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Data Specifications

data_specifications.Rmd

Data Specification

The package requires specific input data columns for risk calculation. A demo dataset is provided to demonstrate the expected format:

# Load the demo data
demo_data <- get_demo_data()
head(demo_data)

Required columns include:

  • Pregnancy details (twins, gestational age in weeks)

  • Maternal characteristics (age, height, weight, race)

  • Medical history (chronic conditions, diabetes)

  • Biophysical measurements (MAP, UtPI)

  • Biochemical measurements (PlGF, PAPP-A)

Allowed and Disallowed Strings

Your data set must adhere to the following standards to be processed. While the calculate_pe_risk() function accepts a data frame, it converts each row to a data list using row_to_list(). The row_to_list() function processes and standardizes specific columns. Below are examples of allowed and disallowed values for key columns:

Twins Status (twins)

Allowed:

  • “no” → Singleton pregnancy

  • “monochorionic” → Twins (Monochorionic)

  • “dichorionic” → Twins (Dichorionic)

Disallowed:

  • “singleton” (use “no” instead)

  • “mono” (use “monochorionic” instead)

  • “di” (use “dichorionic” instead)

Smoking Status (smoking)

Allowed:

  • “yes” → Smoker

  • “no” → Non-smoker

Disallowed:

  • “y”, “n” (use “yes” or “no”)

  • “true”, “false” (use “yes” or “no”)

Race (race)

Allowed (numeric codes):

  • 1 → White

  • 2 → Black

  • 3 → South Asian

  • 4 → East Asian

  • 5 → Mixed

Disallowed:

  • “white”, “black” (use numeric codes)

Diabetes Drugs

Allowed:

  • “diet only”

  • “insulin”

  • “insulin+metformin”

  • “metformin”, “Metformin”

Disallowed:

  • “diet”

  • “insulin + metformin” (spaces)

Biomarker Inclusion (include_plgf, include_pappa)

Allowed:

  • “no” → Not included

  • “mom”, “MoM” → MoM (multiples of the median)

  • “raw”, “Raw” → Raw values

Disallowed:

  • “none” (use “no”)

  • “median”, “raw data” (use “mom” or “raw”)

Biomarker Machines (plgf_machine, pappa_machine)

Allowed:

  • “delfia” → Delfia machine

  • “kryptor” → Kryptor machine

  • “roche” → Roche machine

Disallowed:

  • “kr” (use full names)

Validation and Conversion

To verify and convert your dataset to the appropriate format:

# Validate dataset columns
validate_columns(demo_data)

# Convert a data row to a parameter list
data_row <- demo_data[1, ]
params <- row_to_list(data_row)

The row_to_list() function automatically handles allowed strings and issues warnings if invalid values are detected. This ensures that data passed to the FMF preeclampsia calculator adheres to required standards.