Module:BiologicalAgeBiomarkers

Output the biological age biomarkers table.

Data is stored in Module:BiologicalAgeBiomarkers/Data

---

local p = {}

-- Define biomarkers with their long form and system
local biomarkers = {
   -- Cardiovascular System
	{key = "SBP", name = "Systolic Blood Pressure (SBP)", system = "Cardiovascular System"},
	{key = "DBP", name = "Diastolic Blood Pressure (DBP)", system = "Cardiovascular System"},
	{key = "PP", name = "Pulse Pressure", system = "Cardiovascular System"},
	{key = "MAP", name = "Mean Arterial Pressure", system = "Cardiovascular System"},
	{key = "Pulse", name = "Pulse", system = "Cardiovascular System"},
	{key = "PWV", name = "Pulse Wave Velocity", system = "Cardiovascular System"},
	{key = "HR", name = "Heart Rate", system = "Cardiovascular System"},
	{key = "IMT", name = "Intima-Media Thickness", system = "Cardiovascular System"},
	{key = "MinIMT", name = "Minimum Intima-Media Thickness", system = "Cardiovascular System"},
	{key = "EDV", name = "End Diastolic Velocity", system = "Cardiovascular System"},
	{key = "MVEAP", name = "Mitral Valve E/A Peak", system = "Cardiovascular System"},
	{key = "MVEL_MVES_MVEA", name = "MVEL, MVES, MVEA", system = "Cardiovascular System"},
	{key = "AI", name = "Atherosclerosis Index", system = "Cardiovascular System"},
	{key = "NTproBNP", name = "NT-proBNP", system = "Cardiovascular System"},
	{key = "CTnI", name = "Cardiac Troponin I", system = "Cardiovascular System"},
	{key = "CPK", name = "Creatine Phosphokinase", system = "Cardiovascular System"},
	{key = "Homocysteine", name = "Homocysteine", system = "Cardiovascular System"},

	-- Respiratory System
	{key = "FVC", name = "Forced Vital Capacity (FVC)", system = "Respiratory System"},
	{key = "FEV1", name = "Forced Expiratory Volume in 1 Second (FEV1)", system = "Respiratory System"},
	{key = "VC", name = "Vital Capacity", system = "Respiratory System"},
	{key = "MMFR", name = "Maximal Midexpiratory Flow Rate 75/25", system = "Respiratory System"},
	{key = "VO2Max", name = "VO2 Max", system = "Respiratory System"},
	{key = "CR", name = "Chest Radiography", system = "Respiratory System"},

	-- Nervous System
	{key = "MMSE", name = "Mini-Mental State Examination (MMSE)", system = "Nervous System"},
	{key = "DST", name = "Digital Symbol Test", system = "Nervous System"},
	{key = "NM", name = "Numeric Memory", system = "Nervous System"},
	{key = "AM", name = "Associated Memory", system = "Nervous System"},
	{key = "TM", name = "Topological Memory", system = "Nervous System"},
	{key = "STM", name = "Short-Time Memory", system = "Nervous System"},
	{key = "Concentration", name = "Concentration", system = "Nervous System"},
	{key = "IMD", name = "Intellectuality - Mental Defect", system = "Nervous System"},
	{key = "TMT", name = "Trail Making Test", system = "Nervous System"},
	
