CODEWITHSUNDEEP
rnetcdf
Holzer Manuel
Holzer Manuel

Reputation: 21

Import 4 dimensional netCDF data into R

I've been searching quit a wile to solve my problem, but I still couldn't solve it. I want to Import a nedCDF file into R. Like this:

ncdata <- nc_open("prec_daily_2005-2005.nc")
print(ncdata)

and I get the following

File prec_daily_2005-2005.nc (NC_FORMAT_CLASSIC):

 1 variables (excluding dimension variables):
    float prec[longitude,latitude,z,time]   
        source: Reanalysis daily precipitation, statistically corrected for number of raindays, monthly amounts and diurnal cycle at 1.0deg; interpolated to 0.1deg; available GHCN/GSOD daily station data assimilated into gridded data
        name: prec
        title: Daily bias corrected precipitation
        date: 01/01/05
        time: 00:00
        long_name: Precipitation
        units: kg m-2 s-1
        missing_value: 2.00000004008175e+20
        _FillValue: 2.00000004008175e+20
        valid_min: 0
        valid_max: 0.0045476695522666

 4 dimensions:
    longitude  Size:800
        units: degrees_east
        point_spacing: even
    latitude  Size:300
        units: degrees_north
        point_spacing: even
    z  Size:1
        units: level
        positive: up
    time  Size:365   *** is unlimited ***
        units: days since 2005-01-01 00:00:00
        time_origin: 01-JAN-2005:00:00:00

6 global attributes:
    history: Thu May 22 10:21:12 EDT 2014: created by JS using convert2alma.sh
    title: Princeton University Hydroclimatology Group Bias Corrected African (1979-2005) Meteorological Forcing Dataset V1.0
    institution: Princeton University
    contact: Justin Sheffield ([email protected])
    source: Forcings are a hybrid of NCEP/NCAR reanalysis and observations
    comment: This dataset is described in Chaney and Sheffield (2012) (Chaney, N., and J. Sheffield, 2012: High Resolution Gridded Daily Meteorological Data for Africa: Dataset Development and Analysis of Trends in Means and Extremes, J. Climate, to be submitted) and is related to the original global version reported in Sheffield et al., J. Climate (2006). Updates/changes include: i) African continent domain; ii) extension to 2005; iii) assimilation of available GHCN/GSOD daily station observations; iv) step change detection and correction for observational datasets; v) improved sampling procedure for correction of rain day statistics; vi) use of latest versions of CRU, SRB and TRMM products; vii) improved consistency between specific and relative humidity and air temperature. See Sheffield et al., J. Climate (2006) for details of the observations used and the bias correction and downscaling methodology.

and then I want to extract precipitation data, for example at one grid cell at one day:

n_prec <- ncvar_get(ncdata, 'prec')
print(n_prec[1, 1, 1, 1])

but I get en error message like: error in n_prec[1, 1, 1, 1] : wrong number of dimensions

and I don't get it because the dataset has for dimensions. But I maybe misunderstood something, as I'm pretty new to R.

I'm glad for any help. Manuel

Upvotes: 2

Views: 555

Answers (1)

Justina Pinch
Justina Pinch

Reputation: 397

The number of dimensions for n_prec is 3 instead of 4. The 'z' dimension only has 1 option/level so R ignores it when reading in the precip array. 

> library(ncdf4)
> ncdata <- nc_open("prec_daily_2005-2005.nc")
> n_prec <- ncvar_get(ncdata, 'prec')
> dim(n_prec)
[1] 800 300 365
> n_prec[1,1,1]
[1] NA
> n_prec[400,100,6]
[1] 1.13913e-05

Upvotes: 1

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