# https://github.com/r-lib/pkgdown/issues/2704

Skip to contents

Harmonise Four Labels

Source: R/harmonise.R
harmonise_four_labels.Rd

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

Usage

harmonise_four_labels(
  arg,
  label_one,
  label_two,
  label_three,
  label_four,
  label_unknown,
  harmonise_label_one = "group_1",
  harmonise_label_two = "group_2",
  harmonise_label_three = "group_3",
  harmonise_label_four = "group_4",
  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_four

Input character vector representing the ways to identify harmonise_label_four

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_four

Input character representing the harmonised label for label_four Default: 'group_4'

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 four standardise labels.

Examples

label_cpt_no_chest_pain <- c("no chest pain", "normal")
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 <- "normal"

harmonise_four_labels(
   arg = chest_pain_type,
   label_one = label_cpt_no_chest_pain,
   label_two = label_cpt_nonanginal,
   label_three = label_cpt_atypical,
   label_four = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "no chest pain",
   harmonise_label_two = "nonanginal",
   harmonise_label_three = "atypical",
   harmonise_label_four = "typical",
   harmonise_label_unknown = NA
)
#> [1] "no chest pain"

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

harmonise_four_labels(
   arg = chest_pain_type,
   label_one = label_cpt_no_chest_pain,
   label_two = label_cpt_nonanginal,
   label_three = label_cpt_atypical,
   label_four = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "no chest pain",
   harmonise_label_two = "nonanginal",
   harmonise_label_three = "atypical",
   harmonise_label_four = "typical",
   harmonise_label_unknown = NA
)
#> [1] "nonanginal"

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

harmonise_four_labels(
   arg = chest_pain_type,
   label_one = label_cpt_no_chest_pain,
   label_two = label_cpt_nonanginal,
   label_three = label_cpt_atypical,
   label_four = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "no chest pain",
   harmonise_label_two = "nonanginal",
   harmonise_label_three = "atypical",
   harmonise_label_four = "typical",
   harmonise_label_unknown = NA
)
#> [1] "atypical"

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

harmonise_four_labels(
   arg = chest_pain_type,
   label_one = label_cpt_no_chest_pain,
   label_two = label_cpt_nonanginal,
   label_three = label_cpt_atypical,
   label_four = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "no chest pain",
   harmonise_label_two = "nonanginal",
   harmonise_label_three = "atypical",
   harmonise_label_four = "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_four_labels(
   arg = chest_pain_type,
   label_one = label_cpt_no_chest_pain,
   label_two = label_cpt_nonanginal,
   label_three = label_cpt_atypical,
   label_four = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "no chest pain",
   harmonise_label_two = "nonanginal",
   harmonise_label_three = "atypical",
   harmonise_label_four = "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_four_labels(
   arg = chest_pain_type,
   label_one = label_cpt_no_chest_pain,
   label_two = label_cpt_nonanginal,
   label_three = label_cpt_atypical,
   label_four = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "no chest pain",
   harmonise_label_two = "nonanginal",
   harmonise_label_three = "atypical",
   harmonise_label_four = "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_four_labels(
   arg = chest_pain_type,
   label_one = label_cpt_no_chest_pain,
   label_two = label_cpt_nonanginal,
   label_three = label_cpt_atypical,
   label_four = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "no chest pain",
   harmonise_label_two = "nonanginal",
   harmonise_label_three = "atypical",
   harmonise_label_four = "typical",
   harmonise_label_unknown = NA
))
#> Error in eval(expr, envir) : 
#>   `chest_pain_type` must be one of "no chest pain", "normal",
#> "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_four_labels(
   arg = chest_pain_type,
   label_one = label_cpt_no_chest_pain,
   label_two = label_cpt_nonanginal,
   label_three = label_cpt_atypical,
   label_four = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "no chest pain",
   harmonise_label_two = "nonanginal",
   harmonise_label_three = "atypical",
   harmonise_label_four = "typical",
   harmonise_label_unknown = NA
))
#> Error in eval(expr, envir) : 
#>   `chest_pain_type` must be one of "no chest pain", "normal",
#> "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_four_labels(
   arg = chest_pain_type,
   label_one = label_cpt_no_chest_pain,
   label_two = label_cpt_nonanginal,
   label_three = label_cpt_atypical,
   label_four = label_cpt_typical,
   label_unknown = label_cpt_unknown,
   harmonise_label_one = "no chest pain",
   harmonise_label_two = "nonanginal",
   harmonise_label_three = "atypical",
   harmonise_label_four = "typical",
   harmonise_label_unknown = NA
))
#> Error in eval(expr, envir) : 
#>   `chest_pain_type` must be one of "no chest pain", "normal",
#> "nonanginal", "unspecified", "atypical", "Atypical", "typical", "angina", or
#> "NIL" not NA.