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POset Coordinate System when writing netcdf
 

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  1. POset Coordinate System when writing netcdf
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    <p>I have a SpatialPointsDataFrame in R that I want to save as netCDF. I could use some help with formatting.</p> <pre><code>&gt; str(swe) Formal class 'SpatialPointsDataFrame' [package "sp"] with 5 slots ..@ data :'data.frame': 3487 obs. of 5 variables: .. ..$ site : Factor w/ 6 levels "Dry Lake","Joe Wright",..: 1 1 1 1 1 1 1 1 1 1 ... .. ..$ depth : num [1:3487] 151 157 138 155 145 ... .. ..$ density: num [1:3487] 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 ... .. ..$ swe.obs: num [1:3487] 0.56 0.582 0.512 0.572 0.535 ... .. ..$ date : Date[1:3487], format: "2008-04-04" "2008-04-04" ... ..@ coords.nrs : num(0) ..@ coords : num [1:3487, 1:2] -107 -107 -107 -107 -107 ... .. ..- attr(*, "dimnames")=List of 2 .. .. ..$ : NULL .. .. ..$ : chr [1:2] "utm.e" "utm.n" ..@ bbox : num [1:2, 1:2] -107.9 37.8 -104.1 43.8 .. ..- attr(*, "dimnames")=List of 2 .. .. ..$ : chr [1:2] "utm.e" "utm.n" .. .. ..$ : chr [1:2] "min" "max" ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slots .. .. ..@ projargs: chr "+proj=longlat +datum=NAD83 +ellps=GRS80 +towgs84=0,0,0" </code></pre> <p>I have a <code>date</code> field that is not regular so I think I can't used it as a dimension. These are field measurements of snow so the surveys are approximately once a month in two different years. I do however need to include the date and the site name for each measurement. I also need to preserve the projection information. Below is what I have so far:</p> <pre><code>require(ncdf4) varlat=ncdim_def(name='latitude',units='deg',vals=coordinates(swe)[,2]) varlong=ncdim_def(name='longitude',units='deg',vals=coordinates(swe)[,1]) varswe=ncvar_def(name='swe.obs',units='meters',dim=list(varlat,varlong),missval=-9999) varsite=ncvar_def(name='site',units='site',dim=list(varlat,varlong),missval=-9999) vardate=ncvar_def(name='date',units='day',dim=list(varlat,varlong),missval=-9999) new.nc=nc_create('snow.survey.nc',vars=list(varswe,varsite,vardate)) </code></pre> <p>but when I try to populate values with: </p> <pre><code> ncvar_put(new.nc,varid=varswe,vals=swe$swe.obs) Error in ncvar_put(new.nc, varid = varswe, vals = swe$swe.obs) : ncvar_put: error: you asked to write 12159169 values, but the passed data array only has 3487 entries! </code></pre> <p>here is new.nc:</p> <pre><code>&gt; new.nc [1] "File snow.survey.nc (NC_FORMAT_CLASSIC):" [1] "" [1] " 3 variables:" [1] " float swe.obs[latitude,longitude] " [1] " units: meters" [1] " _FillValue: -9999" [1] " float site[latitude,longitude] " [1] " units: site" [1] " _FillValue: -9999" [1] " float date[latitude,longitude] " [1] " units: day" [1] " _FillValue: -9999" [1] "" [1] " 2 dimensions:" [1] " latitude Size:3487" [1] " units: deg" [1] " long_name: latitude" [1] " longitude Size:3487" [1] " units: deg" [1] " long_name: longitude" </code></pre> <p>Also, How do I define the projection string in the netcdf file? in this case '+proj=longlat +datum=NAD83' so another user knows what they are dealing with? Thanks</p> <p>UPDATE1: I tried this based on @Spacedman but I still get an error. Do I need to make a regular grid of the extents of my coordinates and then try to use that as the extents of my dimension? I'd have ot fill in NA everywhere I don't have a data point. I also don't have evenly spaced measurements.</p> <pre><code>coords=cbind(coordinates(swe)[,1],coordinates(swe)[,2]) nccoords=ncdim_def(name='coords',units='site',vals=coords) varswe=ncvar_def(name='swe.obs',units='meters',dim=nccoords,missval=-9999,longname='survey points') </code></pre> <p>create new 'new.nc' simplified to one variable at the moment.</p> <pre><code>new.nc=nc_create('snow.survey.nc',vars=varswe) ncvar_put(new.nc,varid=varswe,vals=swe$swe.obs) Error in ncvar_put(new.nc, varid = varswe, vals = swe$swe.obs) : ncvar_put: error: you asked to write 6974 values, but the passed data array only has 3487 entries! </code></pre>
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