Skip to contents

Example Dataset: SampleVariableTypes

Source: R/SampleVariableTypes.R
SampleVariableTypes.Rd

An example of a modified VariableTypes file to be used to Revalue SampleData.

Usage

SampleVariableTypes

Format

A data frame with 11 columns and 138 rows:

Variable

Variable name, as listed in column name of data file.

Label

Variable label, as desired in tables and figures.

Type

How the variable should be treated, e.g., continuous (double) or categorical.

Category

Optional for future filtering: the category type this variable belongs to.

Recode

0 or 1, indicating whether or not this variable should be recoded.

Code

If the variable should be recoded, how it should be recoded.

Notes

Optional notes for the variable.

Exclude

Optional for filtering: whether or not this variable should be excluded.

Subcategory

Optional additional categories for the variable.

Include

Optional for filtering: whether or not this variable should be included.

MissingCode

Optional: if a value should be considered NA.

Source

Exported from CreateVariableTypes(SampleData, "SampleData.csv") and modified in Excel.

Details

This is what an edited codebook looks like in practice. It began as the output of CreateVariableTypesTemplate() run on SampleData, and was then filled in by hand: labels written for the columns that needed them, sex marked for recoding with its Code mapping, a missing code recorded where one applies, and Category / Subcategory / Include used to group variables for later selection.

Most rows are left mostly blank, and that is normal. Of 138 variables only a handful carry a recode or a missing code; the rest simply need a readable label. A codebook is a place to record the exceptions, not a form to complete.

Passing it with SampleData to RevalueData() is the first step of nearly every example in this package.

See also

SampleData for the data it describes, CreateVariableTypesTemplate() to generate one for your own data, and RevalueData() to apply it.

Examples

data(SampleVariableTypes)

dim(SampleVariableTypes)
#> [1] 138  11
table(SampleVariableTypes$Type)
#> 
#> Categorical      Double 
#>           8         130 

# \donttest{
# The whole codebook: one row per variable in SampleData
htmltools::browsable(htmltools::HTML(as.character(
  FreezeTableHeader(
    SampleVariableTypes,
    height = "420px", full_width = TRUE
  )
)))

 Variable 
    Label 
    Type 
    Category 
    Recode 
    Code 
    Notes 
    Exclude 
    Subcategory 
    Include 
    MissingCode 
  
 Diagnosis 
    Diagnosis 
    Categorical 
    NA 
    NA 
    NA 
    NA 
    NA 
     
    1 
    NA 
  
 age 
    Age 
    Double 
    NA 
    NA 
    NA 
    NA 
    NA 
     
    1 
    999 
  
 sex 
    Sex 
    Categorical 
    NA 
    yes 
    0 = Female; 1 = Male 
    NA 
    NA 
     
    1 
    NA 
  
 Group 
    Group 
    Categorical 
    NA 
    NA 
    NA 
    NA 
    NA 
     
    NA 
    NA 
  
 Race 
    Race 
    Categorical 
    NA 
    NA 
    NA 
    NA 
    NA 
     
    NA 
    NA 
  
 Marital 
    Marital Status 
    Categorical 
    NA 
    NA 
    NA 
    NA 
    NA 
     
    NA 
    NA 
  
 Height 
    Height 
    Double 
    NA 
    NA 
    NA 
    NA 
    NA 
     
    NA 
    NA 
  
 Income 
    Income 
    Double 
    NA 
    NA 
    NA 
    NA 
    NA 
     
    NA 
    NA 
  
 Smokes 
    Smokes 
    Categorical 
    NA 
    NA 
    NA 
    NA 
    NA 
     
    NA 
    NA 
  
 Smoker 
    Smoker 
    Categorical 
    NA 
    NA 
    NA 
    NA 
    NA 
     
    NA 
    NA 
  
 Genotype 
    Genotype 
    Categorical 
    NA 
    NA 
    NA 
    NA 
    NA 
     
    1 
    NA 
  
 ACE_CD143_Angiotensin_Converti 
    Angiotensin-converting enzyme 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Proteolytic enzyme 
    NA 
    NA 
  
 ACTH_Adrenocorticotropic_Hormon 
    Adrenocorticotropic hormone 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    NA 
    NA 
  
 AXL 
    AXL receptor tyrosine kinase 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Receptor 
    NA 
    NA 
  
 Adiponectin 
    Adiponectin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    NA 
    NA 
  
 Alpha_1_Antichymotrypsin 
    Alpha-1-antichymotrypsin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protease inhibitor 
    NA 
    NA 
  
