/kunu-kutu-data

Data Mining and Analysis for clinical measurements

Primary LanguageRMIT LicenseMIT

Data Wrangling over Excel test Reports

Chemical biomarkers measurements over Ecuadorian Conocoto pacients have been taken since 2018 in a set of Excel files including:

  • Glucose [mg/dL]
  • Sodium
  • Potassium
  • Triglycerides [mg/dL]
  • Cholesterol [mg/dL]
  • Urea [mg/dL]
  • Uric Acid [mg/dL]
  • Transaminases [U/L]
  • Amylases [U/L]
  • Lypases [U/L]
  • Hormones (PSA, \beta HCG, Troponines, D-Dimer, T3, T4, TSH, etc) and more.
  • Toxicological tests [Yes / No]
  • Gasometries Biological measurements also includes:
  • Haematological biometries
  • Elemental and microscopic examination of urine
  • Coproparasitarium

Here, there is a set of scripts for extraction of this valuable information and its conversion from a print-ready state in Excel Spreadsheets to a fully-relational format.

EXAMPLE

These scripts converts a set of excel tables from this:
NOMBRE: RUMI ÑAHUI FECHA 14/04/2024
Muestra: SANGRE HOSPITALIZACION
QUIMICA SANGUINEA RESULTADO VALORES DE REFERENCIA
GLUCOSA BASAL mg/dL 74 - 115 mg/dL
UREA mg/dL 15 - 45 mg/dL
CREATININA 0.74 mg/dL H 0,6-1,1 M 0,5-0,9 mg/dL
ACIDO URICO mg/dL 2,5 - 7 mg/dL
COLESTEROL mg/dL HASTA 220 mg/dL
TRIGLICERIDOS mg/dL HASTA 140 mg/dL
HDL COLESTEROL mg/dL H35-55 M45-65 mg/dL
LDL COLESTEROL mg/dL HASTA 170 mg/dL
TGO U/L HASTA 38 U/L
TGP 24.7 U/L HASTA 40 U/L
FOSFATASA ALCALINA U/L H 53-128 M 42-141 U/L
BILIRUBINA TOTAL mg/dL HASTA 1.00 mg/dL
BILIRUBINA DIRECTA mg/dL HASTA 0.25 mg/dL
BILIRUBINA INDIRECTA mg/dL HASTA 0.75 mg/dL
AMILASA U/L 28-100 U/L
LIPASA U/L 60 U/L
GLUCOSA POSPRANDIAL mg/dL 55 - 115 mg/dL
VALIDADO PHD. GUIVER MAC

Onto this:

Nombre Fecha Tipo Prueba Medicion Tech
RUMI ÑAHUI 14/04/2024 HOSPITALIZACION CREATININA 0.74 PHD. GUIVER MAC
RUMI ÑAHUI 14/04/2024 HOSPITALIZACION TGP 24.7 PHD. GUIVER MAC

HOW TO USE

Load every script onto your R environment with:

source("kunukutu.R")

Which loads all specific manipulation scripts. Then choose what kind of data you need, as "quimica", "emo", "hormones",and run:

extract_quimica("excel_file.xlsx")