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

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

    -- Nervous System
    MMSE = {name = "Mini-Mental State Examination (MMSE)", system = "Nervous System"},
    DST = {name = "Digital Symbol Test", system = "Nervous System"},
    NM = {name = "Numeric Memory", system = "Nervous System"},
    AM = {name = "Associated Memory", system = "Nervous System"},
    TM = {name = "Topological Memory", system = "Nervous System"},
    STM = {name = "Short-Time Memory", system = "Nervous System"},
    Concentration = {name = "Concentration", system = "Nervous System"},
    IMD = {name = "Intellectuality - Mental Defect", system = "Nervous System"},
    TMT = {name = "Trail Making Test", system = "Nervous System"},

    -- Endocrine Metabolic System
    Glucose = {name = "Glucose", system = "Endocrine Metabolic System"},
    HBA1C = {name = "HBA1C", system = "Endocrine Metabolic System"},
    CPeptide = {name = "C-peptide", system = "Endocrine Metabolic System"},
    Insulin = {name = "Insulin", system = "Endocrine Metabolic System"},
    TG = {name = "Triglyceride", system = "Endocrine Metabolic System"},
    TC = {name = "Total Cholesterol (TC)", system = "Endocrine Metabolic System"},
    HDL = {name = "High-Density Lipoprotein (HDL)", system = "Endocrine Metabolic System"},
    LDL = {name = "Low-Density Lipoprotein (LDL)", system = "Endocrine Metabolic System"},
    ApoA1B = {name = "Apolipoprotein A1 and B", system = "Endocrine Metabolic System"},
    TSH = {name = "Thyroid-Stimulating Hormone (TSH)", system = "Endocrine Metabolic System"},
    Testosterone = {name = "Testosterone", system = "Endocrine Metabolic System"},
    VitaminD = {name = "Vitamin D", system = "Endocrine Metabolic System"},
    Calcium = {name = "Calcium", system = "Endocrine Metabolic System"},
    Potassium = {name = "Potassium", system = "Endocrine Metabolic System"},
    Sodium = {name = "Sodium", system = "Endocrine Metabolic System"},
    InorganicPhosphorus = {name = "Inorganic Phosphorus", system = "Endocrine Metabolic System"},
    Urea = {name = "Urea", system = "Endocrine Metabolic System"},
    Creatinine = {name = "Creatinine", system = "Endocrine Metabolic System"},
    eGFR = {name = "Estimated Glomerular Filtration Rate (eGFR)", system = "Endocrine Metabolic System"},
    UricAcid = {name = "Uric Acid", system = "Endocrine Metabolic System"},
    CystatinC = {name = "Cystatin C", system = "Endocrine Metabolic System"},
    CreatinineClearance = {name = "Creatinine Clearance", system = "Endocrine Metabolic System"},
    UrineSG = {name = "Urine Specific Gravity", system = "Endocrine Metabolic System"},
    UrinepH = {name = "Urine pH", system = "Endocrine Metabolic System"},

    -- Digestive System
    ALT = {name = "Alanine Aminotransferase (ALT)", system = "Digestive System"},
    AST = {name = "Aspartate Aminotransferase (AST)", system = "Digestive System"},
    ALP = {name = "Alkaline Phosphatase (ALP)", system = "Digestive System"},
    TotalProtein = {name = "Total Protein", system = "Digestive System"},
    Albumin = {name = "Albumin", system = "Digestive System"},
    AGRatio = {name = "Albumin/Globulin Ratio (A/G)", system = "Digestive System"},
    TotalBilirubin = {name = "Total Bilirubin", system = "Digestive System"},
    DirectBilirubin = {name = "Direct Bilirubin", system = "Digestive System"},
    Amylase = {name = "Amylase", system = "Digestive System"},
    LDH = {name = "Lactate Dehydrogenase", system = "Digestive System"},
    Alpha2Globulin = {name = "Alpha 2 Globulin", system = "Digestive System"},
    GGT = {name = "Gamma Glutamyl Transpeptidase", system = "Digestive System"},

