jtools 1.0.0

Major release

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

Major speed gains (15% faster for small 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.
More model types are supported. In the past, some models failed because the update method was not defined correctly or there was more information needed to refit the model than what can be provided by these functions.
More complicated formula input is supported, with a caveat. If you have, for instance, log-transformed a predictor (with 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 plotting

To 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.

All interaction tools

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.

`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 issues

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.

Survey tools

weights_tests — wgttest and pf_sv_test — now handle missing data in a more sensible and consistent way.

Colors

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

Other stuff

Using the crayon package as a backend, console output is now formatted for most jtools functions for better readability on supported systems. Feedback on this is welcome since this might look better or worse in certain editors/setups.

jtools 0.9.4 (CRAN release)

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!

jtools 0.9.3 (CRAN release)

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.
An upcoming version of R will change a common warning to an error, causing a need to change the internals of gscale.
The default model names in export_summs had an extra space (e.g., ( 1)) due to changes in huxtable. The defaults are now just single numbers.

jtools 0.9.2

Bugfix:

Johnson-Neyman plots misreported the alpha level if 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.

jtools 0.9.1 (CRAN release)

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:

An update to huxtable broke export_summs, but that has been fixed.

Feature updates:

You can now manually provide colors to interact_plot and cat_plot by providing a vector of colors (any format that ggplot2 accepts) for the color.class argument.
Noah Greifer wrote up a tweak to summ that formats the output in a way that lines up the decimal points. It looks great.

jtools 0.9.0 (CRAN release)

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:

A new 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.
A line.thickness argument has been added after Heidi Jacobs pointed out that it cannot be changed after the fact.
The construction of the multiple plots when using sim_slopes for 3-way interactions is much-improved.
The critical test statistic used by default has been slightly altered. It previously used a normal approximation; i.e., if 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:

More improvements to plot.points (see 0.8.1 for more). You can now plot observed data with 3-way interactions.
Another pre-set 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.
A new 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.
When the model used weights, like survey sampling weights, the observed data points are resized according to the observation’s weight when plot.points = TRUE.
New 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:

Users are now informed why the function is taking so long if 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.

jtools 0.8.1

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:

When 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.
Much better support for plotting observed data in 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.

jtools 0.8.0 (CRAN release)

Not many user-facing changes since 0.7.4, but major refactoring internally should speed things up and make future development smoother.

jtools 0.7.4

Bugfixes:

interact_plot and effect_plot would trip up when one of the focal predictors had a name that was a subset of a covariate (e.g., pred = “var” but a covariate is called “var_2”). That’s fixed.
Confidence intervals for merMod objects were not respecting the user-requested confidence level and that has been fixed.
Confidence intervals for merMod objects were throwing a spurious warning on R 3.4.2.
interact_plot was mis-ordering secondary moderators. That has been fixed.
export_summs had a major performance problem when providing extra arguments which may have also caused it to wrongly ignore some arguments. That has been fixed and it is much faster.

Enhancements: * interact_plot now gives more informative labels for secondary moderators when the user has defined the values but not the labels. * confidence intervals are now properly supported with export_summs * changes made to export_summs for compatibility with huxtable 1.0.0 changes

jtools 0.7.3 (CRAN release)

Important bugfix:

When standardize was set to TRUE using summ, the model was not mean-centered as the output stated. This has been fixed. I truly regret the error—double-check any analyses you may have run with this feature.

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.

jtools 0.7.2

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:

With the part.corr = TRUE argument for a linear model, partial and semipartial correlations for each variable are reported.