 Alpha_1_Antitrypsin 
    Alpha-1-antitrypsin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protease inhibitor 
    NA 
    NA 
  
 Alpha_1_Microglobulin 
    Alpha-1-microglobulin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    1 
    NA 
  
 Alpha_2_Macroglobulin 
    Alpha-2-macroglobulin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protease inhibitor 
    NA 
    NA 
  
 Angiopoietin_2_ANG_2 
    Angiopoietin-2 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Growth factor 
    1 
    NA 
  
 Angiotensinogen 
    Angiotensinogen 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    NA 
    NA 
  
 Apolipoprotein_A_IV 
    Apolipoprotein A-IV 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Lipoprotein 
    NA 
    NA 
  
 Apolipoprotein_A1 
    Apolipoprotein A-1 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Lipoprotein 
    1 
    NA 
  
 Apolipoprotein_A2 
    Apolipoprotein A-2 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Lipoprotein 
    NA 
    NA 
  
 Apolipoprotein_B 
    Apolipoprotein B 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Lipoprotein 
    NA 
    NA 
  
 Apolipoprotein_CI 
    Apolipoprotein C-I 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Lipoprotein 
    NA 
    NA 
  
 Apolipoprotein_CIII 
    Apolipoprotein C-III 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Lipoprotein 
    1 
    NA 
  
 Apolipoprotein_D 
    Apolipoprotein D 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Lipoprotein 
    NA 
    NA 
  
 Apolipoprotein_E 
    Apolipoprotein E 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Lipoprotein 
    NA 
    NA 
  
 Apolipoprotein_H 
    Apolipoprotein H 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Lipoprotein 
    NA 
    NA 
  
 B_Lymphocyte_Chemoattractant_BL 
    B-lymphocyte chemoattractant 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    NA 
    NA 
  
 BMP_6 
    Bone morphogenetic protein 6 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Growth factor 
    1 
    NA 
  
 Beta_2_Microglobulin 
    Beta-2-microglobulin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 Betacellulin 
    Betacellulin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Growth factor 
    NA 
    NA 
  
 C_Reactive_Protein 
    C-reactive protein 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Inflammatory marker 
    NA 
    NA 
  
 CD40 
    CD40 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Receptor 
    1 
    NA 
  
 CD5L 
    CD5L 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Receptor 
    NA 
    NA 
  
 Calbindin 
    Calbindin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 Calcitonin 
    Calcitonin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    NA 
    NA 
  
 CgA 
    Chromogranin A 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    1 
    NA 
  
 Clusterin_Apo_J 
    Clusterin (ApoJ) 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 Complement_3 
    Complement component 3 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Immune protein 
    NA 
    NA 
  
 Complement_Factor_H 
    Complement factor H 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Immune protein 
    NA 
    NA 
  
 Connective_Tissue_Growth_Factor 
    Connective tissue growth factor 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Growth factor 
    1 
    NA 
  
 Cortisol 
    Cortisol 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    NA 
    NA 
  
 Creatine_Kinase_MB 
    Creatine kinase-MB 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Enzyme 
    NA 
    NA 
  
 Cystatin_C 
    Cystatin C 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protease inhibitor 
    NA 
    NA 
  
 EGF_R 
    Epidermal growth factor receptor 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Receptor 
    NA 
    NA 
  
 EN_RAGE 
    EN-RAGE (extracellular newly identified RAGE-binding protein) 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 ENA_78 
    ENA-78 (epithelial-derived neutrophil-activating protein 78) 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    NA 
    NA 
  
 Eotaxin_3 
    Eotaxin-3 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    NA 
    NA 
  
 FAS 
    Fas (tumor necrosis factor receptor superfamily member 6) 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Receptor 
    NA 
    NA 
  
 FSH_Follicle_Stimulation_Hormon 
    Follicle-stimulating hormone 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    NA 
    NA 
  
 Fas_Ligand 
    Fas ligand 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 Fatty_Acid_Binding_Protein 
    Fatty acid-binding protein 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 Ferritin 
    Ferritin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 Fetuin_A 
    Fetuin-A 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 Fibrinogen 
    Fibrinogen 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Coagulation factor 
    NA 
    NA 
  
 GRO_alpha 
    Growth-regulated alpha protein 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    NA 
    NA 
  
 Gamma_Interferon_induced_Monokin 
    Gamma interferon-induced monokine 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    NA 
    NA 
  
 Glutathione_S_Transferase_alpha 
    Glutathione S-transferase alpha 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Enzyme 
    NA 
    NA 
  
