In KeachMurakami/li6400xt: Preprocess Gas Exchange Data for R workflow

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

Installation

The present version does not support Windows. You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("KeachMurakami/li6400xt")

core function

Load data using read_licor. Note that file must be tab-separated text, not xls automatically generated by the LI6400XT system.

library(li6400xt)

library(tidyverse)
library(patchwork)

file <- system.file("light_curve.txt", package = "li6400xt")

mydata <- read_licor(file)
print(mydata)

net_photosynthesis <-
  mydata %>%
  ggplot(aes(time, Photo, col = PARi)) +
  geom_line() +
  scale_color_viridis_c()
stomatal_conductance <- 
  mydata %>%
  ggplot(aes(time, Cond, col = PARi)) +
  geom_line() +
  scale_color_viridis_c()

net_photosynthesis / stomatal_conductance

mydata %>%
  ggplot(aes(PARi, Photo, col = PARi)) +
  geom_point() +
  geom_smooth() +
  scale_color_viridis_c()

miscellaneous functions

File remark and operational change logs are available as attributes.

# check remark noted on file creation
attributes(mydata)$remark

# check operational change logs
attributes(mydata)$control

Chamber environments usually fluctuate, making the analysis bothersome. Use track_changes to add a column showing set-point values.

mydata %>%
  track_changes(track = "LCF", variable = "PPFD") %>%
  ggplot(aes(time, PARi)) +
  geom_point() +
  geom_line(aes(y = PPFD), col = "orange")

track = LCF: tracks changes in PARi
track = XXX: tracks change in CO2
track = XXX: tracks change in Tair/Tleaf

Leaves are not always broad enough to cover the chamber (e.g. wheat and rice). Use correct_leaf_area to calculate leaf area sandwitched by the chamber. This function calculates corrected Area, Photo, Cond, and Trmmol from given leaf width (width_mm) and chamber model (model).

# Original area
mydata$Area[1]

# Corrected area
corrected_mydata <- correct_leaf_area(mydata, width_mm = 15, model = "6400-40")
corrected_mydata$Area[1]

standard workflow

data_of_multiple_leaves <-
  dir("PATH_TO_LI6400XT_DIR") %>%
  purrr::map(function(file){

    # read file
    data <- read_licor(file)

    # get leaf width from file remark
    width <- readr::parse_number(attributes(data)$remark)

    # correct area and track PPFD change
    data %>%
      correct_leaf_area(width_mm = width, model = "6400-40") %>%
      track_changes(track = "LCF", variable = "PPFD") %>%
      return()
  })