whippr

Tools for Manipulating Gas Exchange Data 📈

https://github.com/fmmattioni/whippr

Science Score: 26.0%

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Scientific vocabulary similarity
Low similarity (15.3%) to scientific vocabulary

Last synced: 11 months ago · JSON representation

Repository

Tools for Manipulating Gas Exchange Data 📈

Basic Info

Host: GitHub
Owner: fmmattioni
License: other
Language: R
Default Branch: master
Homepage: https://fmmattioni.github.io/whippr/
Size: 51.6 MB

Statistics

Stars: 12
Watchers: 3
Forks: 4
Open Issues: 2
Releases: 1

Created over 6 years ago · Last pushed 12 months ago

Metadata Files

Readme Changelog Funding License

README.Rmd

---
output: github_document
---



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

# whippr 


[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![CRAN status](https://www.r-pkg.org/badges/version/whippr)](https://CRAN.R-project.org/package=whippr)
[![Codecov test coverage](https://codecov.io/gh/fmmattioni/whippr/branch/master/graph/badge.svg)](https://app.codecov.io/gh/fmmattioni/whippr?branch=master)
[![R-CMD-check](https://github.com/fmmattioni/whippr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/fmmattioni/whippr/actions/workflows/R-CMD-check.yaml)


The goal of `whippr` is to provide a set of tools for manipulating gas exchange data from cardiopulmonary exercise testing.

## Why `whippr`?

The name of the package is in honor of [Prof. Brian J Whipp](https://erj.ersjournals.com/content/39/1/1) and his invaluable contribution to the field of exercise physiology.

## Installation

You can install the development version of `whippr` from [Github](https://github.com/fmmattioni/whippr) with:

``` r
# install.packages("remotes")
remotes::install_github("fmmattioni/whippr")
```

## Use

### Read data

```{r}
library(whippr)

## example file that comes with the package for demonstration purposes
path_example <- system.file("example_cosmed.xlsx", package = "whippr")

df <- read_data(path = path_example, metabolic_cart = "cosmed")

df
```

### Interpolate

```{r}
df %>% 
  interpolate()
```

### Perform averages

#### Bin-average

```{r}
## example of performing 30-s bin-averages
df %>% 
  interpolate() %>% 
  perform_average(type = "bin", bins = 30)
```

#### Rolling-average

```{r}
## example of performing 30-s rolling-averages
df %>% 
  interpolate() %>% 
  perform_average(type = "rolling", rolling_window = 30)
```


### Perform VO₂ kinetics analysis

```{r}
results_kinetics <- vo2_kinetics(
  .data = df,
  intensity_domain = "moderate",
  vo2_column = "VO2",
  protocol_n_transitions = 3,
  protocol_baseline_length = 360,
  protocol_transition_length = 360,
  cleaning_level = 0.95,
  cleaning_baseline_fit = c("linear", "exponential", "exponential"),
  fit_level = 0.95,
  fit_bin_average = 5,
  fit_phase_1_length = 20,
  fit_baseline_length = 120,
  fit_transition_length = 240,
  verbose = TRUE
)
```

### Perform VO_2max analysis

```{r}
df_incremental <- read_data(path = system.file("ramp_cosmed.xlsx", package = "whippr"), metabolic_cart = "cosmed")

vo2_max(
  .data = df_incremental, ## data from `read_data()`
  vo2_column = "VO2",
  vo2_relative_column = "VO2/Kg",
  heart_rate_column = "HR",
  rer_column = "R",
  detect_outliers = TRUE,
  average_method = "bin",
  average_length = 30,
  plot = TRUE,
  verbose = TRUE,
  ## arguments for `incremental_normalize()`
  incremental_type = "ramp",
  has_baseline = TRUE,
  baseline_length = 240, ## 4-min baseline
  work_rate_magic = TRUE, ## produce a work rate column
  baseline_intensity = 20, ## baseline was performed at 20 W
  ramp_increase = 25, ## 25 W/min ramp
  ## arguments for `detect_outliers()`
  test_type = "incremental",
  cleaning_level = 0.95, 
  method_incremental = "linear"
)
```

