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Cyclops

Cyclops (Cyclic coordinate descent for logistic, Poisson and survival analysis) is an R package for performing large scale regularized regressions.

https://github.com/ohdsi/cyclops

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 16 committers (18.8%) from academic institutions
  • ○
    Institutional organization owner
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  • ○
    Scientific vocabulary similarity
    Low similarity (16.5%) to scientific vocabulary

Keywords

hades

Keywords from Contributors

mesh interactive serializer packaging network-simulation hacking autograding observability embedded optim
Last synced: 9 months ago · JSON representation

Repository

Cyclops (Cyclic coordinate descent for logistic, Poisson and survival analysis) is an R package for performing large scale regularized regressions.

Basic Info
Statistics
  • Stars: 42
  • Watchers: 42
  • Forks: 33
  • Open Issues: 22
  • Releases: 8
Topics
hades
Created over 12 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog

README.md

Cyclops

Build Status codecov.io CRAN_Status_Badge CRAN_Status_Badge

Cyclops is part of the HADES.

Introduction

Cyclops (Cyclic coordinate descent for logistic, Poisson and survival analysis) is an R package for performing large scale regularized regressions.

Features

  • Regression of very large problems: up to millions of observations, millions of variables
  • Supports (conditional) logistic regression, (conditional) Poisson regression, as well as (conditional) Cox regression
  • Uses a sparse representation of the independent variables when appropriate
  • Supports using no prior, a normal prior or a Laplace prior
  • Supports automatic selection of hyperparameter through cross-validation
  • Efficient estimation of confidence intervals for a single variable using a profile-likelihood for that variable

Examples

r library(Cyclops) cyclopsData <- createCyclopsDataFrame(formula) cyclopsFit <- fitCyclopsModel(cyclopsData)

Technology

Cyclops in an R package, with most functionality implemented in C++. Cyclops uses cyclic coordinate descent to optimize the likelihood function, which makes use of the sparse nature of the data.

System Requirements

Requires R (version 3.1.0 or higher). Compilation on Windows requires RTools >= 3.4.

Installation

In R, to install the latest stable version, install from CRAN:

r install.packages("Cyclops")

To install the latest development version, install from GitHub. Note that this will require RTools to be installed.

r install.packages("devtools") devtools::install_github("OHDSI/Cyclops")

User Documentation

Documentation can be found on the package website.

PDF versions of the documentation are also available: * Package manual: Cyclops manual

Support

Contributing

Read here how you can contribute to this package.

License

Cyclops is licensed under Apache License 2.0. Cyclops contains the TinyThread libray.

The TinyThread library is licensed under the zlib/libpng license as described here.

Development

Cyclops is being developed in R Studio.

Acknowledgements

  • This project is supported in part through the National Science Foundation grants IIS 1251151 and DMS 1264153.

Owner

  • Name: Observational Health Data Sciences and Informatics
  • Login: OHDSI
  • Kind: organization

GitHub Events

Total
  • Create event: 7
  • Commit comment event: 1
  • Release event: 3
  • Issues event: 6
  • Watch event: 3
  • Delete event: 4
  • Member event: 1
  • Issue comment event: 7
  • Push event: 68
  • Pull request event: 5
  • Fork event: 2
Last Year
  • Create event: 7
  • Commit comment event: 1
  • Release event: 3
  • Issues event: 6
  • Watch event: 3
  • Delete event: 4
  • Member event: 1
  • Issue comment event: 7
  • Push event: 68
  • Pull request event: 5
  • Fork event: 2

