Each obspack file has a header with metadata and this function reads selected fields from the metadata and add them as columns. This new columns are used later to be filtered
Usage
obs_read(
index,
categories = "flask",
expr = NULL,
verbose = TRUE,
n_site_code = 15,
n_site_latitude = 18,
n_site_longitude = 19,
n_site_name = 15,
n_site_country = 18,
n_dataset_project = 21,
n_lab = 16,
n_scales = 31,
n_site_elevation = 20,
n_altitude_comment = 22,
n_utc = 18,
fill_value = -1e+34,
as_list = FALSE
)Arguments
- index
data.table
- categories
character; ONE category : of c("aircraft-pfp", "aircraft-insitu", "surface-insitu", "tower-insitu", "aircore", "surface-pfp", "shipboard-insitu", "flask").
- expr
String expressions to filter data.table internally
- verbose
Logical to show more information
- n_site_code
number of characters extratced from metadata after search
- n_site_latitude
number of characters extracted from metadata after search
- n_site_longitude
number of characters extracted from metadata after search
- n_site_name
number of characters extracted from metadata after search
- n_site_country
number of characters extracted from metadata after search
- n_dataset_project
number of characters extracted from metadata after search
- n_lab
number of characters extracted from metadata after search
- n_scales
number of characters extracted from metadata after search
- n_site_elevation
number of characters extracted from metadata after search
- n_altitude_comment
number of characters extracted from metadata after search
- n_utc
number of characters extracted from metadata after search
- fill_value
fill value. Appeared in aoa_aircraft-flask_19_allvalid.txt
- as_list
Logical to return as list
Note
The identification of the altitude and type is critical. The approach used here consists of: 1. Identify agl from the name of the tile. 2. If magl not present, search dill_values used in elevation and transform them into NA (not available) 3. If magl is not present, agl = altitude - elevation 4. If there are some NA in elevation, will result some NA in agl 5. A new column is added named `altitude_final` to store agl or asl 6. Another column named `type_altitude` is added to identify "magl" or "masl" 7. If there is any case NA in `altitude_final`, `type_altitude` is "not available"
Then, the relationship with hysplit is:
| type_altitude | hysplit | magl |
| agl | masl | asl |
| not available | f-PBL |
Examples
{
# Do not run
obs <- system.file("data-raw", package = "rtorf")
index <- obs_summary(obs)
dt <- obs_read(index)
obs_read(index, expr = "altitude_final == '5800'")
}
#> Number of files of index: 1
#> sector N
#> <char> <int>
#> 1: flask 1
#> 2: Total sectors 1
#> Detected 0 files with agl
#> Detected 1 files without agl
#> Searching flask...
#> 1: ch4_aoa_aircraft-flask_19_allvalid.txt
#> Searching flask...
#> 1: ch4_aoa_aircraft-flask_19_allvalid.txt
#> year month day hour minute second time start_time midpoint_time
#> <int> <int> <int> <int> <int> <int> <int> <int> <int>
#> 1: 2011 2 16 2 17 30 1297822650 1297822440 1297822650
