Import gridded "Surface UV" data released by FMI/NASA from NetCDF4 files downloaded from the NASA EARTHDATA server.
Usage
sUV_read_OMUVBd_nc4(
files,
vars.to.read = NULL,
fill = NA_real_,
verbose = interactive()
)
sUV_vars_OMUVBd_nc4(files, set.oper = "intersect")
sUV_grid_OMUVBd_nc4(files, expand = FALSE)
sUV_date_OMUVBd_nc4(files, use.names = length(files > 1))Arguments
- files
character A vector of file names, no other limitation in length than available memory to hold the data.
- vars.to.read
character A vector of variable names. If
NULLall the variables present in the first file are read.- fill
numeric The R value used to replace the fill value used in the file, which is retrieved from the file metadata, and also used to fill missing variables.
- verbose
logical Flag indicating if progress, and time and size of the returned object should be printed.
- set.oper
character One of
"intersect", or"union".- expand
logical Flag indicating whether to return ranges or a full grid.
- use.names
logical. Should names be added to the returned vector?
Value
Function sUV_read_OMUVBd_nc4() returns a data frame with columns
named "Date", "Longitude", "Latitude", and the data variables with
their original names. The data variables have their metadata stored as R
attributes. sUV_vars_OMUVBd_nc4() returns a character vector of
variable names, sUV_grid_OMUVBd_nc4() returns a data frame with two
numeric variables, Longitude and Latitude, with two rows or an expanded
grid depending on the argument passed to expand, while
sUV_date_OMUVBd_nc4() returns a, by default named, vector of class
Date, with file names as names.
Details
Function sUV_read_OMUVBd_nc4() can be used to read the data stored
in a file, either in full or selected variables. Query functions
sUV_vars_OMUVBd_nc4(), sUV_grid_OMUVBd_nc4() and
sUV_date_OMUVBd_nc4() extract the names of the variables, the range of
the grid and the dates of measurements much more efficiently than by using
sUV_read_OMUVBd_nc4(). The dates are decoded from the file names,
expecting these to be those set by the data provider. The grid is expected
to be identical in all files that are imported in a call to
sUV_read_OMUVBd_nc4(), and grid subsetting is currently not supported. If
not all the files named in the argument to files are accessible, an error
is triggered early. If the files differ in the grid, an error is triggered
when reading the first mismatching file. Missing variables named in
vars.to.read if detected when reading the first file, are filled with the
fill value, otherwise they trigger an error when an attempt is made to
read them.
Note
The constraint on the consistency among all files to be read allows very fast reading into a single data frame. If the files differ in the grid or set of variables, this function can be used to read the files individually into separate data frames. These data frames can later be row-bound together.
This function's performance is fast as long as there is enough RAM available to hold the data frame and the files are read from a reasonably fast SSD. The example data included in the package are only for Spain and five summer days. They are used in examples and automated tests.
References
Jari Hovila, Antti Arola, and Johanna Tamminen (2013), OMI/Aura Surface UVB Irradiance and Erythemal Dose Daily L3 Global Gridded 1.0 degree x 1.0 degree V3, NASA Goddard Space Flight Center, Goddard Earth Sciences Data and Information Services Center (GES DISC).
See also
sUV_read_OMUVBd_he5() supporting the same Surface UV data as
stored in the original HDF5 files with a global geographic scope.
Examples
# find location of one example file
path.to.files <-
system.file("extdata",
package = "surfaceuv", mustWork = TRUE)
file.names <- list.files(path.to.files, pattern = "*.nc4$", full.names = TRUE)
one.file.name <- file.names[1]
# available variables
sUV_vars_OMUVBd_nc4(one.file.name)
#> [1] "Date" "Longitude" "Latitude"
#> [4] "CloudOpticalThickness" "ErythemalDailyDose" "ErythemalDoseRate"
#> [7] "Irradiance305" "Irradiance310" "Irradiance324"
#> [10] "Irradiance380" "UVindex"
# available grid
sUV_grid_OMUVBd_nc4(one.file.name)
#> Longitude Latitude
#> 1 24.5 58.5
#> 2 26.5 60.5
sUV_grid_OMUVBd_nc4(one.file.name, expand = TRUE)
