What is the Coordinate Reference System?

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What is the Coordinate Reference System?

Sergio Ibarra
Greetings,

I'm want to read NetCDF spatial data from a meteorological model (WRF
model). The NetCDF can have one of these three projections:

Polar stereographic
Lambert conformal
Mercator projection

(See figure
https://user-images.githubusercontent.com/27447280/41389756-ed23f91a-6f68-11e8-961e-6ba901913c54.png
)

What is the  Coordinate Reference System for each case?

Thanks!

Here an example with ncdf4 and raster:

library(ncdf4)
library(raster)
a <- tempfile()
download.file(url = "
http://www.unidata.ucar.edu/software/netcdf/examples/wrfout_v2_Lambert.nc",
              destfile = a) #78 Mb
wrf <- nc_open(a)
paste("The file has",wrf$nvars,"variables")
paste("The file has",names(wrf$var))
lat <- ncvar_get( wrf, "XLAT" )
lon <- ncvar_get( wrf, "XLONG" )
t2 <- ncvar_get( wrf, "T2" ) - 273.15
dim(t2) #73 60 13
#image
image(t2[, , 12])
# raster
rt2 <- raster(t(t2[1:dim(t2)[1],
                   dim(t2)[2]:1,
                   12]),
              xmn = min(lon),
              xmx = max(lon),
              ymn = min(lat),
              ymx = max(lat),
*              crs="+init=epsg:4326") # ???*
spplot(rt2)



--
​Sergio Ibarra Espinosa
Post Doc
PhD in Atmospheric Sciences
Instituto de Astronomia, Geofísica e Ciências Atmosféricas
Universidade de São Paulo
Rua do Matão, 1226
São Paulo-SP - Brasil -
05508-090
+55-11-97425-3791
Skype: sergio_ibarra1

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Re: What is the Coordinate Reference System?

Michael Sumner-2
Try raster::projection(raster::raster(a)) first, then delve if necessary
into the ncdump summary with print(raster::raster(a)))

But, raster(a) may be enough here? To get that stuff more directly from the
NetCDF API you have to use the inq and att functions of ncdf4 or RNetCDF
and that's no fun.

I'd also try raster(rgdal::readGDAL(a)) which is a totally different but
equivalent read path.

Cheers, Mike

On Thu, 14 Jun 2018, 11:03 Sergio Ibarra, <[hidden email]> wrote:

> Greetings,
>
> I'm want to read NetCDF spatial data from a meteorological model (WRF
> model). The NetCDF can have one of these three projections:
>
> Polar stereographic
> Lambert conformal
> Mercator projection
>
> (See figure
>
> https://user-images.githubusercontent.com/27447280/41389756-ed23f91a-6f68-11e8-961e-6ba901913c54.png
> )
>
> What is the  Coordinate Reference System for each case?
>
> Thanks!
>
> Here an example with ncdf4 and raster:
>
> library(ncdf4)
> library(raster)
> a <- tempfile()
> download.file(url = "
> http://www.unidata.ucar.edu/software/netcdf/examples/wrfout_v2_Lambert.nc
> ",
>               destfile = a) #78 Mb
> wrf <- nc_open(a)
> paste("The file has",wrf$nvars,"variables")
> paste("The file has",names(wrf$var))
> lat <- ncvar_get( wrf, "XLAT" )
> lon <- ncvar_get( wrf, "XLONG" )
> t2 <- ncvar_get( wrf, "T2" ) - 273.15
> dim(t2) #73 60 13
> #image
> image(t2[, , 12])
> # raster
> rt2 <- raster(t(t2[1:dim(t2)[1],
>                    dim(t2)[2]:1,
>                    12]),
>               xmn = min(lon),
>               xmx = max(lon),
>               ymn = min(lat),
>               ymx = max(lat),
> *              crs="+init=epsg:4326") # ???*
> spplot(rt2)
>
>
>
> --
> ​Sergio Ibarra Espinosa
> Post Doc
> PhD in Atmospheric Sciences
> Instituto de Astronomia, Geofísica e Ciências Atmosféricas
> Universidade de São Paulo
> Rua do Matão, 1226
> São Paulo-SP - Brasil -
> 05508-090
> +55-11-97425-3791
> Skype: sergio_ibarra1
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
--
Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia

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Re: What is the Coordinate Reference System?

Ben Tupper
Hi,

That's an interesting approach.  

On the other hand, sometimes I get bitten (well, muddled really) when I use raster to determine the crs of a ncdf resource.  It all sort of depends.

Below is an example for Aqua MODIS imagery from OBPG (https://oceandata.sci.gsfc.nasa.gov/MODIS-Aqua/Mapped/Daily/9km/sst/2017/ <https://oceandata.sci.gsfc.nasa.gov/MODIS-Aqua/Mapped/Daily/9km/sst/2017/>).  The OBPG docs (https://oceancolor.gsfc.nasa.gov/products/ <https://oceancolor.gsfc.nasa.gov/products/>) state that the data is served up as 'Plate Carrée' which I think has a crs ...

'+proj=eqc +lat_ts=0 +lat_0=0 +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs '

... as described here http://spatialreference.org/ref/epsg/32662/ <http://spatialreference.org/ref/epsg/32662/>

You can see below that raster comes up with...

'+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0'

... which is http://spatialreference.org/ref/epsg/4326/ <http://spatialreference.org/ref/epsg/4326/>

Explicitly setting the crs while reading doesn't help.  I have never resolved if it is an OBPG documentation bug, my confusion about projections, or some other mystery.  So, my usual practice is to assume that raster makes the right call.

