Reading a Licor LI-6800 Excel log file

Tool for reading Excel log files created by Licor LI-6800 instruments and storing their contents in exdf objects.

Usage

read_licor_6800_Excel(
    file_name,
    column_name = 'obs',
    get_oxygen = TRUE,
    check_for_zero = c('A', 'gsw'),
    ...
  )

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.

check_for_zero

The names of columns whose values should not all be zero; see below for details.

...

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 (column_name) 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.

"Calculating" formula values: 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 these articles for more information about this issue:

• GitHub issue 261 from the openxlsx package

• GitHub issue 863 from the openxlsx2 package

• GitHub issue 495 from the readxl package

read_licor_6800_Excel attempts to detect this issue by checking the values of key columns (specified by the check_for_zero input argument). If any of these columns are all 0, then an error message will be sent. This feature can be disabled by setting check_for_zero = c() when calling read_licor_6800_Excel or read_gasex_file.

File structure: Not that this function is not foolproof and may not be able to read some LI-6800 log files. For example, this function assumes that the logged points are contained in a single table. If user constants are logged as rows rather than columns, the file will instead contain multiple tables, and this function will not be able to read it.

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.

See also

read_gasex_file

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'
)