Harmonise Three Labels — harmonise_three

Function to map an input from three different list into one of the three standardise labels

Usage

harmonise_three_labels(
  arg,
  label_one,
  label_two,
  label_three,
  label_unknown,
  harmonise_label_one = "group_1",
  harmonise_label_two = "group_2",
  harmonise_label_three = "group_3",
  harmonise_label_unknown = NA,
  error_call = rlang::caller_env()
)

Arguments

arg: Input argument, in characters to be harmonised
label_one: Input character vector representing the ways to identify harmonise_label_one
label_two: Input character vector representing the ways to identify harmonise_label_two
label_three: Input character vector representing the ways to identify harmonise_label_three
label_unknown: Input character vector representing the ways to identify harmonise_label_unknown
harmonise_label_one: Input character representing the harmonised label for label_one Default: 'group_1'
harmonise_label_two: Input character representing the harmonised label for label_two Default: 'group_2'
harmonise_label_three: Input character representing the harmonised label for label_three Default: 'group_3'
harmonise_label_unknown: Input character representing the harmonised label for label_unknown Default: NA
error_call: The execution environment of a currently running function, e.g. caller_env(). The function will be mentioned in error messages as the source of the error. See the call argument of abort() for more information.

Value

Character representing one of the three standardise labels.

Examples

label_cpt_nonanginal <- c("nonanginal", "unspecified")
label_cpt_atypical <- c("atypical", "Atypical")
label_cpt_typical <- c("typical", "angina")
label_cpt_unknown <- c(NA, NaN)

# Gives harmonise_label_one if there is valid input of chest_pain_type
chest_pain_type <- "unspecified"

harmonise_three_labels(
   arg = chest_pain_type,
   label_one = label_cpt_nonanginal,
   label_two = label_cpt_atypical,
   label_three = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "nonanginal",
   harmonise_label_two = "atypical",
   harmonise_label_three = "typical",
   harmonise_label_unknown = NA
)
#> [1] "nonanginal"

# Gives harmonise_label_two if there is valid input of chest_pain_type
chest_pain_type <- "Atypical"

harmonise_three_labels(
   arg = chest_pain_type,
   label_one = label_cpt_nonanginal,
   label_two = label_cpt_atypical,
   label_three = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "nonanginal",
   harmonise_label_two = "atypical",
   harmonise_label_three = "typical",
   harmonise_label_unknown = NA
)
#> [1] "atypical"

# Gives harmonise_label_three if there is valid input of chest_pain_type
chest_pain_type <- "angina"

harmonise_three_labels(
   arg = chest_pain_type,
   label_one = label_cpt_nonanginal,
   label_two = label_cpt_atypical,
   label_three = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "nonanginal",
   harmonise_label_two = "atypical",
   harmonise_label_three = "typical",
   harmonise_label_unknown = NA
)
#> [1] "typical"

# Gives harmonise_label_unknown if there is valid missing input of chest_pain_type
chest_pain_type <- NaN

harmonise_three_labels(
   arg = chest_pain_type,
   label_one = label_cpt_nonanginal,
   label_two = label_cpt_atypical,
   label_three = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "nonanginal",
   harmonise_label_two = "atypical",
   harmonise_label_three = "typical",
   harmonise_label_unknown = NA
)
#> [1] NA

# Gives harmonise_label_unknown if there is valid missing input of chest_pain_type
chest_pain_type <- "NIL"
label_cpt_unknown <- c("NIL")

harmonise_three_labels(
   arg = chest_pain_type,
   label_one = label_cpt_nonanginal,
   label_two = label_cpt_atypical,
   label_three = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "nonanginal",
   harmonise_label_two = "atypical",
   harmonise_label_three = "typical",
   harmonise_label_unknown = NA
)
#> [1] NA

# Gives error of invalid typical chest pain input with partial match
chest_pain_type <- "Typical"
label_cpt_unknown <- c(NA, NaN)

try(harmonise_three_labels(
   arg = chest_pain_type,
   label_one = label_cpt_nonanginal,
   label_two = label_cpt_atypical,
   label_three = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "nonanginal",
   harmonise_label_two = "atypical",
   harmonise_label_three = "typical",
   harmonise_label_unknown = NA
))
#> Error in eval(expr, envir) : 
#>   `chest_pain_type` must be one of "nonanginal", "unspecified",
#> "atypical", "Atypical", "typical", "angina", "NA", or "NaN", not "Typical".
#> ℹ Did you mean "typical"?

# Gives error of invalid typical chest pain input without partial match
chest_pain_type <- "Something"
label_cpt_unknown <- c(NA, NaN)

try(harmonise_three_labels(
   arg = chest_pain_type,
   label_one = label_cpt_nonanginal,
   label_two = label_cpt_atypical,
   label_three = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "nonanginal",
   harmonise_label_two = "atypical",
   harmonise_label_three = "typical",
   harmonise_label_unknown = NA
))
#> Error in eval(expr, envir) : 
#>   `chest_pain_type` must be one of "nonanginal", "unspecified",
#> "atypical", "Atypical", "typical", "angina", "NA", or "NaN", not "Something".

# Gives error of invalid missing input of chest_pain_type
chest_pain_type <- NA
label_cpt_unknown <- c("NIL")

try(harmonise_three_labels(
   arg = chest_pain_type,
   label_one = label_cpt_nonanginal,
   label_two = label_cpt_atypical,
   label_three = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "nonanginal",
   harmonise_label_two = "atypical",
   harmonise_label_three = "typical",
   harmonise_label_unknown = NA
))
#> Error in eval(expr, envir) : 
#>   `chest_pain_type` must be one of "nonanginal", "unspecified",
#> "atypical", "Atypical", "typical", "angina", or "NIL" not NA.