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lgpr

R-package for interpretable nonparametric modeling of longitudinal data using additive Gaussian processes. Contains functionality for inferring covariate effects and assessing covariate relevances. Various models can be specified using a convenient formula syntax.

https://github.com/jtimonen/lgpr

Science Score: 13.0%

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    Low similarity (15.9%) to scientific vocabulary

Keywords

bayesian-inference gaussian-processes longitudinal-data r-packages stan
Last synced: 6 months ago · JSON representation

Repository

R-package for interpretable nonparametric modeling of longitudinal data using additive Gaussian processes. Contains functionality for inferring covariate effects and assessing covariate relevances. Various models can be specified using a convenient formula syntax.

Basic Info
Statistics
  • Stars: 25
  • Watchers: 4
  • Forks: 1
  • Open Issues: 5
  • Releases: 22
Topics
bayesian-inference gaussian-processes longitudinal-data r-packages stan
Created over 6 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing

README.md

lgpr

travis coverage CRAN_Status_Badge metacran downloads license

R-package for interpretable nonparametric modeling of longitudinal data using additive Gaussian processes. Contains functionality for inferring covariate effects and assessing covariate relevances. Various models can be specified using a convenient formula syntax.

[!NOTE] Using this package is computationally viable if your data set has maybe less than 300 observations. But the much more scalable lgpr2 package has been released! It is much faster but unfortunately doesn't have all the special modeling features included in this package.

Getting started

See overview, tutorials, vignettes and documentation at https://jtimonen.github.io/lgpr-usage/index.html.

Requirements

  • The package should work on all major operating systems.
  • R 3.4 or later is required, R 4.2 or later is recommended

Installing from CRAN

  • The latest released version that is available from CRAN can be installed simply via r install.packages("lgpr") Installing from CRAN is probably the easiest option since they might have binaries for your system (so no need to build the package from source yourself).

Installing from source

  • The latest released version (which might not be in CRAN yet) can be installed via r install.packages('devtools') # if you don't have devtools already devtools::install_github('jtimonen/lgpr', build_vignettes = TRUE)

  • The latest development version can be installed via r devtools::install_github('jtimonen/lgpr', ref = "develop") Github installations are source installations (they require a C++ compiler).

  • If you have trouble installing the dependency rstan, see these instructions

  • Installing from source requires that you have your toolchain setup properly. See the instructions for:

Using R < 4.2

If you are using R version 4.1 or earlier, you can get an error cc1plus.exe: out of memory allocating 65536 bytes make: *** [C:/PROGRA~1/R/R-40~1.2/etc/i386/Makeconf:227: stanExports_lgp_latent.o] Error 1 because both 64-bit and 32-bit versions of the package are getting installed. To disable this and resolve error, ugrade to latest R or install the version that has Biarch: false by

r devtools::install_github('jtimonen/lgpr', ref = "no-biarch")

Real data and reproducing the experiments

For code to reproduce the experiments of our manuscript see https://github.com/jtimonen/lgpr-usage. Preprocessed longitudinal proteomics data is also provided there. See also the built-in read_proteomics_data() function.

Owner

  • Name: Juho Timonen
  • Login: jtimonen
  • Kind: user
  • Company: Aalto University

A doctoral candidate at Aalto University, Department of Computer Science

GitHub Events

Total
  • Issues event: 1
Last Year
  • Issues event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 503
  • Total Committers: 3
  • Avg Commits per committer: 167.667
  • Development Distribution Score (DDS): 0.435
Past Year
  • Commits: 19
  • Committers: 2
  • Avg Commits per committer: 9.5
  • Development Distribution Score (DDS): 0.474
Top Committers
Name Email Commits
Juho Timonen j****n@a****i 284
jtimonen j****n@i****i 210
Andrew Johnson a****n@a****m 9
Committer Domains (Top 20 + Academic)
arjohnsonau.com: 1 iki.fi: 1 aalto.fi: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 24
  • Total pull requests: 7
  • Average time to close issues: 2 months
  • Average time to close pull requests: 1 day
  • Total issue authors: 10
  • Total pull request authors: 2
  • Average comments per issue: 2.46
  • Average comments per pull request: 2.71
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jtimonen (12)
  • slhogle (3)
  • barracuda156 (2)
  • teunbrand (1)
  • StaffanBetner (1)
  • YuHsiangLo (1)
  • copernican (1)
  • mike-lawrence (1)
  • spinkney (1)
  • Selbosh (1)
Pull Request Authors
  • jtimonen (5)
  • andrjohns (2)
Top Labels
Issue Labels
enhancement (4) documentation (3) good first issue (1) bug (1) installation problem (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 231 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
cran.r-project.org: lgpr

Longitudinal Gaussian Process Regression

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 231 Last month
Rankings
Stargazers count: 11.3%
Forks count: 17.8%
Dependent packages count: 29.8%
Average: 33.8%
Dependent repos count: 35.5%
Downloads: 74.6%
Maintainers (1)
juho.timonen@iki.fi
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.4.0 depends
  • methods * depends
  • MASS >= 7.3 imports
  • RCurl >= 1.98 imports
  • Rcpp >= 0.12.0 imports
  • RcppParallel >= 5.0.2 imports
  • bayesplot >= 1.7.0 imports
  • ggplot2 >= 3.1.0 imports
  • gridExtra >= 0.3.0 imports
  • rstan >= 2.21.2 imports
  • rstantools >= 2.1.1 imports
  • stats >= 3.4 imports
  • covr * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/R-CMD-check.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