	-- Endocrine Metabolic System
	{key = "Glucose", name = "Glucose", system = "Endocrine Metabolic System"},
	{key = "HBA1C", name = "HBA1C", system = "Endocrine Metabolic System"},
	{key = "CPeptide", name = "C-peptide", system = "Endocrine Metabolic System"},
	{key = "Insulin", name = "Insulin", system = "Endocrine Metabolic System"},
	{key = "TG", name = "Triglyceride", system = "Endocrine Metabolic System"},
	{key = "TC", name = "Total Cholesterol (TC)", system = "Endocrine Metabolic System"},
	{key = "HDL", name = "High-Density Lipoprotein (HDL)", system = "Endocrine Metabolic System"},
	{key = "LDL", name = "Low-Density Lipoprotein (LDL)", system = "Endocrine Metabolic System"},
	{key = "ApoA1B", name = "Apolipoprotein A1 and B", system = "Endocrine Metabolic System"},
	{key = "TSH", name = "Thyroid-Stimulating Hormone (TSH)", system = "Endocrine Metabolic System"},
	{key = "Testosterone", name = "Testosterone", system = "Endocrine Metabolic System"},
	{key = "VitaminD", name = "Vitamin D", system = "Endocrine Metabolic System"},
	{key = "Calcium", name = "Calcium", system = "Endocrine Metabolic System"},
	{key = "Potassium", name = "Potassium", system = "Endocrine Metabolic System"},
	{key = "Sodium", name = "Sodium", system = "Endocrine Metabolic System"},
	{key = "InorganicPhosphorus", name = "Inorganic Phosphorus", system = "Endocrine Metabolic System"},
	{key = "Urea", name = "Urea", system = "Endocrine Metabolic System"},
	{key = "Creatinine", name = "Creatinine", system = "Endocrine Metabolic System"},
	{key = "eGFR", name = "Estimated Glomerular Filtration Rate (eGFR)", system = "Endocrine Metabolic System"},
	{key = "UricAcid", name = "Uric Acid", system = "Endocrine Metabolic System"},
	{key = "CystatinC", name = "Cystatin C", system = "Endocrine Metabolic System"},
	{key = "CreatinineClearance", name = "Creatinine Clearance", system = "Endocrine Metabolic System"},
	{key = "UrineSG", name = "Urine Specific Gravity", system = "Endocrine Metabolic System"},
	{key = "UrinepH", name = "Urine pH", system = "Endocrine Metabolic System"},
	
	-- Digestive System
	{key = "ALT", name = "Alanine Aminotransferase (ALT)", system = "Digestive System"},
	{key = "AST", name = "Aspartate Aminotransferase (AST)", system = "Digestive System"},
	{key = "ALP", name = "Alkaline Phosphatase (ALP)", system = "Digestive System"},
	{key = "TotalProtein", name = "Total Protein", system = "Digestive System"},
	{key = "Albumin", name = "Albumin", system = "Digestive System"},
	{key = "AGRatio", name = "Albumin/Globulin Ratio (A/G)", system = "Digestive System"},
	{key = "TotalBilirubin", name = "Total Bilirubin", system = "Digestive System"},
	{key = "DirectBilirubin", name = "Direct Bilirubin", system = "Digestive System"},
	{key = "Amylase", name = "Amylase", system = "Digestive System"},
	{key = "LDH", name = "Lactate Dehydrogenase", system = "Digestive System"},
	{key = "Alpha2Globulin", name = "Alpha 2 Globulin", system = "Digestive System"},
	{key = "GGT", name = "Gamma Glutamyl Transpeptidase", system = "Digestive System"},
	
	-- Hematologic System
	{key = "RBC", name = "Red Blood Cell", system = "Hematologic System"},
	{key = "RDW", name = "Red Blood Cell Volume Distribution Width", system = "Hematologic System"},
	{key = "Hematocrit", name = "Hematocrit", system = "Hematologic System"},
	{key = "MCV", name = "Mean Corpuscular Volume", system = "Hematologic System"},
	{key = "MCH", name = "Mean Corpuscular Hemoglobin", system = "Hematologic System"},
	{key = "MCHC", name = "Mean Corpuscular Hemoglobin Concentration", system = "Hematologic System"},
	{key = "Hemoglobin", name = "Hemoglobin", system = "Hematologic System"},
	{key = "WBC", name = "White Blood Cell", system = "Hematologic System"},
	{key = "Granulocytes", name = "Granulocytes", system = "Hematologic System"},
	{key = "Neutrophils", name = "Neutrophils", system = "Hematologic System"},
	{key = "BasophilsEosinophils", name = "Basophils, Eosinophils", system = "Hematologic System"},
	{key = "Lymphocytes", name = "Lymphocytes", system = "Hematologic System"},
	{key = "Monocytes", name = "Monocytes", system = "Hematologic System"},
	{key = "Platelet", name = "Platelet", system = "Hematologic System"},
	{key = "MPV", name = "Mean Platelet Volume", system = "Hematologic System"},
	{key = "PDW", name = "Platelet Distribution Width", system = "Hematologic System"},
	{key = "ESR", name = "Erythrocyte Sedimentation Rate", system = "Hematologic System"},
	{key = "DdimerFibrinogen", name = "D-dimer, Fibrinogen", system = "Hematologic System"},
	{key = "Ferritin", name = "Ferritin", system = "Hematologic System"},
	{key = "Transferrin", name = "Transferrin", system = "Hematologic System"},
	