#> 2: 2011 2 16 2 26 30 1297823190 1297822980 1297823190
#> 3: 2011 2 16 2 33 30 1297823610 1297823400 1297823610
#> 4: 2011 2 16 2 40 30 1297824030 1297823820 1297824030
#> 5: 2011 2 16 2 47 30 1297824450 1297824240 1297824450
#> ---
#> 226: 2019 3 14 2 15 30 1552529730 1552529520 1552529730
#> 227: 2019 3 14 2 22 30 1552530150 1552529940 1552530150
#> 228: 2019 5 15 5 10 30 1557897030 1557896820 1557897030
#> 229: 2019 9 4 7 54 30 1567583670 1567583460 1567583670
#> 230: 2020 3 10 6 42 30 1583822550 1583822340 1583822550
#> time_decimal value nvalue latitude longitude altitude elevation
#> <num> <num> <int> <num> <num> <num> <num>
#> 1: 2011.126 1.8464e-06 1 34.429 141.037 5800 -999.999
#> 2: 2011.126 1.8428e-06 1 34.058 141.830 5800 -999.999
#> 3: 2011.126 1.8502e-06 1 33.770 142.447 5800 -999.999
#> 4: 2011.126 1.8477e-06 1 33.480 143.052 5800 -999.999
#> 5: 2011.126 1.8393e-06 1 33.162 143.708 5800 -999.999
#> ---
#> 226: 2019.198 1.9945e-06 1 33.249 143.529 5800 -999.999
#> 227: 2019.198 1.9745e-06 1 32.885 144.267 5800 -999.999
#> 228: 2019.368 1.8902e-06 1 24.819 152.060 5800 -999.999
#> 229: 2019.675 1.8798e-06 1 24.327 152.091 5800 -999.999
#> 230: 2020.189 1.9433e-06 1 24.885 151.834 5800 -999.999
#> intake_height qcflag method unique_sample_location_num obs_flag obs_num
#> <num> <int> <int> <int> <int> <int>
#> 1: -999.999 1 18 8768042 1 1
#> 2: -999.999 1 18 8767980 1 2
#> 3: -999.999 1 18 8767880 1 3
#> 4: -999.999 1 18 8767781 1 4
#> 5: -999.999 1 18 8767708 1 5
#> ---
#> 226: -999.999 1 18 8767761 1 2278
#> 227: -999.999 1 18 8767655 1 2279
#> 228: -999.999 1 18 8766225 1 2339
#> 229: -999.999 1 18 8765601 1 2441
#> 230: -999.999 1 18 44498114 1 2573
#> obspack_num
#> <int>
#> 1: 5536255
#> 2: 5536256
#> 3: 5536257
#> 4: 5536258
#> 5: 5536259
#> ---
#> 226: 5538532
#> 227: 5538533
#> 228: 5538593
#> 229: 5538695
#> 230: 5538827
#> obspack_id
#> <char>
#> 1: obspack_ch4_1_GLOBALVIEWplus_v4.0_2021-10-14~ch4_aoa_aircraft-flask_19_allvalid~5536255
#> 2: obspack_ch4_1_GLOBALVIEWplus_v4.0_2021-10-14~ch4_aoa_aircraft-flask_19_allvalid~5536256
#> 3: obspack_ch4_1_GLOBALVIEWplus_v4.0_2021-10-14~ch4_aoa_aircraft-flask_19_allvalid~5536257
#> 4: obspack_ch4_1_GLOBALVIEWplus_v4.0_2021-10-14~ch4_aoa_aircraft-flask_19_allvalid~5536258
#> 5: obspack_ch4_1_GLOBALVIEWplus_v4.0_2021-10-14~ch4_aoa_aircraft-flask_19_allvalid~5536259
#> ---
#> 226: obspack_ch4_1_GLOBALVIEWplus_v4.0_2021-10-14~ch4_aoa_aircraft-flask_19_allvalid~5538532
#> 227: obspack_ch4_1_GLOBALVIEWplus_v4.0_2021-10-14~ch4_aoa_aircraft-flask_19_allvalid~5538533
#> 228: obspack_ch4_1_GLOBALVIEWplus_v4.0_2021-10-14~ch4_aoa_aircraft-flask_19_allvalid~5538593
#> 229: obspack_ch4_1_GLOBALVIEWplus_v4.0_2021-10-14~ch4_aoa_aircraft-flask_19_allvalid~5538695
#> 230: obspack_ch4_1_GLOBALVIEWplus_v4.0_2021-10-14~ch4_aoa_aircraft-flask_19_allvalid~5538827
#> name sector site_code
#> <char> <char> <char>
#> 1: ch4_aoa_aircraft-flask_19_allvalid.txt flask AOA
#> 2: ch4_aoa_aircraft-flask_19_allvalid.txt flask AOA
#> 3: ch4_aoa_aircraft-flask_19_allvalid.txt flask AOA
