In fmmattioni/whippr: Tools for Manipulating Gas Exchange Data

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whippr

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 and his invaluable contribution to the field of exercise physiology.

Installation

You can install the development version of whippr from Github with:

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

Use

Read data

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

df %>% 
  interpolate()

Perform averages

Bin-average

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

Rolling-average

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

Perform VO₂ kinetics analysis

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

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
• CORTEX
• NSpire
• Parvo Medics
• Geratherm Respiratory
• 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

Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

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fmmattioni/whippr documentation built on Feb. 23, 2024, 11:20 a.m.