Dear R Users,
I am encountering a problem when reading nc files into R using the ncdf and
ncdf4 libraries. The nc files are too large to attach an example (but if
someone is interested in helping out I could send a file privately via an
online drive), but the code is basic:
for(i in 1:length(thesenames[,1])){
data <- nc_open(paste(INDIR, thesenames[i,c("wholename")], sep=""), write=F)
d.vars <- names(data$var)
d.size <- (data$var[[length(d.vars)]])$size
# Obtaining longitude and latitude values
d.lon <- as.vector(ncvar_get(data, varid="lon", start=c(1,1),
count=c(d.size[1],d.size[2])))
d.lat <- as.vector(ncvar_get(data, varid="lat", start=c(1,1),
count=c(d.size[1],d.size[2])))
# Obtaining climate data values
df.clim <- data.frame(rn=seq(1:length(d.lon)))
for(y in 1:d.size[3]){
df.clim[,1+y] <- as.vector(ncvar_get(data, varid=d.vars[length(d.vars)],
start=c(1,1,y), count=c(d.size[1],d.size[2],1)))
names(df.clim)[1+y] <- paste("y",y,sep="") }
tosummarise[,,i] <- as.matrix(df.clim[,-1])
}
The data are temperature or precipitation, across space and time.
For most of the >250 files I have, there are no problems, but for around 8 of
these files, I get strange values. The data should be within a relatively
narrow range, yet I get values such as -8.246508e+07 or 7.659506e+11. The
particularly strange part is that these kind of values occur at regularly
spaced intervals across the data, usually within a single time step.
I have the same problem (including the exact same strange values) when using
ArcMap, yet the data provider assures me that the data look normal when using
CDO (climate data operators) to view them, and that there are no missing values.
I realise this is very difficult to diagnose without the nc files themselves,
so my questions are (1) Has anyone encountered something like this before?, (2)
Is there something I am failing to specify in the code when reading in?, and
(3) Is anyone interested in digging into this and willing to play around with
the nc files if I make them available privately?
Thanks very much in advance!
Louise
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