[R] Extracting subset from netCDF file using lat/lon and converting into .csv in R

[Eeusha Nafi]

Thank you for the kind reply.
1. The order of the dimension is reflected when used as print(ncin)
function. This function has been used to have a quick look at the structure
of the default netCDF file.
2. Firstly, I am in need of subsetting this netCDF file and then have to
convert the slice into .csv format.

So far, I could read the netCDF file (variables and dimensions) and
fragment the time into fields. Therefore, I would be grateful to get
further help to reach the goal.

Regards,
Eeusha

On Mon, Aug 28, 2017 at 11:56 PM, Roy Mendelssohn - NOAA Federal <
roy.mendelssohn at noaa.gov> wrote:

> Two questions:
>
> 1.  Is the order of the dimensions shown what is shown if you look at
> str(ncin) - I mean shown at the end where it describes the variable and its
> dimensions?
>
> 2.  Is you problem how to subset the netcdf file,  how to write to the
> .csv file, or both?
>
> -Roy
>
> > On Aug 28, 2017, at 2:21 PM, Eeusha Nafi <eshad002 at gmail.com> wrote:
> >
> > I have a series of nertCDF files containing global data for a particular
> > variable, e.g. tmin/tmax/precipiation/windspeed/relative
> > humuidity/radiation etc. I get the following information when using
> > *nc_open* function in R:
> >
> > datafile: https://www.dropbox.com/s/xpo7zklcmtm3g5r/gfdl_preci.nc?dl=0
> >
> > File gfdl_preci.nc (NC_FORMAT_NETCDF4_CLASSIC):
> >
> > 1 variables (excluding dimension variables):
> >        float prAdjust[lon,lat,time]
> >            _FillValue: 1.00000002004088e+20
> >            missing_value: 1.00000002004088e+20
> >            comment: includes all types (rain, snow, large-scale,
> > convective, etc.)
> >            long_name: Bias-Corrected Precipitation
> >            units: kg m-2 s-1
> >            standard_name: precipitation_flux
> >
> >     3 dimensions:
> >        lon  Size:720
> >            standard_name: longitude
> >            long_name: longitude
> >            units: degrees_east
> >            axis: X
> >        lat  Size:360
> >            standard_name: latitude
> >            long_name: latitude
> >            units: degrees_north
> >            axis: Y
> >        time  Size:365   *** is unlimited ***
> >            standard_name: time
> >            units: days since 1860-1-1 00:00:00
> >            calendar: standard
> >            axis: T
> >
> >    14 global attributes:
> >        CDI: Climate Data Interface version 1.7.0 (
> http://mpimet.mpg.de/cdi)
> >        Conventions: CF-1.4
> >        title: Model output climate of GFDL-ESM2M r1i1p1 Interpolated
> > to 0.5 degree and bias corrected using observations from 1960 - 1999
> > for EU WATCH project
> >        CDO: Climate Data Operators version 1.7.0 (
> http://mpimet.mpg.de/cdo)
> >        product_id: input
> >        model_id: gfdl-esm2m
> >        institute_id: PIK
> >        experiment_id: historical
> >        ensemble_id: r1i1p1
> >        time_frequency: daily
> >        creator: isimip at pik-potsdam.de
> >        description: GFDL-ESM2M bias corrected impact model input
> > prepared for ISIMIP2
> >
> > Now I want to extract a subset from this dataset using pair of lon and
> lat
> > points, e.g., (12.875, -11.625) & (8.875, 4.125) and convert the file
> into
> > .csv format.
> >
> > so far I could make up to this step:
> >
> > # load the ncdf4 package
> > library(ncdf4)
> > # set path and filename
> > setwd("D:/netcdf")
> > ncname <- "gfdl_preci"
> > ncfname <- paste(ncname, ".nc", sep = "")
> > dname <- "prAdjust"
> > # open a netCDF file
> > ncin <- nc_open(ncfname)
> > print(ncin)# get longitude and latitude
> > lon <- ncvar_get(ncin,"lon")
> > nlon <- dim(lon)
> > head(lon)
> >
> > lat <- ncvar_get(ncin,"lat")
> > nlat <- dim(lat)
> > head(lat)
> >
> > print(c(nlon,nlat))
> > # get time
> > time <- ncvar_get(ncin,"time")
> > time
> >
> > tunits <- ncatt_get(ncin,"time","units")
> > nt <- dim(time)
> > nt
> > tunits
> > # get variable
> > preci.array <- ncvar_get(ncin,dname)
> >
> > dlname <- ncatt_get(ncin,"prAdjust","long_name")
> >
> > dunits <- ncatt_get(ncin,"prAdjust","units")
> >
> > fillvalue <- ncatt_get(ncin,"prAdjust","_FillValue")
> >
> > dim(preci.array)
> > # split the time units string into fields
> > tustr <- strsplit(tunits$value, " ")
> >
> > tdstr <- strsplit(unlist(tustr)[3], "-")
> >
> > tmonth = as.integer(unlist(tdstr)[2])
> >
> > tday = as.integer(unlist(tdstr)[3])
> >
> > tyear = as.integer(unlist(tdstr)[1])
> >
> > chron(time, origin = c(tmonth, tday, tyear))
> >
> > *Any help would be appreciated!!*
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
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> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> **********************
> "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> **********************
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
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> Phone: (831)-420-3666
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>
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> "the arc of the moral universe is long, but it bends toward justice" -MLK
> Jr.
>
>

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