Subsetting and saving netcdf in R











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I am trying to subset 8 netcdf files (one of them is here) in a foor loop according to a shorter period of time and then to save them as a new netcdf file.



I saw that other people already asked on how to subset netcdf files according to different time period (here or here) but once I do it on my netcdf files the "for loop" keeps on running without finishing (not even the first netcdf file) and I can't figure out why.



Here the code I use:



library(raster)
library(netcdf4)
library(lubridate)

#setting wd=indir containing netcdf files

setwd(indir)

files=list.files(pattern="nc")

for (j in seq_along(files)){

#setting wd containing netcdf files in the loop
setwd(indir)

b<-brick(files[j])

nc<-nc_open(files[j])

#variable
varname<-names(nc[['var']][3])
varunits <- ncatt_get(nc,varname,"units")[[2]]

lon<-ncvar_get(nc,"lon")

lat<-ncvar_get(nc,"lat", verbose = F)

time<-ncvar_get(nc, "time")

tunits <- ncatt_get(nc, "time", "units")[[2]]

dlname <- ncatt_get(nc, varname,"long_name")[[2]]

nc_close(nc)

#assigning a crs
proj4string(b)<-"+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"

#setting time as.Date
tm<-ymd(getZ(b))

#setting time to rasterBrick
b<-setZ(b, tm)

# subsetting
b2<-subset(b, which(tm < as.Date('2006-01-01')))

#setting wd where I want to save the "new" netcdf files
setwd(outdir)

writeRaster(b2, filename = paste0(varname, "_1971_2006_Noce.nc"),
format="CDF", varname=varname, varunit=varunits, longname=dlname,
xname="lon", yname="lat", zname="time", zunit=tunits, overwrite=TRUE)
}


Any help on how to get the loop working would be very much appreciated!










share|improve this question




















  • 1




    If your code is indeed files=list.files(pattern="nc) then you've missed a " to close out that string.
    – shians
    Nov 21 at 23:32










  • Try adding a printed out counter at various points in your code (ie print(j) or print(varname)) throughout your loop that might tell you where it is going wrong
    – RAB
    Nov 22 at 7:57












  • Thank you shians, but unfortunately this was just a transcription error when I copy pasted the code here. In the code itself I close out that string.
    – Ste
    Nov 22 at 8:08










  • thanks, I have added some print(j) and now I get this error: Error in R_nc4_create: Invalid argument (creation mode was 0) Error in ncdf4::nc_create(filename, vardef, force_v4 = force_v4) : Error in nc_create! could you help me understanding why it refers to "nc_create" in writeRaster?
    – Ste
    Nov 22 at 9:07










  • hi, your code works well for me. The only thing that I notice is that when you open the subsetted nc file the dates are not well represented. Try to UPDATE your R version and related packages as a start.
    – aaaaa
    Nov 23 at 18:32

















up vote
0
down vote

favorite












I am trying to subset 8 netcdf files (one of them is here) in a foor loop according to a shorter period of time and then to save them as a new netcdf file.



I saw that other people already asked on how to subset netcdf files according to different time period (here or here) but once I do it on my netcdf files the "for loop" keeps on running without finishing (not even the first netcdf file) and I can't figure out why.



Here the code I use:



library(raster)
library(netcdf4)
library(lubridate)

#setting wd=indir containing netcdf files

setwd(indir)

files=list.files(pattern="nc")

for (j in seq_along(files)){

#setting wd containing netcdf files in the loop
setwd(indir)

b<-brick(files[j])

nc<-nc_open(files[j])

#variable
varname<-names(nc[['var']][3])
varunits <- ncatt_get(nc,varname,"units")[[2]]

lon<-ncvar_get(nc,"lon")

lat<-ncvar_get(nc,"lat", verbose = F)

time<-ncvar_get(nc, "time")

tunits <- ncatt_get(nc, "time", "units")[[2]]

dlname <- ncatt_get(nc, varname,"long_name")[[2]]

nc_close(nc)

#assigning a crs
proj4string(b)<-"+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"

#setting time as.Date
tm<-ymd(getZ(b))

#setting time to rasterBrick
b<-setZ(b, tm)

# subsetting
b2<-subset(b, which(tm < as.Date('2006-01-01')))

#setting wd where I want to save the "new" netcdf files
setwd(outdir)

writeRaster(b2, filename = paste0(varname, "_1971_2006_Noce.nc"),
format="CDF", varname=varname, varunit=varunits, longname=dlname,
xname="lon", yname="lat", zname="time", zunit=tunits, overwrite=TRUE)
}


