imports data from the li7500 setup described in Halbritter et al (2024)
Arguments
- path
location of the files. Note that the function is recursive and will import all the files at the location
- version
"till2023"(default) refers to the setup before the li7500 update. For the update version, use"post2023".- plotinfo
character vector of names to use when separating the plot info from the file name. Names in the file name have to be separated with an underscore, ex:
[location]_[date]_[time of day]_[trial].txt.FALSE(default) means no information will be fetched from the filename.
Value
a dataframe with all data present in the files to import. New
datetime and fluxid columns contain respectively the datetime of
measurements and their original filename. If comments are present, a column
will contain the comments. Measurement informations from the file
names are stored in new columns according to plotinfo.
References
Halbritter, A.H., Vandvik, V., Cotner, S.H. et al. Plant trait and vegetation data along a 1314 m elevation gradient with fire history in Puna grasslands, Perú. Sci Data 11, 225 (2024). https://doi.org/10.1038/s41597-024-02980-3
Examples
path_pftc7 <- system.file("extdata/pftc7", package = "licoread")
import7500(path_pftc7, version = "post2023")
#> # A tibble: 330 × 42
#> f_fluxid DATAH Time Date `Sequence Number` `CO2 (mmol/m^3)`
#> <chr> <chr> <chr> <date> <dbl> <dbl>
#> 1 1_2000_east_1_day_… DATA 10:5… 2023-12-14 123540 13.6
#> 2 1_2000_east_1_day_… DATA 10:5… 2023-12-14 123840 13.3
#> 3 1_2000_east_1_day_… DATA 10:5… 2023-12-14 124140 13.2
#> 4 1_2000_east_1_day_… DATA 10:5… 2023-12-14 124440 13.7
#> 5 1_2000_east_1_day_… DATA 10:5… 2023-12-14 124740 13.4
#> 6 1_2000_east_1_day_… DATA 10:5… 2023-12-14 125040 13.1
#> 7 1_2000_east_1_day_… DATA 10:5… 2023-12-14 125340 13.4
#> 8 1_2000_east_1_day_… DATA 10:5… 2023-12-14 125640 13.3
#> 9 1_2000_east_1_day_… DATA 10:5… 2023-12-14 125940 13.2
#> 10 1_2000_east_1_day_… DATA 10:5… 2023-12-14 126240 13.3
#> # ℹ 320 more rows
#> # ℹ 36 more variables: `CO2 (mg/m^3)` <dbl>, `CO2 Absorptance` <dbl>,
#> # `CO2 (umol/mol)` <dbl>, `H2O (mmol/m^3)` <dbl>, `H2O (g/m^3)` <dbl>,
#> # `H2O Absorptance` <dbl>, `H2O (mmol/mol)` <dbl>, `Dew Point (C)` <dbl>,
#> # `Temperature (C)` <dbl>, `Pressure (kPa)` <dbl>, `Diagnostic Value` <dbl>,
#> # `Diagnostic Value 2` <dbl>, `Diagnostic Word` <dbl>, `DSI Vin (v)` <dbl>,
#> # `Cooler Voltage (v)` <dbl>, `Chopper Cooler Voltage (v)` <dbl>, …
path_pftc5 <- system.file("extdata/pftc5", package = "licoread")
import7500(path_pftc5,
plotinfo = c("site", "treatment", "date", "plot", "trial"))
#> # A tibble: 251 × 25
#> f_fluxid `Relative Time` Temperature Pressure `Aux Input` `CO2 Absorptance`
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 ACJ_B_15m… 0.88 20.9 67.9 0 0.0638
#> 2 ACJ_B_15m… 1.94 20.9 67.9 0 0.0637
#> 3 ACJ_B_15m… 2.88 20.9 67.9 0 0.0633
#> 4 ACJ_B_15m… 3.94 20.9 67.9 0 0.063
#> 5 ACJ_B_15m… 4.86 20.9 67.9 0 0.063
#> 6 ACJ_B_15m… 5.88 20.9 67.9 0 0.063
#> 7 ACJ_B_15m… 6.86 20.9 67.9 0 0.0632
#> 8 ACJ_B_15m… 7.88 20.9 67.9 0 0.0625
#> 9 ACJ_B_15m… 8.86 20.9 67.9 0 0.063
#> 10 ACJ_B_15m… 9.88 20.9 67.9 0 0.063
#> # ℹ 241 more rows
#> # ℹ 19 more variables: `CO2 mmol/m3` <dbl>, `CO2 mg/m3` <dbl>,
#> # `CO2 umol/mol` <dbl>, `H2O Absorptance` <dbl>, `H2O mmol/m3` <dbl>,
#> # `H2O g/m3` <dbl>, `H2O mmol/mol` <dbl>, `H2O(°C)` <dbl>,
#> # `Cooler Voltage` <dbl>, f_datetime <dttm>, comment <chr>, f_start <dttm>,
#> # f_end <dttm>, pressure_atm <dbl>, site <chr>, treatment <chr>, date <chr>,
#> # plot <chr>, trial <chr>
path_co2fluxtent <- system.file("extdata/co2fluxtent",
package = "licoread")
import7500(path_co2fluxtent,
plotinfo = c("date", "location", "time_of_day", "trial"))
#> # A tibble: 345 × 24
#> f_fluxid `Relative Time` Temperature Pressure `Aux Input` `CO2 Absorptance`
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 06172020_… 0.91 -65.7 75.7 0 0.0752
#> 2 06172020_… 1.91 -65.7 75.7 0 0.0731
#> 3 06172020_… 2.91 -65.7 75.7 0 0.0737
#> 4 06172020_… 3.98 -65.7 75.7 0 0.0731
#> 5 06172020_… 4.91 -65.7 75.7 0 0.073
#> 6 06172020_… 5.92 -66.2 75.7 0 0.0729
#> 7 06172020_… 6.91 -65.7 75.7 0 0.0733
#> 8 06172020_… 7.92 -65.7 75.7 0 0.0733
#> 9 06172020_… 8.91 -65.7 75.7 0 0.0729
#> 10 06172020_… 9.92 -65.7 75.7 0 0.0728
#> # ℹ 335 more rows
#> # ℹ 18 more variables: `CO2 mmol/m3` <dbl>, `CO2 mg/m3` <dbl>,
#> # `CO2 umol/mol` <dbl>, `H2O Absorptance` <dbl>, `H2O mmol/m3` <dbl>,
#> # `H2O g/m3` <dbl>, `H2O mmol/mol` <dbl>, `H2O(°C)` <dbl>,
#> # `Cooler Voltage` <dbl>, f_datetime <dttm>, comment <chr>, f_start <dttm>,
#> # f_end <dttm>, pressure_atm <dbl>, date <chr>, location <chr>,
#> # time_of_day <chr>, trial <chr>