short_icd10

A lookup table mapping ICD-10 codes to concise human-readable labels.

datasets

We propose an age-dependent topic modelling (ATM) model,
providing a low-rank representation of longitudinal records of
hundreds of distinct diseases in large electronic health record data sets. The model
assigns to each individual topic weights for several disease topics;
each disease topic reflects a set of diseases that tend to co-occur as
a function of age, quantified by age-dependent topic loadings for each
disease. The model assumes that for each disease diagnosis, a topic is
sampled based on the individual’s topic weights (which sum to 1 across
topics, for a given individual), and a disease is sampled based on the
individual’s age and the age-dependent topic loadings (which sum to 1
across diseases, for a given topic at a given age). The model
generalises the Latent Dirichlet Allocation (LDA) model by allowing
topic loadings for each topic to vary with age.
References: Jiang (2023) <doi:10.1038/s41588-023-01522-8>.

Xilin Jiang

AgeTopicModels

Inferring Age-Dependent Disease Topic from Diagnosis Data

short_icd10 function

A data frame/tibble. Common columns include:<dl>
<dt>ICD10</dt>
<dd>ICD-10 code (character).</dd><dt>parent_phecode</dt>
<dd>phecode of parent node (character).</dd><dt>Excl..Phecodes</dt>
<dd>ancestor PheCode range (character).</dd><dt>Excl..Phenotypes</dt>
<dd>ancestor PheCode name (character).</dd><dt>occ</dt>
<dd>number of distinct patient in UKB</dd>
</dl>

Format

Short labels (at most first for letters/digits) for ICD-10 codes — short_icd10

A data frame/tibble. Common columns include:<dl>
<dt>ICD10</dt>
<dd>ICD-10 code (character).</dd>

<dt>parent_phecode</dt>
<dd>phecode of parent node (character).</dd>

<dt>Excl..Phecodes</dt>
<dd>ancestor PheCode range (character).</dd>

<dt>Excl..Phenotypes</dt>
<dd>ancestor PheCode name (character).</dd>

<dt>occ</dt>
<dd>number of distinct patient in UKB</dd>


</dl>

short_icd10: Short labels (at most first for letters/digits) for ICD-10 codes

Description

Usage

Arguments

Format

Examples