comorbidity function doesn't work

[Jeanluc63]

Hi, I have updated the R software to version 4.3.1 and also the 'comorbidity' package. Unfortunately the 'comorbidity' function doesn't work and produces the following error:

Error in comorbidity(x = pat_dati.long, id = "codpaz", code = "ICD", map = "elixhauser_icd9_quan", : unused arguments (x = pat_dati.long, id = "codpaz", code = "ICD", map = "elixhauser_icd9_quan", assign0 = TRUE, labelled = TRUE, tidy.codes = TRUE).

These are my data (pat_dati.long), and my id (codpaz) and code (ICD) names.

head(pat_dati.long) codpaz sesso ETA CLASSI_ETA PESO BMI CLASSE_BMI prog_sdo pat ICD 1 100448 F 79 70-79 83 NA 16612 pat1 71515 2 100448 F 79 70-79 83 NA 16612 pat2 4011 3 100448 F 79 70-79 83 NA 16612 pat3
4 100448 F 79 70-79 83 NA 16612 pat4
5 100448 F 79 70-79 83 NA 16612 pat5
6 100448 F 79 70-79 83 NA 16612 pat6

Thank you for your attention Gianluca

[ellessenne]

Hi, the following works for me on a fully up-to-date system and using the CRAN version of {comorbidity}:

library(comorbidity)
pat_dati.long <- data.frame(
  codpaz = 100448,
  sesso = "F",
  ETA = 79,
  CLASSI_ETA = "70-79",
  PESO = 83,
  BMI = NA,
  CLASSE_BMI = NA,
  pat = c("pat1", "pat2", "pat3", "pat4", "pat5", "pat6"),
  ICD = c("71515", "4011", "", "", "", "")
)
comorbidity(
  x = pat_dati.long,
  id = "codpaz",
  code = "ICD",
  map = "elixhauser_icd9_quan",
  assign0 = TRUE,
  labelled = TRUE,
  tidy.codes = TRUE
)
#>   codpaz chf carit valv pcd pvd hypunc hypc para ond cpd diabunc diabc hypothy
#> 1 100448   0     0    0   0   0      1    0    0   0   0       0     0       0
#>   rf ld pud aids lymph metacanc solidtum rheumd coag obes wloss fed blane dane
#> 1  0  0   0    0     0        0        0      0    0    0     0   0     0    0
#>   alcohol drug psycho depre
#> 1       0    0      0     0

library(devtools)
#> Loading required package: usethis
session_info(info = "platform")
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.1 (2023-06-16)
#>  os       macOS Ventura 13.4
#>  system   x86_64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Europe/Stockholm
#>  date     2023-06-24
#>  pandoc   3.1.3 @ /usr/local/bin/ (via rmarkdown)
#> 
#> ──────────────────────────────────────────────────────────────────────────────

^{Created on 2023-06-24 with reprex v2.0.2}

Could you try the code above and see if that works?

[Jeanluc63]

Hi, I try your code but it give me the same error:

Error in comorbidity(x = pat_dati.long, id = "codpaz", code = "ICD", map = "elixhauser_icd9_quan", : unused arguments (x = pat_dati.long, id = "codpaz", code = "ICD", map = "elixhauser_icd9_quan", assign0 = TRUE, labelled = TRUE, tidy.codes = TRUE)

> Loading required package: usethis

session_info(info = "platform") ─ Session info ──────────────────────────────────────────────────────────────────── setting value version R version 4.3.1 (2023-06-16 ucrt) os Windows 10 x64 (build 19044) system x86_64, mingw32 ui RStudio language (EN) collate Italian_Italy.utf8 ctype Italian_Italy.utf8 tz Europe/Rome date 2023-06-25 rstudio 2023.06.0+421 Mountain Hydrangea (desktop) pandoc 3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)

Thank you Gianluca

[ellessenne]

Interesting, can you try clearing your environment and/or restarting your session and try again the previous code?

[Jeanluc63]

I clean environment and your code and mine work perfectly. Thank you Best regards Gianluca

[ellessenne]

Ok, that's great! Will close this issue then, just let me know if you have any other question.

Best wishes,

Alessandro