count number of missing values in netcdf file - R

Question

Is there a quick way to know how many missing values are in a netcdf file? Possibly using R.

Currently I have to

hum<-nc_open("rhum.sig995.2008.nc")
rhum<-ncvar_get(hum, "rhum")

then manually look up the missing value by typing 'hum' and copy it into this operation

sum(abs(rhum - 9.96920996838687e+36) < -9.96920996838687e+36)

Is there a more direct way, especially if I have to work with hundreds of files? I would like to avoid copying and pasting the missing value, and also I am not sure with what kind of precision the number should be handled.

AF7 · Accepted Answer · 2015-04-30 07:18:22Z

2

My suggestion is to use the excellent raster package:

install.packages(raster)
library(raster)

r <- raster("rhum.sig995.2008.nc", var="rhum")

NAnum <- summary(r)[6]

answered Apr 30, 2015 at 7:18

AF7

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Robert Hijmans Over a year ago

Or use freq(r, value=NA)

ClimateUnboxed · Accepted Answer · 2017-05-10 20:43:58Z

2

The total number of missing data points for variable names "var" can be stored in a new additional variable using

ncap2 -s "nmiss=number_miss(var)" in.nc out.nc

or

ncap2 -s "nmiss=var.number_miss()" in.nc out.nc

If your data has a time dimension and you want to see the total number of missing points summed over the space dimensions, then you can see this with

cdo info in.nc

answered May 10, 2017 at 20:43

ClimateUnboxed

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