imports data from the li7500 setup described in Halbritter et al (2024)
Usage
import7500(
path,
version = "till2023",
plotinfo = TRUE,
plotinfo_names = c("location", "date", "time_of_day", "trial")
)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
TRUE(default), means that the file name contains information about the measurement and that should be added in the output.- plotinfo_names
character vector of column names to use when seperating the plot info from the file name. Default is following the recommanded file naming convention
[location]_[date]_[time of day]_[trial].
Value
a dataframe with all data present in the files to import. New
datetime and filename columns contain respectively the datetime of
measurements and their orginial filename. If comment = TRUE, a column
comment will contain the comments. Measurement informations from the file
names are stored in new columns according to plotinfo_names.
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", plotinfo = FALSE)
#> # A tibble: 330 × 42
#> filename 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_names = c("site", "block", "date", "plot", "trial"))
#> # A tibble: 251 × 25
#> filename `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>,
#> # file_start <dttm>, file_end <dttm>, pressure_atm <dbl>, site <chr>,
#> # block <chr>, date <chr>, plot <chr>, trial <chr>
path_co2fluxtent <- system.file("extdata/co2fluxtent",
package = "licoread")
import7500(path_co2fluxtent,
plotinfo_names = c("date", "location", "time_of_day", "trial"))
#> # A tibble: 345 × 24
#> filename `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>,
#> # file_start <dttm>, file_end <dttm>, pressure_atm <dbl>, date <chr>,
#> # location <chr>, time_of_day <chr>, trial <chr>