Augmenting/Mutating of Model objects in R

Question

So I am running multiple cochrane orcutt regressions, which is no problem. I then display the output of these regressions using modelsummary(). Still no problems up to this point.

However, when I then try to compare the models using modelplot(), there are no confidence intervals computed in the cochrane orcutt model (class "orcutt") and I thus get the following error:

Error in eval(parse(text = text, keep.source = FALSE), envir) : object 'conf.low' not found

I know what the problem here is - there are just no confidence interval "parts" computed by the cochrane.orcutt() command. A partial solution is also obvious - I can just calculate the confidence intervals using the point estimates/coefficients and the standard errors (which are of course included in the model by default).

However my problem arises when I want to use these confidence interval values in modelplot(), because they are not "in" the model object. In my ignorance, I attempted the following to try and create the lower bound of a confidence interval, using mutate():

model %>% 
+   mutate(`conf.low`=`coefficients`-1.96*`std.error`)

I hope this conveys my problem well enough, thank you for reading.

Answer 1

As noted in the comments, mutate is a function from the dplyr package which is intended to work on data frames, and not on model objects or on modelsummary tables.

Also, please note that I can’t diagnose your problem properly because you did not supply a MINIMAL REPRODUCIBLE EXAMPLE and you don’t event tell us which function you used to estimate the model.

One way to do the Cochrane-Orcutt in R is to use the orcutt package:

library(orcutt)
data(icecream, package = "orcutt")
lm <- lm(cons ~ price + income + temp, data = icecream)
coch <- cochrane.orcutt(lm)

Behind the scenes, the modelsummary package uses the tidy function from the broom package to extract estimates from model objects:

library(broom)

tidy(coch)
#> # A tibble: 4 × 5
#>   term        estimate std.error statistic    p.value
#>   <chr>          <dbl>     <dbl>     <dbl>      <dbl>
#> 1 (Intercept)  0.157    0.290        0.543 0.592     
#> 2 price       -0.892    0.811       -1.10  0.282     
#> 3 income       0.00320  0.00155      2.07  0.0488    
#> 4 temp         0.00356  0.000555     6.42  0.00000102

From the output above, you see that broom does NOT extract a confidence interval. This could explain why modelsummary can’t print your table/plot.

One alternative option is to instruct modelsummary to use the parameters package to extract estimates instead of broom. This can be achieved by setting a global option:

library(modelsummary)
options(modelsummary_get = "parameters")
modelsummary(coch, statistic = "conf.int", output = "markdown")

	Model 1
(Intercept)	0.157
	[-0.439, 0.754]
price	-0.892
	[-2.562, 0.778]
income	0.003
	[0.000, 0.006]
temp	0.004
	[0.002, 0.005]
Num.Obs.	30
R2	0.649
R2 Adj.	0.607
rho	0.401
number.interaction	11.000
dw.original	1.021
p.value.original	0.000
dw.transformed	1.549
p.value.transformed	0.051

And modelplot now works too:

modelplot(coch)

Yet another alternative would be to use the broom default, but to customize the output using your own tidy_custom.orcutt method. This is a bit more involved, but you’ll find detailed instruction on the modelsummary website: https://vincentarelbundock.github.io/modelsummary/articles/modelsummary.html#adding-new-information-to-existing-models