Read data from a file (or source) using the NetCDF library directly.
NetCDF file or source as a character vector or an nc_proxy object.
ignored
variable name or names (they must be on matching grids)
matrix of start, count columns (see Details)
length two character named vector with names of variables holding longitude and latitude values for all raster cells. `stars` attempts to figure out appropriate curvilinear coordinates if they are not supplied.
numeric; dimension value increases are considered identical when they differ less than eps
logical; should bounds values for dimensions, if present, be ignored?
if TRUE
(the default), an atttempt is made to provide a date-time class from the "time" variable
if TRUE
(the default), an attempt is made to set the units property of each variable
logical; if TRUE
, an object of class stars_proxy
is read which contains array
metadata only; if FALSE
the full array data is read in memory. If not set, defaults to TRUE
when the number of cells to be read is larger than options(stars.n_proxy)
, or to 1e8 if that option was not set.
integer; number of cells to omit between samples along each dimension.
e.g. c(1,1,2)
would return every other cell in x and y and every third cell
in the third dimension (z or t). If 0, no downsampling is applied. Note that this transformation
is applied AFTER NetCDF data are read using st_downsample. As such, if proxy=TRUE, this
option is ignored.
The following logic is applied to coordinates. If any coordinate axes have regularly spaced coordinate variables they are reduced to the offset/delta form with 'affine = c(0, 0)', otherwise the values of the coordinates are stored and used to define a rectilinear grid.
If the data has two or more dimensions and the first two are regular they are nominated as the 'raster' for plotting.
If the curvilinear
argument is used it specifies the 2D arrays
containing coordinate values for the first two dimensions of the data read. It is currently
assumed that the coordinates are 2D and that they relate to the first two dimensions in
that order.
If var
is not set the first set of variables on a shared grid is used.
start
and count
columns of ncsub must correspond to the variable dimemsion (nrows)
and be valid index using var.get.nc
convention (start is 1-based). If the count value
is NA
then all steps are included. Axis order must match that of the variable/s being read.
f <- system.file("nc/reduced.nc", package = "stars")
if (require(ncmeta, quietly = TRUE)) {
read_ncdf(f)
read_ncdf(f, var = c("anom"))
read_ncdf(f, ncsub = cbind(start = c(1, 1, 1, 1), count = c(10, 12, 1, 1)))
}
#> no 'var' specified, using sst, anom, err, ice
#> other available variables:
#> lon, lat, zlev, time
#> 0-360 longitude crossing the international dateline encountered.
#> Longitude coordinates will be0-360 in output.
#> Will return stars object with 16200 cells.
#> No projection information found in nc file.
#> Coordinate variable units found to be degrees,
#> assuming WGS84 Lat/Lon.
#> 0-360 longitude crossing the international dateline encountered.
#> Longitude coordinates will be0-360 in output.
#> Will return stars object with 16200 cells.
#> No projection information found in nc file.
#> Coordinate variable units found to be degrees,
#> assuming WGS84 Lat/Lon.
#> no 'var' specified, using sst, anom, err, ice
#> other available variables:
#> lon, lat, zlev, time
#> Will return stars object with 120 cells.
#> No projection information found in nc file.
#> Coordinate variable units found to be degrees,
#> assuming WGS84 Lat/Lon.
#> stars object with 4 dimensions and 4 attributes
#> attribute(s):
#> Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
#> sst [°C] -1.39 -0.7200 -0.515 -0.53399999 -0.275 0.03 90
#> anom [°C] -1.07 -0.3625 0.195 0.05866667 0.555 0.92 90
#> err [°C] 0.30 0.3000 0.300 0.30299999 0.300 0.32 90
#> ice [percent] 0.01 0.1100 0.170 0.20937500 0.255 0.52 104
#> dimension(s):
#> from to offset delta refsys values x/y
#> lon 1 10 -1 2 WGS 84 NULL [x]
#> lat 1 12 -90 2 WGS 84 NULL [y]
#> zlev 1 1 NA NA NA 0
#> time 1 1 NA NA POSIXct 1981-12-31 UTC
if (require(ncmeta, quietly = TRUE)) {
#' precipitation data in a curvilinear NetCDF
prec_file = system.file("nc/test_stageiv_xyt.nc", package = "stars")
prec = read_ncdf(prec_file, curvilinear = c("lon", "lat"), ignore_bounds = TRUE)
}
#> no 'var' specified, using Total_precipitation_surface_1_Hour_Accumulation
#> other available variables:
#> lat, lon, time
#> Will return stars object with 236118 cells.
#> No projection information found in nc file.
#> Coordinate variable units found to be degrees,
#> assuming WGS84 Lat/Lon.
##plot(prec) ## gives error about unique breaks
## remove NAs, zeros, and give a large number
## of breaks (used for validating in detail)
qu_0_omit = function(x, ..., n = 22) {
x = units::drop_units(na.omit(x))
c(0, quantile(x[x > 0], seq(0, 1, length.out = n)))
}
if (require(dplyr, quietly = TRUE)) {
prec_slice = slice(prec, index = 17, along = "time")
plot(prec_slice, border = NA, breaks = qu_0_omit(prec_slice[[1]]), reset = FALSE)
nc = sf::read_sf(system.file("gpkg/nc.gpkg", package = "sf"), "nc.gpkg")
plot(st_geometry(nc), add = TRUE, reset = FALSE, col = NA)
}