Testing ggplot2 class

[teunbrand]

Hi there,

We've been preparing a new major release for ggplot2 and found an issue during a reverse dependency check.
The issue is described in tidyverse/ggplot2#6498, where you're welcome to raise discussion.
The issue isn't with your packaged code, but with these expectations:

nlmixr2plot/tests/testthat/test-add.R

Lines 45 to 46 in 386397a

	expect_true(inherits(p2[[1]], "gg"))
	expect_true(inherits(pl[[1]], "gg"))

Similar expectations may exist in other tests. You can test your code with the development version of ggplot2 by installing it as follows:

# install.packages("pak")
pak::pak("tidyverse/ggplot2")

We aim to release the new ggplot2 version in about 2 weeks, and hope you can submit a fix to CRAN around that time. Hopefully this will inform you in a timely manner.

Best wishes,
Teun

[mattfidler]

This was insufficient to fix the issue with adding plots (as you already mentioned)

[mattfidler]

The testing has been integrated (and pushed to CRAN), but the operator + still doesn't work like it did.

[teunbrand]

Thanks for pushing an update to CRAN!
I can confirm it continues to show up in reverse dependency checks.

[mattfidler]

@teunbrand

Do you have any progress on the + operator? (I didn't see anything on the github issue).

[teunbrand]

There is a workaround mentioned in RConsortium/S7#544 (comment). The proper fix should occur in S7 IMO.

[mattfidler]

Hm,

@teunbrand #41 still errors and it uses the work-around you mention.

[mattfidler]

library(nlmixr2)
#> ── Attaching packages ───────────────────────────────────────── nlmixr2 4.0.0 ──
#> ✔ lotri         1.0.1     ✔ ggPMX         1.3.0
#> ✔ nlmixr2data   2.0.9     ✔ monolix2rx    0.0.5
#> ✔ nlmixr2est    4.0.1     ✔ nlmixr2lib    0.3.0
#> ✔ nlmixr2extra  3.0.2     ✔ nlmixr2rpt    0.2.1
#> ✔ nlmixr2plot   3.0.2     ✔ nonmem2rx     0.1.7
#> ✔ rxode2        4.0.2     ✔ shinyMixR     0.5.1
#> ✔ babelmixr2    0.1.8     ✔ xpose.nlmixr2 0.4.1
#> ── Optional Packages Loaded/Ignored ─────────────────────────── nlmixr2 4.0.0 ──
#> ✔ babelmixr2        ✔ nlmixr2rpt   
#> ✔ ggPMX             ✔ nonmem2rx    
#> ✔ monolix2rx        ✔ shinyMixR    
#> ✔ nlmixr2lib        ✔ xpose.nlmixr2
#> ── Conflicts ───────────────────────────────────────────── nlmixr2conflicts() ──
#> ✖ rxode2::boxCox()     masks nlmixr2est::boxCox()
#> ✖ rxode2::yeoJohnson() masks nlmixr2est::yeoJohnson()

PKdata <- nlmixr2data::warfarin %>%
  dplyr::filter(dvid == "cp") %>%
  dplyr::select(-dvid) %>%
  dplyr::mutate(sex = ifelse(sex == "male", 1, 0))

One.comp.KA.solved <- function() {
  ini({
    lka  <- log(1.15)
    lcl  <- log(0.135)
    lv   <- log(8)
    prop.err <- 0.15
    add.err  <- 0.6
    eta.ka ~ 0.5
    eta.cl ~ 0.1
    eta.v  ~ 0.1
  })
  model({
    cl <- exp(lcl + eta.cl)
    v  <- exp(lv + eta.v)
    ka <- exp(lka + eta.ka)
    linCmt() ~ prop(prop.err) + add(add.err)
  })
}

fitOne.comp.KA.solved_S <-
  nlmixr2est::nlmixr(
    One.comp.KA.solved,
    PKdata,
    est = "saem",
    nlmixr2est::saemControl(nBurn = 2,
                            nEm   = 3,
                            print = 0)
  )
#> ℹ parameter labels from comments are typically ignored in non-interactive mode
#> ℹ Need to run with the source intact to parse comments
#> → loading into symengine environment...
#> → pruning branches (`if`/`else`) of saem model...
#> ✔ done
#> → finding duplicate expressions in saem model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> ✔ done
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> ℹ calculate uninformed etas
#> ℹ done
#> Calculating covariance matrix
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → loading into symengine environment...
#> → pruning branches (`if`/`else`) of saem model...
#> ✔ done
#> → finding duplicate expressions in saem predOnly model 0...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → finding duplicate expressions in saem predOnly model 1...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → finding duplicate expressions in saem predOnly model 2...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → optimizing duplicate expressions in saem predOnly model 2...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> ✔ done
#> → Calculating residuals/tables
#> ✔ done
#> → compress origData in nlmixr2 object, save 14912
#> → compress phiM in nlmixr2 object, save 1192
#> → compress parHistData in nlmixr2 object, save 2096
#> → compress saem0 in nlmixr2 object, save 37584

ap <- nlmixr2est::augPred(fitOne.comp.KA.solved_S)

pl <- plot(ap)

p2 <- pl + ggplot2::xlab("cool")

print(p2)
#> NULL

^{Created on 2025-07-23 with reprex v2.1.1}