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Add tidiers for margins and mfx objects #700

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grantmcdermott opened this issue May 2, 2019 · 5 comments · Fixed by alexpghayes/modeltests#33 or #909
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Add tidiers for margins and mfx objects #700

grantmcdermott opened this issue May 2, 2019 · 5 comments · Fixed by alexpghayes/modeltests#33 or #909

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@grantmcdermott
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grantmcdermott commented May 2, 2019

It would be great to have tidy methods for objects from the margins and mfx packages.

Among other things, this would go a long way towards improving the table support for generalized linear models like logit and probit regressions, where you often want to report actual marginal effects rather than the naive coefficient values. (I'm thinking of the fact that modern table-exporting packages like huxtable and gtsummary rely on broom::tidy() as a first step.) AFAIK, there is currently no fully automated way to produce, say, a LaTeX table of marginal effects from a logistic regression in R.

A potential point of convenience here is that margins and mfx both produce output that already closely resemble tidied regression output.

## Run a logistic regression
log_reg <- glm(am ~ cyl + hp + wt, data = mtcars, family = binomial)

## Tidy (but naive) coefficient values
library(broom)
tidy(log_reg)
#> # A tibble: 4 x 5
#>   term        estimate std.error statistic p.value
#>   <chr>          <dbl>     <dbl>     <dbl>   <dbl>
#> 1 (Intercept)  19.7       8.12       2.43   0.0152
#> 2 cyl           0.488     1.07       0.455  0.649 
#> 3 hp            0.0326    0.0189     1.73   0.0840
#> 4 wt           -9.15      4.15      -2.20   0.0276

## Get the actual marginal effects instead

## Option 1: margins package
library(margins, quietly = T)
summary(margins(log_reg))
#>  factor     AME     SE       z      p   lower   upper
#>     cyl  0.0215 0.0470  0.4567 0.6479 -0.0706  0.1135
#>      hp  0.0014 0.0006  2.3197 0.0204  0.0002  0.0026
#>      wt -0.4025 0.1154 -3.4880 0.0005 -0.6287 -0.1764

## Option 2: mfx package
library(mfx, quietly = T, warn.conflicts = F)
logitmfx(log_reg, atmean = F, data = mtcars)
#> Call:
#> logitmfx(formula = log_reg, data = mtcars, atmean = F)
#> 
#> Marginal Effects:
#>          dF/dx  Std. Err.       z  P>|z|
#> cyl  0.0214528  0.0499376  0.4296 0.6675
#> hp   0.0014339  0.0014602  0.9820 0.3261
#> wt  -0.4025475  0.3782646 -1.0642 0.2872

Created on 2019-05-02 by the reprex package (v0.2.1)

@grantmcdermott
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grantmcdermott commented Aug 20, 2019

@alexpghayes I finally got around to writing some tidiers for these objects myself. I still have to update the docs, run coverage tests, etc. But before I do that, would you like me to separate them out into two distinct PRs (one for mfx, one for margins), or just roll them into a single PR?

@alexpghayes
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alexpghayes commented Aug 20, 2019

Separate PRs would be ideal!

@grantmcdermott
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grantmcdermott commented Aug 28, 2019

Alex, I'm about ready to submit this, but I just wanted to check first:

Is there an easy way to add a new column name to the check_arguments() test? I'm not passing this particular test because I've added a new "atmean" column to the tidy.mfxlogit (and related) tidiers. OTOH, I'm happy to ignore for now and just submit the PR as is if you're okay with that...

@alexpghayes
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alexpghayes commented Aug 29, 2019

Yes! You'll need to:

In the meantime go ahead and make the PR!

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github-actions bot commented Mar 7, 2021

This issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with a reprex: https://reprex.tidyverse.org) and link to this issue.

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