R Observatory: Metrics for jmSurface version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

jmSurface

0.1.0Package record

Semi-Parametric Association Surfaces for Joint Longitudinal-Survival Models

0packages depend

1.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Atanu BhattacharjeeCRAN page ↗

Implements interpretable multi-biomarker fusion in joint longitudinal-survival models via semi-parametric association surfaces. Provides a two-stage estimation framework where Stage 1 fits mixed-effects longitudinal models and extracts Best Linear Unbiased Predictors ('BLUP's), and Stage 2 fits transition-specific penalized Cox models with tensor-product spline surfaces linking latent biomarker summaries to transition hazards. Supports multi-state disease processes with transition-specific surfaces, Restricted Maximum Likelihood ('REML') smoothing parameter selection, effective degrees of freedom ('EDF') diagnostics, dynamic prediction of transition probabilities, and three interpretability visualizations (surface plots, contour heatmaps, marginal effect slices). Methods are described in Bhattacharjee (2025, under review).

Install

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

install.packages("jmSurface", 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-jmsurface

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-jmSurface

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-jmSurface

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

13OK

CRAN check page ↗

Slowest check: 2.2 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 338 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 16includes a package overview page
Examples that run: 33%1 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 25%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 13%

How these are measured

Downloads

1.8K

CRAN downloads in the past year

Rank #19,480 · ~5/day · ~152/mo

Releases R versions

Daily download trend is not available in this view yet.

19630 days

68190 days

1.8K1 year

Compare downloads with other packages →

Also on52 r2u5 autocran

How downloads are counted

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing jmSurface adds no packages beyond those that come with R.

Depends (1)

R >= 4.0.0

Imports (7)

nlmesurvivalmgcvstatsutilsgraphicsgrDevices

LinkingTo (0)

none

Suggests (9)

lme4 ggplot2 viridis plotly shiny shinydashboard dplyr tidyr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Atanu Bhattacharjee

Author, Maintainer since 0.1.0 (2026)

Releases (1)

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
record
2026-02-25 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-02-25
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.0.0
Download size: 517 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("jmSurface")

Format

Bhattacharjee, A. (2026). jmSurface: Semi-Parametric Association Surfaces for Joint Longitudinal-Survival Models (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.jmSurface

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 jmSurface version 0.1.0 [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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