#### start

library(raster)
URI = 'https://oceandata.sci.gsfc.nasa.gov/cgi/getfile/A2017175.L3m_DAY_SST_sst_9km.nc'

# ~3.8MB
ok = download.file(URI, basename(URI))

R = raster::raster(basename(URI), varname = 'sst')
R
# class       : RasterLayer
# dimensions  : 2160, 4320, 9331200  (nrow, ncol, ncell)
# resolution  : 0.08333334, 0.08333334  (x, y)
# extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
# coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
# data source : /Users/Shared/code/R/others/record/spnc/A2017175.L3m_DAY_SST_sst_9km.nc
# names       : Sea.Surface.Temperature
# zvar        : sst

S = raster::raster(basename(URI), varname = "sst", crs = '+proj=eqc +lat_ts=0 +lat_0=0 +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs')
# Warning message:
# In .getProj(prj, crs) :
#  argument "crs" ignored because the file provides a crs

#### end


Cheers,
Ben


> On Jun 14, 2018, at 6:42 PM, Michael Sumner <[hidden email]> wrote:
>
> Try raster::projection(raster::raster(a)) first, then delve if necessary
> into the ncdump summary with print(raster::raster(a)))
>
> But, raster(a) may be enough here? To get that stuff more directly from the
> NetCDF API you have to use the inq and att functions of ncdf4 or RNetCDF
> and that's no fun.
>
> I'd also try raster(rgdal::readGDAL(a)) which is a totally different but
> equivalent read path.
>
> Cheers, Mike
>
> On Thu, 14 Jun 2018, 11:03 Sergio Ibarra, <[hidden email]> wrote:
>
>> Greetings,
>>
>> I'm want to read NetCDF spatial data from a meteorological model (WRF
>> model). The NetCDF can have one of these three projections:
>>
>> Polar stereographic
>> Lambert conformal
>> Mercator projection
>>
>> (See figure
>>
>> https://user-images.githubusercontent.com/27447280/41389756-ed23f91a-6f68-11e8-961e-6ba901913c54.png
>> )
>>
>> What is the  Coordinate Reference System for each case?
>>
>> Thanks!
>>
>> Here an example with ncdf4 and raster:
>>
>> library(ncdf4)
>> library(raster)
>> a <- tempfile()
>> download.file(url = "
>> http://www.unidata.ucar.edu/software/netcdf/examples/wrfout_v2_Lambert.nc
>> ",
>>              destfile = a) #78 Mb
>> wrf <- nc_open(a)
>> paste("The file has",wrf$nvars,"variables")
>> paste("The file has",names(wrf$var))
>> lat <- ncvar_get( wrf, "XLAT" )
>> lon <- ncvar_get( wrf, "XLONG" )
>> t2 <- ncvar_get( wrf, "T2" ) - 273.15
>> dim(t2) #73 60 13
>> #image
>> image(t2[, , 12])
>> # raster
>> rt2 <- raster(t(t2[1:dim(t2)[1],
>>                   dim(t2)[2]:1,
>>                   12]),
>>              xmn = min(lon),
>>              xmx = max(lon),
>>              ymn = min(lat),
>>              ymx = max(lat),
>> *              crs="+init=epsg:4326") # ???*
>> spplot(rt2)
>>
>>
>>
>> --
>> ​Sergio Ibarra Espinosa
>> Post Doc
>> PhD in Atmospheric Sciences
>> Instituto de Astronomia, Geofísica e Ciências Atmosféricas
>> Universidade de São Paulo
>> Rua do Matão, 1226
>> São Paulo-SP - Brasil -
>> 05508-090
>> +55-11-97425-3791
>> Skype: sergio_ibarra1
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
> --
> Dr. Michael Sumner
> Software and Database Engineer
> Australian Antarctic Division
> 203 Channel Highway
> Kingston Tasmania 7050 Australia
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org

Ecological Forecasting: https://eco.bigelow.org/






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Re: What is the Coordinate Reference System?

edzer
Plate carree is essentially a linear mapping of long and lat to x and y,
without changing aspect ratio (scale factor 1 at equator).

projecting long/lat towards plate caree using the proj4 string you
mention will however change the units from degrees to m. So while the
plots of of data in linear long/lat (with aspect ration 1) looks
identical to the one obtained in plate caree (with aspect ratio 1), the
numerical values along their axes are very different.

Many netcdf files carry a grid (raster) with the x and y coordinates of
grid cells (centers?) in another coordinate system, but the ones you
mention below don't, as far as I can tell. I think what they mean by
mentioning plate carree is just saying that this is a regular long/lat
degree grid; rather unlucky wording IMO.

