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dataspacer

R Interface to the CAVD DataSpace

https://github.com/ropensci/dataspacer

Science Score: 26.0%

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
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    Institutional organization owner
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  • ○
    Scientific vocabulary similarity
    Low similarity (19.9%) to scientific vocabulary

Keywords

cavd-dataspace

Keywords from Contributors

reproducibility rselenium selenium webdriver webdriver-manager
Last synced: 9 months ago · JSON representation

Repository

R Interface to the CAVD DataSpace

Basic Info
Statistics
  • Stars: 5
  • Watchers: 5
  • Forks: 3
  • Open Issues: 2
  • Releases: 6
Topics
cavd-dataspace
Created about 9 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing Codemeta

README.Rmd 

---
output: github_document
---



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

# DataSpaceR 


[![R build status](https://github.com/ropensci/DataSpaceR/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/DataSpaceR/actions)
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[![](https://badges.ropensci.org/261_status.svg)](https://github.com/ropensci/software-review/issues/261)




`DataSpaceR` is an R interface to [the CAVD DataSpace](https://dataspace.cavd.org), a data sharing and discovery tool that facilitates exploration of HIV immunological data from pre-clinical and clinical HIV vaccine studies.

The package is intended for use by immunologists, bioinformaticians, and statisticians in HIV vaccine research, or anyone interested in the analysis of HIV immunological data across assays, studies, and time.

This package simplifies access to the database by taking advantage of the standardization of the database to hide all the [Rlabkey](https://cran.r-project.org/package=Rlabkey) specific code away from the user, and it allows the users to access the study-specific datasets via [an object-oriented paradigm](https://cran.r-project.org/package=R6/readme/README.html).


## Examples & Documentation

For more detailed examples and detailed documentation, see [the introductory vignette](https://docs.ropensci.org/DataSpaceR/articles/DataSpaceR.html) and [the pkgdown site](https://docs.ropensci.org/DataSpaceR/).


## Installation

Install from CRAN:

```{r, eval=FALSE}
install.packages("DataSpaceR")
```

You can install the latest development version from [GitHub](https://github.com/ropensci/DataSpaceR) with [devtools](https://cran.r-project.org/package=devtools):

```{r, eval=FALSE}
# install.packages("devtools")
devtools::install_github("ropensci/DataSpaceR")
```


## Register and set DataSpace credential

The database is accessed with the user's credentials. A netrc file storing 
login and password information is ***required***.

1. [Create an account](https://dataspace.cavd.org/) and read the terms of use
1. On your R console, create a netrc file using a function from `DataSpaceR`:

```{r, eval=FALSE}
library(DataSpaceR)
writeNetrc(
  login = "yourEmail@address.com", 
  password = "yourSecretPassword",
  netrcFile = "/your/home/directory/.netrc" # use getNetrcPath() to get the default path 
)
```

This will create a netrc file in your home directory.

***Alternatively***, you can manually create a netrc file in the computer running R.

* On Windows, this file should be named `_netrc`
* On UNIX, it should be named `.netrc`
* The file should be located in the user's home directory, and the permissions on the file should be unreadable for everybody except the owner
* To determine home directory, run `Sys.getenv("HOME")` in R

The following three lines must be included in the `.netrc` or `_netrc` file either separated by white space (spaces, tabs, or newlines) or commas. Multiple such blocks can exist in one file.

```
machine dataspace.cavd.org
login myuser@domain.com
password supersecretpassword
```

See [here](https://www.labkey.org/wiki/home/Documentation/page.view?name=netrc) for more information about `netrc`.


## Usage

The general idea is that the user:

1. creates an instance of `DataSpaceConnection` class via `connectDS`
1. browses available studies and groups in the instance via `availableStudies` and `availableGroups`
1. creates a connection to a specific study via `getStudy` or a group via `getGroup`
1. retrieves datasets by name via `getDataset`


### for example:

```{r}
library(DataSpaceR)

con <- connectDS()
con
```

`connectDS()` will create a connection to DataSpace.


### available studies can be listed by `availableStudies` field

```{r}
knitr::kable(head(con$availableStudies))
```


### available groups can be listed by `availableGroups` field

```{r}
knitr::kable(con$availableGroups)
```

***Note***: A group is a curated collection of participants from filtering of treatments, products, studies, or species, and it is created in [the DataSpace App](https://dataspace.cavd.org/cds/CAVD/app.view).