Any help on how to get the loop working would be very much appreciated!










share|improve this question




















  • 1




    If your code is indeed files=list.files(pattern="nc) then you've missed a " to close out that string.
    – shians
    Nov 21 at 23:32










  • Try adding a printed out counter at various points in your code (ie print(j) or print(varname)) throughout your loop that might tell you where it is going wrong
    – RAB
    Nov 22 at 7:57












  • Thank you shians, but unfortunately this was just a transcription error when I copy pasted the code here. In the code itself I close out that string.
    – Ste
    Nov 22 at 8:08










  • thanks, I have added some print(j) and now I get this error: Error in R_nc4_create: Invalid argument (creation mode was 0) Error in ncdf4::nc_create(filename, vardef, force_v4 = force_v4) : Error in nc_create! could you help me understanding why it refers to "nc_create" in writeRaster?
    – Ste
    Nov 22 at 9:07










  • hi, your code works well for me. The only thing that I notice is that when you open the subsetted nc file the dates are not well represented. Try to UPDATE your R version and related packages as a start.
    – aaaaa
    Nov 23 at 18:32















up vote
0
down vote

favorite









up vote
0
down vote

favorite











I am trying to subset 8 netcdf files (one of them is here) in a foor loop according to a shorter period of time and then to save them as a new netcdf file.



I saw that other people already asked on how to subset netcdf files according to different time period (here or here) but once I do it on my netcdf files the "for loop" keeps on running without finishing (not even the first netcdf file) and I can't figure out why.



Here the code I use:



library(raster)
library(netcdf4)
library(lubridate)

#setting wd=indir containing netcdf files

setwd(indir)

files=list.files(pattern="nc")

for (j in seq_along(files)){

#setting wd containing netcdf files in the loop
setwd(indir)

b<-brick(files[j])

nc<-nc_open(files[j])

#variable
varname<-names(nc[['var']][3])
varunits <- ncatt_get(nc,varname,"units")[[2]]

lon<-ncvar_get(nc,"lon")

lat<-ncvar_get(nc,"lat", verbose = F)

time<-ncvar_get(nc, "time")

tunits <- ncatt_get(nc, "time", "units")[[2]]

dlname <- ncatt_get(nc, varname,"long_name")[[2]]

nc_close(nc)

#assigning a crs
proj4string(b)<-"+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"

#setting time as.Date
tm<-ymd(getZ(b))

#setting time to rasterBrick
b<-setZ(b, tm)

# subsetting
b2<-subset(b, which(tm < as.Date('2006-01-01')))

#setting wd where I want to save the "new" netcdf files
setwd(outdir)

writeRaster(b2, filename = paste0(varname, "_1971_2006_Noce.nc"),
format="CDF", varname=varname, varunit=varunits, longname=dlname,
xname="lon", yname="lat", zname="time", zunit=tunits, overwrite=TRUE)
}


Any help on how to get the loop working would be very much appreciated!










share|improve this question















I am trying to subset 8 netcdf files (one of them is here) in a foor loop according to a shorter period of time and then to save them as a new netcdf file.



I saw that other people already asked on how to subset netcdf files according to different time period (here or here) but once I do it on my netcdf files the "for loop" keeps on running without finishing (not even the first netcdf file) and I can't figure out why.



Here the code I use:



library(raster)
library(netcdf4)
library(lubridate)

#setting wd=indir containing netcdf files

setwd(indir)

files=list.files(pattern="nc")

for (j in seq_along(files)){

#setting wd containing netcdf files in the loop
setwd(indir)

b<-brick(files[j])

nc<-nc_open(files[j])

#variable
varname<-names(nc[['var']][3])
varunits <- ncatt_get(nc,varname,"units")[[2]]

lon<-ncvar_get(nc,"lon")

lat<-ncvar_get(nc,"lat", verbose = F)

time<-ncvar_get(nc, "time")

tunits <- ncatt_get(nc, "time", "units")[[2]]

dlname <- ncatt_get(nc, varname,"long_name")[[2]]

nc_close(nc)

#assigning a crs
proj4string(b)<-"+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"

#setting time as.Date
tm<-ymd(getZ(b))

#setting time to rasterBrick
b<-setZ(b, tm)

# subsetting
b2<-subset(b, which(tm < as.Date('2006-01-01')))

#setting wd where I want to save the "new" netcdf files
setwd(outdir)

writeRaster(b2, filename = paste0(varname, "_1971_2006_Noce.nc"),
format="CDF", varname=varname, varunit=varunits, longname=dlname,
xname="lon", yname="lat", zname="time", zunit=tunits, overwrite=TRUE)
}


