used to fit the model via the data
argument. You’ll receive a warning if the function thinks this is needed to work right.As noted, there is a new data
argument for these functions. You do not normally need to use this if your model is fit with a y ~ x + z
type of formula. But if you start doing things like y ~ factor(x) + z
, then you need to provide the source data frame. Another benefit is that this allows for fitting polynomials with effect_plot
or even interactions with polynomials with interact_plot
. For instance, if my model was fit using this kind of formula — y ~ poly(x, 2) + z
— I could then plot the predicted curve with effect_plot(fit, pred = x, data = data)
substituting fit
with whatever my model is called and data
with whatever data frame I used is called.
There are some possible drawbacks for these changes. One is that no longer are factor predictors supported in interact_plot
and effect_plot
, even two-level ones. This worked before by coercing them to 0/1 continuous variables and re-fitting the model. Since the model is no longer re-fit, this can’t be done. To work around it, either transform the predictor to numeric before fitting the model or use cat_plot
. Relatedly, two-level factor covariates are no longer centered and are simply set to their reference value.
Robust confidence intervals: Plotting robust standard errors for compatible models (tested on lm
, glm
). Just use the robust
argument like you would for sim_slopes
or summ
.
Preliminary support for confidence intervals for merMod
models: You may now get confidence intervals when using merMod
objects as input to the plotting functions. Of importance, though, is the uncertainty is only for the fixed effects. For now, a warning is printed. See the next section for another option for merMod
confidence intervals.
Rug plots in the margins: So-called “rug” plots can be included in the margins of the plots for any of these functions. These show tick marks for each of the observed data points, giving a non-obtrusive impression of the distribution of the pred
variable and (optionally) the dependent variable. See the documentation for interact_plot
and effect_plot
and the rug
/rug.sides
arguments.
Facet by the modx
variable: Some prefer to visualize the predicted lines on separate panes, so that is now an option available via the facet.modx
argument. You can also use plot.points
with this, though the division into groups is not straightforward is the moderator isn’t a factor. See the documentation for more on how that is done.
make_predictions
and plot_predictions
: New tools for advanced plottingTo let users have some more flexibility, jtools
now lets users directly access the (previously internal) functions that make effect_plot
, cat_plot
, and interact_plot
work. This should make it easier to tailor the outputs for specific needs. Some features may be implemented for these functions only to keep the _plot
functions from getting any more complicated than they already are.
The simplest use of the two functions is to use make_predictions
just like you would effect_plot
/interact_plot
/cat_plot
. The difference is, of course, that make_predictions
only makes the data that would be used for plotting. The resulting predictions
object has both the predicted and original data as well as some attributes describing the arguments used. If you pass this object to plot_predictions
with no further arguments, it should do exactly what the corresponding _plot
function would do. However, you might want to do something entirely different using the predicted data which is part of the reason these functions are separate.
One such feature specific to make_predictions
is bootstrap confidence intervals for merMod
models.
You may no longer use these tools to scale the models. Use scale_mod
, save the resulting object, and use that as your input to the functions if you want scaling.
All these tools have a new default centered
argument. They are now set to centered = "all"
, but "all"
no longer means what it used to. Now it refers to all variables not included in the interaction, including the dependent variable. This means that in effect, the default option does the same thing that previous versions did. But instead of having that occur when centered = NULL
, that’s what centered = "all"
means. There is no NULL
option any longer. Note that with sim_slopes
, the focal predictor (pred
) will now be centered — this only affects the conditional intercept.
sim_slopes
This function now supports categorical (factor) moderators, though there is no option for Johnson-Neyman intervals in these cases. You can use the significance of the interaction term(s) for inference about whether the slopes differ at each level of the factor when the moderator is a factor.
You may now also pass arguments to summ
, which is used internally to calculate standard errors, p values, etc. This is particularly useful if you are using a merMod
model for which the pbkrtest
-based p value calculation is too time-consuming.
gscale
The interface has been changed slightly, with the actual numbers always provided as the data
argument. There is no x
argument and instead a vars
argument to which you can provide variable names. The upshot is that it now fits much better into a piping workflow.
