In bgctw/ncdfTools: Handling NetCDF Files

# do not execute on CRAN: 
# https://stackoverflow.com/questions/28961431/computationally-heavy-r-vignettes
is_check <- ("CheckExEnv" %in% search()) || any(c("_R_CHECK_TIMINGS_",
             "_R_CHECK_LICENSE_") %in% names(Sys.getenv()))
#knitr::opts_chunk$set(eval = !is_check)

#rmarkdown::render("vignettes/useCase.Rmd")
#knitr::opts_knit$set(root.dir = '..')
knitr::opts_chunk$set(
    #, fig.align = "center"
    #, fig.width = 3.27, fig.height = 2.5, dev.args = list(pointsize = 10)
    #,cache = TRUE
    #, fig.width = 4.3, fig.height = 3.2, dev.args = list(pointsize = 10)
    #, fig.width = 6.3, fig.height = 6.2, dev.args = list(pointsize = 10)
    # works with html but causes problems with latex
    #,out.extra = 'style = "display:block; margin: auto"' 
    )
knitr::knit_hooks$set(spar = function(before, options, envir) {
    if (before) {
        par(las = 1 )                   #also y axis labels horizontal
        par(mar = c(2.0,3.3,0,0) + 0.3 )  #margins
        par(tck = 0.02 )                          #axe-tick length inside plots             
        par(mgp = c(1.1,0.2,0) )  #positioning of axis title, axis labels, axis
     }
})

#themeTw <- theme_bw(base_size = 10) + theme(axis.title = element_text(size = 9))
#bgiDir <- "~/bgi"

NetCDF in R Tutorial

from Dept. Geography, Univ. Oregon

Reading a netCDF data set using the ncdf4 package

The ndcf4 package works much the same way as the ncdf package, but the functions in this package are a little more similar to the functions in the netCDF Fortran or C libraries than are those in the ncdf package. To begin, load the ncdf4 package.

library(ncdf4)

Open the NetCDF data set, and print some basic information. The print() function applied to the ncin object produces information similar to that produced by the command-line utility ncdump.

ncname <- "cru10min30_tmp"  
ncfname <- paste(ncname,".nc", sep = "")
dname <- "tmp"  # note: tmp means temperature (not temporary)
# open a netCDF file
getwd()
ncin <- nc_open(ncfname)
print(ncin)

Get the longtiudes and latitudes as before, using now the ncvar_get() function in ncdf4.

lon <- ncvar_get(ncin,"lon")
nlon <- dim(lon)
head(lon)

lat <- ncvar_get(ncin,"lat",verbose = F)
nlat <- dim(lat)
head(lat)

print(c(nlon,nlat))

Get the time variable and its attributes using the ncvar_get() and ncatt_get() functions, and list them, and also get the number of times using the dim() function.

t <- ncvar_get(ncin,"time")
t

tunits <- ncatt_get(ncin,"time","units")
nt <- dim(t)
nt

Print the time units string. Note the structure of the time units attribute. The object tunits has two components hasatt (a logical variable), and tunits$value, the actual “time since” string.

tunits

Get the input variable (tmp) and its attributes, and verify the size of the array.

tmp_array <- ncvar_get(ncin,dname)
dlname <- ncatt_get(ncin,dname,"long_name")
dunits <- ncatt_get(ncin,dname,"units")
fillvalue <- ncatt_get(ncin,dname,"_FillValue")
dim(tmp_array)

Get the global attributes.

title <- ncatt_get(ncin,0,"title")
institution <- ncatt_get(ncin,0,"institution")
datasource <- ncatt_get(ncin,0,"source")
references <- ncatt_get(ncin,0,"references")
history <- ncatt_get(ncin,0,"history")
Conventions <- ncatt_get(ncin,0,"Conventions")

Close the netCDF file using the nc_close() function.

nc_close(ncin)

Check what’s in the current workspace:

ls()
outworkspace = "netCDF01.RData"
save.image(file = outworkspace)

bgctw/ncdfTools documentation built on Jan. 29, 2020, 1:16 p.m.