Skip to contents padding-top: 70px;

Reading a CR3000 data file

read_cr3000.Rd

Tool for reading output files created by Campbell Scientific CR3000 data loggers and storing their contents in exdf objects.

Usage

read_cr3000(
    file_name,
    rows_to_skip = 1,
    variable_name_row = 2,
    variable_unit_row = 3,
    data_start_row = 5,
    remove_NA_rows = TRUE,
    ...
  )

Arguments

file_name

A relative or absolute path to a .dat file containing TDL data.

rows_to_skip

The number of rows to skip at the beginning of the file; the first row in a TDL file typically has fewer columns than the others, which causes problems when storing it as a table.

variable_name_row

The row number in the TDL file containing the names of the variables (RECORD, Conc12C_Avg, etc).

variable_unit_row

The row number in the TDL file containing the units of the variables (ppm, V, etc).

data_start_row

The first row number of the table containing the measured data.

remove_NA_rows

A logical value indicating whether to remove any rows whose values are all NA.

...

Additional arguments to be passed to read.csv.

Value

An exdf object that fully includes all the data from the CR3000 output file. In addition to the elements described in the documentation for read_gasex_file, the following "extra" elements are also included:

  • rows_to_skip: A copy of the input argument with the same name

  • variable_name_row: A copy of the input argument with the same name.

  • variable_unit_row: A copy of the input argument with the same name.

  • data_start_row: A copy of the input argument with the same name.

See also

read_gasex_file

Examples

# Example: reading a TDL file that is included with the PhotoGEA package.
tdl_file <- read_cr3000(
  PhotoGEA_example_file_path('tdl_sampling_1.dat')
)

