AgeTopicModels

0.3.0

Inferring Age-Dependent Disease Topic from Diagnosis Data

0packages depend

2.4Kdownloads / year

53.7%test coverage

13/13checks pass

Overview

About

Maintained by Xilin JiangFirst published 2025-10-212 releasesCRAN page ↗

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.

Install

R (CRAN)Ubuntu (r2u)openSUSE (OBS)

install.packages("AgeTopicModels", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-agetopicmodels

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-AgeTopicModels

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 10.7 min · r-devel-linux-x86_64-fedora-clang

Check history

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

2.4K

CRAN downloads in the past year

Rank #13,399 · ~6/day · ~197/mo

AgeTopicModels Releases R versions

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26330 days

78690 days

2.4K1 year

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Also on104 r2u96 autocran

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (15)

data.table dplyr ggplot2 ggrepelgrDevicesgtools magrittr pROC reshape2 rlangstatsstringr tibble tidyrutils

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Xilin Jiang

Author, Maintainer

Authors (1)

Xilin Jiang

Author, Maintainer

Package Timeline

2 releases. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.3.0Latest
2026-02-28 · current release · diff ↗
0.1.0
2025-10-21
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-10-21
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 4.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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