Analyze Cardiopulmonary Exercise Testing (CPET) data from COSMED Quark metabolic carts in R — type-safe S7 data structures, ATS/ACCP-based peak and threshold detection, a Shiny clinical interface, and bilingual (EN/FR) Typst PDF reports.

• Import COSMED Quark Excel exports with automatic parsing
• S7 classes with built-in physiological validation
• Peak detection via rolling averages (ATS/ACCP)
• Ventilatory threshold methods: V-slope, VE/VO2, VE/VCO2, end-tidal gases
• Test-quality and maximal-effort assessment
• Nine-panel clinical CPET plot
• Interactive Shiny app with EN/FR toggle
• Typst-based PDF reports (bilingual)
• Normative comparison against athlete and general-population registries

# Install from GitHub
# install.packages("pak")
pak::pak("jotremblay/cardiometR")

library(cardiometR)

# Import COSMED file
data <- read_cpet("path/to/cosmed_export.xlsx")

# Validate and analyze
validation <- validate(data)
averaged <- average(data, method = "rolling", window = 30)
peaks <- find_peaks(averaged)

# Create analysis object
analysis <- CpetAnalysis(
  data = averaged,
  peaks = peaks,
  validation = validation
)

# Generate 9-panel CPET plot
plot_cpet_panel(analysis)

# Launch interactive app
run_app()

Access properties with the @ operator:

# View participant info
data@participant@age
data@participant@weight_kg

# View peak values
peaks@vo2_peak       # mL/min
peaks@vo2_kg_peak    # mL/kg/min
peaks@hr_peak        # bpm

The 9-panel CPET display follows clinical standards:

# English labels
plot_cpet_panel(analysis, language = "en")

# French labels
plot_cpet_panel(analysis, language = "fr")

Individual plots available:

• plot_v_slope() - V-slope for threshold detection
• plot_ventilatory_equivalents() - VE/VO2 and VE/VCO2
• plot_heart_rate() - HR response with zones
• plot_power() - Power output with VO2 overlay

Generate professional bilingual reports:

config <- ReportConfig(
  language = "fr",
  institution = "Centre ÉPIC",
  technician = "Dr. Smith"
)

generate_report(
  analysis = analysis,
  output_file = "cpet_report.pdf",
  config = config
)

Launch the Shiny app for clinical use:

run_app()           # English interface
run_app(language = "fr")  # French interface

The app provides:

• Drag-and-drop file import
• Participant info editing
• Interactive visualization
• Quality assessment
• PDF report generation

Assess test quality based on ACSM guidelines:

quality <- assess_quality(data, rpe = 18, lactate = 9.5)

# Check maximal effort criteria
quality@exercise_criteria@determination
#> "maximal"

# Overall quality grade
quality@overall_grade
#> "A"

• Vignette: vignette("introduction", package = "cardiometR")
• Function reference: See ?cardiometR for package help
• Translations: inst/translations/labels_{en,fr}.yml

• ATS/ACCP Statement on Cardiopulmonary Exercise Testing. Am J Respir Crit Care Med. 2003;167(2):211-277.
• Beaver WL, Wasserman K, Whipp BJ. A new method for detecting anaerobic threshold by gas exchange. J Appl Physiol. 1986;60(6):2020-2027.

• spiro - rOpenSci CPET package
• whippr - VO2 kinetics analysis

MIT License. See LICENSE for details.

Tremblay J (2026). cardiometR: Cardiopulmonary Exercise Testing Analysis with S7 Classes.
R package version 0.6.0. https://github.com/jotremblay/cardiometR