Import Experimental Data from agroclimR Data Workbook
import_exp_data.Rdimport_exp_data() performs extraction of experimental data from the agroclimR data workbook, including
location, soil, climate data, and observed data for phenology, leaf area index,
dry matter, and yield.
Reads data from agroclimR workbook sheets.
Arguments
- files
Vector of strings with workbook names (.xls extension file included).
- model
String indicating the model name, default "oryza",options: ("dssat", "aquacrop").
- workbook_name
String with the workbook name (full name).
Value
List containing raw and observed data by component ("data", "soil", "wth", "phen", "lai", "dry_matter", "yield").
agroclimR list. A List of data frames for each sheet in the workbook.
Examples
#' # File names vector, extension include
name_file = c("agroclimR_workbook.xlsx")
# Files directory
test_file = system.file("extdata", name_file, package = "agroclimR")
# Import data to R lists and tibble formats
obs_data = import_exp_data(test_file, model = "oryza")
head(obs_data)
#> $data
#> # A tibble: 1 × 2
#> file input_data
#> <chr> <list>
#> 1 /home/runner/work/_temp/Library/agroclimR/extdata/agroclimR_work… <named list>
#>
#> $soil
#> # A tibble: 1 × 5
#> site soil lat lon elev
#> <chr> <list> <dbl> <dbl> <dbl>
#> 1 SDTO <tibble [3 × 20]> 3.91 -75.0 415
#>
#> $wth
#> # A tibble: 1 × 6
#> site ws_id wth lat lon elev
#> <chr> <dbl> <list> <dbl> <dbl> <dbl>
#> 1 SDTO 1 <tibble [1,461 × 7]> 3.91 -75.0 415
#>
#> $phen
#> # A tibble: 21 × 4
#> exp_file data var value
#> <chr> <list> <chr> <dbl>
#> 1 SDTO_FED2000_MADRI_S1 <tibble [5 × 2]> IDAT 51
#> 2 SDTO_FED2000_MADRI_S1 <tibble [5 × 2]> FDAT 81
#> 3 SDTO_FED2000_MADRI_S1 <tibble [5 × 2]> MDAT 104
#> 4 SDTO_FED2000_MADRII_S1 <tibble [5 × 2]> IDAT 48
#> 5 SDTO_FED2000_MADRII_S1 <tibble [5 × 2]> FDAT 85
#> 6 SDTO_FED2000_MADRII_S1 <tibble [5 × 2]> MDAT 115
#> 7 SDTO_FED2000_MADRI_S2 <tibble [5 × 2]> IDAT 49
#> 8 SDTO_FED2000_MADRI_S2 <tibble [5 × 2]> FDAT 85
#> 9 SDTO_FED2000_MADRI_S2 <tibble [5 × 2]> MDAT 105
#> 10 SDTO_FED2000_MADRII_S2 <tibble [5 × 2]> IDAT 40
#> # ℹ 11 more rows
#>
#> $lai
#> # A tibble: 77 × 5
#> exp_file date var value se
#> <chr> <date> <chr> <dbl> <dbl>
#> 1 SDTO_FED2000_MADRI_S1 2013-05-21 LAI NA NA
#> 2 SDTO_FED2000_MADRI_S1 2013-05-28 LAI NA NA
#> 3 SDTO_FED2000_MADRI_S1 2013-06-07 LAI NA NA
#> 4 SDTO_FED2000_MADRI_S1 2013-06-12 LAI NA NA
#> 5 SDTO_FED2000_MADRI_S1 2013-06-18 LAI NA NA
#> 6 SDTO_FED2000_MADRI_S1 2013-06-25 LAI NA NA
#> 7 SDTO_FED2000_MADRI_S1 2013-07-07 LAI NA NA
#> 8 SDTO_FED2000_MADRI_S1 2013-07-10 LAI NA NA
#> 9 SDTO_FED2000_MADRI_S1 2013-07-17 LAI NA NA
#> 10 SDTO_FED2000_MADRI_S1 2013-07-22 LAI NA NA
#> # ℹ 67 more rows
#>
#> $dry_matter
#> # A tibble: 385 × 5
#> exp_file date var value se
#> <chr> <date> <chr> <dbl> <dbl>
#> 1 SDTO_FED2000_MADRI_S1 2013-05-21 WAGT 610. 37.2
#> 2 SDTO_FED2000_MADRI_S1 2013-05-21 WLVD 0 0
#> 3 SDTO_FED2000_MADRI_S1 2013-05-21 WLVG 316. 20.4
#> 4 SDTO_FED2000_MADRI_S1 2013-05-21 WSO 0 0
#> 5 SDTO_FED2000_MADRI_S1 2013-05-21 WST 294. 20
#> 6 SDTO_FED2000_MADRI_S1 2013-05-28 WAGT 1188 254
#> 7 SDTO_FED2000_MADRI_S1 2013-05-28 WLVD 0 0
#> 8 SDTO_FED2000_MADRI_S1 2013-05-28 WLVG 544. 122.
