Read data from a file (or source) using the NetCDF library directly.

read_ncdf(
  .x,
  ...,
  var = NULL,
  ncsub = NULL,
  curvilinear = character(0),
  eps = 1e-12,
  ignore_bounds = FALSE,
  make_time = TRUE,
  make_units = TRUE
)

Arguments

.x

NetCDF file or source

...

ignored

var

variable name or names (they must be on matching grids)

ncsub

matrix of start, count columns (see Details)

curvilinear

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.

eps

numeric; dimension value increases are considered identical when they differ less than eps

ignore_bounds

logical; should bounds values for dimensions, if present, be ignored?

make_time

if TRUE (the default), an atttempt is made to provide a date-time class from the "time" variable

make_units

if TRUE (the default), an attempt is made to set the units property of each variable

Details

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.

Examples

f <- system.file("nc/reduced.nc", package = "stars") read_ncdf(f)
#> no 'var' specified, using sst, anom, err, ice
#> other available variables: #> lon, lat, zlev, time
#> 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): #> sst [°C] anom [°C] err [°C] ice [percent] #> Min. :-1.80 Min. :-7.950 Min. :0.110 Min. :0.010 #> 1st Qu.:-0.03 1st Qu.:-0.580 1st Qu.:0.160 1st Qu.:0.470 #> Median :13.65 Median :-0.080 Median :0.270 Median :0.920 #> Mean :12.99 Mean :-0.185 Mean :0.263 Mean :0.718 #> 3rd Qu.:24.81 3rd Qu.: 0.210 3rd Qu.:0.320 3rd Qu.:0.960 #> Max. :32.97 Max. : 2.990 Max. :0.840 Max. :1.000 #> NA's :4448 NA's :4449 NA's :4448 NA's :13266 #> dimension(s): #> from to offset delta refsys point values #> lon 1 180 -1 2 EPSG:4326 NA NULL [x] #> lat 1 90 -90 2 EPSG:4326 NA NULL [y] #> zlev 1 1 NA NA NA NA 0 #> time 1 1 NA NA POSIXct NA 1981-12-31 UTC
read_ncdf(f, var = c("anom"))
#> No projection information found in nc file. #> Coordinate variable units found to be degrees, #> assuming WGS84 Lat/Lon.
#> stars object with 4 dimensions and 1 attribute #> attribute(s): #> anom [°C] #> Min. :-7.950 #> 1st Qu.:-0.580 #> Median :-0.080 #> Mean :-0.185 #> 3rd Qu.: 0.210 #> Max. : 2.990 #> NA's :4449 #> dimension(s): #> from to offset delta refsys point values #> lon 1 180 -1 2 EPSG:4326 NA NULL [x] #> lat 1 90 -90 2 EPSG:4326 NA NULL [y] #> zlev 1 1 NA NA NA NA 0 #> time 1 1 NA NA POSIXct NA 1981-12-31 UTC
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
#> 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): #> sst [°C] anom [°C] err [°C] ice [percent] #> Min. :-1.390 Min. :-1.07000 Min. :0.300 Min. :0.0100 #> 1st Qu.:-0.720 1st Qu.:-0.36250 1st Qu.:0.300 1st Qu.:0.1100 #> Median :-0.515 Median : 0.19500 Median :0.300 Median :0.1700 #> Mean :-0.534 Mean : 0.05867 Mean :0.303 Mean :0.2094 #> 3rd Qu.:-0.275 3rd Qu.: 0.55500 3rd Qu.:0.300 3rd Qu.:0.2550 #> Max. : 0.030 Max. : 0.92000 Max. :0.320 Max. :0.5200 #> NA's :90 NA's :90 NA's :90 NA's :104 #> dimension(s): #> from to offset delta refsys point values #> lon 1 10 -1 2 EPSG:4326 NA NULL [x] #> lat 1 12 -90 2 EPSG:4326 NA NULL [y] #> zlev 1 1 NA NA NA NA 0 #> time 1 1 NA NA POSIXct NA 1981-12-31 UTC
#' 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: #> time_bounds, lon, lat, time
#> 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))) } library(dplyr) 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)