Subsetting and saving netcdf in R

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!

edited Nov 22 '18 at 9:20

Bart

4,72132043

asked Nov 21 '18 at 22:53

Ste

1

If your code is indeed files=list.files(pattern="nc) then you've missed a " to close out that string.

– shians
Nov 21 '18 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 '18 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 '18 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 '18 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 '18 at 18:32

add a comment |

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.

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!

edited Nov 22 '18 at 9:20

Bart

4,72132043

asked Nov 21 '18 at 22:53

Ste

1

If your code is indeed files=list.files(pattern="nc) then you've missed a " to close out that string.

– shians
Nov 21 '18 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 '18 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 '18 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 '18 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 '18 at 18:32

add a comment |

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.

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!

edited Nov 22 '18 at 9:20

Bart

4,72132043

asked Nov 21 '18 at 22:53

Ste

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.

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

edited Nov 22 '18 at 9:20

Bart

4,72132043

asked Nov 21 '18 at 22:53

Ste

edited Nov 22 '18 at 9:20

Bart

4,72132043

asked Nov 21 '18 at 22:53

Ste

edited Nov 22 '18 at 9:20

Bart

4,72132043

edited Nov 22 '18 at 9:20

Bart

4,72132043

edited Nov 22 '18 at 9:20

Bart

4,72132043

asked Nov 21 '18 at 22:53

Ste

asked Nov 21 '18 at 22:53

Ste

asked Nov 21 '18 at 22:53

Ste

1

If your code is indeed files=list.files(pattern="nc) then you've missed a " to close out that string.

– shians
Nov 21 '18 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 '18 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 '18 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 '18 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 '18 at 18:32

add a comment |

1

If your code is indeed files=list.files(pattern="nc) then you've missed a " to close out that string.

– shians
Nov 21 '18 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 '18 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 '18 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 '18 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 '18 at 18:32

If your code is indeed files=list.files(pattern="nc) then you've missed a " to close out that string.

– shians
Nov 21 '18 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 '18 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 '18 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 '18 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 '18 at 18:32

add a comment |

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