The entire function has gotten an extensive reworking, which in some cases should result in significant speed gains. And if that’s not enough, just know that the code was an absolute monstrosity before and now it’s not.
There are two new functions that are wrappers around gscale
: standardize
and center
, which call gscale
but with n.sd = 1
in the first case and with center.only = TRUE
in the latter case.
summ
Tired of specifying your preferred configuration every time you use summ
? Now, many arguments will by default check your options so you can set your own defaults. See ?set_summ_defaults
for more info.
Rather than having separate scale.response
and center.response
arguments, each summ
function now uses transform.response
to collectively cover those bases. Whether the response is centered or scaled depends on the scale
and center
arguments.
The robust.type
argument is deprecated. Now, provide the type of robust estimator directly to robust
. For now, if robust = TRUE
, it defaults to "HC3"
with a warning. Better is to provide the argument directly, e.g., robust = "HC3"
. robust = FALSE
is still fine for using OLS/MLE standard errors.
Whereas summ.glm
, summ.svyglm
, and summ.merMod
previously offered an odds.ratio
argument, that has been renamed to exp
(short for exponentiate) to better express the quantity.
vifs
now works when there are factor variables in the model.
One of the first bugs summ
ever had occurred when the function was given a rank-deficient model. It is not straightforward to detect, especially since I need to make a space for an almost empty row in the outputted table. At long last, this release can handle such models gracefully.
Like the rest of R, when summ
rounded your output, items rounded exactly to zero would be treated as, well, zero. But this can be misleading if the original value was actually negative. For instance, if digits = 2
and a coefficient was -0.003
, the value printed to the console was 0.00
, suggesting a zero or slightly positive value when in fact it was the opposite. This is a limitation of the round
(and trunc
) function. I’ve now changed it so the zero-rounded value retains its sign.
summ.merMod
now calculates pseudo-R^2 much, much faster. For only modestly complex models, the speed-up is roughly 50x faster. Because of how much faster it now is and how much less frequently it throws errors or prints cryptic messages, it is now calculated by default. The confidence interval calculation is now “Wald” for these models (see confint.merMod
for details) rather than “profile”, which for many models can take a very long time and sometimes does not work at all. This can be toggled with the conf.method
argument.
summ.glm
/summ.svyglm
now will calculate pseudo-R^2 for quasibinomial and quasipoisson families using the value obtained from refitting them as binomial/poisson. For now, I’m not touching AIC/BIC for such models because the underlying theory is a bit different and the implementation more challenging.
summ.lm
now uses the t-distribution for finding critical values for confidence intervals. Previously, a normal approximation was used.
The summ.default
method has been removed. It was becoming an absolute terror to maintain and I doubted anyone found it useful. It’s hard to provide the value added for models of a type that I do not know (robust errors don’t always apply, scaling doesn’t always work, model fit statistics may not make sense, etc.). Bug me if this has really upset things for you.
One new model type has been supported: rq
models from the quantreg
package. Please feel free to provide feedback for the output and support of these models.
scale_lm
and center_lm
are now scale_mod
/center_mod
To better reflect the capabilities of these functions (not restricted to lm
objects), they have been renamed. The old names will continue to work to preserve old code.
However, scale.response
and center.response
now default to FALSE
to reflect the fact that only OLS models can support transformations of the dependent variable in that way.
There is a new vars =
argument for scale_mod
that allows you to only apply scaling to whichever variables are included in that character vector.
I’ve also implemented a neat technical fix that allows the updated model to itself be updated while not also including the actual raw data in the model call.
plot_coefs
and plot_summs
A variety of fixes and optimizations have been added to these functions. Now, by default, there are two confidence intervals plotted, a thick line representing (with default settings) the 90% interval and a thinner line for the 95% intervals. You can set inner_ci_level
to NULL
to get rid of the thicker line.
With plot_summs
, you can also set per-model summ
arguments by providing the argument as a vector (e.g., robust = c(TRUE, FALSE)
). Length 1 arguments are applied to all models. plot_summs
will now also support models not accepted by summ
by just passing those models to plot_coefs
without using summ
on them.
