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

[Roy Mendelssohn - NOAA Federal]

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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> 

**********************
"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
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/

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