gasanalyzer

Provides support for reading and preprocessing data from various portable photosynthesis systems. Includes options to parse xlsx equations from the data files, for recalculating data based on sets of pre-defined equations, or based on user-specified equations.

Installation

GasAnalyzeR can be found on CRAN, which greatly simplifies installation (if you are using an up-to-date R install, it can for example be found in RStudio under Tools, Install Packages).

It is also possible to install the development version of the package from gitlab. Please make sure to run the following command to install all requirements first:

install.packages(c("units", "stringi", "jsonify", "xml2", "tidyxl", "tibble", "vctrs", "devtools"))

Then, download the zip (or tar.gz, etc) from gitlab and run:

devtools::install_local("gasanalyzer-master.zip")

You may need to adopt the command above to point to the correct folder and name of the file you just downloaded. R may give a warning about missing Rtools , however, Rtools is currently not needed to install this package.

Documentation

Portable photosynthesis systems are infra-red gas-analyzers for measuring gas-exchange characteristics on plant leaves. They typically measure \(CO_{2}\) and \(H_{2}O\) mol fractions, gas flow and various other relevant parameters (temperature, light intensity, fan speed, pressure). These measurements are combined with user-defined parameters (leaf area or weight, stomatal ratios, oxygen concentration) and used by the instrument firmware or external software to calculate physiological relevant traits such as the rate of photosynthesis, evapotranspiration, or intercellular \(CO_{2}\) concentrations.

These calculations are described in scientific publications1,2 and user manuals for the instruments3,4,5. Some instruments optionally save data in the form of spreadsheet documents that contain the used equations. Unfortunately, these sources often made different assumptions for deriving gas-exchange equations. Moreover, they all use very different terminology and symbols. This makes it difficult to compare the different approaches. A unified way of dealing with gas-exchange data would benefit the research in this field. Moreover, a change in assumptions, configuration or externally measured data (leaf area, stomatal ratio, \(O_2\)) makes it necessary to recalculate gas-exchange data. Although the vendor-provided spreadsheets provide some options to recalculate data, they are not available and limited in scope and usability. A tool to reliably recalculate gas-exchange data is currently not available. To this end, this package uses a unified set of symbols and equations for gas-exchange data.

An advantage of using R is that it allows us to read and modify many datafiles as part of a single scripted procedure. Afterwards the data can be quickly summarized, analyzed and plotted. It ensures a repeatable and traceable pipeline to turn raw measurements into analyzed results.

Please see the package vignette for more detailed information.

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  1. von Caemmerer and Farquhar (1981). Some relationships between the biochemistry of photosynthesis and the gas exchange of leaves. Planta 153, 376–387. doi: 10.1007/bf00384257↩

  2. Márquez, Stuart-Williams and Farquhar. An improved theory for calculating leaf gas exchange more precisely accounting for small fluxes. Nat. Plants 7, 317–326 (2021). doi: 10.1038/s41477-021-00861-w↩

  3. https://www.licor.com/env/support/LI-6400/topics/system-description.html#Equation↩

  4. https://www.licor.com/env/support/LI-6800/topics/equation-summary.html↩

  5. https://www.walz.com/files/downloads/manuals/gfs-3000/GFS-3000_Manual_9.pdf↩