HES_age_example         Example HES diagnosis ages
HES_icd10_example       Example HES ICD-10 diagnoses
SNOMED_ICD10CM          SNOMED <-> ICD-10(-CM) mapping (excerpt)
UKB_349_disease         List of 349 UK Biobank diseases (example)
UKB_HES_10topics        Example topic model output (10 topics, UKB HES)
age_imputation          imputing missing age if you can't find some of
                        them The function does two stage imputation: i.
                        if the individual has other age label - use the
                        mean, min, or max of other age labels for the
                        missing ones. ii. if the individual has no age
                        label - use the mean, min, max for all the
                        diagnosis codes iii. if there is no age info
                        available for any of this code, we will impute
                        it as the mean of all age codes in the data
disease_info_phecode_icd10
                        Disease information linking PheCodes and ICD-10
diseasematrix2longdata
                        Disease matrix reformatting for ATM
icd2phecode             Mapping the disease code from icd10 to phecode
loading2weights         Mapping individuals to fixed topic loadings.
longdata2diseasematrix
                        Title
phecode_icd10           ICD-10 <-> PheCode mapping
phecode_icd10cm         ICD-10-CM <-> PheCode mapping
plot_age_topics         Title plot the topic loadings across age.
plot_lfa_topics         Title plot topic loadings for LFA.
prediction_OR           Title Compute prediction odds ratio for a
                        testing data set using pre-training ATM topic
                        loading. Note only diseases listed in the
                        ds_list will be used. The prediction odds ratio
                        is the odds predicted by ATM versus a naive
                        prediction using disease probability.
short_icd10             Short labels (at most first for letters/digits)
                        for ICD-10 codes
short_icd10cm           Short labels (at most first for letters/digits)
                        for ICD-10-CM codes
simulate_genetic_disease_from_topic
                        Simulate genetic-disease-topic structure (step
                        2)
simulate_topics         Simulate genetic-disease-topic structure (step
                        1)
wrapper_ATM             Run ATM on diagnosis data.
wrapper_LFA             Run LFA on diagnosis data.