More tweaks to summ.merMod:

Default behavior with regard to p values depends on model type (lmer vs. glmer/nlmer) and, in the case of linear models, whether the 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.
There is an 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.

jtools 0.7.1

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.

jtools 0.7.0

New features:

j_summ can now provide cluster-robust standard errors for lm models.
j_summ output now gives info about missing observations for supported models.
At long last, j_summ/scale_lm/center_lm can standardize/center models with logged terms and other functions applied.
interact_plot and effect_plot will now also support predictors that have functions applied to them.
j_summ now supports confidence intervals at user-specified widths.
j_summ now allows users to not display p-values if requested.
I’ve added a warning to j_summ output with merMod objects, since it provides p-values calculated on the basis of the estimated t-values. These are not to be interpreted in the same way that OLS and GLM p-values are, since with smaller samples mixed model t-values will give inflated Type I error rates.
By default, j_summ will not show p-values for merMod objects.

Bug fix:

scale_lm did not have its center argument implemented and did not explain the option well in its documentation.
johnson_neyman got confused when a factor variable was given as a predictor

jtools 0.6.1

Bug fix release:

wgttest acted in a way that might be unexpected when providing a weights variable name but no data argument. Now it should work as expected by getting the data frame from the model call.
gscale had a few situations in which it choked on missing data, especially when weights were used. This in turn affected j_summ, scale_lm, and center_lm, which each rely on gscale for standardization and mean-centering. That’s fixed now.
gscale wasn’t playing nicely with binary factors in survey designs, rendering the scaling incorrect. If you saw a warning, re-check your outputs after this update.

jtools 0.6.0

A lot of changes!

New functions:

effect_plot: If you like the visualization of moderation effects from interact_plot, then you should enjoy effect_plot. It is a clone of interact_plot, but shows a single regression line rather than several. It supports GLMs and lme4 models and can plot original, observed data points.
pf_sv_test: Another tool for survey researchers to test whether it’s okay to run unweighted regressions. Named after Pfefferman and Svervchkov, who devised the test.
weights_tests: Like probe_interaction does for the interaction functions, weights_tests will run the new pf_sv_test as well as wgttest simultaneously with a common set of arguments.

Enhancements:

Set a default number of digits to print for all jtools functions with the option “jtools-digits”.
wgttest now accepts and tests GLMs and may work for other regression models.

Bug fixes:

j_summ would print significance stars based on the rounded p value, sometimes resulting in misleading output. Now significance stars are based on the non-rounded p values.
probe_interaction did not pass an “alpha” argument to sim_slopes, possibly confusing users of johnson_neyman. The argument sim_slopes is looking for is called “jnalpha”. Now probe_interaction will pass “alpha” arguments as “jn_alpha”.
interact_plot would stop on an error when the model included a two-level factor not involved in the interaction and not centered. Now those factors in that situation are treated like other factors.
interact_plot sometimes gave misleading output when users manually defined moderator labels. It is now more consistent with the ordering the labels and values and will not wrongly label them when the values are provided in an odd order.
wgttest now functions properly when a vector of weights is provided to the weights argument rather than a column name.
gscale now works properly on tibbles, which requires a different style of column indexing than data frames.
Related to the prior point, j_summ/standardize_lm/center_lm now work properly on models that were originally fit with tibbles in the data argument.
sim_slopes would fail for certain weighted lm objects depending on the way the weights were specified in the function call. It should now work for all weighted lm objects.

jtools 0.5.0

More goodies for users of interact_plot:

Added support for models with a weights parameter in interact_plot. It would work previously, but didn’t use a weighted mean or SD in calculating values of the moderator(s) and for mean-centering other predictors. Now it does.
Added support for two-level factor predictors in interact_plot. Previously, factor variables had to be a moderator.
When predictor in interact_plot has only two unique values (e.g., dummy variables that have numeric class), by default only those two values have tick marks on the x-axis. Users may use the pred.labels argument to specify labels for those ticks.
Offsets are now supported (especially useful for Poisson GLMs), but only if specified via the offset argument rather than included in the model formula. You can (and should) specify the offset used for the plot using the set.offset argument. By default it is 1 so that the y-axis represents a proportion.

Other feature changes:

sim_slopes now supports weights (from the weights argument rather than a svyglm model). Previously it used unweighted mean and standard deviation for non-survey models with weights.
Improved printing features of wgttest