Another new option is point.shape
, similar to the model plotting functions. This is most useful for when you are planning to distribute your output in grayscale or to colorblind audiences (although the new default color scheme is meant to be colorblind friendly, it is always best to use another visual cue).
The coolest is the new plot.distributions
argument, which if TRUE will plot normal distributions to even better convey the uncertainty. Of course, you should use this judiciously if your modeling or estimation approach doesn’t produce coefficient estimates that are asymptotically normally distributed. Inspiration comes from https://twitter.com/BenJamesEdwards/status/979751070254747650.
Minor fixes: broom
’s interface for Bayesian methods is inconsistent, so I’ve hacked together a few tweaks to make brmsfit
and stanreg
models work with plot_coefs
.
You’ll also notice vertical gridlines on the plots, which I think/hope will be useful. They are easily removable (see drop_x_gridlines()
) with ggplot2’s built-in theming options.
export_summs
Changes here are not too major. Like plot_summs
, you can now provide unsupported model types to export_summs
and they are just passed through to huxreg
. You can also provide different arguments to summ
on a per-model basis in the way described under the plot_summs
heading above.
There are some tweaks to the model info (provided by glance
). Most prominent is for merMod
models, for which there is now a separate N for each grouping factor.
theme_apa
plus new functions add_gridlines
, drop_gridlines
New arguments have been added to theme_apa
: remove.x.gridlines
and remove.y.gridlines
, both of which are TRUE
by default. APA hates giving hard and fast rules, but the norm is that gridlines should be omitted unless they are crucial for interpretation. theme_apa
is also now a “complete” theme, which means specifying further options via theme
will not revert theme_apa
’s changes to the base theme.
Behind the scenes the helper functions add_gridlines
and drop_gridlines
are used, which do what they sound like they do. To avoid using the arguments to those functions, you can also use add_x_gridlines
/add_y_gridlines
or drop_x_gridlines
/drop_y_gridlines
which are wrappers around the more general functions.
weights_tests
— wgttest
and pf_sv_test
— now handle missing data in a more sensible and consistent way.
There is a new default qualitative palette, based on Color Universal Design (designed to be readable by the colorblind) that looks great to all. There are several other new palette choices as well. These are all documented at ?jtools_colors
This release is limited to dealing with the huxtable
package’s temporary removal from CRAN, which in turn makes this package out of compliance with CRAN policies regarding dependencies on non-CRAN packages.
Look out for jtools
1.0.0 coming very soon!
Bugfixes:
johnson_neyman
and sim_slopes
were both encountering errors with merMod
input. Thanks to Seongho Bae for reporting these issues and testing out development versions.gscale
.export_summs
had an extra space (e.g., ( 1)
) due to changes in huxtable
. The defaults are now just single numbers.Bugfix:
control.fdr
was TRUE
. It was reporting alpha * 2
in the legend, but now it is accurate again.Feature update:
johnson_neyman
now handles multilevel models from lme4
.Bugfix update:
Jonas Kunst helpfully pointed out some odd behavior of interact_plot
with factor moderators. No longer should there be occasions in which you have two different legends appear. The linetype and colors also should now be consistent whether there is a second moderator or not. For continuous moderators, the darkest line should also be a solid line and it is by default the highest value of the moderator.
Other fixes:
huxtable
broke export_summs
, but that has been fixed.Feature updates:
interact_plot
and cat_plot
by providing a vector of colors (any format that ggplot2
accepts) for the color.class
argument.summ
that formats the output in a way that lines up the decimal points. It looks great.This may be the single biggest update yet. If you downloaded from CRAN, be sure to check the 0.8.1 update as well.
