[R] Extracting subset from netCDF file using lat/lon and converting into .csv in R
Eeusha Nafi
eshad002 at gmail.com
Mon Aug 28 23:21:28 CEST 2017
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!!*
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