Dear list, sorry about the file. The files from the CMIP5 are public, but need a registration first. You can access the same file in any of these links: https://www.sendspace.com/file/famgz3 and https://drive.google.com/file/d/1L1T03iQ6LU1yYRYeRypxwMB3E7fLjkJI/view?usp=sharing .
In this meantime I will try the Mike' advices. Best regards, Frederico <https://www.sendspace.com/file/famgz3> On Thu, Aug 22, 2019 at 3:41 PM Frederico Faleiro <fvfale...@gmail.com> wrote: > Dear list, > > sorry about the file. The files from the CMIP5 are public, but need a > registration first. I am sending the same file attached. > > In this meantime I will try the Mike' advices. > > Best regards, > > Frederico > > > > > > On Thu, Aug 22, 2019 at 5:03 AM Michael Sumner <mdsum...@gmail.com> wrote: > >> raster does the wrong thing here in my opinion, the right outcome is to >> give a grid in index-extent (0, ncol, 0, nrow) and with no projection >> metadata (crs). There will be coordinate arrays in this file, and they need >> to be handled as though they are data (with local, x*y dependent values in >> every cell). >> >> With brick() you can proceed to process the data with no problem (using >> stopIfNotEqualSpaced = FALSE), but you can't rely on the extent being >> relevant, or any function that works in geographic space to do the right >> thing. To map a layer of these data you might try >> >> grd <- raster(yourfile, stopIfNotEqualSpaced = FALSE) >> coords <- brick(raster(yourfile, varname = "lon"), >> raster(yourfile, varname = "lat")) ## but only >> you will know the names of these variables values "lon", "lat" (might be >> "TLON", "TLAT" ? ) >> >> In quadmesh there is a way to plot in geographic space that's not >> impossibly slow (possibly the coords will need a re-orientation transpose >> ...): >> >> quadmesh::mesh_plot(grd, coords = coords) >> >> It's likely that will "map" it properly, but CMIP is likely to wrap >> around an odd longitude (or something), and so cropping to your area and/or >> choosing a good project for the crs argument to mesh_plot is probably >> needed. You can investigate with plot(coords[[1]]) and plot(coords[[2]]) >> to get a sense of their layout. >> >> In the stars package this is all internalized, with >> stars::read_stars(yourfile) catching all the information required as much >> as possible, and with plotting methods - but variable choice and actual >> results vary widely, and depend a lot on very specific details. (angstroms >> package has similar helpers for the approach but is unlikely to help here >> without access to the file to try) >> >> To help us guess further you can use the "ncdump" output, raster will >> print this with >> >> print(raster("yourfile")) >> >> and from that we could provide better guesses at variable names and >> subsetting etc. >> >> But, as Edzer asked, nothing is as good as having the file - any chance >> you can share it? (Personally I think the world rather needs more R >> attention on climate model output.) >> >> Cheers, Mike. >> >> On Thu, Aug 22, 2019 at 1:53 PM Frederico Faleiro <fvfale...@gmail.com> >> wrote: >> > >> > Dear list, >> > >> > I am using some netCDF files from the CMIP5 climate models in raster >> > package, but I am having some issues with one model. >> > The netCDF file from the GFDL-ESM2G model (e.g. >> > >> http://aims3.llnl.gov/thredds/fileServer/css03_data/cmip5/output1/NOAA-GFDL/GFDL-ESM2G/rcp45/mon/atmos/Amon/r1i1p1/v20120412/pr/pr_Amon_GFDL-ESM2G_rcp45_r1i1p1_204101-204512.nc >> > ) >> > have the error message as in bellow example. >> > >> > #Example >> > library(raster) >> > s1 <- stack("pr_Amon_GFDL-ESM2G_rcp45_r1i1p1_204101-204512.nc") >> > Error in .rasterObjectFromCDF(x, type = objecttype, band = band, ...) : >> > cells are not equally spaced; you should extract values as points >> > >> > # I check some solutions that recomend force read the file with the >> > argument "stopIfNotEqualSpaced = F" as bellow. >> > sf <- stack("pr_Amon_GFDL-ESM2G_rcp45_r1i1p1_204101-204512.nc", >> > *stopIfNotEqualSpaced >> > = F*) >> > bf <- brick("pr_Amon_GFDL-ESM2G_rcp45_r1i1p1_204101-204512.nc", >> > *stopIfNotEqualSpaced >> > = F*) >> > >> > I performed some tests and only "works" with brick. However I did not >> find >> > any solution to check where is the problem and fix it in the file. >> > >> > How can I check if it is really an issue and fix it? >> > >> > sessionInfo() >> > R version 3.5.1 (2018-07-02) >> > Platform: x86_64-w64-mingw32/x64 (64-bit) >> > Running under: Windows 10 x64 (build 18362) >> > >> > Matrix products: default >> > >> > locale: >> > [1] LC_COLLATE=Portuguese_Brazil.1252 LC_CTYPE=Portuguese_Brazil.1252 >> > [3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C >> > [5] LC_TIME=Portuguese_Brazil.1252 >> > >> > attached base packages: >> > [1] stats graphics grDevices utils datasets methods base >> > >> > other attached packages: >> > [1] raster_2.8-19 sp_1.3-1 >> > >> > loaded via a namespace (and not attached): >> > [1] compiler_3.5.1 rgdal_1.4-3 Rcpp_1.0.1 codetools_0.2-15 >> > ncdf4_1.16.1 >> > [6] grid_3.5.1 lattice_0.20-35 >> > >> > Best regards, >> > >> > Frederico >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > R-sig-Geo mailing list >> > R-sig-Geo@r-project.org >> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo >> >> >> >> -- >> Michael Sumner >> Software and Database Engineer >> Australian Antarctic Division >> Hobart, Australia >> e-mail: mdsum...@gmail.com >> > [[alternative HTML version deleted]] _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo