GasanalyzeR: advancing reproducible research using a new R package for photosynthesis data workflows

Area of Science:

• Plant physiology and ecophysiology
• Computational biology
• Environmental science

Background:

• Photosynthetic traits are crucial in plant (eco-)physiology but often derived from complex calculations.
• Existing gas-exchange instruments report derived variables using inconsistent definitions and assumptions.
• A lack of standardized, reproducible software hinders data analysis and interpretation.

Purpose of the Study:

• To introduce the R package gasanalyzer for standardized analysis of photosynthetic traits.
• To provide reproducible workflows for importing, pre-processing, and recalculating derived gas-exchange variables.
• To enable sensitivity analyses for assessing the robustness of calculated photosynthetic parameters.

Main Methods:

• Development of the R package gasanalyzer.
• Implementation of standardized nomenclature for photosynthetic variables.
• Integration of standardized equations for recalculating derived quantities.
• Inclusion of functions for sensitivity analysis of input variables and assumptions.

Main Results:

• The gasanalyzer package offers a unified approach to handling gas-exchange data from various instruments.
• It ensures consistent definitions and calculations of derived photosynthetic traits.
• The package facilitates reproducible research by enabling scripted data analysis and sensitivity assessments.

Conclusions:

• The R package gasanalyzer addresses critical needs for standardization and reproducibility in plant gas-exchange analysis.
• It empowers researchers to improve the reliability and comparability of their findings in plant (eco-)physiology.
• The package supports robust scientific inquiry by allowing rigorous assessment of calculation assumptions.