#> Longitude Latitude
#> 1 24.5 58.5
#> 2 25.5 58.5
#> 3 26.5 58.5
#> 4 24.5 59.5
#> 5 25.5 59.5
#> 6 26.5 59.5
#> 7 24.5 60.5
#> 8 25.5 60.5
#> 9 26.5 60.5
# decode date from file name
sUV_date_OMUVBd_nc4(one.file.name)
#> OMI-Aura_L3-OMUVBd_2023m1001_v003.nc4
#> "2023-10-01"
sUV_date_OMUVBd_nc4(one.file.name, use.names = FALSE)
#> [1] "2023-10-01"
# read all variables
midsummer_spain.tb <- sUV_read_OMUVBd_nc4(one.file.name)
dim(midsummer_spain.tb)
#> [1] 9 11
summary(midsummer_spain.tb)
#> Date Longitude Latitude CloudOpticalThickness
#> Min. :2023-10-01 Min. :24.5 Min. :58.5 Min. :0.5107
#> 1st Qu.:2023-10-01 1st Qu.:24.5 1st Qu.:58.5 1st Qu.:0.9730
#> Median :2023-10-01 Median :25.5 Median :59.5 Median :1.1728
#> Mean :2023-10-01 Mean :25.5 Mean :59.5 Mean :1.3821
#> 3rd Qu.:2023-10-01 3rd Qu.:26.5 3rd Qu.:60.5 3rd Qu.:1.6853
#> Max. :2023-10-01 Max. :26.5 Max. :60.5 Max. :2.4806
#> ErythemalDailyDose ErythemalDoseRate Irradiance305 Irradiance310
#> Min. :653.3 Min. :32.80 Min. :4.786 Min. :15.97
#> 1st Qu.:686.6 1st Qu.:34.48 1st Qu.:5.025 1st Qu.:16.76
#> Median :769.5 Median :38.68 Median :5.745 Median :18.86
#> Mean :757.1 Mean :38.09 Mean :5.734 Mean :18.66
#> 3rd Qu.:813.2 3rd Qu.:40.99 3rd Qu.:6.367 3rd Qu.:20.27
#> Max. :861.1 Max. :43.34 Max. :6.669 Max. :21.31
#> Irradiance324 Irradiance380 UVindex
#> Min. :117.6 Min. :240.8 Min. :1.309
#> 1st Qu.:123.8 1st Qu.:255.4 1st Qu.:1.376
#> Median :137.5 Median :290.4 Median :1.543
#> Mean :134.6 Mean :281.4 Mean :1.523
#> 3rd Qu.:143.0 3rd Qu.:300.6 3rd Qu.:1.648
#> Max. :151.3 Max. :321.2 Max. :1.739
# read only UVindex
midsummer_spain_daily.tb <-
sUV_read_OMUVBd_nc4(one.file.name,
vars.to.read = "UVindex")
dim(midsummer_spain_daily.tb)
#> [1] 9 4
summary(midsummer_spain_daily.tb)
#> Date Longitude Latitude UVindex
#> Min. :2023-10-01 Min. :24.5 Min. :58.5 Min. :1.309
#> 1st Qu.:2023-10-01 1st Qu.:24.5 1st Qu.:58.5 1st Qu.:1.376
#> Median :2023-10-01 Median :25.5 Median :59.5 Median :1.543
#> Mean :2023-10-01 Mean :25.5 Mean :59.5 Mean :1.523
#> 3rd Qu.:2023-10-01 3rd Qu.:26.5 3rd Qu.:60.5 3rd Qu.:1.648
#> Max. :2023-10-01 Max. :26.5 Max. :60.5 Max. :1.739
# read multiple files
sUV_vars_OMUVBd_nc4(file.names)
#> [1] "Date" "Longitude" "Latitude"
#> [4] "CloudOpticalThickness" "ErythemalDailyDose" "ErythemalDoseRate"
#> [7] "Irradiance305" "Irradiance310" "Irradiance324"
#> [10] "Irradiance380" "UVindex"
sUV_grid_OMUVBd_nc4(file.names)
#> Longitude Latitude
#> 1 24.5 58.5
#> 2 26.5 60.5
sUV_grid_OMUVBd_nc4(file.names, expand = TRUE)
#> Longitude Latitude
#> 1 24.5 58.5
#> 2 25.5 58.5
#> 3 26.5 58.5
#> 4 24.5 59.5
#> 5 25.5 59.5
#> 6 26.5 59.5
#> 7 24.5 60.5
#> 8 25.5 60.5
#> 9 26.5 60.5
sUV_date_OMUVBd_nc4(file.names)
#> OMI-Aura_L3-OMUVBd_2023m1001_v003.nc4 OMI-Aura_L3-OMUVBd_2023m1002_v003.nc4
#> "2023-10-01" "2023-10-02"
#> OMI-Aura_L3-OMUVBd_2023m1003_v003.nc4
#> "2023-10-03"
sUV_date_OMUVBd_nc4(file.names, use.names = FALSE)
#> [1] "2023-10-01" "2023-10-02" "2023-10-03"
summer_3days_spain.tb <- sUV_read_OMUVBd_nc4(file.names)
dim(summer_3days_spain.tb)
#> [1] 27 11
summary(summer_3days_spain.tb)
#> Date Longitude Latitude CloudOpticalThickness
#> Min. :2023-10-01 Min. :24.5 Min. :58.5 Min. : 0.5107
#> 1st Qu.:2023-10-01 1st Qu.:24.5 1st Qu.:58.5 1st Qu.: 1.1440
#> Median :2023-10-02 Median :25.5 Median :59.5 Median : 1.6853
#> Mean :2023-10-02 Mean :25.5 Mean :59.5 Mean : 5.8036
#> 3rd Qu.:2023-10-03 3rd Qu.:26.5 3rd Qu.:60.5 3rd Qu.: 7.5133
#> Max. :2023-10-03 Max. :26.5 Max. :60.5 Max. :28.9309
#> ErythemalDailyDose ErythemalDoseRate Irradiance305 Irradiance310
#> Min. :347.0 Min. :17.82 Min. :3.471 Min. : 9.188
#> 1st Qu.:564.0 1st Qu.:28.88 1st Qu.:5.057 1st Qu.:14.752
#> Median :769.5 Median :38.68 Median :5.745 Median :18.863
#> Mean :695.2 Mean :35.32 Mean :6.155 Mean :17.745
#> 3rd Qu.:836.6 3rd Qu.:42.68 3rd Qu.:7.869 3rd Qu.:21.571
#> Max. :867.6 Max. :44.34 Max. :8.442 Max. :22.666
#> Irradiance324 Irradiance380 UVindex
#> Min. : 52.85 Min. : 95.49 Min. :0.7085
#> 1st Qu.: 89.09 1st Qu.:170.28 1st Qu.:1.1526
#> Median :131.81 Median :263.52 Median :1.5431
#> Mean :114.22 Mean :231.07 Mean :1.4099
#> 3rd Qu.:135.12 3rd Qu.:278.49 3rd Qu.:1.7008
#> Max. :151.29 Max. :321.25 Max. :1.7763