FastJM

1.7.0

Semi-Parametric Joint Modeling of Longitudinal and Survival Data

2packages depend

4.9Kdownloads / year

6.7%test coverage

12/13checks pass

Overview

About

Maintained by Shanpeng LiFirst published 2022-01-0617 releasesCRAN page ↗

Implements scalable joint models for large-scale competing risks time-to-event data with one or multiple longitudinal biomarkers using the efficient algorithms developed by Li et al. (2022) doi:10.1155/2022/1362913 and doi:10.48550/arXiv.2506.12741. The time-to-event process is modeled using a cause-specific Cox proportional hazards model with time-fixed covariates, while longitudinal biomarkers are modeled using linear mixed-effects models. The association between the longitudinal and survival processes is captured through shared random effects. The package enables analysis of large-scale biomedical data to model biomarker trajectories, estimate their effects on event risks, and perform dynamic prediction of future events based on patients' longitudinal histories. Functions for simulating survival and longitudinal data for multiple biomarkers are included, along with built-in example datasets. The package also supports modeling a single biomarker with heterogeneous within-subject variability via functionality adapted from the 'JMH' package.

Install

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

install.packages("FastJM", 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-fastjm

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-FastJM

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-FastJM

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

Health

CRAN checks

1NOTE12OK

Failing flavors

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

Slowest check: 27.6 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.00

6.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 3 earlier snapshots

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 · 679 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 36%
Documented parameters: 97%
Return-value docs: 100%
References docs: 0%

Downloads

4.9K

CRAN downloads in the past year

Rank #5,417 · ~13/day · ~409/mo

Releases R versions

Daily download trend is not available in this view yet.

38930 days

1.6K90 days

4.9K1 year

Compare downloads with other packages →

Also on519 r2u

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (7)

R >= 3.5.0survivalutilsMASSstatmod magrittrstats

Imports (12)

Rcpp dplyrnlmecaret pec future future.apply tidycmprsk rlang ggsurvfit ggplot2 ggpubr

LinkingTo (2)

Rcpp RcppEigen

Suggests (3)

testthat spelling rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

JMbdirect jmBIG

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Shanpeng Li

Author, Maintainer

Authors (1)

Shanpeng Li

Author, Maintainer

Contributors (3)

Gang Li

Contributor

Ace Mejia-Sanchez

Contributor · added in 1.7.0

Emily Ouyang

Contributor · added in 1.5.3

Listed in earlier versions (4)

Ning Li

no longer listed · 1.0.0 to 1.5.3

Hong Wang

no longer listed · 1.0.0 to 1.5.3

Hua Zhou

no longer listed · 1.0.0 to 1.5.3

Jin Zhou

no longer listed · 1.0.0 to 1.5.3

Package Timeline

17 releases. Pick two to compare their code metrics. R releases are shown for context.

1.7.0Latest
2026-07-22 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.6.0
2026-03-28 · diff ↗
1.5.3
2025-11-08 · diff ↗
1.5.2
2025-10-18 · diff ↗
1.5.1
2025-07-24 · diff ↗
1.5.0
2025-06-22 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.4.2
2024-03-01 · diff ↗
1.4.1
2024-01-09 · diff ↗
1.4.0
2023-10-10 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.3.1
2023-03-26 · diff ↗
1.2.0
2022-08-06 · diff ↗
1.1.3
2022-06-01 · diff ↗

Show 7 earlier events

R
R 4.2.0 released · 2022-04-22
1.1.2
2022-02-16 · diff ↗
1.1.1
2022-02-14 · diff ↗
1.1.0
2022-02-08 · diff ↗
1.0.1
2022-01-12 · diff ↗
1.0.0
2022-01-06
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-01-06
Total releases: 17 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Bundled data: 181 KB / 6 files
Download size: 327 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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