read_universal_data: Read and Process Universal PAM Data

In pam: Fast and Efficient Processing of PAM Data

Read and Process Universal PAM Data

Description

Reads a standardized CSV file containing PAR and yield data for photosystem I and/or II, calculates electron transport rates (ETR), and returns a cleaned and validated dataset. The function is device-agnostic but requires a predefined column structure.

Usage

read_universal_data(
  csv_path,
  etr_factor = 0.84,
  fraction_photosystem_I = 0.5,
  fraction_photosystem_II = 0.5
)

Arguments

csv_path	File path to the CSV file.
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 using:

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

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

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", package = "pam"), "universal_data", "universal_data.csv")
data <- read_universal_data(path)

pam documentation built on April 11, 2026, 5:06 p.m.