build_list: build_list function

In ManuelLamothe/RapidACi: Automated Rapid A-Ci curve correction for Li-Cor system

Description

Generates a list of the files present in a specified directory. By default, the function uses the MATCH timestamp generated by the Li-Cor system to pair an A-Ci measurement file to its identify which corresponding 'empty chamber' file is to used to for its correction. If the Li-Cor MATCH function is not used, the option can be turned off and the closest empty chamber file will be used.

Usage

build_list(path_to_licor_files = "data/",
  sampleID_format = "[:upper:]{3}_[:digit:]{3}",
  pattern_empty = "(mpty).*\\.xls",
  pattern_rapidACi = "(fast).*\\.xls",
  pattern_standardACi = "(slow).*\\.xls",
  pattern_dark = "(dark).*\\.xls", timestamp_column = "BN",
  leafArea_df = NULL)

Arguments

path_to_licor_files	Directory path where all files are stored
sampleID_format	Regex pattern that uniquely identifies the sample ID in filenames. For example (default), "[:upper:]3_[:digit:]3" will extract sample ID of the format ABC_123 from a filename like "2019-03-20_456_Logdata_ABC_123_Fast_KF.xlsx"
pattern_empty	Regex pattern that must only match filenames for empty chamber files
pattern_rapidACi	Regex pattern that must only match filenames for rapid A-Ci measurement files
pattern_standardACi	Regex pattern that must only match filenames for standard A-Ci measurement files
pattern_dark	Regex pattern that identifies measurements in dark chamber files
timestamp_column	Column index corresponding to the MATCH TIME column in all Li-Cor Excel files. By default this corresponds to column BN (index = 66) in Excel files.
leafArea_df	A dataframe containing at least a "sample_ID" column and a "leafArea_mm2" column (default = NULL)

Value

The function returns a dataframe that includes the path to the Li-Cor files to use, the type of measurements, the starting time of the measure, the timestamps, and how the timestamp was acquired. It also includes leaf area if available.

ManuelLamothe/RapidACi documentation built on Sept. 16, 2020, 9:53 p.m.