spiro

spiro: An R package for analyzing data from cardiopulmonary exercise testing - Published in JOSS (2023)

https://github.com/ropensci/spiro

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Repository

Work with data from cardiopulmonary exercise testing

Basic Info

Host: GitHub
Owner: ropensci
License: other
Language: R
Default Branch: main
Homepage: https://docs.ropensci.org/spiro/
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Created over 4 years ago · Last pushed 5 months ago

Metadata Files

Readme Changelog Contributing License Citation Codemeta

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
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)
```

# spiro    

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![CRAN status](https://www.r-pkg.org/badges/version/spiro)](https://CRAN.R-project.org/package=spiro)
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05089/status.svg)](https://doi.org/10.21105/joss.05089)
[![R-CMD-check](https://github.com/ropensci/spiro/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/spiro/actions)
[![codecov](https://codecov.io/gh/ropensci/spiro/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ropensci/spiro)
[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/541_status.svg)](https://github.com/ropensci/software-review/issues/541)


## Overview

This R package offers a fast, standardized and reproducible workflow for data
from cardiopulmonary exercise testing. It offers tools for data import,
processing, summary and visualization.

## Background

Measuring gas exchange during physical exercise is a common procedure in sports science and medicine. It allows to assess the functional limit of the cardiovascular system, evaluate the success of training interventions, and diagnose cardio-respiratory diseases. The measuring devices of cardiopulmonary exercise testing --- so-called metabolic carts --- output their data in different formats. Moreover, measured breath-by-breath data is noisy and requires post-processing. This package standardizes the import and processing of raw data from different metabolic carts.

## Installation

Install `spiro` from CRAN:

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

Install the current development version of `spiro` from GitHub:

``` {r install-dev, eval = FALSE}
if (!require(remotes)) install.packages("remotes")
remotes::install_github("ropensci/spiro")
```

## Usage

Main functions:

* Use `spiro()` to automatically import and process raw data from
  cardiopulmonary exercise testing.
* Use `spiro_summary()`  for a summary of cardiopulmonary parameters (e.g., relative oxygen uptake, respiratory quotient, heart rate, ...) for each load step.
* Use `spiro_max()` to calculate maximum parameter values (e.g., VO2max).
* Use `spiro_plot()` to visualize the data as a modifiable Wassermann 9-Panel Plot.

Further functionality:

* Add external heart rate data from a .tcx file.
* Automated guessing or manual setting of exercise protocols.
* Different data filtering strategies for VO~2max~ determination (moving time averages, moving breath averages, Butterworth filters)
  
#### Metabolic Carts

The following metabolic carts are currently supported by `spiro`:

* Cortex
* Cosmed
* Vyntus
* ZAN

Support for further metabolic carts is planned for future releases.

## Example

```{r example, warning = FALSE, fig.width = 10, fig.height = 8}
library(spiro)

# get data path for example
file <- spiro_example("zan_gxt")

# import and process the raw data
gxt_data <- spiro(file)

# summary of parameters by load step
spiro_summary(gxt_data)

# maximum values
spiro_max(gxt_data)

# Wassermann 9-Panel Plot
spiro_plot(gxt_data)
```

## Citation

```{r citation, collapse=FALSE, comment=""}
citation("spiro")
```

## Related Work

The [whippr](https://github.com/fmmattioni/whippr) package offers a different
approach to working with data from cardiopulmonary exercise testing. It
additionally offers functions for analyzing VO2 kinetics.

## Acknowledgment

The following persons contributed to this package by providing raw data files, reviewing code and/or suggesting features:
Daniel Appelhans, Michael Beaven, James Hunter, Virgile Lecoultre, Sebastian Mühlenhoff, Manuel Ramon, Anton Schiffer, Yannick Schwarz, Adrian Swoboda, Andreas Wagner.

## Contributing

If you consider contributing to this package, read the [CONTRIBUTING.md](https://github.com/ropensci/spiro/blob/main/.github/CONTRIBUTING.md). Please note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). By contributing to this project, you agree to abide by its terms.

Owner

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

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

JOSS Publication

spiro: An R package for analyzing data from cardiopulmonary exercise testing

Published

January 22, 2023

DOI

10.21105/joss.05089

Volume 8, Issue 81, Page 5089

Authors

Simon Nolte

Institute of Movement and Neurosciences, German Sport University Cologne, Cologne, Germany

Editor

Kevin M. Moerman

Citation (CITATION.cff)

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Watch event: 2
Delete event: 1
Push event: 5
Pull request event: 2
Create event: 3

Last Year

Release event: 2
Watch event: 2
Delete event: 1
Push event: 5
Pull request event: 2
Create event: 3

Committers

Last synced: 5 months ago

All Time

Total Commits: 380
Total Committers: 2
Avg Commits per committer: 190.0
Development Distribution Score (DDS): 0.003

Past Year

Commits: 10
Committers: 1
Avg Commits per committer: 10.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Simon Nolte	8****t	379
Maëlle Salmon	m**n@y**e	1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 1
Total pull requests: 12
Average time to close issues: about 1 month
Average time to close pull requests: 4 days
Total issue authors: 1
Total pull request authors: 2
Average comments per issue: 1.0
Average comments per pull request: 0.0
Merged pull requests: 12
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 2
Average time to close issues: N/A
Average time to close pull requests: 11 minutes
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

thomasp85 (1)

Pull Request Authors

smnnlt (13)
maelle (2)

Top Labels

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Packages

Total packages: 1
Total downloads:
- cran 248 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 5
Total maintainers: 1

cran.r-project.org: spiro

Manage Data from Cardiopulmonary Exercise Testing

Homepage: https://github.com/ropensci/spiro
Documentation: http://cran.r-project.org/web/packages/spiro/spiro.pdf
License: MIT + file LICENSE
Latest release: 0.2.3
published 10 months ago

Versions: 5
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 248 Last month

Rankings

Stargazers count: 17.9%

Forks count: 28.8%

Dependent packages count: 29.8%

Dependent repos count: 35.5%

Average: 37.6%

Downloads: 76.3%

Maintainers (1)

s.nolte@dshs-koeln.de

Last synced: 4 months ago

spiro

Science Score: 98.0%

Repository

Basic Info

Statistics

Metadata Files

README.Rmd

Owner

JOSS Publication

spiro: An R package for analyzing data from cardiopulmonary exercise testing

Authors

Editor

Tags

Citation (CITATION.cff)

CodeMeta (codemeta.json)

GitHub Events

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Packages

cran.r-project.org: spiro

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Maintainers (1)

Dependencies