Check out [the reference page](https://docs.ropensci.org/DataSpaceR/reference/DataSpaceConnection.html) of `DataSpaceConnection` for all available fields and methods.


### create an instance of `cvd408`

```{r}
cvd408 <- con$getStudy("cvd408")
cvd408
class(cvd408)
```


### available datasets can be listed by `availableDatasets` field

```{r}
knitr::kable(cvd408$availableDatasets)
```

which will print names of available datasets.


### Neutralizing Antibody dataset (`NAb`) can be retrieved by:

```{r}
NAb <- cvd408$getDataset("NAb")
dim(NAb)
colnames(NAb)
```

Check out [the reference page](https://docs.ropensci.org/DataSpaceR/reference/DataSpaceStudy.html) of `DataSpaceStudy` for all available fields and methods.

***Note***: The package uses a [R6](https://cran.r-project.org/package=R6) class to represent the connection to a study and get around some of R's copy-on-change behavior.


## Meta

* Please [report any issues or bugs](https://github.com/ropensci/DataSpaceR/issues).
* License: GPL-3
* Get citation information for `DataSpaceR` in R doing `citation(package = 'DataSpaceR')`
* Please note that this project is released with a [Contributor Code of Conduct](https://github.com/ropensci/DataSpaceR/blob/main/CONDUCT.md). By participating in this project you agree to abide by its terms.

[![ropensci_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)

Owner

  • Name: rOpenSci
  • Login: ropensci
  • Kind: organization
  • Email: info@ropensci.org
  • Location: Berkeley, CA

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GitHub Events

Total
  • Release event: 1
  • Delete event: 3
  • Member event: 1
  • Issue comment event: 1
  • Push event: 8
  • Pull request review comment event: 1
  • Pull request review event: 4
  • Pull request event: 3
  • Create event: 3
Last Year
  • Release event: 1
  • Delete event: 3
  • Member event: 1
  • Issue comment event: 1
  • Push event: 8
  • Pull request review comment event: 1
  • Pull request review event: 4
  • Pull request event: 3
  • Create event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 325
  • Total Committers: 11
  • Avg Commits per committer: 29.545
  • Development Distribution Score (DDS): 0.338
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Ju Yeong Kim j****5@f****g 215
J. Kim jk@j****m 34
Jason Taylor j****r@f****g 28
Helen Miller h****r@f****g 13
Helen Miller h****n@o****g 9
jmtaylor-fhcrc 4****c 9
Jason Taylor y****u@e****m 8
J. Kim j****m 6
Jeroen Ooms j****s@g****m 1
Sean Hughes s****n@g****m 1
ropenscibot m****t@g****m 1
Committer Domains (Top 20 + Academic)
fredhutch.org: 3 ohana.org: 1 juyeongkim.com: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 18
  • Total pull requests: 32
  • Average time to close issues: 7 months
  • Average time to close pull requests: 2 months
  • Total issue authors: 2
  • Total pull request authors: 5
  • Average comments per issue: 0.61
  • Average comments per pull request: 0.34
  • Merged pull requests: 28
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: 3 months
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.5
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • juyeongkim (15)
  • jmtaylor-fhcrc (3)
Pull Request Authors
  • jmtaylor-fhcrc (21)
  • helenmiller16 (6)
  • maelle (2)
  • juyeongkim (2)
  • seaaan (1)
Top Labels
Issue Labels
enhancement (8) bug (4) documentation (3) infrastructure (1)
Pull Request Labels
enhancement (3)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 372 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
cran.r-project.org: DataSpaceR

Interface to 'the CAVD DataSpace'

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 372 Last month
Rankings
Forks count: 12.8%
Stargazers count: 22.5%
Average: 26.6%
Dependent packages count: 29.8%
Downloads: 32.4%
Dependent repos count: 35.5%
Maintainers (1)
jmtaylor@fredhutch.org
Last synced: 9 months ago

Dependencies

DESCRIPTION cran
  • R6 * imports
  • Rlabkey >= 2.2.0 imports
  • assertthat * imports
  • curl * imports
  • data.table * imports
  • digest * imports
  • httr * imports
  • jsonlite * imports
  • utils * imports
  • covr * suggests
  • knitr * suggests
  • pryr * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc master composite
  • r-lib/actions/setup-r master composite
.github/workflows/pr-commands.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/pr-fetch v1 composite
  • r-lib/actions/pr-push v1 composite
  • r-lib/actions/setup-r v1 composite