New features are organized by function.
johnson_neyman:
control.fdr
option is added to control the false discovery rate, building on new research. This makes the test more conservative but less likely to be a Type 1 error.line.thickness
argument has been added after Heidi Jacobs pointed out that it cannot be changed after the fact.sim_slopes
for 3-way interactions is much-improved.alpha = .05
the critical test statistic was always 1.96. Now, the residual degrees of freedom are used with the t distribution. You can do it the old way by setting df = "normal"
or any arbitrary number.interact_plot:
plot.points
(see 0.8.1 for more). You can now plot observed data with 3-way interactions.modxvals
and mod2vals
specification has been added: "terciles"
. This splits the observed data into 3 equally sized groups and chooses as values the mean of each of those groups. This is especially good for skewed data and for second moderators.linearity.check
option for two-way interactions. This facets by each level of the moderator and lets you compare the fitted line with a loess smoothed line to ensure that the interaction effect is roughly linear at each level of the (continuous) moderator.plot.points = TRUE
.jitter
argument added for those using plot.points
. If you don’t want the points jittered, you can set jitter = 0
. If you want more or less, you can play with the value until it looks right. This applies to effect_plot
as well.summ:
r.squared
or pbkrtest
are slowing things down. r.squared
is now set to FALSE by default.New functions!
plot_summs
: A graphic counterpart to export_summs
, which was introduced in the 0.8.0 release. This plots regression coefficients to help in visualizing the uncertainty of each estimate and facilitates the plotting of nested models alongside each other for comparison. This allows you to use summ
features like robust standard errors and scaling with this type of plot that you could otherwise create with some other packages.
plot_coefs
: Just like plot_summs
, but no special summ
features. This allows you to use models unsupported by summ
, however, and you can provide summ
objects to plot the same model with different summ
argument alongside each other.
cat_plot
: This was a long time coming. It is a complementary function to interact_plot
, but is designed to deal with interactions between categorical variables. You can use bar plots, line plots, dot plots, and box and whisker plots to do so. You can also use the function to plot the effect of a single categorical predictor without an interaction.
Thanks to Kim Henry who reported a bug with johnson_neyman
in the case that there is an interval, but the entire interval is outside of the plotted area: When that happened, the legend wrongly stated the plotted line was non-significant.
Besides that bugfix, some new features:
johnson_neyman
fails to find the interval (because it doesn’t exist), it no longer quits with an error. The output will just state the interval was not found and the plot will still be created.interact_plot
has been added. Previously, if the moderator was a factor, you would get very nicely colored plotted points when using plot.points = TRUE
. But if the moderator was continuous, the points were just black and it wasn’t very informative beyond examining the main effect of the focal predictor. With this update, the plotted points for continous moderators are shaded along a gradient that matches the colors used for the predicted lines and confidence intervals.Not many user-facing changes since 0.7.4, but major refactoring internally should speed things up and make future development smoother.
Bugfixes:
Enhancements:
Important bugfix:
New function: export_summs
.
This function outputs regression models supported by summ in table formats useful for RMarkdown output as well as specific options for exporting to Microsoft Word files. This is particularly helpful for those wanting an efficient way to export regressions that are standardized and/or use robust standard errors.
The documentation for j_summ has been reorganized such that each supported model type has its own, separate documentation. ?j_summ
will now just give you links to each supported model type.
More importantly, j_summ will from now on be referred to as, simply, summ. Your old code is fine; j_summ will now be an alias for summ and will run the same underlying code. Documentation will refer to the summ function, though. That includes the updated vignette.
One new feature for summ.lm:
part.corr = TRUE
argument for a linear model, partial and semipartial correlations for each variable are reported.More tweaks to summ.merMod:
pbkrtest
package is installed. If it is, p values are calculated based on the Kenward-Roger degrees of freedom calculation and printed. Otherwise, p values are not shown by default with lmer models. P values are shown with glmer models, since that is also the default behavior of lme4
.r.squared
option, which for now is FALSE by default. It adds runtime since it must fit a null model for comparison and sometimes this also causes convergence issues.Returning to CRAN!
A very strange bug on CRAN’s servers was causing jtools updates to silently fail when I submitted updates; I’d get a confirmation that it passed all tests, but a LaTeX error related to an Indian journal I cited was torpedoing it before it reached CRAN servers.
The only change from 0.7.0 is fixing that problem, but if you’re a CRAN user you will want to flip through the past several releases as well to see what you’ve missed.
New features:
Bug fix:
Bug fix release:
A lot of changes!
New functions:
Enhancements:
Bug fixes:
More goodies for users of interact_plot:
Other feature changes:
Bug fixes: