data-raw/prep_pbc_data.R

In Big-Life-Lab/recodeflow: Contains functions to interface with variable details sheets, including recoding variables and converting them to PMML

## code to prepare dataset goes here
library(yaml)
library(readr)
library(usethis)
library(survival)

variables_sheet_cols <- cols(
    variable = col_character(),
    label = col_character(),
    labelLong = col_character(),
    subject = col_character(),
    section = col_character(),
    variableType = col_character(),
    databaseStart = col_character(),
    units = col_character(),  # changed from logical
    variableStart = col_character(),
    notes = col_logical(),
    description = col_logical()
)

variable_details_sheet_cols <- cols(
    variable = col_character(),
    dummyVariable = col_character(),
    typeEnd = col_character(),
    typeStart = col_character(),
    databaseStart = col_character(),
    variableStart = col_character(),
    variableStartLabel = col_character(),
    numValidCat = col_double(),
    recEnd = col_character(),
    catLabel = col_character(),
    catLabelLong = col_character(),
    units = col_character(),
    recStart = col_character(),
    catLabelLong = col_character(),
    variableStartShortLabel = col_character(),
    notes = col_character(),
    .default = col_character()  # for any remaining columns
)

# ------ pbc.rda data ------
# Get PBC data from survival package
data(pbc, package = "survival")

# Save both the original pbc data 
usethis::use_data(pbc, overwrite = TRUE)

# ------ import the pbc_metadata.yaml file ------
pbc_metadata <- read_yaml("inst/extdata/pbc_metadata.yaml")
usethis::use_data(pbc_metadata, overwrite = TRUE)

# ------ import the pbc_variables.csv file --------
pbc_variables <- read_csv("inst/extdata/pbc_variables.csv",
    show_col_types = FALSE,
    col_types = variables_sheet_cols
)

# Check for any parsing problems
if(nrow(problems(pbc_variables)) != 0) {
    print("Problems with pbc_variables:")
    print(problems(pbc_variables))
}

usethis::use_data(pbc_variables, overwrite = TRUE)

# ------- import the pbc_variable_details.csv file ------
pbc_variable_details <- read_csv("inst/extdata/pbc_variable_details.csv",
    show_col_types = FALSE,
    col_types = variable_details_sheet_cols
)

# Check for any parsing problems
if(nrow(problems(pbc_variable_details)) != 0) {
    print("Problems with pbc_variable_details:")
    print(problems(pbc_variable_details))
}

usethis::use_data(pbc_variable_details, overwrite = TRUE)

# ------ import the tester_variables.csv file --------
tester_variables <- read_csv("inst/extdata/tester_variables.csv",
    show_col_types = FALSE,
    col_types = variables_sheet_cols
)

# Check for any parsing problems
if(nrow(problems(tester_variables)) != 0) {
    print("Problems with tester_variables:")
    print(problems(tester_variables))
}

usethis::use_data(tester_variables, overwrite = TRUE)

# ------- import the tester_variable_details.csv file ------
tester_variable_details <- read_csv("inst/extdata/tester_variable_details.csv",
    show_col_types = FALSE,
    col_types = variable_details_sheet_cols
)

# Check for any parsing problems
if(nrow(problems(tester_variable_details)) != 0) {
    print("Problems with tester_variable_details:")
    print(problems(tester_variable_details))
}

usethis::use_data(tester_variable_details, overwrite = TRUE)