An R package to help with the import of Li6400 files and to help with recalculation of gas exchange parameters when the leaf area is updated after the measurement.
For documentation see the online help:
help(package = "Li6400helper")
Installation:
devtools::install_github("MarkusLoew/Li6400helper")
This is an updated version due to changes changes between LPL version 3 and LPL version 6 (yes, I didn't update it in a while...).
Acknowledgement
The development of this package was supported by ARC grant LP130101183.
Imports a csv or tsv text file from a Licor 6400. As I was not happy that the date is not included by default in each sample, this function uses the date from the header and updates the HHMMSS vector to create a full date and time information. Makes it easier to keep track of regular, or diurnal measurements. Remarks and data are separated and provided individually. The function returns a list with two data frames. The first data frame holds the data without remarks, the second data frame provides the remarks and an index of the row number that each remark was in.
If the leaf does not fill the full area of the IRGA cuvette, some of the gas exchange parameters need to be recalculated once the actual leaf area is known. This function returns either a data frame with the changed parameters only, or returns the data frame with the updated parameters in place, in context of the full file. The calculations are taken from the default compute list of a Li6400 IRGA. The source code shows the compute list entry and the corresponding R code. Be aware that rounding errors occur! And, as usual, no guarantee for error-free recalculation.
This packages provides a rather simplistic approach to processing the between-observations remarks created by the Li6400 IRGA. Whether this approach makes sense is up to the specific use case! Assuming a block of samples (observations, Obs) is always preceeded by a remark, this approach works as the last remark is carried over to all following observations until a new remark is found. But as there can be many more remarks in the file than samples and the last remark might not be the correct remark for a block of samples, the merge between the actual sample observations and remarks needs further processing afterwards. For convenience, the orginal remarks vector with gaps and the filled remarks are both provided in the output.