Tools for summarizing and visualizing regression models

In jtools: Analysis and Presentation of Social Scientific Data

required <- c("survey", "huxtable", "broom", "lme4", "quantreg")
if (!all(sapply(required, requireNamespace, quietly = TRUE)))
  knitr::opts_chunk$set(eval = FALSE)
knitr::opts_chunk$set(message = FALSE, warning = FALSE, fig.width = 6, 
                      fig.height = 4, dpi = 125, render = knitr::normal_print)
library(jtools)

The support jtools provides for helping to understand and report the results of regression models falls into a few broad categories:

• Generating flexible table output in the console that includes multiple standard error specifications, toggles for confidence intervals, VIFs, p values, and so on (summ)
• Plotting predicted data from models to aid in substantive interpretation and understanding model fit, including models with interactions (effect_plot; see other vignette)
• Plotting regression coefficients and their uncertainty in a visually appealing way (plot_coefs, plot_summs)
• Exporting regression summaries as tables in PDF/LaTeX and Word formats for publication (export_summs)

summ

When sharing analyses with colleagues unfamiliar with R, I found that the output generally was not clear to them. Things were even worse if I wanted to give them information that is not included in the summary() like robust standard errors, scaled coefficients, and VIFs since the functions for estimating these don't append them to a typical regression table. After creating output tables "by hand" on multiple occasions, I thought it would be best to pack things into a reusable function: It became summ().

For example purposes, we'll create a model using the movies data from this package. These data comprise information about over 800 movies across several decades. We will be predicting the Metacritic metascore, which ranges from 0 to 100 (where higher numbers reflect more positive reviews) using the gross revenue in the United States (us_gross), the fan rating at IMDB (imdb_rating), and a categorical variable reflecting the genre (genre5) with "Action" as the reference level.

With no user-specified arguments except a fitted model, the output of summ() looks like this:

library(jtools) # Load jtools
data(movies) # Telling R we want to use this data
fit <- lm(metascore ~ imdb_rating + log(us_gross) + genre5, data = movies)
summ(fit)

Like any output, this one is somewhat opinionated — some information is shown that perhaps not everyone would be interested in, some may be missing. That, of course, was the motivation behind the creation of the function; I didn't like the choices made by R's core team with summary()!

Here's a quick (not comprehensive) list of functionality supported by summ:

• Summaries for lm, glm, svyglm (survey), merMod (lme4), and rq (quantreg) models.
• Variable scaling and centering (i.e., calculating standardized coefficients)
• Robust standard errors (for lm and glm plus quantreg's built-in options for rq models)
• Confidence intervals, VIFs, and partial correlations (lm only) can optionally be included in the output
• p-values can be dropped from the output
• R^2 (lm, linear svyglm), pseudo-R^2 (glm, svyglm, merMod), R^1 (rq), and other model fit statistics are calculated and reported. These can also be suppressed if you don't want them.
• Ability to choose defaults for many options using set_summ_defaults() to reduce the need to do redundant typing in interactive use.

Model types supported are lm, glm, svyglm, merMod, and rq, though not all will be reviewed in detail here.

Note: The output in this vignette will mimic how it looks in the R console, but if you are generating your own RMarkdown documents and have kableExtra installed, you'll instead get some prettier looking tables like this:

summ(fit)

You can force knitr to give the console style of output by setting the chunk option render = 'normal_print'.

Report robust standard errors

One of the problems that originally motivated the creation of summ() was the desire to efficiently report robust standard errors — while it is easy enough for an experienced R user to calculate robust standard errors, there are not many simple ways to include the results in a regression table as is common with the likes of Stata, SPSS, etc.

Robust standard errors require the user to have the sandwich package installed. It does not need to be loaded.