On 06/15/2018 08:14 PM, Ben Tupper wrote:

> Hi,
>
> That's an interesting approach.  
>
> On the other hand, sometimes I get bitten (well, muddled really) when I use raster to determine the crs of a ncdf resource.  It all sort of depends.
>
> Below is an example for Aqua MODIS imagery from OBPG (https://oceandata.sci.gsfc.nasa.gov/MODIS-Aqua/Mapped/Daily/9km/sst/2017/ <https://oceandata.sci.gsfc.nasa.gov/MODIS-Aqua/Mapped/Daily/9km/sst/2017/>).  The OBPG docs (https://oceancolor.gsfc.nasa.gov/products/ <https://oceancolor.gsfc.nasa.gov/products/>) state that the data is served up as 'Plate Carrée' which I think has a crs ...
>
> '+proj=eqc +lat_ts=0 +lat_0=0 +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs '
>
> ... as described here http://spatialreference.org/ref/epsg/32662/ <http://spatialreference.org/ref/epsg/32662/>
>
> You can see below that raster comes up with...
>
> '+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0'
>
> ... which is http://spatialreference.org/ref/epsg/4326/ <http://spatialreference.org/ref/epsg/4326/>
>
> Explicitly setting the crs while reading doesn't help.  I have never resolved if it is an OBPG documentation bug, my confusion about projections, or some other mystery.  So, my usual practice is to assume that raster makes the right call.
>
> #### start
>
> library(raster)
> URI = 'https://oceandata.sci.gsfc.nasa.gov/cgi/getfile/A2017175.L3m_DAY_SST_sst_9km.nc'
>
> # ~3.8MB
> ok = download.file(URI, basename(URI))
>
> R = raster::raster(basename(URI), varname = 'sst')
> R
> # class       : RasterLayer
> # dimensions  : 2160, 4320, 9331200  (nrow, ncol, ncell)
> # resolution  : 0.08333334, 0.08333334  (x, y)
> # extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
> # coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
> # data source : /Users/Shared/code/R/others/record/spnc/A2017175.L3m_DAY_SST_sst_9km.nc
> # names       : Sea.Surface.Temperature
> # zvar        : sst
>
> S = raster::raster(basename(URI), varname = "sst", crs = '+proj=eqc +lat_ts=0 +lat_0=0 +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs')
> # Warning message:
> # In .getProj(prj, crs) :
> #  argument "crs" ignored because the file provides a crs
>
> #### end
>
>
> Cheers,
> Ben
>
>
>> On Jun 14, 2018, at 6:42 PM, Michael Sumner <[hidden email]> wrote:
>>
>> Try raster::projection(raster::raster(a)) first, then delve if necessary
>> into the ncdump summary with print(raster::raster(a)))
>>
>> But, raster(a) may be enough here? To get that stuff more directly from the
>> NetCDF API you have to use the inq and att functions of ncdf4 or RNetCDF
>> and that's no fun.
>>
>> I'd also try raster(rgdal::readGDAL(a)) which is a totally different but
>> equivalent read path.
>>
>> Cheers, Mike
>>
>> On Thu, 14 Jun 2018, 11:03 Sergio Ibarra, <[hidden email]> wrote:
>>
>>> Greetings,
>>>
>>> I'm want to read NetCDF spatial data from a meteorological model (WRF
>>> model). The NetCDF can have one of these three projections:
>>>
>>> Polar stereographic
>>> Lambert conformal
>>> Mercator projection
>>>
>>> (See figure
>>>
>>> https://user-images.githubusercontent.com/27447280/41389756-ed23f91a-6f68-11e8-961e-6ba901913c54.png
>>> )
>>>
>>> What is the  Coordinate Reference System for each case?
>>>
>>> Thanks!
>>>
>>> Here an example with ncdf4 and raster:
>>>
>>> library(ncdf4)
>>> library(raster)
>>> a <- tempfile()
>>> download.file(url = "
>>> http://www.unidata.ucar.edu/software/netcdf/examples/wrfout_v2_Lambert.nc
>>> ",
>>>              destfile = a) #78 Mb
>>> wrf <- nc_open(a)
>>> paste("The file has",wrf$nvars,"variables")
>>> paste("The file has",names(wrf$var))
>>> lat <- ncvar_get( wrf, "XLAT" )
>>> lon <- ncvar_get( wrf, "XLONG" )
>>> t2 <- ncvar_get( wrf, "T2" ) - 273.15
>>> dim(t2) #73 60 13
>>> #image
>>> image(t2[, , 12])
>>> # raster
>>> rt2 <- raster(t(t2[1:dim(t2)[1],
>>>                   dim(t2)[2]:1,
>>>                   12]),
>>>              xmn = min(lon),
>>>              xmx = max(lon),
>>>              ymn = min(lat),
>>>              ymx = max(lat),
>>> *              crs="+init=epsg:4326") # ???*
>>> spplot(rt2)
>>>
>>>
>>>
>>> --
>>> ​Sergio Ibarra Espinosa
>>> Post Doc
>>> PhD in Atmospheric Sciences
>>> Instituto de Astronomia, Geofísica e Ciências Atmosféricas
>>> Universidade de São Paulo
>>> Rua do Matão, 1226
>>> São Paulo-SP - Brasil -
>>> 05508-090
>>> +55-11-97425-3791
>>> Skype: sergio_ibarra1
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>> --
>> Dr. Michael Sumner
>> Software and Database Engineer
>> Australian Antarctic Division
>> 203 Channel Highway
>> Kingston Tasmania 7050 Australia
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org
>
> Ecological Forecasting: https://eco.bigelow.org/
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

--
Edzer Pebesma
Institute for Geoinformatics
Heisenbergstrasse 2, 48151 Muenster, Germany
Phone: +49 251 8333081

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Re: What is the Coordinate Reference System?

Michael Sumner-2
Agree with Edzer this application of eqc is anomalous and after it confused
us initially we now ignore it and apply the unproblematic proj=longlat
interpretation to these products (after checking).

