Package compatibility

[ellessenne]

Following some e-mail feedback, I think it would be good to add to the package the following functions:

• comorbidity_check() (or some similar name) to verify if a user-supplied comorbidity dataset is compatible with the package;
• set_comorbidity() (or similar) to add the required internal structure/attributes to yield a comorbidity-compatible object.

Example code using the current (2022-08-16) dev version:

library(comorbidity)
#> This is {comorbidity} version 1.0.3.
#> A lot has changed since the pre-1.0.0 release on CRAN, please check-out breaking changes here:
#> -> https://ellessenne.github.io/comorbidity/articles/C-changes.html
df <- data.frame(
  id = 1,
  mi = 1,
  chf = 0,
  pvd = 0,
  cevd = 0,
  dementia = 0,
  cpd = 0,
  rheumd = 0,
  pud = 0,
  mld = 0,
  diab = 0,
  diabwc = 1,
  hp = 1,
  rend = 0,
  canc = 0,
  msld = 0,
  metacanc = 0,
  aids = 0
)
score(x = df)
#> Error: This function can only be used on an object of class 'comorbidity', which you can obtain by using the 'comorbidity()' function. See ?comorbidity for more details.

class(df) <- c("comorbidity", class(df))
attr(df, "map") <- "charlson_icd10_quan"
score(x = df, assign0 = FALSE)
#> [1] 3
#> attr(,"map")
#> [1] "charlson_icd10_quan"
score(x = df, weights = "quan", assign0 = FALSE)
#> [1] 3
#> attr(,"map")
#> [1] "charlson_icd10_quan"
#> attr(,"weights")
#> [1] "quan"

df$mi <- NULL
score(x = df, assign0 = FALSE)
#> Error in `[.data.frame`(x, , names(.maps[[map]])): undefined columns selected

^{Created on 2022-08-16 by the reprex package (v2.0.1)}