example_data_files: Example data files

In PhotoGEA: Photosynthetic Gas Exchange Analysis

Example data files

Description

The PhotoGEA package includes several data files that can be used to demonstrate different functions and analysis techniques.

Details

The following files are included with the package:

• ball_berry_1.xlsx and ball_berry_2.xlsx: Two log files created by Licor Li-6800 portable gas exchange measurement systems. These log files each contain several Ball-Berry curves. Several user constants were defined in these logs that can be used to identify individual curves or subsets of curves: species, plot, and instrument. These files are used in the "Analyzing Ball-Berry Data" vignette and in other examples.

• ball_berry_1.csv: A CSV version of ball_berry_1.xlsx, which was created by reading the Excel file with read_gasex_file and then saving it using write.csv.exdf. This can be done as follows: tmp <- read_gasex_file(PhotoGEA_example_file_path('ball_berry_1.xlsx')); write.csv.exdf(tmp, 'ball_berry_1.csv')

• c3_aci_1.xlsx and c3_aci_2.xlsx: Two log files created by Licor Li-6800 portable gas exchange measurement systems. These log files each contain several C3 CO2 response (or A-Ci) curves. Several user constants were defined in these logs that can be used to identify individual curves or subsets of curves: species, plot, and instrument. These files are used in the "Analyzing C3 A-Ci Curves" vignette and in other examples. The Remarks sheet of c3_aci_2.xlsx was deleted from the original version as a test for read_licor_6800_Excel.

• c4_aci_1.xlsx and c4_aci_2.xlsx: Two log files created by Licor Li-6800 portable gas exchange measurement systems. These log files each contain several C4 CO2 response (or A-Ci) curves. Several user constants were defined in these logs that can be used to identify individual curves or subsets of curves: species, plot, and instrument. These files are used in the "Analyzing C4 A-Ci Curves" vignette and in other examples.

• tdl_sampling_1.dat and tdl_sampling_2.dat: Two log files created by a Campbell Scientific CR3000 data logger, representing data from a tunable diode laser (TDL) system. These files are used in the "Analyzing TDL Data" vignette and in other examples.

• plaintext_licor_file: A log file created by a Licor Li-6800 portable gas exchange measurement system. This file contains several CO2 response (or A-Ci) curves. Several user constants were defined in this log that can be used to identify individual curves or subsets of curves: species, plot, and instrument.

• plaintext_licor_file_v2: A log file based on plaintext_licor_file that has two separate [Data] and [Header] sections, as if the log file had been closed and reopened halfway through the measurement sequence.

• licor_for_gm_site11.xlsx, licor_for_gm_site13.xslsx, and tdl_for_gm: Two Licor Li-6800 log files and a CR3000 TDL log file, respectively. These files are used as an example of loading and processing combined gas exchange and isotope discrimination measurements. Each Licor log file includes 6 points measured with the CO2_r setpoint set to 715 ppm and 6 points with the setpoint set to 450 ppm.

Since none of these data files have been published, noise has been added to the original data. Thus, they are similar to real measurements, but no useful conclusions can be drawn from them.

After installing 'PhotoGEA', copies of these files will be stored in the R package directory (in the PhotoGEA/extdata subdirectory). This location will be unique to your computer, but full paths to these files can be obtained using the PhotoGEA_example_file_path function.

Examples

# Print full paths to the example files
PhotoGEA_example_file_path('ball_berry_1.xlsx')
PhotoGEA_example_file_path('ball_berry_2.xlsx')
PhotoGEA_example_file_path('c3_aci_1.xlsx')
PhotoGEA_example_file_path('c3_aci_2.xlsx')
PhotoGEA_example_file_path('c4_aci_1.xlsx')
PhotoGEA_example_file_path('c4_aci_2.xlsx')
PhotoGEA_example_file_path('licor_for_gm_site11.xlsx')
PhotoGEA_example_file_path('licor_for_gm_site13.xlsx')
PhotoGEA_example_file_path('plaintext_licor_file')
PhotoGEA_example_file_path('plaintext_licor_file_v2')
PhotoGEA_example_file_path('tdl_for_gm.dat')
PhotoGEA_example_file_path('tdl_sampling_1.dat')
PhotoGEA_example_file_path('tdl_sampling_2.dat')

PhotoGEA documentation built on April 11, 2025, 5:48 p.m.