read_pam_2500_data: Read and Process PAM 2500 Data

In pam: Fast and Efficient Processing of PAM Data

Read and Process PAM 2500 Data

Description

Reads raw CSV files generated by PAM 2500 software, calculates electron transport rate (ETR) values, and returns a cleaned dataset.

Usage

read_pam_2500_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 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.

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/pam_2500_data", package = "pam"), "20260422_pam_2500.CSV")
data <- read_pam_2500_data(path)

pam documentation built on April 23, 2026, 5:08 p.m.