Package: AgeTopicModels
Title: Inferring Age-Dependent Disease Topic from Diagnosis Data
Version: 0.3.0
Authors@R: 
    person("Xilin", "Jiang", , "jiangxilin1@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-6773-9182"))
Description: 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>.
License: MIT + file LICENSE
Depends: R (>= 3.5)
Imports: data.table, dplyr, ggplot2, ggrepel, grDevices, gtools,
        magrittr, pROC, reshape2, rlang, stats, stringr, tibble, tidyr,
        utils
Suggests: testthat (>= 3.0.0)
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
RoxygenNote: 7.3.3
NeedsCompilation: no
Packaged: 2026-02-28 12:00:26 UTC; xj262
Author: Xilin Jiang [aut, cre] (ORCID: <https://orcid.org/0000-0001-6773-9182>)
Maintainer: Xilin Jiang <jiangxilin1@gmail.com>
Repository: CRAN
Date/Publication: 2026-02-28 12:20:02 UTC
Built: R 4.4.3; ; 2026-04-15 04:32:34 UTC; windows
