read_junior_pam_data: Read and Process Junior PAM Data

In pam: Fast and Efficient Processing of PAM Data

Read and Process Junior PAM Data

Description

Reads raw CSV files generated by Junior PAM software, calculates electron transport rate (ETR) values, and returns a cleaned dataset. Customization may be needed for non-DualPAM devices.

Usage

read_junior_pam_data(
  csv_path,
  remove_recovery = TRUE,
  etr_factor = 0.84,
  fraction_photosystem_I = 0.5,
  fraction_photosystem_II = 0.5
)

Arguments

csv_path	File path to the CSV file.
remove_recovery	Logical. Removes recovery measurements if TRUE. Default is TRUE.
etr_factor	Numeric. Factor for ETR calculation. Default is 0.84.
fraction_photosystem_I	Numeric. Relative distribution of absorbed PAR to photosystem I. Default is 0.5.
fraction_photosystem_II	Numeric. Relative distribution of absorbed PAR to photosystem II. Default is 0.5.

Details

Calculates ETR II using:

\text{ETR II} = \text{PAR} \cdot \text{ETR-Factor} \cdot \text{Fraction of Photosystem (II)} \cdot \text{Yield (II)}

A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file

Value

A 'data.table' with processed data and calculated ETR values.

References

Heinz Walz GmbH. (2024). DUAL-PAM-100 DUAL-PAM/F MANUAL, 5th Edition, April 2024, Chapter 7 (pp. 162-172). Heinz Walz GmbH, Effeltrich, Germany. Available at: https://www.walz.com/files/downloads/dualpamed05.pdf

Examples

path <- file.path(system.file("extdata/junior_pam", package = "pam"), "junior_pam_20250613.csv")
data <- read_junior_pam_data(path)

pam documentation built on Aug. 27, 2025, 5:10 p.m.