Reading a Licor LI-6800 Excel log file
read_licor_6800_Excel.Rd
Tool for reading Excel log files created by Licor LI-6800 instruments and
storing their contents in exdf
objects.
Arguments
- file_name
A relative or absolute path to an Excel file containing Licor data.
- column_name
A column name that should be present in the log file; used to identify the beginning of the data block in the file.
- get_oxygen
A logical value indicating whether to get the oxygen percentage from the file's preamble using
get_oxygen_from_preamble
.- ...
Additional arguments; currently unused.
Details
Licor LI-6800 instruments create two types of log files: a plain-text file and
an Excel file, each containing the same information. In general, the Excel
files are much easier to modify, for example, deleting rows or adding new
columns. For this reason, it is helpful to be able to read these files in R.
Unfortunately, base R does not have any functionality for reading Excel files,
so here the openxlsx
package is used.
read_licor_6800_Excel
looks for a particular data column in order to
identify the start of the data table within the contents of the Licor file.
Rows above the main data table are assumed to be part of the preamble (or
header), which are broken into pairs of rows representing names and values.
IMPORTANT NOTE ABOUT LICOR EXCEL FILES: by default, Licor Excel files
do not "calculate" formula values. This causes a problem when reading them in
R, since any data entry determined from a formula will be read as 0. To fix
this issue for a Licor Excel file, open it in in Excel, go to the
Formulas
menu, and choose Calculate Now
. (Alternatively, press
F9.) Then save the file and close it. See
GitHub issue 495 from the readxl package
for more details.
Value
An exdf
object that fully includes all the data from the Licor Excel
file. In addition to the elements described in the documentation for
read_gasex_file
, the following "extra" elements are also
included:
preamble
: A data frame containing the "preamble" (or "header") information from the file.data_row
: The line of the file where the column name was found.
Examples
# Example 1: Reading a Licor Excel file that is included with the PhotoGEA
# package.
licor_file <- PhotoGEA:::read_licor_6800_Excel(
PhotoGEA_example_file_path('ball_berry_1.xlsx')
)
# Example 2: Reading a Licor Excel file that is included with the PhotoGEA
# package; here we use a different column name to identify the data block within
# the file's contents.
licor_file <- PhotoGEA:::read_licor_6800_Excel(
PhotoGEA_example_file_path('ball_berry_1.xlsx'),
column_name = 'A'
)