I might explore the L3 products to find out why this occurred, but the
ocean colour forum is the usual place to find discussion.

Cheers, Mike

On Mon, 18 Jun 2018, 15:59 Edzer Pebesma, <[hidden email]>
wrote:

> Plate carree is essentially a linear mapping of long and lat to x and y,
> without changing aspect ratio (scale factor 1 at equator).
>
> projecting long/lat towards plate caree using the proj4 string you
> mention will however change the units from degrees to m. So while the
> plots of of data in linear long/lat (with aspect ration 1) looks
> identical to the one obtained in plate caree (with aspect ratio 1), the
> numerical values along their axes are very different.
>
> Many netcdf files carry a grid (raster) with the x and y coordinates of
> grid cells (centers?) in another coordinate system, but the ones you
> mention below don't, as far as I can tell. I think what they mean by
> mentioning plate carree is just saying that this is a regular long/lat
> degree grid; rather unlucky wording IMO.
>
> On 06/15/2018 08:14 PM, Ben Tupper wrote:
> > Hi,
> >
> > That's an interesting approach.
> >
> > On the other hand, sometimes I get bitten (well, muddled really) when I
> use raster to determine the crs of a ncdf resource.  It all sort of depends.
> >
> > Below is an example for Aqua MODIS imagery from OBPG (
> https://oceandata.sci.gsfc.nasa.gov/MODIS-Aqua/Mapped/Daily/9km/sst/2017/
> <https://oceandata.sci.gsfc.nasa.gov/MODIS-Aqua/Mapped/Daily/9km/sst/2017/>).
> The OBPG docs (https://oceancolor.gsfc.nasa.gov/products/ <
> https://oceancolor.gsfc.nasa.gov/products/>) state that the data is
> served up as 'Plate Carrée' which I think has a crs ...
> >
> > '+proj=eqc +lat_ts=0 +lat_0=0 +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84
> +datum=WGS84 +units=m +no_defs '
> >
> > ... as described here http://spatialreference.org/ref/epsg/32662/ <
> http://spatialreference.org/ref/epsg/32662/>
> >
> > You can see below that raster comes up with...
> >
> > '+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0'
> >
> > ... which is http://spatialreference.org/ref/epsg/4326/ <
> http://spatialreference.org/ref/epsg/4326/>
> >
> > Explicitly setting the crs while reading doesn't help.  I have never
> resolved if it is an OBPG documentation bug, my confusion about
> projections, or some other mystery.  So, my usual practice is to assume
> that raster makes the right call.
> >
> > #### start
> >
> > library(raster)
> > URI = '
> https://oceandata.sci.gsfc.nasa.gov/cgi/getfile/A2017175.L3m_DAY_SST_sst_9km.nc
> '
> >
> > # ~3.8MB
> > ok = download.file(URI, basename(URI))
> >
> > R = raster::raster(basename(URI), varname = 'sst')
> > R
> > # class       : RasterLayer
> > # dimensions  : 2160, 4320, 9331200  (nrow, ncol, ncell)
> > # resolution  : 0.08333334, 0.08333334  (x, y)
> > # extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
> > # coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
> > # data source : /Users/Shared/code/R/others/record/spnc/
> A2017175.L3m_DAY_SST_sst_9km.nc
> > # names       : Sea.Surface.Temperature
> > # zvar        : sst
> >
> > S = raster::raster(basename(URI), varname = "sst", crs = '+proj=eqc
> +lat_ts=0 +lat_0=0 +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84
> +units=m +no_defs')
> > # Warning message:
> > # In .getProj(prj, crs) :
> > #  argument "crs" ignored because the file provides a crs
> >
> > #### end
> >
> >
> > Cheers,
> > Ben
> >
> >
> >> On Jun 14, 2018, at 6:42 PM, Michael Sumner <[hidden email]> wrote:
> >>
> >> Try raster::projection(raster::raster(a)) first, then delve if necessary
> >> into the ncdump summary with print(raster::raster(a)))
> >>
> >> But, raster(a) may be enough here? To get that stuff more directly from
> the
> >> NetCDF API you have to use the inq and att functions of ncdf4 or RNetCDF
> >> and that's no fun.
> >>
> >> I'd also try raster(rgdal::readGDAL(a)) which is a totally different but
> >> equivalent read path.
> >>
> >> Cheers, Mike
> >>
> >> On Thu, 14 Jun 2018, 11:03 Sergio Ibarra, <[hidden email]>
> wrote:
> >>
> >>> Greetings,
> >>>
> >>> I'm want to read NetCDF spatial data from a meteorological model (WRF
> >>> model). The NetCDF can have one of these three projections:
> >>>
> >>> Polar stereographic
> >>> Lambert conformal
> >>> Mercator projection
> >>>
> >>> (See figure
> >>>
> >>>
> https://user-images.githubusercontent.com/27447280/41389756-ed23f91a-6f68-11e8-961e-6ba901913c54.png
> >>> )
> >>>
> >>> What is the  Coordinate Reference System for each case?
> >>>
> >>> Thanks!
> >>>
> >>> Here an example with ncdf4 and raster:
> >>>
> >>> library(ncdf4)
> >>> library(raster)
> >>> a <- tempfile()
> >>> download.file(url = "
> >>>
> http://www.unidata.ucar.edu/software/netcdf/examples/wrfout_v2_Lambert.nc
> >>> ",
> >>>              destfile = a) #78 Mb
> >>> wrf <- nc_open(a)
> >>> paste("The file has",wrf$nvars,"variables")
> >>> paste("The file has",names(wrf$var))
> >>> lat <- ncvar_get( wrf, "XLAT" )
> >>> lon <- ncvar_get( wrf, "XLONG" )
> >>> t2 <- ncvar_get( wrf, "T2" ) - 273.15
> >>> dim(t2) #73 60 13
> >>> #image
> >>> image(t2[, , 12])
> >>> # raster
> >>> rt2 <- raster(t(t2[1:dim(t2)[1],
> >>>                   dim(t2)[2]:1,
> >>>                   12]),
> >>>              xmn = min(lon),
> >>>              xmx = max(lon),
> >>>              ymn = min(lat),
> >>>              ymx = max(lat),
> >>> *              crs="+init=epsg:4326") # ???*
> >>> spplot(rt2)
> >>>
> >>>
> >>>
> >>> --
> >>> ​Sergio Ibarra Espinosa
> >>> Post Doc
> >>> PhD in Atmospheric Sciences
> >>> Instituto de Astronomia, Geofísica e Ciências Atmosféricas
> >>> Universidade de São Paulo
> >>> Rua do Matão, 1226
> >>> São Paulo-SP - Brasil -
> >>> 05508-090
> >>> +55-11-97425-3791
> >>> Skype: sergio_ibarra1
> >>>
> >>>        [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> R-sig-Geo mailing list
> >>> [hidden email]
> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>>
> >> --
> >> Dr. Michael Sumner
> >> Software and Database Engineer
> >> Australian Antarctic Division
> >> 203 Channel Highway
> >> Kingston Tasmania 7050 Australia
> >>
> >>      [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> R-sig-Geo mailing list
> >> [hidden email]
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>
> >
> > Ben Tupper
> > Bigelow Laboratory for Ocean Sciences
> > 60 Bigelow Drive, P.O. Box 380
> > East Boothbay, Maine 04544
> > http://www.bigelow.org
> >
> > Ecological Forecasting: https://eco.bigelow.org/
> >
> >
> >
> >
> >
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > [hidden email]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
>
> --
> Edzer Pebesma
> Institute for Geoinformatics
> Heisenbergstrasse 2, 48151 Muenster, Germany
> Phone: +49 251 8333081
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
--
Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia

        [[alternative HTML version deleted]]

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Re: What is the Coordinate Reference System?

Ben Tupper
Hi,

I will blissfully proceed as I have in the past.   Thanks to each of you for the clear explanations.  

Cheers,
Ben

> On Jun 18, 2018, at 6:26 AM, Michael Sumner <[hidden email]> wrote:
>
> Agree with Edzer this application of eqc is anomalous and after it confused
> us initially we now ignore it and apply the unproblematic proj=longlat
> interpretation to these products (after checking).
>
> I might explore the L3 products to find out why this occurred, but the
> ocean colour forum is the usual place to find discussion.
>
> Cheers, Mike
>
> On Mon, 18 Jun 2018, 15:59 Edzer Pebesma, <[hidden email]>
> wrote:
>
>> Plate carree is essentially a linear mapping of long and lat to x and y,
>> without changing aspect ratio (scale factor 1 at equator).
>>
>> projecting long/lat towards plate caree using the proj4 string you
>> mention will however change the units from degrees to m. So while the
>> plots of of data in linear long/lat (with aspect ration 1) looks
>> identical to the one obtained in plate caree (with aspect ratio 1), the
>> numerical values along their axes are very different.
>>
>> Many netcdf files carry a grid (raster) with the x and y coordinates of
>> grid cells (centers?) in another coordinate system, but the ones you
>> mention below don't, as far as I can tell. I think what they mean by
>> mentioning plate carree is just saying that this is a regular long/lat
>> degree grid; rather unlucky wording IMO.
>>
>> On 06/15/2018 08:14 PM, Ben Tupper wrote:
>>> Hi,
>>>
>>> That's an interesting approach.
>>>
>>> On the other hand, sometimes I get bitten (well, muddled really) when I
>> use raster to determine the crs of a ncdf resource.  It all sort of depends.
>>>
>>> Below is an example for Aqua MODIS imagery from OBPG (
>> https://oceandata.sci.gsfc.nasa.gov/MODIS-Aqua/Mapped/Daily/9km/sst/2017/
>> <https://oceandata.sci.gsfc.nasa.gov/MODIS-Aqua/Mapped/Daily/9km/sst/2017/>).
>> The OBPG docs (https://oceancolor.gsfc.nasa.gov/products/ <
>> https://oceancolor.gsfc.nasa.gov/products/>) state that the data is
>> served up as 'Plate Carrée' which I think has a crs ...
>>>
>>> '+proj=eqc +lat_ts=0 +lat_0=0 +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84
>> +datum=WGS84 +units=m +no_defs '
>>>
>>> ... as described here http://spatialreference.org/ref/epsg/32662/ <
>> http://spatialreference.org/ref/epsg/32662/>
>>>
>>> You can see below that raster comes up with...
>>>
>>> '+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0'
>>>
>>> ... which is http://spatialreference.org/ref/epsg/4326/ <
>> http://spatialreference.org/ref/epsg/4326/>
>>>
>>> Explicitly setting the crs while reading doesn't help.  I have never
>> resolved if it is an OBPG documentation bug, my confusion about
>> projections, or some other mystery.  So, my usual practice is to assume
>> that raster makes the right call.
>>>
>>> #### start
>>>
>>> library(raster)
>>> URI = '
>> https://oceandata.sci.gsfc.nasa.gov/cgi/getfile/A2017175.L3m_DAY_SST_sst_9km.nc
>> '
>>>
>>> # ~3.8MB
>>> ok = download.file(URI, basename(URI))
>>>
>>> R = raster::raster(basename(URI), varname = 'sst')
>>> R
>>> # class       : RasterLayer
>>> # dimensions  : 2160, 4320, 9331200  (nrow, ncol, ncell)
>>> # resolution  : 0.08333334, 0.08333334  (x, y)
>>> # extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
>>> # coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
>>> # data source : /Users/Shared/code/R/others/record/spnc/
>> A2017175.L3m_DAY_SST_sst_9km.nc
>>> # names       : Sea.Surface.Temperature
>>> # zvar        : sst
>>>
>>> S = raster::raster(basename(URI), varname = "sst", crs = '+proj=eqc
>> +lat_ts=0 +lat_0=0 +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84
