Environmental Risk Surface

Thank you very much Mike.

I have the rasters made with the package ratser, using the function
rasterize, distance and distance from points.  I know how to model when you
have presence or presence/absence data, but in this situation I don?t have
those type of data and I am looking for a way to do a risk assessment in R.
 I was reading, an apparently Environmental Risk Surface is something that
could be done with that type of information.  A software like Marxan seems
to do that type of analysis, but I don?t know the capabilities of R to do
such type of analysis.

Best,

Manuel


2014-03-20 9:07 GMT-06:00 Michael Treglia <mtreglia at gmail.com>:

Manuel,

Please correct me if I misunderstand, but you've got vector layers of
Roads, Wetlands, and specific locations, and are need to make Raster layers
of how far each pixel would be from these types features, and then combine
these distance rasters through some sort of computation to map risk. Right?

I don't think there is package that would do this all for you
automatically (and there are a lot of decisions you'll probably have to
make), but I think the Raster package should have all of the necessary
tools - in particular the functions rasterize(), distance() , and the
raster algebra functions [though to initially import shapefiles you'll have
to use another package, maybe rGDAL]. The documentation for the Raster
package is here: http://cran.r-project.org/web/packages/raster/index.html

Post-back as you have specific questions on how to execute specific steps,
(and look at examples for specific steps in the documentation - the raster
package is very well documented).

Cheers,
Mike


On Wed, Mar 19, 2014 at 9:05 PM, Manuel Sp?nola <mspinola10 at gmail.com>wrote:

Thank you Mike,

I am thinking in overlay several raster layers, mainly distance raster
(distance to roads, to specific locations, to wetlands, etc) to assess the
risk of a disease spread that is not yet in the country but could enter
through migratory birds.

Best,

Manuel


2014-03-19 19:08 GMT-06:00 Michael Treglia <mtreglia at gmail.com>:

Hi Manuel,

There may be multiple types of environmental risk surfaces, based on
different variables, and using different methods to effectively create
indices of risk. Can you provide some more detail about what you are trying
to do? If there is a paper that explains the general methodology, that
would be helpful? If not, perhaps an explanation of the general workflow
you are thinking, with the data types (raster/vector) would be helpful.
Also, are there specific steps for which you need help? (e.g.,
data-processing, multi-layer raster calculations, etc?)

Cheers,
Mike



2014-03-19 17:37 GMT-05:00 Manuel Sp?nola <mspinola10 at gmail.com>:

Dear list members,

Is there any way to do an Environmental Risk Surface in R?

Best,

Manuel


--
*Manuel Sp?nola, Ph.D.*

Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.ac.cr
mspinola10 at gmail.com
Tel?fono: (506) 2277-3598
Fax: (506) 2237-7036
Personal website: Lobito de r?o <
https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>

        [[alternative HTML version deleted]]

Thank you very much Alex.

I want to do simple calculations.

Best,

Manuel


2014-03-20 10:35 GMT-06:00 Alex Mandel <tech_dev at wildintellect.com>:

All such tools are algorithms applied in some way via a raster
calculator. So the question is what formula or model of Risk Assessment
do you want to use. It can be a simple calculation based on your layers
and your knowledge of how important they are.

Or you can use many statistical formulas if you wanted. Marxan is just
one particular method of doing such calculations. There is no 1 way to
calculate risk. See
http://cran.r-project.org/web/views/Environmetrics.html

Once you have the statistical model you want to apply, you can use
predict to generate values over your area based on your other layers.

The question is not if R can do it, but what do you want R to do.

Thanks,
Alex


On 03/20/2014 09:00 AM, Manuel Sp?nola wrote:

Thank you very much Mike.

I have the rasters made with the package ratser, using the function
rasterize, distance and distance from points.  I know how to model when

you

have presence or presence/absence data, but in this situation I don?t

have

those type of data and I am looking for a way to do a risk assessment in

R.

 I was reading, an apparently Environmental Risk Surface is something

that

could be done with that type of information.  A software like Marxan

seems

to do that type of analysis, but I don?t know the capabilities of R to do
such type of analysis.

Best,

Manuel


2014-03-20 9:07 GMT-06:00 Michael Treglia <mtreglia at gmail.com>:

Manuel,

Please correct me if I misunderstand, but you've got vector layers of
Roads, Wetlands, and specific locations, and are need to make Raster

layers

of how far each pixel would be from these types features, and then

combine

these distance rasters through some sort of computation to map risk.

Right?

I don't think there is package that would do this all for you
automatically (and there are a lot of decisions you'll probably have to
make), but I think the Raster package should have all of the necessary
tools - in particular the functions rasterize(), distance() , and the
raster algebra functions [though to initially import shapefiles you'll

have

to use another package, maybe rGDAL]. The documentation for the Raster
package is here:

http://cran.r-project.org/web/packages/raster/index.html

Post-back as you have specific questions on how to execute specific

steps,

(and look at examples for specific steps in the documentation - the

raster

package is very well documented).

Cheers,
Mike


On Wed, Mar 19, 2014 at 9:05 PM, Manuel Sp?nola <mspinola10 at gmail.com

wrote:

Thank you Mike,

I am thinking in overlay several raster layers, mainly distance raster
(distance to roads, to specific locations, to wetlands, etc) to assess

the

risk of a disease spread that is not yet in the country but could enter
through migratory birds.

Best,

Manuel


2014-03-19 19:08 GMT-06:00 Michael Treglia <mtreglia at gmail.com>:

Hi Manuel,

There may be multiple types of environmental risk surfaces, based on
different variables, and using different methods to effectively create
indices of risk. Can you provide some more detail about what you are

trying

to do? If there is a paper that explains the general methodology, that
would be helpful? If not, perhaps an explanation of the general

workflow

you are thinking, with the data types (raster/vector) would be

helpful.

Also, are there specific steps for which you need help? (e.g.,
data-processing, multi-layer raster calculations, etc?)

Cheers,
Mike



2014-03-19 17:37 GMT-05:00 Manuel Sp?nola <mspinola10 at gmail.com>:

Dear list members,

Is there any way to do an Environmental Risk Surface in R?

Best,

Manuel


--
*Manuel Sp?nola, Ph.D.*

Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.ac.cr
mspinola10 at gmail.com
Tel?fono: (506) 2277-3598
Fax: (506) 2237-7036
Personal website: Lobito de r?o <
https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>

        [[alternative HTML version deleted]]