#> 9 SDTO_FED2000_MADRI_S1 2013-05-28 WSO 0 0
#> 10 SDTO_FED2000_MADRI_S1 2013-05-28 WST 644. 132.
#> # ℹ 375 more rows
#>
#' # File names vector, extension include
name_file = c("agroclimR_workbook.xlsx")
# Files directory
test_file = system.file("extdata", name_file, package = "agroclimR")
# Import data to R lists and tibble formats
agroclimr_list = read_agroclimr_data(test_file)
agroclimr_list
#> $AGRO_man
#> # A tibble: 7 × 14
#> ID LOC_ID PROJECT CULTIVAR TR_N LAT LONG ALT PDAT CROP_SYS ESTAB
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <chr> <chr> <chr>
#> 1 SDTOS1MA… SDTO MADRI FED2000 S1 3.91 -75.0 415 2013… IRRIGAT… DIRE…
#> 2 SDTOS1MA… SDTO MADRII FED2000 S1 3.91 -75.0 415 2015… IRRIGAT… DIRE…
#> 3 SDTOS2MA… SDTO MADRI FED2000 S2 3.91 -75.0 415 2013… IRRIGAT… DIRE…
#> 4 SDTOS2MA… SDTO MADRII FED2000 S2 3.91 -75.0 415 2015… IRRIGAT… DIRE…
#> 5 SDTOS3COL SDTO COL FED2000 S3 3.91 -75.0 415 2014… IRRIGAT… DIRE…
#> 6 SDTOS3MA… SDTO MADRI FED2000 S3 3.91 -75.0 415 2014… IRRIGAT… DIRE…
#> 7 SDTOS4COL SDTO COL FED2000 S4 3.91 -75.0 415 2015… IRRIGAT… DIRE…
#> # ℹ 3 more variables: NPLDS <dbl>, SBDUR <lgl>, TRDAT <lgl>
#>
#> $PLANT_obs
#> # A tibble: 77 × 22
#> ID LOC_ID CULTIVAR SAMPLING_DATE WLVG_OBS WLVG_SE LAI_OBS LAI_SE
#> <chr> <chr> <chr> <dttm> <dbl> <dbl> <dbl> <dbl>
#> 1 SDTOS1MA… SDTO FED2000 2013-05-21 00:00:00 316. 20.4 NA NA
#> 2 SDTOS1MA… SDTO FED2000 2013-05-28 00:00:00 544. 122. NA NA
#> 3 SDTOS1MA… SDTO FED2000 2013-06-07 00:00:00 752. 168. NA NA
#> 4 SDTOS1MA… SDTO FED2000 2013-06-12 00:00:00 816. 169. NA NA
#> 5 SDTOS1MA… SDTO FED2000 2013-06-18 00:00:00 1495. 250. NA NA
#> 6 SDTOS1MA… SDTO FED2000 2013-06-25 00:00:00 1665. 387. NA NA
#> 7 SDTOS1MA… SDTO FED2000 2013-07-07 00:00:00 2740. 400. NA NA
#> 8 SDTOS1MA… SDTO FED2000 2013-07-10 00:00:00 3476. 270 NA NA
#> 9 SDTOS1MA… SDTO FED2000 2013-07-17 00:00:00 3985. 129. NA NA
#> 10 SDTOS1MA… SDTO FED2000 2013-07-22 00:00:00 3419. 48.8 NA NA
#> # ℹ 67 more rows
#> # ℹ 14 more variables: WLVD_OBS <dbl>, WLVD_SE <dbl>, WST_OBS <dbl>,
#> # WST_SE <dbl>, WSO_OBS <dbl>, WSO_SE <dbl>, WAGT_OBS <dbl>, WAGT_SE <dbl>,
#> # NLV_OBS <lgl>, NLV_SE <lgl>, NST_OBS <lgl>, NST_SE <lgl>, NP_OBS <lgl>,
#> # NP_SE <lgl>
#>
#> $FERT_obs
#> # A tibble: 37 × 7
#> ID LOC_ID FERT_No DDE N P K
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 SDTOS1MADRI SDTO 1 10 42 21.5 33
#> 2 SDTOS1MADRI SDTO 2 23 58 1.5 33
#> 3 SDTOS1MADRI SDTO 3 38 56.5 0 30
#> 4 SDTOS1MADRI SDTO 4 52 51.2 0 15
#> 5 SDTOS1MADRI SDTO 5 64 18.4 0 0
#> 6 SDTOS1MADRII SDTO 1 9 42 21.5 48
#> 7 SDTOS1MADRII SDTO 2 23 58 31.5 33
#> 8 SDTOS1MADRII SDTO 3 37 56.5 0 30
#> 9 SDTOS1MADRII SDTO 4 50 51.2 0 15
#> 10 SDTOS1MADRII SDTO 5 62 36.8 0 0
#> # ℹ 27 more rows
#>
#> $PHEN_obs
#> # A tibble: 7 × 8
#> ID LOC_ID CULTIVAR PDAT EDAT
#> <chr> <chr> <chr> <dttm> <dttm>
#> 1 SDTOS1MADRI SDTO FED2000 2013-04-29 00:00:00 2013-05-08 00:00:00
#> 2 SDTOS1MADRII SDTO FED2000 2015-06-05 00:00:00 2015-06-14 00:00:00
#> 3 SDTOS2MADRI SDTO FED2000 2013-12-05 00:00:00 2013-12-12 00:00:00
#> 4 SDTOS2MADRII SDTO FED2000 2015-11-03 00:00:00 2015-11-12 00:00:00
#> 5 SDTOS3COL SDTO FED2000 2014-10-07 00:00:00 2014-10-16 00:00:00
#> 6 SDTOS3MADRI SDTO FED2000 2014-02-05 00:00:00 2014-02-11 00:00:00
#> 7 SDTOS4COL SDTO FED2000 2015-02-20 00:00:00 2015-03-03 00:00:00
#> # ℹ 3 more variables: IDAT <dttm>, FDAT <dttm>, MDAT <dttm>
#>
#> $YIELD_obs
#> # A tibble: 7 × 20
#> ID LOC_ID CULTIVAR YIELD_AVG YIELD_MIN YIELD_MAX HIAD HIAD_SE PAN_fert
#> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 SDTOS1MA… SDTO FED2000 8103. 7331. 8931. 0.335 8.90e-3 88.9
#> 2 SDTOS2MA… SDTO FED2000 4474. 3795. 5244. 0.300 5.65e-4 95.5
#> 3 SDTOS3MA… SDTO FED2000 5032. 4247. 5951. 0.305 2.95e-3 92.9
#> 4 SDTOS3COL SDTO FED2000 4935. 4403. 5365. 0.415 1.19e-2 88.5
#> 5 SDTOS4COL SDTO FED2000 5542. 4927. 6056. 0.390 2.98e-2 81.3
#> 6 SDTOS1MA… SDTO FED2000 5430. 5120. 5719. 0.405 7.22e-3 86.1
#> 7 SDTOS2MA… SDTO FED2000 5114. 4676. 5550. 0.356 2.01e-2 88.4
#> # ℹ 11 more variables: PAN_fert_SE <dbl>, GW1000 <dbl>, GW1000_SE <dbl>,
#> # ST_M2 <dbl>, ST_M2_SE <dbl>, PAN_M2 <dbl>, PAN_M2_SE <dbl>, GT_PAN <dbl>,
#> # GT_PAN_SE <dbl>, GF_PAN <dbl>, GF_PAN_SE <dbl>
#>
#> $WTH_obs
#> # A tibble: 1,461 × 9
#> LOC_ID WS_ID DATE TMAX TMIN RAIN SRAD RHUM WSPD
#> <chr> <dbl> <dttm> <dbl> <dbl> <dbl> <dbl> <dbl> <lgl>
#> 1 SDTO 1 2013-01-01 00:00:00 36.0 25.7 0 20.9 66.3 NA
#> 2 SDTO 1 2013-01-02 00:00:00 35.7 25.1 0.2 21.6 73.3 NA
#> 3 SDTO 1 2013-01-03 00:00:00 38.5 24.0 0 23.1 61.4 NA
#> 4 SDTO 1 2013-01-04 00:00:00 35.7 22.9 0 21.4 68.9 NA
#> 5 SDTO 1 2013-01-05 00:00:00 38.8 23.8 0 22.9 69.5 NA
#> 6 SDTO 1 2013-01-06 00:00:00 37.2 22.7 1.2 24.2 65.9 NA
#> 7 SDTO 1 2013-01-07 00:00:00 38.4 23.7 0 22.9 60.3 NA
#> 8 SDTO 1 2013-01-08 00:00:00 34.7 22.5 0 22.1 74.3 NA
#> 9 SDTO 1 2013-01-09 00:00:00 38.9 23.9 0 22.7 72.1 NA
#> 10 SDTO 1 2013-01-10 00:00:00 38.9 24.2 0 22.8 72.2 NA
#> # ℹ 1,451 more rows
#>
#> $SOIL_obs
#> # A tibble: 18 × 21
#> ID LOC_ID SAMPLING_DATE NL DEPTH STC SAND SILT CLAY SBDM
#> <chr> <chr> <dttm> <dbl> <dbl> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 SDTOS1M… SDTO 2013-05-10 00:00:00 1 20 Lo 39.2 45.6 15.2 1.53
#> 2 SDTOS1M… SDTO 2013-05-10 00:00:00 2 20 Lo 37.9 46.9 15.2 1.71
#> 3 SDTOS1M… SDTO 2013-05-10 00:00:00 3 20 Lo 40.3 44.5 15.2 1.66
#> 4 SDTOS1M… SDTO 2015-08-10 00:00:00 1 20 SaLo 70.9 17.6 11.6 1.40
#> 5 SDTOS1M… SDTO 2015-08-10 00:00:00 2 20 SaLo 79.7 8.77 11.6 1.49
#> 6 SDTOS1M… SDTO 2015-08-10 00:00:00 3 20 SaLo 77.7 7.83 14.4 1.46
#> 7 SDTOS2M… SDTO 2014-04-10 00:00:00 1 20 Lo 41.3 45.3 13.4 1.79
#> 8 SDTOS2M… SDTO 2014-04-10 00:00:00 2 20 Lo 47.6 39.0 13.4 1.76
#> 9 SDTOS2M… SDTO 2014-04-10 00:00:00 3 20 SaLo 77.9 8.78 13.3 1.59
#> 10 SDTOS2M… SDTO 2015-12-23 00:00:00 1 20 Lo 42.6 39.1 18.3 1.56
#> 11 SDTOS2M… SDTO 2015-12-23 00:00:00 2 20 Lo 47.7 37.9 14.5 1.69
#> 12 SDTOS2M… SDTO 2015-12-23 00:00:00 3 20 Lo 43.9 40.4 15.7 1.70
#> 13 SDTOS3M… SDTO 2014-02-26 00:00:00 1 20 SiLo 28.3 56.0 15.7 1.59
#> 14 SDTOS3M… SDTO 2014-02-26 00:00:00 2 20 Lo 45.0 36.9 18.1 1.80
#> 15 SDTOS3M… SDTO 2014-02-26 00:00:00 3 20 SaLo 81.4 2.96 15.6 1.54
#> 16 SDTOS4M… SDTO 2014-07-24 00:00:00 1 20 Lo 50.3 40.7 8.96 1.45
#> 17 SDTOS4M… SDTO 2014-07-24 00:00:00 2 20 SaLo 81.9 5.43 12.7 1.53
#> 18 SDTOS4M… SDTO 2014-07-24 00:00:00 3 20 SaLo 83.1 2.93 13.9 1.47
#> # ℹ 11 more variables: SOC <dbl>, SLON <dbl>, SNH4 <dbl>, SNO3 <dbl>, PH <dbl>,
#> # SCEC <dbl>, WCST <dbl>, WCFC <dbl>, WCWP <dbl>, WCAD <dbl>, SSKS <dbl>
#>
#> $Metadata
#> # A tibble: 85 × 7
#> COMPONENT VAR_NAME DESCRIPTION TYPE UNITS Calculation method /…¹ Agrovoc
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 AGRO ID Trial ID char… XXXX NA NA
#> 2 AGRO LOC_ID locality ID char… name NA NA
#> 3 AGRO PROJECT Project ID char… name NA NA
#> 4 AGRO CULTIVAR Cultivar name char… name NA NA
#> 5 AGRO TR_N Treatment numb… char… cn NA NA
#> 6 AGRO LAT Latitude nume… Deci… GPS, G-EARTH http:/…
#> 7 AGRO LONG Longitude nume… Deci… GPS, G-EARTH http:/…
#> 8 AGRO ALT Elevation(m ab… nume… mete… GPS, G-EARTH http:/…
#> 9 AGRO PDAT Planting date date MM/D… Field Manual http:/…
#> 10 AGRO CROP_SYS Crop system char… IRRI… Field Manual NA
#> # ℹ 75 more rows
#> # ℹ abbreviated name: ¹`Calculation method / Observation`
#>