 HB_EGF 
    Heparin-binding epidermal growth factor 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Growth factor 
    NA 
    NA 
  
 HCC_4 
    HCC-4 (hemofiltrate CC chemokine-4) 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    NA 
    NA 
  
 Hepatocyte_Growth_Factor_HGF 
    Hepatocyte growth factor 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Growth factor 
    NA 
    NA 
  
 I_309 
    I-309 (TCA-3) 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    NA 
    NA 
  
 ICAM_1 
    Intercellular adhesion molecule 1 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Adhesion molecule 
    NA 
    NA 
  
 IGF_BP_2 
    Insulin-like growth factor-binding protein 2 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Binding protein 
    NA 
    NA 
  
 IL_11 
    Interleukin 11 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Cytokine 
    NA 
    NA 
  
 IL_13 
    Interleukin 13 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Cytokine 
    NA 
    NA 
  
 IL_16 
    Interleukin 16 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Cytokine 
    NA 
    NA 
  
 IL_17E 
    Interleukin 17E 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Cytokine 
    1 
    NA 
  
 IL_1alpha 
    Interleukin 1 alpha 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Cytokine 
    NA 
    NA 
  
 IL_3 
    Interleukin 3 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Cytokine 
    NA 
    NA 
  
 IL_4 
    Interleukin 4 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Cytokine 
    NA 
    NA 
  
 IL_5 
    Interleukin 5 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Cytokine 
    NA 
    NA 
  
 IL_6 
    Interleukin 6 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Cytokine 
    NA 
    NA 
  
 IL_6_Receptor 
    Interleukin 6 receptor 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Receptor 
    NA 
    NA 
  
 IL_7 
    Interleukin 7 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Cytokine 
    NA 
    NA 
  
 IL_8 
    Interleukin 8 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Cytokine 
    NA 
    NA 
  
 IP_10_Inducible_Protein_10 
    Inducible protein 10 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    NA 
    NA 
  
 IgA 
    Immunoglobulin A 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Antibody 
    NA 
    NA 
  
 Insulin 
    Insulin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    1 
    NA 
  
 Kidney_Injury_Molecule_1_KIM_1 
    Kidney injury molecule 1 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Biomarker 
    1 
    NA 
  
 LOX_1 
    Lectin-like oxidized LDL receptor 1 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Receptor 
    NA 
    NA 
  
 Leptin 
    Leptin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    NA 
    NA 
  
 Lipoprotein_a 
    Lipoprotein(a) 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Lipoprotein 
    NA 
    NA 
  
 MCP_1 
    Monocyte chemoattractant protein 1 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    1 
    NA 
  
 MCP_2 
    Monocyte chemoattractant protein 2 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    NA 
    NA 
  
 MIF 
    Macrophage migration inhibitory factor 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Cytokine 
    NA 
    NA 
  
 MIP_1alpha 
    Macrophage inflammatory protein 1 alpha 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    NA 
    NA 
  
 MIP_1beta 
    Macrophage inflammatory protein 1 beta 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    NA 
    NA 
  
 MMP_2 
    Matrix metalloproteinase 2 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Enzyme 
    NA 
    NA 
  
 MMP_3 
    Matrix metalloproteinase 3 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Enzyme 
    NA 
    NA 
  
 MMP10 
    Matrix metalloproteinase 10 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Enzyme 
    NA 
    NA 
  
 MMP7 
    Matrix metalloproteinase 7 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Enzyme 
    NA 
    NA 
  
 Myoglobin 
    Myoglobin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 NT_proBNP 
    N-terminal pro b-type natriuretic peptide 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    NA 
    NA 
  
 NrCAM 
    Neuron-glia cell adhesion molecule 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Adhesion molecule 
    NA 
    NA 
  
 Osteopontin 
    Osteopontin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    1 
    NA 
  
 PAI_1 
    Plasminogen activator inhibitor 1 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Inhibitor 
    NA 
    NA 
  
 PAPP_A 
    Pregnancy-associated plasma protein A 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 PLGF 
    Placental growth factor 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Growth factor 
    NA 
    NA 
  
 PYY 
    Peptide YY 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    NA 
    NA 
  
 Pancreatic_polypeptide 
    Pancreatic polypeptide 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    NA 
    NA 
  
 Prolactin 
    Prolactin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    NA 
    NA 
  
 Prostatic_Acid_Phosphatase 
    Prostatic acid phosphatase 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Enzyme 
    NA 
    NA 
  
 Protein_S 
    Protein S 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Coagulation factor 
    NA 
    NA 
  
