R Observatory: Metrics for spect version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

spect

1.0

Survival Prediction Ensemble Classification Tool

0packages depend

1.8Kdownloads / year

90.6%test coverage

13/13checks pass

Overview

About

Maintained by Stephen AbramsFirst published 2025-04-081 releasesCRAN page ↗GitHub ↗

A tool for survival analysis using a discrete time approach with ensemble binary classification. 'spect' provides a simple interface consistent with commonly used R data analysis packages, such as 'caret', a variety of parameter options to help facilitate search automation, a high degree of transparency to the end-user - all intermediate data sets and parameters are made available for further analysis and useful, out-of-the-box visualizations of model performance. Methods for transforming survival data into discrete-time are adapted from the 'autosurv' package by Suresh et al., (2022) doi:10.1186/s12874-022-01679-6.

Install

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

install.packages("spect", 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("dawdawdo/spect")

Development version from dawdawdo/spect. 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-spect

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-spect

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-spect

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

Health

CRAN checks

13OK

Slowest check: 6.0 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.75

90.6%

Coverage · measured lines

100%

Documentation · exports

10

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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

Show 2 earlier snapshots

ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 34 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

1.8K

CRAN downloads in the past year

Rank #21,814 · ~5/day · ~152/mo

Releases R versions

Daily download trend is not available in this view yet.

12430 days

50290 days

1.8K1 year

Compare downloads with other packages →

Also on103 r2u7 autocran

Repository

GitHub ↗ dawdawdo/spect

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2025-04-13

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/dawdawdo/spect on 2026-08-16.

Continuous integration (1)

GitHub Actions

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (3)

R >= 4.0futile.logger dplyr

Imports (8)

doParallel ggplot2 survminer riskRegression caret caretEnsemblesurvivalrlang

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown randomForest kernlab testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Stephen Abrams

Author, Maintainer

Authors (1)

Stephen Abrams

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-04-08
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0
Download size: 113 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("spect")

Format

Abrams, S. (2025). spect: Survival Prediction Ensemble Classification Tool (Version 1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.spect

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 spect version 1.0 [Data set]. HJJB, LLC. Data release v2026-08-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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