There are multiple types of robust standard errors that you may use, ranging from "HC0" to "HC5". Per the recommendation of the authors of the sandwich package, the default is "HC3" so this is what you get if you set robust = TRUE. Stata's default is "HC1", so you may want to use that if your goal is to replicate Stata analyses. To toggle the type of robust errors, provide the desired type as the argument to robust.

summ(fit, robust = "HC1")

Robust standard errors can also be calculated for generalized linear models (i.e., glm objects) though there is some debate whether they should be used for models fit iteratively with non-normal errors. In the case of svyglm, the standard errors that package calculates are already robust to heteroskedasticity, so any argument to robust will be ignored with a warning.

You may also specify with cluster argument the name of a variable in the input data or a vector of clusters to get cluster-robust standard errors.

Standardized/scaled coefficients

Some prefer to use scaled coefficients in order to avoid dismissing an effect as "small" when it is just the units of measure that are small. scaled betas are used instead when scale = TRUE. To be clear, since the meaning of "standardized beta" can vary depending on who you talk to, this option mean-centers the predictors as well but does not alter the dependent variable whatsoever. If you want to scale the dependent variable too, just add the transform.response = TRUE argument. This argument does not do anything to factor variables and doesn't scale binary variables by default.

summ(fit, scale = TRUE)

If you have transformed variables (e.g., log(us_gross)), the function will scale the already-transformed variable. In other words, it is similar to the result you would get if you did scale(log(us_gross)) rather than log(scale(us_gross)) which would cause an error since you cannot apply log() to numbers <== 0.

You can also choose a different number of standard deviations to divide by for standardization. Andrew Gelman has been a proponent of dividing by 2 standard deviations; if you want to do things that way, give the argument n.sd = 2.

summ(fit, scale = TRUE, n.sd = 2)

Note that this is achieved by refitting the model. If the model took a long time to fit initially, expect a similarly long time to refit it.

Mean-centered variables

In the same vein as the standardization feature, you can keep the original scale while still mean-centering the predictors with the center = TRUE argument. As with scale, this is not applied to the response variable unless transform.response = TRUE.

summ(fit, center = TRUE)

Confidence intervals

In many cases, you'll learn more by looking at confidence intervals than p-values. You can request them from summ.

summ(fit, confint = TRUE, digits = 3)

You can adjust the width of the confidence intervals, which are by default 95% CIs.

summ(fit, confint = TRUE, ci.width = .5)

Removing p values

You might also want to drop the p-values altogether.

summ(fit, confint = TRUE, pvals = FALSE)

Remember that you can omit p-values regardless of whether you have requested confidence intervals.

Generalized and Mixed models

summ has been expanding its range of supported model types. glm models are a straightforward choice. Here we can take our previous model, but make it a probit model to reflect the fact that metascore is bound at 0 and 100 (analogous to 0 and 1). We'll use the quasibinomial family since this is a percentage rather a binary outcome.

fitg <- glm(metascore/100 ~ imdb_rating + log(us_gross) + genre5, data = movies,
            family = quasibinomial())

summ(fitg)

For exponential family models, especially logit and Poisson, you may be interested in getting the exponentiated coefficients rather than the linear estimates. summ can handle that!

summ(fitg, exp = TRUE)

Standard errors are omitted for odds ratio estimates since the confidence intervals are not symmetrical.

You can also get summaries of merMod objects, the mixed models from the lme4 package.

library(lme4)
fm1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)

summ(fm1)

Note that the summary of linear mixed models will omit p-values by default unless the \code{pbkrtest} package is installed for linear models. There's no clear-cut way to derive p-values with linear mixed models and treating the t-values as you would for OLS models can lead to inflated Type 1 error rates. Confidence intervals are better, but not perfect. Kenward-Roger calculated degrees of freedom are fairly good under many circumstances and those are used by default when \code{pbkrtest} package is installed. Be aware that for larger datasets, this procedure can take a long time. See the documentation (?summ.merMod) for more info.

You also get an estimated model R-squared for mixed models using the Nakagawa & Schielzeth (2013) procedure with code adapted from the piecewiseSEM package.

svyglm

I won't run through any examples here, but svyglm models are supported and provide near-equivalent output to what you see here depending on whether they are linear models or generalized linear models. See ?summ.svyglm for details.