 Pulmonary_and_Activation_Regulat 
    Pulmonary and activation-regulated chemokine 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    NA 
    NA 
  
 RANTES 
    Regulated on activation, normal T cell expressed and secreted 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    NA 
    NA 
  
 Resistin 
    Resistin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    NA 
    NA 
  
 S100b 
    S100 calcium-binding protein B 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 SGOT 
    Serum glutamic-oxaloacetic transaminase 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Enzyme 
    NA 
    NA 
  
 SHBG 
    Sex hormone-binding globulin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Binding protein 
    NA 
    NA 
  
 SOD 
    Superoxide dismutase 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Enzyme 
    NA 
    NA 
  
 Serum_Amyloid_P 
    Serum amyloid P component 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 Sortilin 
    Sortilin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Receptor 
    NA 
    NA 
  
 Stem_Cell_Factor 
    Stem cell factor 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Growth factor 
    NA 
    NA 
  
 TGF_alpha 
    Transforming growth factor alpha 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Growth factor 
    NA 
    NA 
  
 TIMP_1 
    Tissue inhibitor of metalloproteinases 1 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Inhibitor 
    NA 
    NA 
  
 TNF_RII 
    Tumor necrosis factor receptor II 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Receptor 
    NA 
    NA 
  
 TRAIL_R3 
    TNF-related apoptosis-inducing ligand receptor 3 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Receptor 
    NA 
    NA 
  
 TTR_prealbumin 
    Transthyretin (prealbumin) 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 Tamm_Horsfall_Protein_THP 
    Tamm-Horsfall protein 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 Thrombomodulin 
    Thrombomodulin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Receptor 
    NA 
    NA 
  
 Thrombopoietin 
    Thrombopoietin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    1 
    NA 
  
 Thymus_Expressed_Chemokine_TECK 
    Thymus-expressed chemokine (TECK) 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Chemokine 
    NA 
    NA 
  
 Thyroid_Stimulating_Hormone 
    Thyroid-stimulating hormone 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Hormone 
    NA 
    NA 
  
 Thyroxine_Binding_Globulin 
    Thyroxine-binding globulin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Binding protein 
    NA 
    NA 
  
 Tissue_Factor 
    Tissue factor 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Coagulation factor 
    NA 
    NA 
  
 Transferrin 
    Transferrin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Transport protein 
    NA 
    NA 
  
 Trefoil_Factor_3_TFF3 
    Trefoil factor 3 (TFF3) 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 VCAM_1 
    Vascular cell adhesion molecule 1 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Adhesion molecule 
    NA 
    NA 
  
 VEGF 
    Vascular endothelial growth factor 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Growth factor 
    NA 
    NA 
  
 Vitronectin 
    Vitronectin 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 von_Willebrand_Factor 
    von Willebrand factor 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Coagulation factor 
    1 
    NA 
  
 tau 
    Tau protein 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    1 
    NA 
  
 p_tau 
    Phosphorylated tau protein 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    NA 
    NA 
  
 Ab_42 
    Amyloid beta 42 
    Double 
    Lab Measures 
    NA 
    NA 
    NA 
    NA 
    Protein 
    1 
    NA 
  

# Only the rows carrying an instruction
rows_WithRules <- !is.na(SampleVariableTypes$Code) |
  (!is.na(SampleVariableTypes$MissingCode) & SampleVariableTypes$MissingCode != "")

htmltools::browsable(htmltools::HTML(as.character(
  FreezeTableHeader(
    SampleVariableTypes[
      rows_WithRules,
      c("Variable", "Label", "Type", "Recode", "Code", "MissingCode")
    ],
    full_width = TRUE
  )
)))

   
    Variable 
    Label 
    Type 
    Recode 
    Code 
    MissingCode 
  
 2 
    age 
    Age 
    Double 
    NA 
    NA 
    999 
  
 3 
    sex 
    Sex 
    Categorical 
    yes 
    0 = Female; 1 = Male 
    NA 
  

# The grouping columns define variable sets
vars_Labs <- SampleVariableTypes$Variable[
  !is.na(SampleVariableTypes$Category) &
    SampleVariableTypes$Category == "Lab Measures"
]
length(vars_Labs)
#> [1] 127
utils::head(vars_Labs)
#> [1] "ACE_CD143_Angiotensin_Converti"  "ACTH_Adrenocorticotropic_Hormon"
#> [3] "AXL"                             "Adiponectin"                    
#> [5] "Alpha_1_Antichymotrypsin"        "Alpha_1_Antitrypsin"            
# }