Problem `.x` is empty in pammtools packages

Question

I am trying to replicate the example code in Bender and Schleip for Piece-wise exponential Additive Mixed modelling tools. Specifically a survival exercise with time varying effects. https://arxiv.org/pdf/1806.01042.pdf

   library(dplyr); library(tidyr); library(purrr); library(ggplot2)
library(survival); library(mgcv); library(pammtools)

data("pbc", package="survival")
# event time information
pbc <- pbc %>%
  filter(id <= 312) %>%
  mutate(status = ifelse(status==0,0,1) )%>%
  select(id:status, trt:sex, bili, protime)
pbc %>% slice(1:6)


pbc_ped <- as_ped(
  data = list(pbc, pbcseq),
  formula = Surv(pbc$time, pbc$status)~sex|concurrent(bili, protime, tz_var = "day"),
  id = "id")

I always get the error

Error: .x is empty, and no .init supplied

I installed and checked Rtools, I tried with different (older) version of Purrr, which sometimes is related with this error. I tried to run the code also on https://rdrr.io/snippets/.

Any idea? thank you very much...

Answer 1

You have not used the code in that vignette. And you added pbc$ to the arguments in Surv(), a common mistake but generally not a productive strategy

# Need to narrow the material from pbcseq
pbcseq <- pbcseq %>% select(id, day, bili, protime)
# I would have given it a different name

#------ Error when using "|" rather than "+"
pbc_ped <- as_ped(
    data = list(pbc, pbcseq),
    formula = Surv(time, status)~sex|concurrent(bili, protime, tz_var = "day"),
    id = "id")
#Error: `.x` is empty, and no `.init` supplied
#________________

pbc_ped <- as_ped(
    data = list(pbc, pbcseq),
    formula = Surv(time, status)~sex + concurrent(bili, protime, tz_var = "day"),
    id = "id")    # No error

I think there may be an error in the vignette. I don't see any examples using the construct ...

Surv(time,status)~ variates | special(.)

They all use a "+" sign for adding the time-dependent covariates. If you go to https://adibender.github.io/pammtools//articles/data-transformation.html you see them using a "+" rather than a "|". I think there is some sloppiness in that package's documentation. But your additions only made the problem worse.