tdl_file$file_name # A record of where the data came from
#> NULL
str(tdl_file)      # View the contents of the exdf object's main_data
#> 
#> Converting an `exdf` object to a `data.frame` before printing
#> 
#> 'data.frame':	922 obs. of  97 variables:
#>  $ TIMESTAMP [read_cr3000] (TS)            : chr  "2022-07-12 06:12:43" "2022-07-12 06:13:03" "2022-07-12 06:13:23" "2022-07-12 06:13:43" ...
#>  $ RECORD [read_cr3000] (RN)               : num  0 1 2 3 4 5 6 7 8 9 ...
#>  $ valve_number [read_cr3000] ()           : num  20 21 23 26 2 10 11 12 13 20 ...
#>  $ diag_system_Avg [read_cr3000] ()        : num  128 128 128 132 128 128 128 128 128 128 ...
#>  $ NumSamples [read_cr3000] ()             : num  100 100 100 100 100 100 100 100 100 100 ...
#>  $ Conc12C_Avg [read_cr3000] (ppm)         : num  2.9 68.8 311.9 1022.5 294.3 ...
#>  $ Conc13C_Avg [read_cr3000] (ppm)         : num  0.132 0.847 3.481 11.114 3.299 ...
#>  $ TGAStatus_Avg [read_cr3000] ()          : num  96 96 96 96 96 96 96 96 96 96 ...
#>  $ TGAPressure_Avg [read_cr3000] (mb)      : num  30 30 30 30 30 ...
#>  $ LaserTemp_Avg [read_cr3000] (degC)      : num  -4 -4 -4 -4 -4 ...
#>  $ DCCurrentA_Avg [read_cr3000] (mA)       : num  50.4 50.4 50.4 50.4 50.4 ...
#>  $ DCCurrentB_Avg [read_cr3000] (mA)       : num  38.9 38.9 38.9 38.9 38.9 ...
#>  $ TGAAnalog1_Avg [read_cr3000] (V)        : num  0.0244 0.0244 0.0244 0.0244 0.0244 ...
#>  $ TGATemp1_Avg [read_cr3000] (degC)       : num  30 30 30 30 30 ...
#>  $ TGATemp2_Avg [read_cr3000] (degC)       : num  30 30 30 30 30 ...
#>  $ LaserCooler_Avg [read_cr3000] (V)       : num  2.02 2.02 2.02 2.02 2.02 ...
#>  $ RefDetSigA_Avg [read_cr3000] (mV)       : num  2.48 2.48 2.48 2.48 2.48 ...
#>  $ RefDetSigB_Avg [read_cr3000] (mV)       : num  0.503 0.503 0.502 0.502 0.502 ...
#>  $ RefDetTransA_Avg [read_cr3000] (%)      : num  41.2 41.2 41.1 41.1 41.1 ...
#>  $ RefDetTransB_Avg [read_cr3000] (%)      : num  54.8 54.8 54.7 54.7 54.7 ...
#>  $ RefDetTemp_Avg [read_cr3000] (degC)     : num  -35 -35 -35 -35 -35 ...
#>  $ RefDetCooler_Avg [read_cr3000] ()       : num  1461 1461 1461 1461 1461 ...
#>  $ RefDetGainOffset_Avg [read_cr3000] ()   : num  8217 8217 8217 8217 8217 ...
#>  $ SmpDetSigA_Avg [read_cr3000] (mV)       : num  57.8 56.5 51.6 39.8 52 ...
#>  $ SmpDetSigB_Avg [read_cr3000] (mV)       : num  10.08 9.88 9.17 7.38 9.22 ...
#>  $ SmpDetTransA_Avg [read_cr3000] (%)      : num  99.8 97.4 89.2 68.8 89.8 ...
#>  $ SmpDetTransB_Avg [read_cr3000] (%)      : num  114.4 112.2 104.2 84.2 104.8 ...
#>  $ SmpDetTemp_Avg [read_cr3000] (degC)     : num  -39 -39 -39 -39 -39 ...
#>  $ SmpDetCooler_Avg [read_cr3000] ()       : num  1449 1449 1449 1449 1449 ...
#>  $ SmpDetGainOffset_Avg [read_cr3000] ()   : num  8456 8456 8456 8456 8456 ...
#>  $ TGATemp1DutyCycle_Avg [read_cr3000] ()  : num  0.13 0.121 0.132 0.129 0.138 ...
#>  $ TGATemp2DutyCycle_Avg [read_cr3000] ()  : num  0.0601 0.077 0.0677 0.0676 0.0649 ...
#>  $ SampleFlow_Avg [read_cr3000] (ml_min)   : num  167 167 167 164 162 ...
#>  $ ExcessFlow_Avg [read_cr3000] (ml_min)   : num  95.77 105.457 140.852 0.123 53.341 ...
#>  $ SamplePress_Avg [read_cr3000] (mb)      : num  400 400 400 396 400 ...
#>  $ BypassPress_Avg [read_cr3000] (mb)      : num  400 400 400 400 400 ...
#>  $ SampleP_control_Avg [read_cr3000] ()    : num  0.4 0.404 0.414 0.2 0.385 ...
#>  $ BypassP_control_Avg [read_cr3000] ()    : num  0.477 0.475 0.471 0.484 0.496 ...
#>  $ TGAPress_control_Avg [read_cr3000] ()   : num  0.528 0.529 0.53 0.53 0.53 ...
#>  $ panel_tmpr_Avg [read_cr3000] (degC)     : num  24.7 24.7 24.7 24.7 24.7 ...
#>  $ batt_volt_Avg [read_cr3000] (V)         : num  11.8 11.8 11.8 11.8 11.8 ...
#>  $ buff_depth_Max [read_cr3000] ()         : num  0 0 0 0 0 0 0 0 0 0 ...
#>  $ Conc12C_Std [read_cr3000] (ppm)         : num  0.5244 0.0946 0.2025 1.1064 1.5535 ...
#>  $ Conc13C_Std [read_cr3000] (ppm)         : num  0.00797 0.00637 0.00849 0.02317 0.018 ...
#>  $ TGAStatus_Std [read_cr3000] ()          : num  0 0 0 0 0 0 0 0 0 0 ...
#>  $ TGAPressure_Std [read_cr3000] (mb)      : num  0.0101 0.0105 0.0115 0.0102 0.0112 ...
#>  $ LaserTemp_Std [read_cr3000] (degC)      : num  0.000244 0.000289 0.000272 0.000287 0.00025 ...
#>  $ DCCurrentA_Std [read_cr3000] (mA)       : num  0.000454 0.0006 0.000338 0.000492 0.000503 ...
