Package index • leo.ukb

Regression Analyses

Unified regression wrappers and formatters for Cox, logistic, and linear models.

leo_cox() leo_cox_format(): Cox regression fitting and formatting helpers

leo_cox_interaction() leo_cox_add_interaction() experimental: Cox interaction analyses

leo_cox_subgroup() leo_cox_subgroup_format() experimental: Cox subgroup analysis

leo_cox_mediation() leo_cox_mediation_plot() experimental: Cox mediation analysis

leo_logistic() leo_logistic_format() experimental: Logistic regression fitting and formatting helpers

leo_linear() leo_linear_format() experimental: Linear regression fitting and formatting helpers

Analysis Tools

leo_impute_na(): Basic imputation function for missing values

leo_quantile(): Bin a continuous variable by quantiles

leo_heterogeneity_p(): Calculate P-value for Heterogeneity from Subgroup Summary Statistics

Clinical Variables

combine_two_eye(): Combine Measurements from Two Eyes

convert_iop(): Convert IOP Measurements

convert_to_logMAR(): Convert Visual Acuity Measurements to logMAR

get_max_date(): Find the max date in given date columns

leo_age(): Recode age (years) https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=21003

leo_gender(): Recode sex (Male/Female) https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=31

leo_ethnicity(): Recode ethnicity to White vs non-White https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=21000

leo_ethnicity_finer(): Recode ethnicity into finer categories (top-level 1–6) https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=21000

leo_BMI(): Recode BMI into categories (Underweight/Normal weight/Overweight/Obese) https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=21001

leo_tdi(): Recode Townsend deprivation index (TDI) https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=22189

leo_education(): Recode UKB qualifications into 3 categories

leo_smoking_status(): Recode smoking status (Never/Previous/Current) https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=20116

leo_drinking_status(): Recode drinking status (Never/Previous/Current) https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=20117

leo_drinking_consumption(): Recode drinking consumption

leo_diet_us(): healthy diet score by U.S. Dietary Guidelines

leo_sleep_score(): Calculate Sleep Score and Pattern

leo_physical_activity(): Calculate Physical Activity Indicator

leo_household_income(): Recode household income (UKB 738) into readable categories

leo_household_income_2(): Recode household income (UKB 738) into readable categories (2 categories)

leo_career(): Recode employment status

leo_hba1c(): Recode HbA1c (IFCC, mmol/mol) https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=30750

leo_hba1c_percent(): Convert HbA1c from IFCC (mmol/mol) to NGSP (%) https://ngsp.org/ifcc.asp

leo_eGFR_v2009() experimental: Calculate eGFR by CKD-EPI 2009 (untested)

leo_eGFR_v2021() experimental: Calculate eGFR by CKD-EPI 2021 (untested)

leo_eGDR(): Calculate Estimated Glucose Disposal Rate (eGDR)

leo_LGI(): Calculate Low-Grade Inflammation Score (LGI / INFLA-score)

leo_TyG(): Calculate Triglyceride-Glucose Index (TyG)

leo_new_clinical_indicators(): Generate New Clinical Indicators

Diagnosis and RAP

dx_login(): Log in to DNAnexus

dx_extract(): Extract UKB data using DNAnexus Table Exporter

dx_status(): Check DNAnexus Job Status & Dashboard

dx_run(): Robust dx runner

Diagnosis Processing

diagnosis_process_fo(): Process first occurrence (FO) data in UKB —-

diagnosis_process_icd(): Process UKB ICD data for survival analysis

diagnosis_process_icd_multi(): Process multiple ICD definitions in bulk

HLA Typing

ukb_hla_clean(): Clean HLA carrier output to a wide format

ukb_hla_header(): Read UK Biobank HLA v2 header (ukb_hla_v2.txt)

ukb_hla_specify(): Specify carrier status for given HLA allele(s) in UK Biobank

ukb_hla_typing(): HLA Genotyping in UKB

DAG Tools

leo_dag(): Create a leo_dag object

leo_dag_write(): Write outputs for a leo_dag object

leo_dag_write(<leo_dag>): Write a leo_dag object to disk

Table 1

leo.table1.help(): Table 1 Help

leo.table1.step1(): Step 1: Check Normality for Variables

leo.table1.step2(): Step 2: Generate Table 1 for Cohort Study

leo.table1.save(): Save Table 1 to Word or CSV