    -- Hematologic System
    RBC = {name = "Red Blood Cell", system = "Hematologic System"},
    RDW = {name = "Red Blood Cell Volume Distribution Width", system = "Hematologic System"},
    Hematocrit = {name = "Hematocrit", system = "Hematologic System"},
    MCV = {name = "Mean Corpuscular Volume", system = "Hematologic System"},
    MCH = {name = "Mean Corpuscular Hemoglobin", system = "Hematologic System"},
    MCHC = {name = "Mean Corpuscular Hemoglobin Concentration", system = "Hematologic System"},
    Hemoglobin = {name = "Hemoglobin", system = "Hematologic System"},
    WBC = {name = "White Blood Cell", system = "Hematologic System"},
    Granulocytes = {name = "Granulocytes", system = "Hematologic System"},
    Neutrophils = {name = "Neutrophils", system = "Hematologic System"},
    BasophilsEosinophils = {name = "Basophils, Eosinophils", system = "Hematologic System"},
    Lymphocytes = {name = "Lymphocytes", system = "Hematologic System"},
    Monocytes = {name = "Monocytes", system = "Hematologic System"},
    Platelet = {name = "Platelet", system = "Hematologic System"},
    MPV = {name = "Mean Platelet Volume", system = "Hematologic System"},
    PDW = {name = "Platelet Distribution Width", system = "Hematologic System"},
    ESR = {name = "Erythrocyte Sedimentation Rate", system = "Hematologic System"},
    DdimerFibrinogen = {name = "D-dimer, Fibrinogen", system = "Hematologic System"},
    Ferritin = {name = "Ferritin", system = "Hematologic System"},
    Transferrin = {name = "Transferrin", system = "Hematologic System"},

    -- Sensory System
    VisualAcc = {name = "Visual Accommodation", system = "Sensory System"},
    VisualReactTime = {name = "Visual Reaction Time", system = "Sensory System"},
    VisualAcuity = {name = "Visual Acuity", system = "Sensory System"},
    Hearing = {name = "Hearing", system = "Sensory System"},
    Vibrotactile = {name = "Vibrotactile", system = "Sensory System"},
    RetinalPhotos = {name = "Retinal Photos", system = "Sensory System"},

    -- Inflammatory Index
    CRP = {name = "C-Reactive Protein (CRP)", system = "Inflammatory Index"},
    CMVOptDensity = {name = "Cytomegalovirus Optical Density", system = "Inflammatory Index"},
    IL6 = {name = "Interleukin-6", system = "Inflammatory Index"},
    Pselectin = {name = "P-selectin", system = "Inflammatory Index"},

    -- Motion Index
    GripStrength = {name = "Grip Strength", system = "Motion Index"},
    VerticalJump = {name = "Vertical Jump", system = "Motion Index"},
    TUGTest = {name = "Timed Up and Go Test", system = "Motion Index"},
    ChairRiseTime = {name = "Chair Rise Time", system = "Motion Index"},
    PhysicalActivityWeek = {name = "1-Week Physical Activity", system = "Motion Index"},

    -- Body Morphology Index
    WaistCirc = {name = "Waist Circumference (WC)", system = "Body Morphology Index"},
    WaistHipRatio = {name = "Waist-to-Hip Ratio", system = "Body Morphology Index"},
    WaistHeightRatio = {name = "Waist-to-Height Ratio", system = "Body Morphology Index"},
    BMI = {name = "Body Mass Index (BMI)", system = "Body Morphology Index"},
    Weight = {name = "Weight", system = "Body Morphology Index"},
    Height = {name = "Height", system = "Body Morphology Index"},
    BodyFat = {name = "Body Fat", system = "Body Morphology Index"},
    LeanBodyMass = {name = "Lean Body Mass", system = "Body Morphology Index"},
    SoftLeanMass = {name = "Soft Lean Mass", system = "Body Morphology Index"},

    -- Genetic Index
    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 abbr, details in pairs(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[abbr] or ""
            wikitable = wikitable .. ' || ' .. cellValue
        end
		wikitable = wikitable .. '\n'
    end

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

    return wikitable
end

return p