[R-sig-Geo] Problems with mask (raster)

[Robert J. Hijmans]

Here is alternative (non-computational) approach to ensure that the
files are read as signed integers:

library(raster)
bio <- raster("bio1_23.bil", native=T)
dataType(bio) <- 'INT2S'
NAvalue(bio) <- -9999

plot(bio)

Robert

On Fri, Oct 15, 2010 at 4:10 AM, Jaime R. Garcia Marquez
<jaime.garcia at uni-bonn.de> wrote:
> Hola Manuel,
>
> Regarding the values of the .bil files I was dealing with that also sometime
> ago.
>
> I found this link in a forum who helped me understand what is going on with
> these files:
>
> http://pvanb.wordpress.com/2010/02/06/importing-worldclim-climate-bil-datalayers-in-grass-gis/
>
> So I wrote in R something like this to get the right values:
>
> library(raster)
> bio <- raster("bio1_23.bil")
> ind <- which(bio[] > 32767)
> bio[ind] <- bio[ind] - (65535+1)
> bio[bio[] == -9999] <- NA
> bio
> plot(bio)
>
> Hope this helps.
>
> Saludos, pura vida
>
> Jaime
>
> On Thu, 14 Oct 2010 16:17:25 -0600
>  Manuel Spínola <mspinola10 at gmail.com> wrote:
>>
>>  Thank you very much Robert,
>>
>> Now I have this error:
>>
>> > me <- maxent(bio1res, arb)
>> Error en .local(x, p, ...) :
>>  more than half of the presence points have NA predictor values
>>
>> It could be related to the raster "bio1res"?  The origin of this file is
>> .bil files.  Which is the best file format to work with bioclim data?
>> The plot(bio1res) display with a legend with values from 0 to 50000 and
>> the raster is for temperature.
>>
>> bio1res
>> class       : RasterLayer
>> filename    :
>> nrow        : 382
>> ncol        : 407
>> ncell       : 155474
>> min value   : 47
>> max value   : 55537
>> projection  : NA
>> xmin        : -85.95
>> xmax        : -82.55833
>> ymin        : 8.041667
>> ymax        : 11.225
>> xres        : 0.008333333
>> yres        : 0.008333333
>>
>> Best,
>>
>> Manuel
>>
>>
>> On 14/10/2010 02:44 p.m., Robert J. Hijmans wrote:
>>>
>>> I think it should be:
>>>
>>> res<- mask(bio1cr, crmask)
>>>
>>> On Thu, Oct 14, 2010 at 1:22 PM, Manuel Spínola<mspinola10 at gmail.com>
>>>  wrote:
>>>>
>>>>  Dear list members,
>>>>
>>>> I am working with bioclim variables to model species distribution.
>>>> The files downloaded from Worldclim.org are generic raster files (.bil)
>>>> I transform this files to raster:
>>>>
>>>> bio1<- raster("bio1_23.bil")
>>>>
>>>> cr = readOGR(dsn="C:/ProyectoRespacial/EvalHab_reporte",
>>>> layer="Cr_wgs84_meso")
>>>>
>>>> bio1cr<- crop(bio1, cr)
>>>> crmask<- polygonsToRaster(cr, bio1cr)
>>>> res<- mask(bio1, crmask)
>>>> Error en compare(x, mask) : Different bounding box
>>>>
>>>> plot(bio1cr) the scale legend shows numbers from 0 to 55000
>>>>
>>>> Best,
>>>>
>>>> Manuel
>>>>
>>>>
>>>> --
>>>> *Manuel Spínola, Ph.D.*
>>>> Instituto Internacional en Conservación y Manejo de Vida Silvestre
>>>> Universidad Nacional
>>>> Apartado 1350-3000
>>>> Heredia
>>>> COSTA RICA
>>>> mspinola at una.ac.cr
>>>> mspinola10 at gmail.com
>>>> Teléfono: (506) 2277-3598
>>>> Fax: (506) 2237-7036
>>>> Personal website: Lobito de río
>>>> <https://sites.google.com/site/lobitoderio/>
>>>> Institutional website: ICOMVIS<http://www.icomvis.una.ac.cr/>
>>>>
>>>>        [[alternative HTML version deleted]]
>>>>
>>>>
>>>> _______________________________________________
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>>>> R-sig-Geo at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>
>>>>
>>
>>
>> --
>> *Manuel Spínola, Ph.D.*
>> Instituto Internacional en Conservación y Manejo de Vida Silvestre
>> Universidad Nacional
>> Apartado 1350-3000
>> Heredia
>> COSTA RICA
>> mspinola at una.ac.cr
>> mspinola10 at gmail.com
>> Teléfono: (506) 2277-3598
>> Fax: (506) 2237-7036
>> Personal website: Lobito de río
>> <https://sites.google.com/site/lobitoderio/>
>> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>>
>>        [[alternative HTML version deleted]]
>>
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