Quantile regression

summ() also supports quantile regression models, as estimated by the rq package. See ?summ.rq for details.

effect_plot()

Sometimes to really understand what your model is telling you, you need to see the kind of predictions it will give you. For that, you can use effect_plot(), which does what it sounds like. There is a separate vignette available to explore all it can offer, but here's a basic example with our glm model:

effect_plot(fitg, pred = imdb_rating, interval = TRUE, plot.points = TRUE, 
            jitter = 0.05)

Now we're really learning something about our model---and you can see the close but imperfect agreement between fans and critics.

plot_summs() and plot_coefs()

When it comes time to share your findings, especially in talks, tables are often not the best way to capture people's attention and quickly convey the results. Variants on what are known by some as "forest plots" have been gaining popularity for presenting regression results.

For that, jtools provides plot_summs() and plot_coefs(). plot_summs() gives you a plotting interface to summ() and allows you to do so with multiple models simultaneously (assuming you want to apply the same arguments to each model).

Here's a basic, single-model use case.

plot_summs(fit)

Note that the intercept is omitted by default because it often distorts the scale and generally isn't of theoretical interest. You can change this behavior or omit other coefficients with the omit.coefs argument.

We may still want to use other features of summ(), like having robust standard errors. No problem.

plot_summs(fit, robust = TRUE)

Note that by default the width of the confidence interval is .95, but this can be changed with the ci_level argument. You can also add a thicker band to convey a narrow interval using the inner_ci_level argument:

plot_summs(fit, inner_ci_level = .9)

Plot coefficient uncertainty as normal distributions

Most of our commonly used regression models make an assumption that the coefficient estimates are asymptotically normally distributed, which is how we derive our confidence intervals, p values, and so on. Using the plot.distributions = TRUE argument, you can plot a normal distribution along the width of your specified interval to convey the uncertainty. This is also great for didactic purposes.

While the common OLS model assumes a t distribution, I decided that they are visually sufficiently close that I have opted not to try to plot the points along a t distribution.

plot_summs(fit, plot.distributions = TRUE, inner_ci_level = .9)

Comparing model coefficients visually

Comparison of multiple models simultaneously is another benefit of plotting. This is especially true when the models are nested. Let's fit a second model and compare.

fit2 <- lm(metascore ~ imdb_rating + log(us_gross) + log(budget) + genre5,
           data = movies)
plot_summs(fit, fit2)

Doing this with plot.distributions = TRUE creates a nice effect:

plot_summs(fit, fit2, plot.distributions = TRUE)

By providing a list of summ() arguments to plot_summs(), you can compare results with different summ() arguments (each item in the list corresponds to one model; the second list item to the second model, etc.). For instance, we can look at how the standard errors differ with different robust arguments:

plot_summs(fit, fit, fit, robust = list(FALSE, "HC0", "HC5"),
           model.names = c("OLS", "HC0", "HC5"))

Support for models with no summ() method

plot_coefs() is very similar to plot_summs(), but does not offer the features that summ() does. The tradeoff, though, is that it allows for model types that summ() does not — any model supported by tidy() from the broom or broom.mixed packages should work.

Note: If you provide unsupported model types to plot_summs(), it just passes them to plot_coefs().

Table output for Word and RMarkdown documents

Sometimes you really do want a table, but it can't be standard R output. For that, you can use export_summs(). It is a wrapper around huxtable's huxreg() function that will give you nice looking output if used in RMarkdown documents or, if requested, printed to a Word file. In the latter case, complicated models often need more fine-tuning in Word, but it gets you started.

Like plot_summs(), export_summs() is designed to give you the features available in summ(), so you can request things like robust standard errors and variable scaling.

Here's an example of what to expect in a document like this one:

export_summs(fit, fit2, scale = TRUE)

huxtable::print_html(export_summs(fit, fit2, scale = TRUE))

When using RMarkdown, set results = 'asis' for the chunk with export_summs() to get the right formatting for whatever type of output document (HTML, PDF, etc.)