Any help on how to get the loop working would be very much appreciated!







r netcdf






share|improve this question















share|improve this question













share|improve this question




share|improve this question








edited Nov 22 at 9:20









Bart

4,41721841




4,41721841










asked Nov 21 at 22:53









Ste

11




11








  • 1




    If your code is indeed files=list.files(pattern="nc) then you've missed a " to close out that string.
    – shians
    Nov 21 at 23:32










  • Try adding a printed out counter at various points in your code (ie print(j) or print(varname)) throughout your loop that might tell you where it is going wrong
    – RAB
    Nov 22 at 7:57












  • Thank you shians, but unfortunately this was just a transcription error when I copy pasted the code here. In the code itself I close out that string.
    – Ste
    Nov 22 at 8:08










  • thanks, I have added some print(j) and now I get this error: Error in R_nc4_create: Invalid argument (creation mode was 0) Error in ncdf4::nc_create(filename, vardef, force_v4 = force_v4) : Error in nc_create! could you help me understanding why it refers to "nc_create" in writeRaster?
    – Ste
    Nov 22 at 9:07










  • hi, your code works well for me. The only thing that I notice is that when you open the subsetted nc file the dates are not well represented. Try to UPDATE your R version and related packages as a start.
    – aaaaa
    Nov 23 at 18:32
















  • 1




    If your code is indeed files=list.files(pattern="nc) then you've missed a " to close out that string.
    – shians
    Nov 21 at 23:32










  • Try adding a printed out counter at various points in your code (ie print(j) or print(varname)) throughout your loop that might tell you where it is going wrong
    – RAB
    Nov 22 at 7:57












  • Thank you shians, but unfortunately this was just a transcription error when I copy pasted the code here. In the code itself I close out that string.
    – Ste
    Nov 22 at 8:08










  • thanks, I have added some print(j) and now I get this error: Error in R_nc4_create: Invalid argument (creation mode was 0) Error in ncdf4::nc_create(filename, vardef, force_v4 = force_v4) : Error in nc_create! could you help me understanding why it refers to "nc_create" in writeRaster?
    – Ste
    Nov 22 at 9:07










  • hi, your code works well for me. The only thing that I notice is that when you open the subsetted nc file the dates are not well represented. Try to UPDATE your R version and related packages as a start.
    – aaaaa
    Nov 23 at 18:32










1




1




If your code is indeed files=list.files(pattern="nc) then you've missed a " to close out that string.
– shians
Nov 21 at 23:32




If your code is indeed files=list.files(pattern="nc) then you've missed a " to close out that string.
– shians
Nov 21 at 23:32












Try adding a printed out counter at various points in your code (ie print(j) or print(varname)) throughout your loop that might tell you where it is going wrong
– RAB
Nov 22 at 7:57






Try adding a printed out counter at various points in your code (ie print(j) or print(varname)) throughout your loop that might tell you where it is going wrong
– RAB
Nov 22 at 7:57














Thank you shians, but unfortunately this was just a transcription error when I copy pasted the code here. In the code itself I close out that string.
– Ste
Nov 22 at 8:08




Thank you shians, but unfortunately this was just a transcription error when I copy pasted the code here. In the code itself I close out that string.
– Ste
Nov 22 at 8:08












thanks, I have added some print(j) and now I get this error: Error in R_nc4_create: Invalid argument (creation mode was 0) Error in ncdf4::nc_create(filename, vardef, force_v4 = force_v4) : Error in nc_create! could you help me understanding why it refers to "nc_create" in writeRaster?
– Ste
Nov 22 at 9:07




thanks, I have added some print(j) and now I get this error: Error in R_nc4_create: Invalid argument (creation mode was 0) Error in ncdf4::nc_create(filename, vardef, force_v4 = force_v4) : Error in nc_create! could you help me understanding why it refers to "nc_create" in writeRaster?
– Ste
Nov 22 at 9:07












hi, your code works well for me. The only thing that I notice is that when you open the subsetted nc file the dates are not well represented. Try to UPDATE your R version and related packages as a start.
– aaaaa
Nov 23 at 18:32






hi, your code works well for me. The only thing that I notice is that when you open the subsetted nc file the dates are not well represented. Try to UPDATE your R version and related packages as a start.
– aaaaa
Nov 23 at 18:32



















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