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.- 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.
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.
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.
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.
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.
Not many user-facing changes since 0.7.4, but major refactoring internally should speed things up and make future development smoother.
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
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.
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.
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:
- 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
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.
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.
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
Bug fixes:
- R 3.4 introduced a change that caused warning messages when return objects are created in a certain way. This was first addressed in jtools 0.4.5, but a few instances slipped through the cracks. Thanks to Kim Henry for pointing out one such instance.
- When sim_slopes called johnson_neyman while the robust argument was set to TRUE, the robust.type argument was not being passed (causing the default of “HC3” to be used). Now it is passing that argument correctly.
- Added better support for plotting nonlinear interactions with interact_plot, providing an option to plot on original (nonlinear) scale.
- interact_plot can now plot fixed effects interactions from merMod objects
- Fixed warning messages when using j_summ with R 3.4.x
- Added preliminary merMod support for j_summ. Still needs convergence warnings, some other items.
- Under the hood changes to j_summ
- Cleaned up examples
- Added wgttest function, which runs a test to assess need for sampling weights in linear regression
- No matter what you do, there’s nothing like seeing your package on CRAN to open your eyes to all the typos, etc. you’ve put into your package.
- This is the first CRAN release. Compared to 0.4.1, the prior Github release, dependencies have been removed and several functions optimized for speed.