## Metabolic carts currently supported

* [COSMED](https://www.cosmed.com/en/)
* [CORTEX](https://cortex-medical.com/EN)
* [NSpire](https://www.pressebox.de/pressemitteilung/nspire-health-gmbh/ZAN-100-Diagnostische-Spirometrie/boxid/745555)
* Parvo Medics
* [Geratherm Respiratory](https://www.geratherm-respiratory.com/product-groups/cpet/)
* [CardioCoach](https://korr.com/go/cardiocoach/)

## Online app

Would you like to perform VO₂ kinetics analyses but don't know R? No problem! You can use our online app: [VO2 Kinetics App](https://exphyslab.com/kinetics/)

## Code of Conduct

Please note that this project is released with a [Contributor Code of Conduct](https://www.contributor-covenant.org/version/1/0/0/code-of-conduct.html).
By participating in this project you agree to abide by its terms.

Icons made by monkik from www.flaticon.com

Owner

Name: Felipe Mattioni Maturana, Ph.D.
Login: fmmattioni
Kind: user
Location: Germany
Company: enhance-d

Website: fmattioni.me
Twitter: felipe_mattioni
Repositories: 33
Profile: https://github.com/fmmattioni

My goal is to help making exercise physiology reproducible and open and accessible for everyone

GitHub Events

Total

Release event: 1
Issues event: 1
Watch event: 1
Issue comment event: 1
Push event: 2
Fork event: 1

Last Year

Release event: 1
Issues event: 1
Watch event: 1
Issue comment event: 1
Push event: 2
Fork event: 1

Committers

Last synced: over 2 years ago

All Time

Total Commits: 153
Total Committers: 2
Avg Commits per committer: 76.5
Development Distribution Score (DDS): 0.007

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Felipe Mattioni Maturana	f**2@g**m	152
Felipe Mattioni Maturana	3****i	1

Issues and Pull Requests

Last synced: 11 months ago

All Time

Total issues: 9
Total pull requests: 4
Average time to close issues: 4 months
Average time to close pull requests: 17 days
Total issue authors: 5
Total pull request authors: 2
Average comments per issue: 2.33
Average comments per pull request: 0.5
Merged pull requests: 4
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

Scott-S-Hannah (4)
marikaecarr (2)
Jeffrothschild (1)
kizen777 (1)
saragracebiddle (1)

Pull Request Authors

fmmattioni (3)
olivroy (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 287 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 4
Total maintainers: 1

cran.r-project.org: whippr

Tools for Manipulating Gas Exchange Data

Homepage: https://fmmattioni.github.io/whippr/
Documentation: http://cran.r-project.org/web/packages/whippr/whippr.pdf
License: MIT + file LICENSE
Latest release: 0.1.4
published about 1 year ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 287 Last month

Rankings

Forks count: 14.9%

Stargazers count: 19.8%

Dependent packages count: 29.8%

Average: 33.6%

Dependent repos count: 35.5%

Downloads: 68.0%

Maintainers (1)

felipe.mattioni@med.uni-tuebingen.de

Last synced: 11 months ago

Dependencies

DESCRIPTION cran

broom >= 0.7.0 imports
cli * imports
dplyr >= 1.0.1 imports
ggplot2 >= 3.3.2 imports
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lubridate >= 1.7.9 imports
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patchwork >= 1.0.1 imports
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readxl >= 1.3.1 imports
rlang * imports
stringr >= 1.4.0 imports
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tidyr >= 1.1.1 imports
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anomalize * suggests
collapsibleTree * suggests
covr * suggests
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readr * suggests
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rstudioapi * suggests
shiny * suggests
testthat * suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v3 composite
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r-lib/actions/setup-pandoc v2 composite
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.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action v4.4.1 composite
actions/checkout v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pr-commands.yaml actions

actions/checkout v3 composite
r-lib/actions/pr-fetch v2 composite
r-lib/actions/pr-push v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v3 composite
actions/upload-artifact v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

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Data

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Open Source Science

whippr

Science Score: 26.0%

Repository

Basic Info

Statistics

Metadata Files

README.Rmd

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Issues and Pull Requests

All Time

Past Year

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cran.r-project.org: whippr

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Maintainers (1)

Dependencies