CODEWITHSUNDEEP
rlibrariesgammgcv
TimW
TimW

Reputation: 65

How to use 2 different functions in 2 different libraries that have the same name

I'm trying to explore the difference in how the gam function works in the mgcv package versus the gam package. But I'm not able to run both gam functions in one R session. I thought if I preface with mgcv::gam or gam::gam it would be able to run the right function, but it looks like I have to detach mgcv in order to run the gam function in the gam package.

library(ISLR)
library(mgcv)
library(gam)

# I get an error message when it runs this
gam.m3 <- gam::gam(wage~s(year,4)+s(age,5)+education,data=Wage)

# No error message when I detach mgcv
detach(package:mgcv)
gam.m3 <- gam::gam(wage~s(year,4)+s(age,5)+education,data=Wage)

Is there a way I can run both gam functions in one session?

Below is the output:

> library(ISLR)
> library(mgcv)
> library(gam)
> #I get an error message when it runs this
> gam.m3 <- gam::gam(wage~s(year,4)+s(age,5)+education,data=Wage)
Error in terms.formula(reformulate(term[i])) : 
  invalid model formula in ExtractVars
> #No error message when I detach mgcv
> detach(package:mgcv)
> gam.m3 <- gam::gam(wage~s(year,4)+s(age,5)+education,data=Wage)
Warning message:
In model.matrix.default(mt, mf, contrasts) :
  non-list contrasts argument ignored

Update: I re-ran this with a clean R session and the story is different. Before, I cleared the workspace but did not have a clear R session. Now, if I run with a clean session the gam.m3 model seems to work. BUT - if I change the order of the library load, and load gam before mgcv, I get the same error. When mgcv is loaded after gam is loaded, I do get this message:

The following objects are masked from ‘package:gam’:

gam, gam.control, gam.fit, s

So I guess just part of the deal of loading mgcv is that you can no longer use certain functions in gam? That is annoying. FYI I get the analogous warning message when loading gam after mgcv is loaded - that certain objects will be masked from package:mgcv.

Upvotes: 2

Views: 279

Answers (1)

Roland
Roland

Reputation: 132706

As shown in my answer to your other question, you can't use gam::s.

However, you can tell R to evaluate the call in the gam package namespace:

library(ISLR)
library(gam)

fit1 <- gam(wage~s(year,4)+s(age,5)+education,data=Wage)

library(mgcv)

gam::gam(wage~s(year,4)+s(age,5)+education,data=Wage)
#errors

fit2 <- eval(quote(gam(wage~s(year,4)+s(age,5)+education,data=Wage)), 
               envir = asNamespace("gam"))
#works

all.equal(coef(fit1), coef(fit2))
#[1] TRUE

Upvotes: 3

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