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eHDPrep

Electronic Health Data Preparation (eHDPrep) R package

https://github.com/overton-group/ehdprep

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
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.9%) to scientific vocabulary

Keywords

data-quality health-informatics r semantic-enrichment
Last synced: 6 months ago · JSON representation

Repository

Electronic Health Data Preparation (eHDPrep) R package

Basic Info
  • Host: GitHub
  • Owner: overton-group
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 6.05 MB
Statistics
  • Stars: 8
  • Watchers: 0
  • Forks: 2
  • Open Issues: 0
  • Releases: 2
Topics
data-quality health-informatics r semantic-enrichment
Created over 3 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# eHDPrep


[![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/eHDPrep)](https://cranlogs.r-pkg.org/badges/grand-total/eHDPrep)
[![CRAN status](https://www.r-pkg.org/badges/version/eHDPrep)](https://cran.r-project.org/package=eHDPrep)
[![R-CMD-check](https://github.com/overton-group/eHDPrep/actions/workflows/r.yml/badge.svg)](https://github.com/overton-group/eHDPrep/actions/workflows/r.yml/badge.svg)


The goal of 'eHDPrep' is to provide robust quality control and semantic enrichment tools for preparation of health datasets. High-level and low-level functionality are included for general and specialist 'R' users, respectively. A detailed vignette can be accessed using: `vignette("Introduction_to_eHDPrep", package = "eHDPrep")`.

## Installation

You can install the released version of 'eHDPrep' from [CRAN](https://CRAN.R-project.org) with:

``` r
install.packages("eHDPrep")
```

Or from [GitHub](https://github.com) with:

``` r
install.packages("devtools")
devtools::install_github("overton-group/eHDPrep")
```

## Example

'eHDPrep' can prepare health data for analysis with several approaches. For example, standardising strings representing missing values to `NA`:

```{r example}
library(eHDPrep)
data("example_data")

# original values in t_stage variable
unique(example_data$t_stage)

# predefined value "equivocal" is removed
unique(eHDPrep::strings_to_NA(example_data, strings_to_replace = "equivocal")$t_stage)


```

## System Requirements

Some additional system dependencies are required for 'eHDPrep'. These are detailed below:

### Ubuntu

```{r ubuntu-req}
remotes::system_requirements(".", os = "ubuntu", os_release = "18.04")
remotes::system_requirements(".", os = "ubuntu", os_release = "20.04")
```

### Opensuse

```{r opensuse-req}
remotes::system_requirements(".", os = "opensuse", os_release = "42.3")
```

### CentOS

```{r centos-req}
remotes::system_requirements(".", os = "centos", os_release = "7")
remotes::system_requirements(".", os = "centos", os_release = "8")
```

### Red Hat

```{r redhat-req}
remotes::system_requirements(".", os = "redhat", os_release = "7")
remotes::system_requirements(".", os = "redhat", os_release = "8")
```

Owner

  • Name: overton-group
  • Login: overton-group
  • Kind: organization

GitHub Events

Total
  • Delete event: 1
  • Member event: 1
  • Push event: 1
  • Fork event: 1
Last Year
  • Delete event: 1
  • Member event: 1
  • Push event: 1
  • Fork event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 73
  • Total Committers: 3
  • Avg Commits per committer: 24.333
  • Development Distribution Score (DDS): 0.041
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Tom Toner t****3@q****k 70
DavisVaughan d****s@r****m 2
Hadley Wickham h****m@g****m 1
Committer Domains (Top 20 + Academic)
rstudio.com: 1 qub.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 day
  • Total issue authors: 0
  • Total pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.33
  • Merged pull requests: 3
  • 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
Pull Request Authors
  • tommtoner (1)
  • hadley (1)
  • DavisVaughan (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 172 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
cran.r-project.org: eHDPrep

Quality Control and Semantic Enrichment of Datasets

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 172 Last month
Rankings
Forks count: 17.8%
Stargazers count: 22.5%
Dependent packages count: 29.8%
Average: 34.3%
Dependent repos count: 35.5%
Downloads: 65.8%
Maintainers (1)
I.Overton@qub.ac.uk
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.6.0 depends
  • dplyr >= 1.0.3 imports
  • forcats >= 0.5.0 imports
  • ggplot2 >= 3.3.3 imports
  • igraph >= 1.2.6 imports
  • kableExtra >= 1.3.1 imports
  • knitr >= 1.31 imports
  • magrittr >= 2.0.1 imports
  • pheatmap >= 1.0.12 imports
  • purrr >= 0.3.4 imports
  • quanteda >= 2.1.2 imports
  • readr >= 1.4.0 imports
  • readxl >= 1.3.1 imports
  • rlang >= 0.4.10 imports
  • scales >= 1.1.1 imports
  • stringr >= 1.4.0 imports
  • tibble >= 3.0.5 imports
  • tidygraph >= 1.2.0 imports
  • tidyr >= 1.1.2 imports
  • tm >= 0.7 imports
  • ggraph >= 2.0.5 suggests
  • testthat >= 2.1.0 suggests
.github/workflows/r.yml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r f57f1301a053485946083d7a45022b278929a78a composite