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

Abstract

The analysis of photosynthetic traits has become an integral part of plant (eco-)physiology. Many of these characteristics are not directly measured, but calculated from combinations of several, more direct, measurements. The calculations of such derived variables are based on underlying physical models and may use additional constants or assumed values. Commercially available gas-exchange instruments typically report such derived variables, but the available implementations use different definitions and assumptions. Moreover, no software is currently available to allow a fully scripted and reproducible workflow that includes importing data, pre-processing and recalculating derived quantities. The R package gasanalyzer aims to address these issues by providing methods to import data from different instruments, by translating photosynthetic variables to a standardized nomenclature, and by optionally recalculating derived quantities using standardized equations. In addition, the package facilitates performing sensitivity analyses on variables or assumptions used in the calculations to allow researchers to better assess the robustness of the results. The use of the package and how to perform sensitivity analyses are demonstrated using three different examples.

Plant phenotyping relevance

植物の光合成形質データを標準化・再計算・感度分析するRパッケージを開発しており、植物生理形質の取得後処理と再現可能な解析ワークフローが中心である。

Code and data availability

The paper's gas-exchange phenotyping data (poplar, tobacco, GFS-3000 examples) and all analysis code for the gasanalyzer package are publicly available in the authors' GitLab repository, with a stable release on CRAN.