<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>Hi! </div>
<div>Thanks a lot !!! I could get the raster now. </div>
<div>This is what I got:</div>
<div>> r<br/>
class : RasterLayer <br/>
band : 1 (of 365 bands)<br/>
dimensions : 4823, 5268, 25407564 (nrow, ncol, ncell)<br/>
resolution : 1000, 1000 (x, y)<br/>
extent : -2015000, 3253000, -3037000, 1786000 (xmin, xmax, ymin, ymax)<br/>
coord. ref. : +proj=lcc +lon_0=-100 +lat_0=42.5 +x_0=0 +y_0=0 +lon_0=0 +lat_1=25 +lat_2=60 <br/>
data source : C:\Users\Andi\Desktop\1980\tmin_1980.nc4 <br/>
names : daily.minimum.temperature <br/>
z-value : 1980-01-01 <br/>
zvar : tmin </div>
<div> </div>
<div>
<div> </div>
<div>and </div>
<div>
<div><br/>
> print(ncic)<br/>
[1] "File tmin_1980.nc4 (NC_FORMAT_NETCDF4_CLASSIC):"<br/>
[1] ""<br/>
[1] " 6 variables (excluding dimension variables):"<br/>
[1] " short lambert_conformal_conic[] "<br/>
[1] " grid_mapping_name: lambert_conformal_conic"<br/>
[1] " longitude_of_central_meridian: -100"<br/>
[1] " latitude_of_projection_origin: 42.5"<br/>
[1] " false_easting: 0"<br/>
[1] " false_northing: 0"<br/>
[1] " standard_parallel: 25" " standard_parallel: 60"<br/>
[1] " longitude_of_prime_meridian: 0"<br/>
[1] " float lat[x,y] "<br/>
[1] " units: degrees_north"<br/>
[1] " long_name: latitude coordinate"<br/>
[1] " standard_name: latitude"<br/>
[1] " float lon[x,y] "<br/>
[1] " units: degrees_east"<br/>
[1] " long_name: longitude coordinate"<br/>
[1] " standard_name: longitude"<br/>
[1] " float time_bnds[nv,time] "<br/>
[1] " float tmin[x,y,time] "<br/>
[1] " long_name: daily minimum temperature"<br/>
[1] " units: degrees C"<br/>
[1] " missing_value: -9999"<br/>
[1] " _FillValue: -9999"<br/>
[1] " valid_range: -50" " valid_range: 50" <br/>
[1] " coordinates: lat lon"<br/>
[1] " grid_mapping: lambert_conformal_conic"<br/>
[1] " cell_methods: area: mean time: minimum"<br/>
[1] " short yearday[time] "<br/>
[1] " long_name: yearday"<br/>
[1] " valid_range: 1" " valid_range: 365"<br/>
[1] ""<br/>
[1] " 4 dimensions:"<br/>
[1] " y Size:4823"<br/>
[1] " units: m"<br/>
[1] " long_name: y coordinate of projection"<br/>
[1] " standard_name: projection_y_coordinate"<br/>
[1] " x Size:5268"<br/>
[1] " units: m"<br/>
[1] " long_name: x coordinate of projection"<br/>
[1] " standard_name: projection_x_coordinate"<br/>
[1] " time Size:365 *** is unlimited ***"<br/>
[1] " long_name: time"<br/>
[1] " calendar: standard"<br/>
[1] " units: days since 1980-01-01 00:00:00 UTC"<br/>
[1] " bounds: time_bnds"<br/>
[1] " nv Size:2"<br/>
[1] ""<br/>
[1] " 8 global attributes:"<br/>
[1] " start_year: 1980"<br/>
[1] " source: Daymet Software Version 2.0"<br/>
[1] " Version_software: Daymet Software Version 2.0"<br/>
[1] " Version_data: Daymet Data Version 2.1"<br/>
[1] " Conventions: CF-1.4"<br/>
[1] " citation: Please see http://daymet.ornl.gov/ for current Daymet data citation information"<br/>
[1] " references: Please see http://daymet.ornl.gov/ for current information on Daymet references"<br/>
[1] " institution: Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC)"</div>
<div> </div>
<div>The file can be downloaded from: http://daymet.ornl.gov/mosaics.html (The files with the daylength data are much smaller.)</div>
<div>When I open the lat layer I see that the differences between consecutive cells are different depending on the location on the file, so I think that the sizes are not uniform. </div>
<div>I am not sure how I can fix that. </div>
<div> </div>
<div>Thanks a lot. </div>
<div>Andi</div>
</div>
<div name="quote" style="margin:10px 5px 5px 10px; padding: 10px 0 10px 10px; border-left:2px solid #C3D9E5; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Freitag, 05. Juni 2015 um 23:53 Uhr<br/>
<b>Von:</b> "Michael Sumner" <mdsumner@gmail.com><br/>
<b>An:</b> "Andrea Timmermann" <timmermann@gmx.at>, r-sig-geo@r-project.org<br/>
