pam (version 2.0.0)

read_junior_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
)

Value

A data.table containing:

• par: Photosynthetically active radiation.

• yield_1: Yield for photosystem I.

• yield_2: Yield for photosystem II.

• etr_1: Calculated ETR for photosystem I.

• etr_2: Calculated ETR for photosystem II.

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

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)