>> +units=m +no_defs')
>>> # Warning message:
>>> # In .getProj(prj, crs) :
>>> #  argument "crs" ignored because the file provides a crs
>>>
>>> #### end
>>>
>>>
>>> Cheers,
>>> Ben
>>>
>>>
>>>> On Jun 14, 2018, at 6:42 PM, Michael Sumner <[hidden email]> wrote:
>>>>
>>>> Try raster::projection(raster::raster(a)) first, then delve if necessary
>>>> into the ncdump summary with print(raster::raster(a)))
>>>>
>>>> But, raster(a) may be enough here? To get that stuff more directly from
>> the
>>>> NetCDF API you have to use the inq and att functions of ncdf4 or RNetCDF
>>>> and that's no fun.
>>>>
>>>> I'd also try raster(rgdal::readGDAL(a)) which is a totally different but
>>>> equivalent read path.
>>>>
>>>> Cheers, Mike
>>>>
>>>> On Thu, 14 Jun 2018, 11:03 Sergio Ibarra, <[hidden email]>
>> wrote:
>>>>
>>>>> Greetings,
>>>>>
>>>>> I'm want to read NetCDF spatial data from a meteorological model (WRF
>>>>> model). The NetCDF can have one of these three projections:
>>>>>
>>>>> Polar stereographic
>>>>> Lambert conformal
>>>>> Mercator projection
>>>>>
>>>>> (See figure
>>>>>
>>>>>
>> https://user-images.githubusercontent.com/27447280/41389756-ed23f91a-6f68-11e8-961e-6ba901913c54.png
>>>>> )
>>>>>
>>>>> What is the  Coordinate Reference System for each case?
>>>>>
>>>>> Thanks!
>>>>>
>>>>> Here an example with ncdf4 and raster:
>>>>>
>>>>> library(ncdf4)
>>>>> library(raster)
>>>>> a <- tempfile()
>>>>> download.file(url = "
>>>>>
>> http://www.unidata.ucar.edu/software/netcdf/examples/wrfout_v2_Lambert.nc
>>>>> ",
>>>>>             destfile = a) #78 Mb
>>>>> wrf <- nc_open(a)
>>>>> paste("The file has",wrf$nvars,"variables")
>>>>> paste("The file has",names(wrf$var))
>>>>> lat <- ncvar_get( wrf, "XLAT" )
>>>>> lon <- ncvar_get( wrf, "XLONG" )
>>>>> t2 <- ncvar_get( wrf, "T2" ) - 273.15
>>>>> dim(t2) #73 60 13
>>>>> #image
>>>>> image(t2[, , 12])
>>>>> # raster
>>>>> rt2 <- raster(t(t2[1:dim(t2)[1],
>>>>>                  dim(t2)[2]:1,
>>>>>                  12]),
>>>>>             xmn = min(lon),
>>>>>             xmx = max(lon),
>>>>>             ymn = min(lat),
>>>>>             ymx = max(lat),
>>>>> *              crs="+init=epsg:4326") # ???*
>>>>> spplot(rt2)
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ​Sergio Ibarra Espinosa
>>>>> Post Doc
>>>>> PhD in Atmospheric Sciences
>>>>> Instituto de Astronomia, Geofísica e Ciências Atmosféricas
>>>>> Universidade de São Paulo
>>>>> Rua do Matão, 1226
>>>>> São Paulo-SP - Brasil -
>>>>> 05508-090
>>>>> +55-11-97425-3791
>>>>> Skype: sergio_ibarra1
>>>>>
>>>>>       [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-Geo mailing list
>>>>> [hidden email]
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>
>>>> --
>>>> Dr. Michael Sumner
>>>> Software and Database Engineer
>>>> Australian Antarctic Division
>>>> 203 Channel Highway
>>>> Kingston Tasmania 7050 Australia
>>>>
>>>>     [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> [hidden email]
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>
>>>
>>> Ben Tupper
>>> Bigelow Laboratory for Ocean Sciences
>>> 60 Bigelow Drive, P.O. Box 380
>>> East Boothbay, Maine 04544
>>> http://www.bigelow.org
>>>
>>> Ecological Forecasting: https://eco.bigelow.org/
>>>
>>>
>>>
>>>
>>>
>>>
>>>      [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>
>> --
>> Edzer Pebesma
>> Institute for Geoinformatics
>> Heisenbergstrasse 2, 48151 Muenster, Germany
>> Phone: +49 251 8333081
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
> --
> Dr. Michael Sumner
> Software and Database Engineer
> Australian Antarctic Division
> 203 Channel Highway
> Kingston Tasmania 7050 Australia
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org

Ecological Forecasting: https://eco.bigelow.org/






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Re: What is the Coordinate Reference System?

