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hdme

hdme: High-Dimensional Regression with Measurement Error - Published in JOSS (2019)

https://github.com/osorensen/hdme

Science Score: 95.0%

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
    Found 4 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ✓
    Committers with academic emails
    2 of 4 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software
Last synced: 6 months ago · JSON representation

Repository

R-package containing penalized regression methods for High-Dimensional Measurement Error problems (errors-in-variables)

Basic Info
  • Host: GitHub
  • Owner: osorensen
  • License: gpl-3.0
  • Language: R
  • Default Branch: master
  • Size: 472 KB
Statistics
  • Stars: 9
  • Watchers: 1
  • Forks: 3
  • Open Issues: 0
  • Releases: 12
Created over 9 years ago · Last pushed almost 3 years ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
bibliography: ./inst/REFERENCES.bib
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```

# hdme

[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/hdme)](https://cran.r-project.org/package=hdme)
[![codecov](https://codecov.io/gh/osorensen/hdme/branch/master/graph/badge.svg)](https://app.codecov.io/gh/osorensen/hdme)
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01404/status.svg)](https://doi.org/10.21105/joss.01404)
[![R-CMD-check](https://github.com/osorensen/hdme/workflows/R-CMD-check/badge.svg)](https://github.com/osorensen/hdme/actions)



The goal of hdme is to provide penalized regression methods for High-Dimensional Measurement Error problems (errors-in-variables).

## Installation

Install `hdme` from CRAN using.
```{r, eval=FALSE}
install.packages("hdme")
```

You can install the latest development version from github with:

```{r gh-installation, eval = FALSE}
# install.packages("devtools")
devtools::install_github("osorensen/hdme", build_vignettes = TRUE)
```


### Dependency on Rglpk

`hdme` uses the [Rglpk package](https://cran.r-project.org/package=Rglpk), which requires the GLPK library package to be installed. On some platforms this requires a manual installation. 

On Debian/Ubuntu, you might use:

```{sh, eval=FALSE}
sudo apt-get install libglpk-dev
```

On macOS, you might use:

```{sh, eval=FALSE}
brew install glpk
```


## Methods
hdme provides implementations of the following algorithms:

The methods implemented in the package include

* Corrected Lasso for Linear Models (@loh2012)
* Corrected Lasso for Generalized Linear Models (@sorensen2015)
* Matrix Uncertainty Selector for Linear Models (@rosenbaum2010)
* Matrix Uncertainty Selector for Generalized Linear Models (@sorensen2018)
* Matrix Uncertainty Lasso for Generalized Linear Models (@sorensen2018)
* Generalized Dantzig Selector (@james2009)

## Contributions

Contributions to `hdme` are very welcome. If you have a question or suspect you have found a bug, please [open an Issue](https://github.com/osorensen/hdme/issues). Code contribution by pull requests are also appreciated.

## Citation

If using hdme in a scientific publication, please cite the following paper:

```{r}
citation("hdme")
```


## References

Owner

  • Name: Øystein Sørensen
  • Login: osorensen
  • Kind: user
  • Location: Oslo, Norway
  • Company: @LCBC-UiO

Associate Professor in Statistics, Center for Lifespan Changes in Brain and Cognition, University of Oslo.

JOSS Publication

hdme: High-Dimensional Regression with Measurement Error
Published
May 19, 2019
DOI
Volume 4, Issue 37, Page 1404
Authors
Øystein Sørensen ORCID
Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo
Editor
Charlotte Soneson ORCID
Tags
regression variable selection measurement error
View PDF Review Thread Software Archive

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 197
  • Total Committers: 4
  • Avg Commits per committer: 49.25
  • Development Distribution Score (DDS): 0.421
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Øystein Sørensen o****n@h****m 114
Øystein Sørensen o****s@m****o 79
Øystein Sørensen o****o@n****o 3
Øystein Sørensen o****s@u****o 1
Committer Domains (Top 20 + Academic)
uio.no: 1 nextbridge.no: 1 medisin.uio.no: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 22
  • Total pull requests: 28
  • Average time to close issues: 9 months
  • Average time to close pull requests: 35 minutes
  • Total issue authors: 6
  • Total pull request authors: 1
  • Average comments per issue: 1.77
  • Average comments per pull request: 0.0
  • Merged pull requests: 28
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
  • osorensen (17)
  • dirmeier (1)
  • michaelpollmann (1)
  • arcruz0 (1)
  • davidaknowles (1)
  • YuxiaoRuoyao (1)
Pull Request Authors
  • osorensen (28)
Top Labels
Issue Labels
bug (4) enhancement (3)
Pull Request Labels
enhancement (2) bug (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 331 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 14
  • Total maintainers: 1
cran.r-project.org: hdme

High-Dimensional Regression with Measurement Error

  • Versions: 14
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 331 Last month
Rankings
Forks count: 14.9%
Stargazers count: 19.8%
Downloads: 24.4%
Average: 24.9%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Maintainers (1)
oystein.sorensen.1985@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • Rcpp >= 0.12.15 imports
  • Rdpack * imports
  • Rglpk >= 0.6 imports
  • ggplot2 >= 2.2.1 imports
  • glmnet >= 3.0.0 imports
  • stats * imports
  • covr * suggests
  • dplyr * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • tidyr * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite