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Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(eva3dm) > > test_check("eva3dm") calculating wind speed ... calculating wind direction... VVIbes has only 0 valid observations (lesser than 8 obs) Ibirapuera not found in observation input Americana has 227 valid observations using 0 for min cutoff 227 values left using 999 for max cutoff 227 values left using 0 for min NME cutoff 227 values left using 935 for max NME cutoff 227 values left Terradonunca not found in observation input Americana not found in model input zeros contains only zeros (or constant values) and NA values for model zeros contains only zeros (or constant values) and NA values for observations zeros contains only zeros (or constant values) and NA values for observations combining all sites... considering a fair comparison for other domain... Americana SAndre VVIbes zero zeros ... ALL has 914 valid observations combining all sites... considering a fair comparison for other domain... Americana SAndre VVIbes zero zeros ... ALL has 914 valid observations using model in obs combining all sites... Americana SAndre VVIbes zero zeros ... ALL has 914 valid observations using model in names(obs) combining all sites... Americana SAndre VVIbes zero zeros ... ALL has 914 valid observations n Obs Sim r IOA FA2 VVIbes 0 NA NA NA NA NA Ibirapuera 0 NA NA NA NA NA am 2 227 440.9295 378.18197 0.6492022 0.4366783 1.00000000 Terradonunca 0 NA NA NA NA NA Americana 0 NA NA NA NA NA model zero 0 NA NA NA NA NA obs zero 0 NA NA NA NA NA obs cke 0 NA NA NA NA NA all fair 914 155.6685 39.70511 -0.3543786 0.3421893 0.03829322 all fair 2 914 155.6685 39.70511 -0.3543786 0.3421893 0.03829322 all model in obs 914 155.6685 39.70511 -0.3543786 0.3421893 0.03829322 all names model in obs 914 155.6685 39.70511 -0.3543786 0.3421893 0.03829322 RMSE MB ME NMB (%) NME (%) VVIbes NA NA NA NA NA Ibirapuera NA NA NA NA NA am 2 66.89005 -62.74754 62.74754 -14.23074 14.23074 Terradonunca NA NA NA NA NA Americana NA NA NA NA NA model zero NA NA NA NA NA obs zero NA NA NA NA NA obs cke NA NA NA NA NA all fair 235.09955 -115.96338 177.83271 -74.49381 114.23809 all fair 2 235.09955 -115.96338 177.83271 -74.49381 114.23809 all model in obs 235.09955 -115.96338 177.83271 -74.49381 114.23809 all names model in obs 235.09955 -115.96338 177.83271 -74.49381 114.23809 Americana has 227 valid observations SAndre has 207 valid observations VVIbes has only 0 valid observations (lesser than 8 obs) georeferencing stats at sites extracting series of o3 field 4d for 2 points dim of lat/lon: 125 125 used dim of lat/lon: 125 125 inside lat / lon range: 2 points calculating distances... extracting series of o3 field 4d for 2 points dim of lat/lon: 125 125 used dim of lat/lon: 125 125 using i & j to extract points: lat lon name agency class city state BA0001 -12.68638 -38.33360 Gravatá INEMA Não classificada Camaçari BA BA0002 -12.63026 -38.35853 Cobre INEMA Não classificada Dias D'Ávila BA start i j model_lat model_lon BA0001 2000 110 67 -12.70324 -38.39191 BA0002 2000 110 67 -12.70324 -38.39191 reading o3 : D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrf.day1.o3.nc file 1 of 3 reading o3 : D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrf.day2.o3.nc file 2 of 3 reading o3 : D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrf.day3.o3.nc file 3 of 3 output: D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/SERIE/serie.o3.Rds extracting series of o3 field 4d for 5 points dim of lat/lon: 125 125 used dim of lat/lon: 125 125 inside lat / lon range: 5 points calculating distances... * station Gravatá ouside the domain * station Cobre ouside the domain * station Areias ouside the domain * station Lamarão ouside the domain lon lat i j model_lat model_lon Escola -38.27318 -12.63532 110 67 -12.70324 -38.39191 reading o3 : D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrf.day1.o3.nc file 1 of 3 reading o3 : D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrf.day2.o3.nc file 2 of 3 reading o3 : D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrf.day3.o3.nc file 3 of 3 output: D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/SERIE/serie.o3.Rds extracting series of o3 field 4d for 5 points dim of lat/lon: 125 125 used dim of lat/lon: 125 125 inside lat / lon range: 5 points calculating distances... * station Gravatá ouside the domain * station Cobre ouside the domain * station Areias ouside the domain * station Lamarão ouside the domain lon lat i j model_lat model_lon Escola -38.27318 -12.63532 110 67 -12.70324 -38.39191 reading o3 : D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrf.day1.o3.nc file 1 of 3 reading o3 : D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrf.day2.o3.nc file 2 of 3 reading o3 : D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrf.day3.o3.nc file 3 of 3 output: D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/SERIE/serie.o3.Rds extracting mean of o3 field 4d reading: D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrf.day1.o3.nc file 1 of 1 min: 2.123069e-05 mean: 0.007767247 max: 0.03175572 total times: 1 output: D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/MEAN/mean.o3.nc extracting 8h max of o3 field 3d units: ug m-3 reading: D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/test_small_o3.nc file 1 of 1 min: 2.010639e-13 mean: 23.42075 max: 99.85495 total times: 24 output: D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/MDA8/mean.o3.nc terra 1.7.83 Attaching package: 'terra' The following objects are masked from 'package:testthat': compare, describe writing XLAT in D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrfinput_d01 units of XLAT set to 'degree north' in D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrfinput_d01 reading D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/sat_cat.csv reading D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/sat_cat.txt writing D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/s/sat_cat.csv writing D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/s/sat_cat.txt croping m with o removing 6 points for the model (y) boundaryes ... interpolating obs. (x) to model grid (y)... removing 6 points for the model (y) boundaryes ... interpolating obs. (x) to model grid (y)... seting min value to 2 seting max value to 110 using 0.05 for min cutoff 97 values left using 3 for max cutoff 97 values left folder D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/WRF/case : link wrf output files here! bash D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/post-R_wrf.sh : post processing job script r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/extract_metar.R : source code to extract metar using eva3dm::extract_serie() r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/extract_inpet.R : source code to extract inmet using eva3dm::extract_serie() folder D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/WRF/case : link wrf output files here! bash D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/post-R_wrf.sh : post processing job script r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/extract_metar.R : source code to extract metar using eva3dm::extract_serie() folder D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/CAMx/case : link CAMx output files here! bash D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/post-R_CAMx.sh : post processing job script r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/extract_camx.R : source code to extract time-series from AERONET site locations using eva3dm::extract_serie() folder D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/CAMx/case : link CAMx output files here! bash D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/post-R_CAMx.sh : post processing job script r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/extract_camx.R : source code to extract time-series from AERONET site locations using eva3dm::extract_serie() folder D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/WRF/case : link wrf output files here! bash D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/post-R_wrfchem.sh : post processing job script r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/extract_metar.R : source code to extract metar using eva3dm::extract_serie() r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/extract_aq.R : source code to extract AQ stations from Brazil using eva3dm::extract_serie() r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/extract_pm.R : source code to extract PM compositon from AERONET sites using eva3dm::extract_serie() folder D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/WRF/case : link wrf output files here! bash D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/post-R_exp.sh : post processing job script r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/extract_expr.R : source code to extract metar using eva3dm::extract_serie() new locations can be added to the data.frame with the list of sites. folder D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/ : copy wrfinput_d01 gere! folder D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/METAR : destination folder r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/download_METAR.R : script that download metar data using riem package and information from eva3dm and wrfinput_d01 file r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/all_tables.R : setup and run script r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/table_metar_T2.R : evaluation of Temperature using METAR r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/table_metar_Q2.R : evaluation of absolute humidity using METAR r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/table_metar_WS.R : evaluation of wind speed using METAR r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/table_metar_WD.R : evaluation of wind direction using METAR r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/all_tables.R : setup and run script r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/table_metar_T2.R : evaluation of Temperature using METAR r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/table_metar_Q2.R : evaluation of absolute humidity using METAR r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/table_metar_WS.R : evaluation of wind speed using METAR r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/table_metar_WD.R : evaluation of wind direction using METAR folder D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/WRF/case : link WRF or CAMx post-rocessed output here! r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/all_tables.R : setup and run script r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/table_aq_o3.R : evaluation of hourly 8h O3 r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/table_aq_max_o3.R : evaluation of daily max 8h O3 r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/table_aq_pm2.5.R : evaluation of daily pm2.5 NOTE 1: Other scripts in all_tables.R not provided, use previous as template NOTE 2: other templates provide templates for metar folder D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/WRF/case : copy wrf post-proced files here! folder D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/GPCP : folder to copy satellite data here! r-script D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/table_GPCP_rain.R : script for satellite evaluation (CHANGE the file names!!) bash D:\temp\2024_11_18_17_55_02_26821\RtmpyiTmdR/POST/post-sate.sh : post processing for satellite evaluation using CDO processing hourly data ... processing 8-hour moving avarage ... processing daily maximum ... processing hourly data ... processing 8-hour moving avarage ... processing hourly data ... processing daily statistcis ... File D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrfinput_d01 (NC_FORMAT_CLASSIC): 3 variables (excluding dimension variables): char Times[DateStrLen,Time] float XLAT[west_east,south_north] MemoryOrder: XY description: LATITUDE, SOUTH IS NEGATIVE units: degree north stagger: FieldType: 104 float XLONG[west_east,south_north] MemoryOrder: XY description: LONGITUDE, WEST IS NEGATIVE units: degree east stagger: FieldType: 104 4 dimensions: DateStrLen Size:19 Time Size:1 *** is unlimited *** west_east Size:149 south_north Size:99 79 global attributes: TITLE: OUTPUT FROM REAL_EM V3.9.1.1 PREPROCESSOR START_DATE: 2011-08-01_00:00:00 SIMULATION_START_DATE: 2011-08-01_00:00:00 WEST-EAST_GRID_DIMENSION: 150 SOUTH-NORTH_GRID_DIMENSION: 100 BOTTOM-TOP_GRID_DIMENSION: 35 DX: 9000 DY: 9000 GRIDTYPE: C DIFF_OPT: 1 KM_OPT: 4 DAMP_OPT: 3 DAMPCOEF: 0.200000002980232 KHDIF: 0 KVDIF: 0 MP_PHYSICS: 10 RA_LW_PHYSICS: 4 RA_SW_PHYSICS: 4 SF_SFCLAY_PHYSICS: 1 SF_SURFACE_PHYSICS: 2 BL_PBL_PHYSICS: 1 CU_PHYSICS: 11 SF_LAKE_PHYSICS: 0 SURFACE_INPUT_SOURCE: 1 SST_UPDATE: 0 GRID_FDDA: 0 GFDDA_INTERVAL_M: 0 GFDDA_END_H: 0 GRID_SFDDA: 0 SGFDDA_INTERVAL_M: 0 SGFDDA_END_H: 0 HYPSOMETRIC_OPT: 2 USE_THETA_M: 0 USE_MAXW_LEVEL: 0 USE_TROP_LEVEL: 0 GWD_OPT: 0 SF_URBAN_PHYSICS: 1 SF_OCEAN_PHYSICS: 0 SIMULATION_INITIALIZATION_TYPE: REAL-DATA CASE WEST-EAST_PATCH_START_UNSTAG: 1 WEST-EAST_PATCH_END_UNSTAG: 149 WEST-EAST_PATCH_START_STAG: 1 WEST-EAST_PATCH_END_STAG: 150 SOUTH-NORTH_PATCH_START_UNSTAG: 1 SOUTH-NORTH_PATCH_END_UNSTAG: 99 SOUTH-NORTH_PATCH_START_STAG: 1 SOUTH-NORTH_PATCH_END_STAG: 100 BOTTOM-TOP_PATCH_START_UNSTAG: 1 BOTTOM-TOP_PATCH_END_UNSTAG: 34 BOTTOM-TOP_PATCH_START_STAG: 1 BOTTOM-TOP_PATCH_END_STAG: 35 GRID_ID: 1 PARENT_ID: 1 I_PARENT_START: 1 J_PARENT_START: 1 PARENT_GRID_RATIO: 1 DT: 45 CEN_LAT: -23.5499954223633 CEN_LON: -45 TRUELAT1: -23 TRUELAT2: -24 MOAD_CEN_LAT: -23.5499954223633 STAND_LON: -45 POLE_LAT: 90 POLE_LON: 0 GMT: 0 JULYR: 2011 JULDAY: 213 MAP_PROJ: 1 MAP_PROJ_CHAR: Lambert Conformal MMINLU: MODIFIED_IGBP_MODIS_NOAH NUM_LAND_CAT: 21 ISWATER: 17 ISLAKE: 21 ISICE: 15 ISURBAN: 13 ISOILWATER: 14 HYBRID_OPT: -1 ETAC: 0 global attributes: TITLE START_DATE SIMULATION_START_DATE WEST-EAST_GRID_DIMENSION SOUTH-NORTH_GRID_DIMENSION BOTTOM-TOP_GRID_DIMENSION DX DY GRIDTYPE DIFF_OPT KM_OPT DAMP_OPT DAMPCOEF KHDIF KVDIF MP_PHYSICS RA_LW_PHYSICS RA_SW_PHYSICS SF_SFCLAY_PHYSICS SF_SURFACE_PHYSICS BL_PBL_PHYSICS CU_PHYSICS SF_LAKE_PHYSICS SURFACE_INPUT_SOURCE SST_UPDATE GRID_FDDA GFDDA_INTERVAL_M GFDDA_END_H GRID_SFDDA SGFDDA_INTERVAL_M SGFDDA_END_H HYPSOMETRIC_OPT USE_THETA_M USE_MAXW_LEVEL USE_TROP_LEVEL GWD_OPT SF_URBAN_PHYSICS SF_OCEAN_PHYSICS SIMULATION_INITIALIZATION_TYPE WEST-EAST_PATCH_START_UNSTAG WEST-EAST_PATCH_END_UNSTAG WEST-EAST_PATCH_START_STAG WEST-EAST_PATCH_END_STAG SOUTH-NORTH_PATCH_START_UNSTAG SOUTH-NORTH_PATCH_END_UNSTAG SOUTH-NORTH_PATCH_START_STAG SOUTH-NORTH_PATCH_END_STAG BOTTOM-TOP_PATCH_START_UNSTAG BOTTOM-TOP_PATCH_END_UNSTAG BOTTOM-TOP_PATCH_START_STAG BOTTOM-TOP_PATCH_END_STAG GRID_ID PARENT_ID I_PARENT_START J_PARENT_START PARENT_GRID_RATIO DT CEN_LAT CEN_LON TRUELAT1 TRUELAT2 MOAD_CEN_LAT STAND_LON POLE_LAT POLE_LON GMT JULYR JULDAY MAP_PROJ MAP_PROJ_CHAR MMINLU NUM_LAND_CAT ISWATER ISLAKE ISICE ISURBAN ISOILWATER HYBRID_OPT ETACvariable Times attritutes: not found XLAT attribute units: degree north global attribute DT: 45 writing 'degree north' on attribute 'units' of XLAT at file D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrfinput_d01 writing '45' on global attribute 'DT' at file D:/RCompile/CRANincoming/R-devel/lib/eva3dm/extdata/wrfinput_d01 Times XLAT XLONG [ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ] > > proc.time() user system elapsed 7.12 0.29 7.42