Sergio Ibarra
Yes, thanks for the explanations.


Have a nice week! :)

Em seg, 18 de jun de 2018 às 10:29, Ben Tupper <[hidden email]>
escreveu:

> Hi,
>
> I will blissfully proceed as I have in the past.   Thanks to each of you
> for the clear explanations.
>
> Cheers,
> Ben
>
> > On Jun 18, 2018, at 6:26 AM, Michael Sumner <[hidden email]> wrote:
> >
> > Agree with Edzer this application of eqc is anomalous and after it
> confused
> > us initially we now ignore it and apply the unproblematic proj=longlat
> > interpretation to these products (after checking).
> >
> > I might explore the L3 products to find out why this occurred, but the
> > ocean colour forum is the usual place to find discussion.
> >
> > Cheers, Mike
> >
> > On Mon, 18 Jun 2018, 15:59 Edzer Pebesma, <[hidden email]
> >
> > wrote:
> >
> >> Plate carree is essentially a linear mapping of long and lat to x and y,
> >> without changing aspect ratio (scale factor 1 at equator).
> >>
> >> projecting long/lat towards plate caree using the proj4 string you
> >> mention will however change the units from degrees to m. So while the
> >> plots of of data in linear long/lat (with aspect ration 1) looks
> >> identical to the one obtained in plate caree (with aspect ratio 1), the
> >> numerical values along their axes are very different.
> >>
> >> Many netcdf files carry a grid (raster) with the x and y coordinates of
> >> grid cells (centers?) in another coordinate system, but the ones you
> >> mention below don't, as far as I can tell. I think what they mean by
> >> mentioning plate carree is just saying that this is a regular long/lat
> >> degree grid; rather unlucky wording IMO.
> >>
> >> On 06/15/2018 08:14 PM, Ben Tupper wrote:
> >>> Hi,
> >>>
> >>> That's an interesting approach.
> >>>
> >>> On the other hand, sometimes I get bitten (well, muddled really) when I
> >> use raster to determine the crs of a ncdf resource.  It all sort of
> depends.
> >>>
> >>> Below is an example for Aqua MODIS imagery from OBPG (
> >>
> https://oceandata.sci.gsfc.nasa.gov/MODIS-Aqua/Mapped/Daily/9km/sst/2017/
> >> <
> https://oceandata.sci.gsfc.nasa.gov/MODIS-Aqua/Mapped/Daily/9km/sst/2017/
> >).
> >> The OBPG docs (https://oceancolor.gsfc.nasa.gov/products/ <
> >> https://oceancolor.gsfc.nasa.gov/products/>) state that the data is
> >> served up as 'Plate Carrée' which I think has a crs ...
> >>>
> >>> '+proj=eqc +lat_ts=0 +lat_0=0 +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84
> >> +datum=WGS84 +units=m +no_defs '
> >>>
> >>> ... as described here http://spatialreference.org/ref/epsg/32662/ <
> >> http://spatialreference.org/ref/epsg/32662/>
> >>>
> >>> You can see below that raster comes up with...
> >>>
> >>> '+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0'
> >>>
> >>> ... which is http://spatialreference.org/ref/epsg/4326/ <
> >> http://spatialreference.org/ref/epsg/4326/>
> >>>
> >>> Explicitly setting the crs while reading doesn't help.  I have never
> >> resolved if it is an OBPG documentation bug, my confusion about
> >> projections, or some other mystery.  So, my usual practice is to assume
> >> that raster makes the right call.
> >>>
> >>> #### start
> >>>
> >>> library(raster)
> >>> URI = '
> >>
> https://oceandata.sci.gsfc.nasa.gov/cgi/getfile/A2017175.L3m_DAY_SST_sst_9km.nc
> >> '
> >>>
> >>> # ~3.8MB
> >>> ok = download.file(URI, basename(URI))
> >>>
> >>> R = raster::raster(basename(URI), varname = 'sst')
> >>> R
> >>> # class       : RasterLayer
> >>> # dimensions  : 2160, 4320, 9331200  (nrow, ncol, ncell)
> >>> # resolution  : 0.08333334, 0.08333334  (x, y)
> >>> # extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
> >>> # coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
> >>> # data source : /Users/Shared/code/R/others/record/spnc/
> >> A2017175.L3m_DAY_SST_sst_9km.nc
> >>> # names       : Sea.Surface.Temperature
> >>> # zvar        : sst
> >>>
> >>> S = raster::raster(basename(URI), varname = "sst", crs = '+proj=eqc
> >> +lat_ts=0 +lat_0=0 +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84
> >> +units=m +no_defs')
> >>> # Warning message:
> >>> # In .getProj(prj, crs) :
> >>> #  argument "crs" ignored because the file provides a crs
> >>>
> >>> #### end
> >>>
> >>>
> >>> Cheers,
> >>> Ben
> >>>
> >>>
> >>>> On Jun 14, 2018, at 6:42 PM, Michael Sumner <[hidden email]>
> wrote:
> >>>>
> >>>> Try raster::projection(raster::raster(a)) first, then delve if
> necessary
> >>>> into the ncdump summary with print(raster::raster(a)))
> >>>>