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 1,494
  • Total Committers: 16
  • Avg Commits per committer: 93.375
  • Development Distribution Score (DDS): 0.283
Past Year
  • Commits: 45
  • Committers: 4
  • Avg Commits per committer: 11.25
  • Development Distribution Score (DDS): 0.089
Top Committers
Name Email Commits
Marc Suchard m****d@g****m 1,071
jianxiaoyang y****x@g****u 201
schuemie s****e@o****g 65
yuxitian y****n@g****m 53
Eric Kawaguchi e****i@u****u 46
Trevor Shaddox t****x@u****u 19
Sushil Mittal s****l@g****m 15
Schuemie M****I@i****m 9
Admin_mschuemi A****i@i****m 5
Steve Peak s****e@c****o 3
Yuxi Tian y****n@H****l 2
Chris Knoll c****l@o****g 1
Henrik John l****n@e****l 1
Tomas Kalibera t****a@g****m 1
dependabot[bot] 4****] 1
Coki Ta c****h@g****m 1
Committer Domains (Top 20 + Academic)
its.jnj.com: 2 ucla.edu: 2 ohdsi.org: 2 erasmusmc.nl: 1 codecov.io: 1 g.ucla.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 63
  • Total pull requests: 24
  • Average time to close issues: 7 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 18
  • Total pull request authors: 12
  • Average comments per issue: 2.57
  • Average comments per pull request: 1.5
  • Merged pull requests: 15
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 4
  • Pull requests: 7
  • Average time to close issues: 3 days
  • Average time to close pull requests: 6 days
  • Issue authors: 3
  • Pull request authors: 3
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • schuemie (28)
  • msuchard (15)
  • egillax (3)
  • azimov (3)
  • PRijnbeek (2)
  • huanpipt (1)
  • daniellameeker (1)
  • louisahsmith (1)
  • jepark315 (1)
  • myoung3 (1)
  • aperotte (1)
  • jduke99 (1)
  • chrisknoll (1)
  • jreps (1)
  • warya7 (1)
Pull Request Authors
  • erickawaguchi (6)
  • egillax (4)
  • schuemie (4)
  • ApproximateIdentity (2)
  • dependabot[bot] (2)
  • kalibera (2)
  • lhjohn (1)
  • jianxiaoyang (1)
  • yuxitian (1)
  • stevepeak (1)
  • chrisknoll (1)
  • azimov (1)
Top Labels
Issue Labels
enhancement (15) bug (5)
Pull Request Labels
dependencies (2)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 1,122 last-month
  • Total docker downloads: 43,390
  • Total dependent packages: 2
  • Total dependent repositories: 39
  • Total versions: 23
  • Total maintainers: 1
cran.r-project.org: Cyclops

Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis

  • Versions: 23
  • Dependent Packages: 2
  • Dependent Repositories: 39
  • Downloads: 1,122 Last month
  • Docker Downloads: 43,390
Rankings
Docker downloads count: 0.6%
Forks count: 2.4%
Dependent repos count: 4.2%
Average: 7.1%
Stargazers count: 8.6%
Downloads: 13.0%
Dependent packages count: 13.7%
Maintainers (1)
msuchard@ucla.edu
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.1.0 depends
  • Andromeda >= 0.3.1 imports
  • Matrix * imports
  • Rcpp >= 0.12.12 imports
  • bit64 * imports
  • dplyr * imports
  • methods * imports
  • rlang * imports
  • survival * imports
  • MASS * suggests
  • cmprsk * suggests
  • ggplot2 * suggests
  • gnm * suggests
  • microbenchmark * suggests
  • readr * suggests
  • testthat * suggests
.github/workflows/R_CMD_check_Hades.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/create-release v1 composite
  • actions/download-artifact v2 composite
  • actions/upload-artifact v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
  • r-lib/actions/setup-tinytex v1 composite
.github/workflows/nightly_cleanup_Hades.yml actions
  • c-hive/gha-remove-artifacts v1 composite
docker/r-devel-san/Dockerfile docker
  • rocker/r-devel-san latest build
docker/r-devel-san-clang/Dockerfile docker
  • rocker/r-devel-ubsan-clang latest build
.github/workflows/R_CMD_check_main_weekly.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
  • r-lib/actions/setup-tinytex v2 composite