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imports data from the li7500 setup described in Halbritter et al (2024)

Usage

import7500(path, version = "till2023", plotinfo = FALSE)

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>