> >>>> But, raster(a) may be enough here? To get that stuff more directly
> from
> >> the
> >>>> NetCDF API you have to use the inq and att functions of ncdf4 or
> RNetCDF
> >>>> and that's no fun.
> >>>>
> >>>> I'd also try raster(rgdal::readGDAL(a)) which is a totally different
> but
> >>>> equivalent read path.
> >>>>
> >>>> Cheers, Mike
> >>>>
> >>>> On Thu, 14 Jun 2018, 11:03 Sergio Ibarra, <[hidden email]>
> >> wrote:
> >>>>
> >>>>> Greetings,
> >>>>>
> >>>>> I'm want to read NetCDF spatial data from a meteorological model (WRF
> >>>>> model). The NetCDF can have one of these three projections:
> >>>>>
> >>>>> Polar stereographic
> >>>>> Lambert conformal
> >>>>> Mercator projection
> >>>>>
> >>>>> (See figure
> >>>>>
> >>>>>
> >>
> https://user-images.githubusercontent.com/27447280/41389756-ed23f91a-6f68-11e8-961e-6ba901913c54.png
> >>>>> )
> >>>>>
> >>>>> What is the  Coordinate Reference System for each case?
> >>>>>
> >>>>> Thanks!
> >>>>>
> >>>>> Here an example with ncdf4 and raster:
> >>>>>
> >>>>> library(ncdf4)
> >>>>> library(raster)
> >>>>> a <- tempfile()
> >>>>> download.file(url = "
> >>>>>
> >>
> http://www.unidata.ucar.edu/software/netcdf/examples/wrfout_v2_Lambert.nc
> >>>>> ",
> >>>>>             destfile = a) #78 Mb
> >>>>> wrf <- nc_open(a)
> >>>>> paste("The file has",wrf$nvars,"variables")
> >>>>> paste("The file has",names(wrf$var))
> >>>>> lat <- ncvar_get( wrf, "XLAT" )
> >>>>> lon <- ncvar_get( wrf, "XLONG" )
> >>>>> t2 <- ncvar_get( wrf, "T2" ) - 273.15
> >>>>> dim(t2) #73 60 13
> >>>>> #image
> >>>>> image(t2[, , 12])
> >>>>> # raster
> >>>>> rt2 <- raster(t(t2[1:dim(t2)[1],
> >>>>>                  dim(t2)[2]:1,
> >>>>>                  12]),
> >>>>>             xmn = min(lon),
> >>>>>             xmx = max(lon),
> >>>>>             ymn = min(lat),
> >>>>>             ymx = max(lat),
> >>>>> *              crs="+init=epsg:4326") # ???*
> >>>>> spplot(rt2)
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> ​Sergio Ibarra Espinosa
> >>>>> Post Doc
> >>>>> PhD in Atmospheric Sciences
> >>>>> Instituto de Astronomia, Geofísica e Ciências Atmosféricas
> >>>>> Universidade de São Paulo
> >>>>> Rua do Matão, 1226
> >>>>> São Paulo-SP - Brasil -
> >>>>> 05508-090
> >>>>> +55-11-97425-3791 <(11)%2097425-3791>
> >>>>> Skype: sergio_ibarra1
> >>>>>
> >>>>>       [[alternative HTML version deleted]]
> >>>>>
> >>>>> _______________________________________________
> >>>>> R-sig-Geo mailing list
> >>>>> [hidden email]
> >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>>>>
> >>>> --
> >>>> Dr. Michael Sumner
> >>>> Software and Database Engineer
> >>>> Australian Antarctic Division
> >>>> 203 Channel Highway
> >>>> Kingston Tasmania 7050 Australia
> >>>>
> >>>>     [[alternative HTML version deleted]]
> >>>>
> >>>> _______________________________________________
> >>>> R-sig-Geo mailing list
> >>>> [hidden email]
> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>>>
> >>>
> >>> Ben Tupper
> >>> Bigelow Laboratory for Ocean Scien
> <https://maps.google.com/?q=for+Ocean+Scien&entry=gmail&source=g>ces
> >>> 60 Bigelow Drive, P.O. Box 380
> >>> East Boothbay, Maine 04544
> >>> http://www.bigelow.org
> >>>
> >>> Ecological Forecasting: https://eco.bigelow.org/
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>      [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> R-sig-Geo mailing list
> >>> [hidden email]
> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>>
> >>
> >> --
> >> Edzer Pebesma
> >> Institute for Geoinformatics
> >> Heisenbergstrasse 2, 48151 Muenster, Germany
> >> Phone: +49 251 8333081 <+49%20251%208333081>
> >>
> >> _______________________________________________
> >> R-sig-Geo mailing list
> >> [hidden email]
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>
> > --
> > Dr. Michael Sumner
> > Software and Database Engineer
> > Australian Antarctic Division
> > 203 Channel Highway
> > Kingston Tasmania 7050 Australia
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > [hidden email]
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> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org
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> Ecological Forecasting: https://eco.bigelow.org/
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--
​Sergio Ibarra Espinosa
Post Doc
PhD in Atmospheric Sciences
Instituto de Astronomia, Geofísica e Ciências Atmosféricas
Universidade de São Paulo
Rua do Matão, 1226
São Paulo-SP - Brasil -
05508-090
+55-11-97425-3791
Skype: sergio_ibarra1

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