#>  $ DCCurrentB_Std [read_cr3000] (mA)       : num  0.000677 0.000844 0.00061 0.000753 0.000625 ...
#>  $ TGAAnalog1_Std [read_cr3000] (V)        : num  1.56e-05 1.39e-05 1.31e-05 1.30e-05 1.31e-05 ...
#>  $ TGATemp1_Std [read_cr3000] (degC)       : num  0.000994 0.00121 0.003558 0.001737 0.001128 ...
#>  $ TGATemp2_Std [read_cr3000] (degC)       : num  0.00215 0.00137 0.00141 0.00126 0.00227 ...
#>  $ LaserCooler_Std [read_cr3000] (V)       : num  0.000293 0.000347 0.000326 0.000345 0.000301 ...
#>  $ RefDetSigA_Std [read_cr3000] (mV)       : num  0.00155 0.00185 0.00155 0.00199 0.00154 ...
#>  $ RefDetSigB_Std [read_cr3000] (mV)       : num  0.00169 0.00148 0.00145 0.0015 0.00188 ...
#>  $ RefDetTransA_Std [read_cr3000] (%)      : num  0.0298 0.0354 0.0268 0.0366 0.0293 ...
#>  $ RefDetTransB_Std [read_cr3000] (%)      : num  0.255 0.233 0.223 0.226 0.258 ...
#>  $ RefDetTemp_Std [read_cr3000] (degC)     : num  0.00364 0.0032 0.00361 0.00365 0.00315 ...
#>  $ RefDetCooler_Std [read_cr3000] ()       : num  0.354 0.316 0.356 0.357 0.299 ...
#>  $ RefDetGainOffset_Std [read_cr3000] ()   : num  0 0 0 0 0 0 0 0 0 0 ...
#>  $ SmpDetSigA_Std [read_cr3000] (mV)       : num  0.01137 0.00519 0.00502 0.01354 0.02786 ...
#>  $ SmpDetSigB_Std [read_cr3000] (mV)       : num  0.00497 0.00576 0.00366 0.00388 0.00501 ...
#>  $ SmpDetTransA_Std [read_cr3000] (%)      : num  0.0214 0.00781 0.00875 0.02549 0.05127 ...
#>  $ SmpDetTransB_Std [read_cr3000] (%)      : num  0.0631 0.0441 0.0564 0.0485 0.0763 ...
#>  $ SmpDetTemp_Std [read_cr3000] (degC)     : num  0.00136 0.00128 0.00116 0.00148 0.00128 ...
#>  $ SmpDetCooler_Std [read_cr3000] ()       : num  0.1147 0.1077 0.1009 0.1203 0.0931 ...
#>  $ SmpDetGainOffset_Std [read_cr3000] ()   : num  0 0 0 0 0 0 0 0 0 0 ...
#>  $ TGATemp1DutyCycle_Std [read_cr3000] ()  : num  0.00923 0.00826 0.0119 0.00883 0.00886 ...
#>  $ TGATemp2DutyCycle_Std [read_cr3000] ()  : num  0.00837 0.00978 0.00828 0.00849 0.00862 ...
#>  $ SampleFlow_Std [read_cr3000] (ml_min)   : num  0.1467 0.2004 0.1747 0.0871 0.1594 ...
#>  $ ExcessFlow_Std [read_cr3000] (ml_min)   : num  0.10026 0.11171 0.1207 0.00958 0.08248 ...
#>  $ SamplePress_Std [read_cr3000] (mb)      : num  0.0214 0.0234 0.0199 0.0935 0.0242 ...
#>  $ BypassPress_Std [read_cr3000] (mb)      : num  0.1431 0.0428 0.1358 0.4229 0.3114 ...
#>  $ SampleP_control_Std [read_cr3000] ()    : num  9.05e-05 8.99e-05 7.08e-05 0.00 2.21e-04 ...
#>  $ BypassP_control_Std [read_cr3000] ()    : num  1.85e-04 5.47e-05 1.52e-04 4.63e-04 3.60e-04 ...
#>  $ TGAPress_control_Std [read_cr3000] ()   : num  0.000536 0.000541 0.000592 0.000525 0.000577 ...
#>  $ panel_tmpr_Std [read_cr3000] (degC)     : num  0.00641 0.00222 0.00214 0.0023 0.00224 ...
#>  $ batt_volt_Std [read_cr3000] (V)         : num  0.00241 0.00235 0.00224 0.00218 0.00232 ...
#>  $ Li64Match_Avg(1) [read_cr3000] ()       : num  1 1 1 1 1 1 1 1 1 1 ...
#>  $ Li64Match_Avg(2) [read_cr3000] ()       : num  0 0 0 0 0 0 0 0 0 0 ...
#>  $ Li64Tmpr_Avg(1) [read_cr3000] (degC)    : num  -79.2 -77.6 -81.6 -79.4 -79.7 ...
#>  $ Li64Tmpr_Avg(2) [read_cr3000] (degC)    : num  NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ...
#>  $ Li64Heat_Avg(1) [read_cr3000] ()        : num  1 1 1 1 1 1 1 1 1 1 ...
#>  $ Li64Heat_Avg(2) [read_cr3000] ()        : num  0 0 0 0 0 0 0 0 0 0 ...
#>  $ _Mix_diag_system_Avg [read_cr3000] ()   : num  NaN 960 960 960 960 960 960 960 960 960 ...
#>  $ _Mix_ExcessZeroFlow_Avg [read_cr3000] (): num  NaN 0.42 0.379 0.441 0.411 ...
#>  $ _Mix_ExcessMixFlow_Avg [read_cr3000] () : num  NaN 159 158 158 158 ...
#>  $ _Mix_CO2Press_Avg [read_cr3000] ()      : num  NaN 11.4 11.4 11.4 11.4 ...
#>  $ _Mix_ZeroPress_Avg [read_cr3000] ()     : num  NaN 16.5 16.5 16.5 16.5 ...
#>  $ _Mix_CO2P_control_Avg [read_cr3000] ()  : num  NaN 0 0 0 0 0 0 0 0 0 ...
#>  $ _Mix_ZeroP_control_Avg [read_cr3000] () : num  NaN 0 0 0 0 0 0 0 0 0 ...
#>  $ _Mix_MixTmpr1_Avg [read_cr3000] ()      : num  NaN 32 32 32 32 ...
#>  $ _Mix_MixTmpr2_Avg [read_cr3000] ()      : num  NaN 31.7 31.7 31.7 31.7 ...
#>  $ _Mix_MixHeat1_Avg [read_cr3000] ()      : num  NaN 1 1 1 1 1 1 1 1 1 ...
#>  $ _Mix_MixHeat2_Avg [read_cr3000] ()      : num  NaN 1 1 1 1 1 1 1 1 1 ...
#>  $ _Mix_panel_tmpr_Avg [read_cr3000] ()    : num  NaN 24.1 24.1 24.1 24.1 ...
#>  $ _Mix_batt_volt_Avg [read_cr3000] ()     : num  NaN 9.62 9.62 9.62 9.62 ...