GXread: Read in Licor-6400 raw Data
In KevinCrab/Instant-Gas-Exchange-Measurements: Instant Gas Exchange Analysis

Description Usage Arguments Value Author(s) References Examples

This function reads the raw csv files generated from licor-6400 gas exchange measurement.It records measurement conditions, extracts each measurement observations, trims unnecessary parameters, matches genotype names and reformats digit numbers in names. Data from machines with different output structure settings are unified and reorganized.

1	read.GX(filename, leaf_rep, genolist, condition = FALSE)

`filename`	character of a licor-6400 output csv file name.
`leaf_rep`	a numeric number to indicate replicate number, usually start from 1. each day we sample a whole set of replication for each plot. Thus, each file comprise of same leaf replicate number.
`genolist`	a dataframe with at least two columns indicating plot indexes and their corresponding genotype names.
`condition`	if TRUE, check whether measurement conditions are complete. (measurement_time/machine/lightsource/AD.avgtime/flow/par/CO2_mixer/Tblock)

Returns a class GXcurve table that includes all observations in the raw dataset with measurements (Photo; Cond; Ci/Ca) and properties (plot name; leaf replicate number; genotype name; original dataset; range; row; block; time)

Jiayang Xie <kevinxie@illinois.edu>

https://www.licor.com/documents/ifuhfcjga0wvh94lkysz

# Assume "cm 07-21-2017 ril leak1_.csv" is exported from Licor-6400 machine
# "genotypic imformation.csv" has matching of plot names with genotype names.

input <- system.file("extdata", "cm_07-21-2017_ril_leak1_.csv", package = "IGEA")
genolist <- system.file("extdata", "genotypic_information.csv", package = "IGEA")
leak1_721 = read.GX(filename = input ,leaf_rep = 1, genolist = genolist,condition = TRUE)