sureLDA

0.1.0-1

A Novel Multi-Disease Automated Phenotyping Method for the EHR

0packages depend

2.2Kdownloads / year

–test coverage

10/13checks pass

Overview

About

Maintained by Yuri AhujaFirst published 2020-11-101 releasesCRAN page ↗GitHub ↗

A statistical learning method to simultaneously predict a range of target phenotypes using codified and natural language processing (NLP)-derived Electronic Health Record (EHR) data. See Ahuja et al (2020) JAMIA doi:10.1093/jamia/ocaa079 for details.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("celehs/sureLDA")

Development version from celehs/sureLDA. Installs pak first if it is not already available.

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-surelda

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-sureLDA

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# 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-sureLDA

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

Health

CRAN checks

3NOTE10OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 7.6 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 151 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.2K

CRAN downloads in the past year

Rank #18,738 · ~6/day · ~180/mo

Releases R versions

Daily download trend is not available in this view yet.

16030 days

58590 days

2.2K1 year

Compare downloads with other packages →

Also on375 r2u1 autocran

Repository

GitHub ↗ celehs/surelda

4Stars

2Forks

1Open issues

1Open PRs

0Releases

85Commits

5Contributors

85 commits · Last activity 2025-04-12 · 0% stars, 30d

Stars over time

2023-01-11 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/celehs/surelda on 2026-08-02.

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.0Matrix

Imports (6)

pROC glmnet MAP Rcpp foreach doParallel

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Yuri Ahuja

Author, Maintainer

Authors (3)

Yuri Ahuja

Author, Maintainer

Tianxi Cai

Author

PARSE LTD

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0-1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2020-11-10
Total releases: 1 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0
Bundled data: 16 KB / 1 file
Download size: 34 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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