	-- Sensory System
	{key = "VisualAcc", name = "Visual Accommodation", system = "Sensory System"},
	{key = "VisualReactTime", name = "Visual Reaction Time", system = "Sensory System"},
	{key = "VisualAcuity", name = "Visual Acuity", system = "Sensory System"},
	{key = "Hearing", name = "Hearing", system = "Sensory System"},
	{key = "Vibrotactile", name = "Vibrotactile", system = "Sensory System"},
	{key = "RetinalPhotos", name = "Retinal Photos", system = "Sensory System"},
	
	-- Inflammatory Index
	{key = "CRP", name = "C-Reactive Protein (CRP)", system = "Inflammatory Index"},
	{key = "CMVOptDensity", name = "Cytomegalovirus Optical Density", system = "Inflammatory Index"},
	{key = "IL6", name = "Interleukin-6", system = "Inflammatory Index"},
	{key = "Pselectin", name = "P-selectin", system = "Inflammatory Index"},
	
	-- Motion Index
	{key = "GripStrength", name = "Grip Strength", system = "Motion Index"},
	{key = "VerticalJump", name = "Vertical Jump", system = "Motion Index"},
	{key = "TUGTest", name = "Timed Up and Go Test", system = "Motion Index"},
	{key = "ChairRiseTime", name = "Chair Rise Time", system = "Motion Index"},
	{key = "PhysicalActivityWeek", name = "1-Week Physical Activity", system = "Motion Index"},
	
	-- Body Morphology Index
	{key = "WaistCirc", name = "Waist Circumference (WC)", system = "Body Morphology Index"},
	{key = "WaistHipRatio", name = "Waist-to-Hip Ratio", system = "Body Morphology Index"},
	{key = "WaistHeightRatio", name = "Waist-to-Height Ratio", system = "Body Morphology Index"},
	{key = "BMI", name = "Body Mass Index (BMI)", system = "Body Morphology Index"},
	{key = "Weight", name = "Weight", system = "Body Morphology Index"},
	{key = "Height", name = "Height", system = "Body Morphology Index"},
	{key = "BodyFat", name = "Body Fat", system = "Body Morphology Index"},
	{key = "LeanBodyMass", name = "Lean Body Mass", system = "Body Morphology Index"},
	{key = "SoftLeanMass", name = "Soft Lean Mass", system = "Body Morphology Index"},
	
	-- Genetic Index
	{key = "TelomereLength", name = "Terminal Telomere Restriction Fragment", system = "Genetic Index"}
}

local rows = {
	method = "Biological Age Estimation Method",
	year = "Year"
}

-- Incorporate data directly into studies identified by PMID
local studies = {
    PMID12345 = {
    	pmid = "12345",
        name = "Study1",
        method = "MLR",
        year = "1995",
        data = {
            SBP = "x",
            DBP = "x",
            HDL = "x",
            LDL = "x"
        }
    },
    PMID67890 = {
        pmid = "67890",
        method = "MLR",
        year = "1995",
        data = {
            SBP = "x",
            DBP = "x",
            HDL = "x",
            LDL = "x"
        }
    },
    PMID13579 = {
        pmid = "13579",
        method = "MLR",
        year = "1995",
        data = {
            SBP = "x",
            DBP = "x",
            HDL = "x",
            LDL = "x"
        }
    }
}

function p.createCrossTable()
    -- Start of the wiki table
    local wikitable = '{| class="wikitable"\n!'

    -- Column headers: Biomarker and System
    wikitable = wikitable .. ' System !! Biomarker'
    for _, study in pairs(studies) do
        wikitable = wikitable .. ' !! '  .. study.pmid
	end
	wikitable = wikitable .. '\n'

    for key, name in pairs(rows) do
        wikitable = wikitable .. '|-\n'
        wikitable = wikitable .. '| ' .. name .. ' || ' .. ''
        for _, study in pairs(studies) do
            local cellValue = study[key] or ""
			wikitable = wikitable .. ' || ' .. cellValue
        end
		wikitable = wikitable .. '\n'
	end

    -- Generate rows for each biomarker
    for i, details in ipairs(biomarkers) do
        wikitable = wikitable .. '|-\n'
        wikitable = wikitable .. '| '  .. details.system .. ' || ' .. details.name
        for _, study in pairs(studies) do
            -- Retrieve data value for the current cell, using the nested structure
            local cellValue = study.data[details.key] or ""
            wikitable = wikitable .. ' || ' .. cellValue
        end
		wikitable = wikitable .. '\n'
    end

    -- End of the table
    wikitable = wikitable .. '\n|}'

    return wikitable
end

return p