#> 4: ch4_aoa_aircraft-flask_19_allvalid.txt flask AOA
#> 5: ch4_aoa_aircraft-flask_19_allvalid.txt flask AOA
#> ---
#> 226: ch4_aoa_aircraft-flask_19_allvalid.txt flask AOA
#> 227: ch4_aoa_aircraft-flask_19_allvalid.txt flask AOA
#> 228: ch4_aoa_aircraft-flask_19_allvalid.txt flask AOA
#> 229: ch4_aoa_aircraft-flask_19_allvalid.txt flask AOA
#> 230: ch4_aoa_aircraft-flask_19_allvalid.txt flask AOA
#> site_name site_country
#> <char> <char>
#> 1: Aircraft Observation of Atmospheric trace gases by JMA Japan
#> 2: Aircraft Observation of Atmospheric trace gases by JMA Japan
#> 3: Aircraft Observation of Atmospheric trace gases by JMA Japan
#> 4: Aircraft Observation of Atmospheric trace gases by JMA Japan
#> 5: Aircraft Observation of Atmospheric trace gases by JMA Japan
#> ---
#> 226: Aircraft Observation of Atmospheric trace gases by JMA Japan
#> 227: Aircraft Observation of Atmospheric trace gases by JMA Japan
#> 228: Aircraft Observation of Atmospheric trace gases by JMA Japan
#> 229: Aircraft Observation of Atmospheric trace gases by JMA Japan
#> 230: Aircraft Observation of Atmospheric trace gases by JMA Japan
#> site_elevation site_latitude site_longitude dataset_project lab_1_abbr
#> <lgcl> <char> <char> <char> <char>
#> 1: NA -1e+34 -1e+34 aircraft-flask JMA
#> 2: NA -1e+34 -1e+34 aircraft-flask JMA
#> 3: NA -1e+34 -1e+34 aircraft-flask JMA
#> 4: NA -1e+34 -1e+34 aircraft-flask JMA
#> 5: NA -1e+34 -1e+34 aircraft-flask JMA
#> ---
#> 226: NA -1e+34 -1e+34 aircraft-flask JMA
#> 227: NA -1e+34 -1e+34 aircraft-flask JMA
#> 228: NA -1e+34 -1e+34 aircraft-flask JMA
#> 229: NA -1e+34 -1e+34 aircraft-flask JMA
#> 230: NA -1e+34 -1e+34 aircraft-flask JMA
#> dataset_calibration_scale
#> <char>
#> 1: WMO CH4 X2004A
#> 2: WMO CH4 X2004A
#> 3: WMO CH4 X2004A
#> 4: WMO CH4 X2004A
#> 5: WMO CH4 X2004A
#> ---
#> 226: WMO CH4 X2004A
#> 227: WMO CH4 X2004A
#> 228: WMO CH4 X2004A
#> 229: WMO CH4 X2004A
#> 230: WMO CH4 X2004A
#> altitude_comment
#> <char>
#> 1: Altitude (in meters above sea level). See provider_comment if available.
#> 2: Altitude (in meters above sea level). See provider_comment if available.
#> 3: Altitude (in meters above sea level). See provider_comment if available.
#> 4: Altitude (in meters above sea level). See provider_comment if available.
#> 5: Altitude (in meters above sea level). See provider_comment if available.
#> ---
#> 226: Altitude (in meters above sea level). See provider_comment if available.
#> 227: Altitude (in meters above sea level). See provider_comment if available.
#> 228: Altitude (in meters above sea level). See provider_comment if available.
#> 229: Altitude (in meters above sea level). See provider_comment if available.
#> 230: Altitude (in meters above sea level). See provider_comment if available.
#> site_utc2lst agl type_altitude altitude_final id
#> <num> <num> <num> <num> <int>
#> 1: 9 NA 1 5800 1
#> 2: 9 NA 1 5800 1
#> 3: 9 NA 1 5800 1
#> 4: 9 NA 1 5800 1
#> 5: 9 NA 1 5800 1
#> ---
#> 226: 9 NA 1 5800 1
#> 227: 9 NA 1 5800 1
#> 228: 9 NA 1 5800 1
#> 229: 9 NA 1 5800 1
#> 230: 9 NA 1 5800 1