[R-sig-Geo] Multi-file raster stack from netcdf specifying levels

[Vijay Lulla]

Maybe you can try something like this?

h2osoil.l1 <- do.call(stack, lapply(files, function(file) raster(file,
varname='H2OSOI', level=1)))
h2osoil.l2 <- do.call(stack, lapply(files, function(file) raster(file,
varname='H2OSOI', level=2)))
...
h2osoil.l15 <- do.call(stack, lapply(files, function(file) raster(file,
varname='H2OSOI', level=15)))


On Thu, Oct 19, 2017 at 6:33 PM, Thiago V. dos Santos via R-sig-Geo <
r-sig-geo at r-project.org> wrote:

> Dear all,
>
> I am working with several netcdf files that contain soil moisture in 15
> soil layers.
>
> I am trying to create raster stacks of individual layers, but I am getting
> a strange error.
>
> # Get list of files
> files <- list.files('~/Downloads', pattern='.nc', full.names=T)
>
> # Stack all the files
> h2osoil.l1 <- stack(files, varname='H2OSOI', level=1) # this would be the
> first layer
> h2osoil.l2 <- stack(files, varname='H2OSOI', level=2) # this would be the
> second layer
>
> And this is the error I get:
>
> Error in (function (classes, fdef, mtable)  :
> unable to find an inherited method for function ‘raster’ for signature
> ‘"numeric"’
> In addition: Warning messages:
> 1: In .rasterObjectFromCDF(x, type = objecttype, band = band, ...) :
> "level" set to 1 (there are 15 levels)
> 2: In .rasterObjectFromCDF(x, type = objecttype, band = band, ...) :
> "level" set to 1 (there are 15 levels)
> 3: In .rasterObjectFromCDF(x, type = objecttype, band = band, ...) :
> "level" set to 1 (there are 15 levels)
>
> Here are some files to reproduce this issue (3 MB each file):
>
> https://www.dropbox.com/s/9z3fnadqdf1rzuz/cam5clm45_ctl.
> clm2.h0.1980-01.nc?dl=0
> https://www.dropbox.com/s/0snz58au8ic196p/cam5clm45_ctl.
> clm2.h0.1980-02.nc?dl=0
> https://www.dropbox.com/s/v5ps5bkyrkflki7/cam5clm45_ctl.
> clm2.h0.1980-03.nc?dl=0
>
>
> I know netcdf files can be quite tricky to work with, but is there any way
> to get this file read in the right way using the raster package? Any other
> option?
>
>
> Greetings,
>  -- Thiago V. dos Santos
>
> Postdoctoral Research Fellow
> Department of Climate and Space Science and Engineering
> University of Michigan
>
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo




-- 
Vijay Lulla, Ph.D.

Assistant Professor,
Dept. of Geography,
Indiana University Purdue University Indianapolis (IUPUI)
425 University Blvd, CA-207C.
Indianapolis, IN-46202
vlulla at iupui.edu

<http://vijaylulla.com>
http://vijaylulla.com

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