R Observatory: Metrics for MAP version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MAP

1.0.0Package record

Multimodal Automated Phenotyping

1packages depend

4.6Kdownloads / year

85.3%test coverage

11/13flavors OK

Overview

About

Maintained by Thomas CharlonCRAN page ↗GitHub ↗Website ↗Issues ↗

Electronic health records (EHR) linked with biorepositories are a powerful platform for translational studies. A major bottleneck exists in the ability to phenotype patients accurately and efficiently. Towards that end, we developed an automated high-throughput phenotyping method integrating International Classification of Diseases (ICD) codes and narrative data extracted using natural language processing (NLP). Specifically, our proposed method, called MAP (Map Automated Phenotyping algorithm), fits an ensemble of latent mixture models on aggregated ICD and NLP counts along with healthcare utilization. The MAP algorithm yields a predicted probability of phenotype for each patient and a threshold for classifying subjects with phenotype yes/no (See Katherine P. Liao, et al. (2019) doi:10.1093/jamia/ocz066.).

Install

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

install.packages("MAP", 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/MAP")

Development version from celehs/MAP. 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-map

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-MAP

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-MAP

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2NOTE11OK

Check messages

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘compound.Rd’ ‘exposition.Rd’ ‘pipe.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 2.0 min · r-oldrel-macos-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 1 NOTE2026-07-11
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMEYes · 710 wordsVignettesYes · 2 · dynamicNEWSNoCitation fileNoWebsiteYes · pkgdown

Help pages: 5
Examples that run: 100%2 run in a plain check
Exported functions with examples: 25%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 20%

Vignettes (2)

MAP: Multimodal Automated Phenotyping HTML
Simulated Example HTML

How these are measured

Downloads

4.6K

CRAN downloads in the past year

Rank #9,600 · ~13/day · ~384/mo

Releases R versions

Daily download trend is not available in this view yet.

36630 days

1K90 days

4.6K1 year

Compare downloads with other packages →

Also on70 r2u3 autocran

How downloads are counted

Repository

celehs/map ↗Account: celehs

7Stars

3Forks

0Open issues

0Open PRs

0Releases

27Commits

4Commit identities

27 commits · Last activity 2025-01-08 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-06-24 · 72026-07-07 · 7

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/celehs/map on 2026-10-21.

Docs source (2)

pkgdown

GitHub Pages site last deployed 2025-01-08

pkgdown site last built 2025-01-08

Reproducibility and dev environment (2)

MakefileDockerfile

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing MAP adds 3 packages (1 with compiled code, 1.4 MB of source tarballs). Heaviest: flexmix 1.1 MB, magrittr 275 KB, modeltools 15 KB.

Depends (3)

R >= 3.4.0flexmixMatrix

Imports (1)

magrittr

LinkingTo (0)

none

Suggests (4)

knitr pROC rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

sureLDA

How these are counted

Code & Tests

Datasets

People & History

People (8)

Thomas Charlon

Author, Maintainer since 1.0.0 (2024) · added in 1.0.0

CELEHS

Author · added in 1.0.0

<https://celehs.hms.harvard.edu>

PARSE Health

Author · added in 1.0.0

<https://parse-health.org>

Tianxi Cai

Author

Chuan Hong

Author · added in 1.0.0

Katherine Liao

Author · added in 1.0.0

Jiehuan Sun

Author

Sheng Yu

Author

Previously maintained by Jiehuan Sun (0.1.3).

Listed in earlier versions (1)

Katherine P. Liao

no longer listed · 0.1.3

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0.0Latest
record
2024-12-02 · current release · diff ↗ ·
added 3 exports
%$%, %<>%, %>%
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
0.1.3
record
2019-04-01
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-04-01
Total releases: 2 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.4.0
Bundled data: 58 KB / 1 file
Download size: 76 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MAP")

Format

Charlon, T., CELEHS, PARSE Health, Cai, T., Hong, C., Liao, K., Sun, J., & Yu, S. (2024). MAP: Multimodal Automated Phenotyping (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.MAP

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for MAP version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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