To format the error statistics, simply put the statistics desired in curly braces wherever you want them in a character string. For example, if you want the standard error in parentheses, the argument would be "({std.error})", which is the default. Some other ideas:

• "({statistic})", which gives you the test statistic in parentheses.

• "({statistic}, p = {p.value})", which gives the test statistic followed by a "p =" p value all in parentheses. Note that you'll have to pay special attention to rounding if you do this to keep cells sufficiently narrow.

• "[{conf.low}, {conf.high}]", which gives the confidence interval in the standard bracket notation. You could also explicitly write the confidence level, e.g., "95% CI [{conf.low}, {conf.high}]".

Here's an example with confidence intervals instead of standard errors:

export_summs(fit, fit2, scale = TRUE,
             error_format = "[{conf.low}, {conf.high}]")

huxtable::print_html(export_summs(fit, fit2, scale = TRUE,
                     error_format = "[{conf.low}, {conf.high}]"))

There's a lot more customization that I'm not covering here: Renaming the columns, renaming/excluding coefficients, realigning the errors, and so on.

If you want to save to a Word doc, use the to.file argument (requires the officer and flextable packages):

export_summs(fit, fit2, scale = TRUE, to.file = "docx", file.name = "test.docx")

You can likewise export to PDF ("PDF"), HTML ("HTML"), or Excel format ("xlsx").

Other options

Adding and removing written output

Much of the output with summ can be removed while there are several other pieces of information under the hood that users can ask for.

To remove the written output at the beginning, set model.info = FALSE and/or model.fit = FALSE.

summ(fit, model.info = FALSE, model.fit = FALSE)

Choose how many digits past the decimal to round to

With the digits = argument, you can decide how precise you want the outputted numbers to be. It is often inappropriate or distracting to report quantities with many digits past the decimal due to the inability to measure them so precisely or interpret them in applied settings. In other cases, it may be necessary to use more digits due to the way measures are calculated.

The default argument is digits = 2.

summ(fit, model.info = FALSE, digits = 5)

summ(fit, model.info = FALSE, digits = 1)

You can pre-set the number of digits you want printed for all jtools functions with the jtools-digits option.

options("jtools-digits" = 2)
summ(fit, model.info = FALSE)

options("jtools-digits" = NULL)

Note that the summ object contains the non-rounded values if you want to use them later. The digits option just affects the printed output.

j <- summ(fit, digits = 3)

j$coeftable

Set default arguments to summ

You may like some of the options afforded to you by summ() but may not like the inconvenience of typing them over and over. To streamline your sessions, you can use the set_summ_defaults() function to avoid redundant typing.

It works like this:

set_summ_defaults(digits = 2, pvals = FALSE, robust = "HC3")

If you do that, you will have 2 digits in your output, no p values displayed, and "HC3" sandwich robust standard errors in your summ output for the rest of the R session. You can also use this in a .RProfile, but remember that it should be included in scripts so that your code runs the same on every computer and every session.

Here are all the options that can be toggled via set_summ_defaults:

• digits
• model.info
• model.fit
• pvals
• robust
• confint
• ci.width
• vifs
• conf.method (merMod models only)

Calculate and report variance inflation factors (VIF)

When multicollinearity is a concern, it can be useful to have VIFs reported alongside each variable. This can be particularly helpful for model comparison and checking for the impact of newly-added variables. To get VIFs reported in the output table, just set vifs = TRUE.

summ(fit, vifs = TRUE)

There are many standards researchers apply for deciding whether a VIF is too large. In some domains, a VIF over 2 is worthy of suspicion. Others set the bar higher, at 5 or 10. Others still will say you shouldn't pay attention to these at all. Ultimately, the main thing to consider is that small effects are more likely to be "drowned out" by higher VIFs, but this may just be a natural, unavoidable fact with your model (e.g., there is no problem with high VIFs when you have an interaction effect).

jtools documentation built on Sept. 11, 2024, 7 p.m.