<b>Betreff:</b> Re: [R-sig-Geo] Problem with raster package and nc4 file</div>
<div name="quoted-content">
<div>
<div class="gmail_quote">
<div>On Sat, 6 Jun 2015 at 08:04 Andrea Timmermann <<a href="timmermann@gmx.at" target="_parent">timmermann@gmx.at</a>> wrote:</div>
<blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex;border-left: 1.0px rgb(204,204,204) solid;padding-left: 1.0ex;">Hi,<br/>
<br/>
I have daymet data in nc4 format and could open it with the ncdf4 package. I also have the coordinates of some polygons representing ecological areas.<br/>
Both, the polygon vertices and the nc4 file have the same projection (LCC) and units (degrees).</blockquote>
<div> </div>
<div> </div>
<div>Do you have grid data in LCC but stored with longitude/latitude coordinates? This is unfortunate, but you can restore the LCC grid probably. I would try</div>
<div> </div>
<div>r <- <span style="font-size: 13.2px;line-height: 17.999998px;">raster(</span><span style="font-size: 13.2px;line-height: 17.999998px;">"tmin_1980.</span><span class="lG" style="font-size: 13.2px;line-height: 17.999998px;">nc4</span><span style="font-size: 13.2px;line-height: 17.999998px;">")</span></div>
<div> </div>
<div><span style="font-size: 13.2px;line-height: 17.999998px;">and then print it out and tell us the result (or post the errors if it fails): </span></div>
<div> </div>
<div><span style="font-size: 13.2px;line-height: 17.999998px;">r</span></div>
<div> </div>
<div><span style="font-size: 13.2px;line-height: 17.999998px;">Do you have the details of the LCC projection? At a bare minimum you need the centre longitude and centre latitude, and the two standard parallels, and the datum/ellipsoid. Can you open the file with ncdf4 and print out this? </span></div>
<div> </div>
<div><span style="font-size: 13.2px;line-height: 17.999998px;">ncic <- nc_open("tmin_1980.</span><span class="lG" style="font-size: 13.2px;line-height: 17.999998px;">nc4</span><span style="font-size: 13.2px;line-height: 17.999998px;">")</span></div>
<div><span style="font-size: 13.2px;line-height: 17.999998px;">print(ncic)</span></div>
<div> </div>
<div> You are not supposed to mix use of the ncdf4 package functions with those of raster, raster is designed to do all the work - but it does expect sensibly specified regular grids. If your data really are regular in LCC I would recommend sorting that out. Can you share the file, or a link to an analogous one? </div>
<div> </div>
<div>Once you have it sorted out in raster, you can read your shapefile in and do this</div>
<div> </div>
<div>meanpolydata <- extract(r, poly, fun = mean)</div>
<div> </div>
<div>Cheers, Mike. </div>
<div> </div>
<blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex;border-left: 1.0px rgb(204,204,204) solid;padding-left: 1.0ex;">What I would like to do is to get the average temperature for each ecological area. So I wanted to use the polygons as a mask for the temperature raster and then get the average temperature for each polygon.<br/>
<br/>
I wanted to create a raster object (using the raster function in the raster package):<br/>
<br/>
ncic <- nc_open("tmin_1980.nc4")<br/>
raster(ncic, 'tmin')<br/>
<br/>
But I get this error:<br/>
Error in (function (classes, fdef, mtable) :<br/>
unable to find an inherited method for function ‘raster’ for signature ‘"ncdf4"’<br/>
<br/>
Does anyone know how to fix this? Is there another way to get the data that I need?<br/>
<br/>
I am a bit confused by the fact that the temperature data consists of one matrix with latitude data, one with longitude data and one with the temperature values. And by the fact that the spacing between the latitude and longitude matrices is not uniform. Is the raster package accounting somehow for this?<br/>
<br/>
Thanks a lot. Andi.<br/>
<br/>
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