[R-sig-Geo] as.im in spatstat::ppm not working as before

Sat May 11 18:03:18 CEST 2024

On 11/05/2024 10:21, Roozbeh Valavi wrote:
> This might also help:

the solution below will not raise the error if x has geographic 
(unprojected) coordinates, a case for which you should not use spatstat.

> 
> library(spatstat)
> library(terra)
> 
> .raster_to_im <- function(x){
>          r <- as.data.frame(x, xy = TRUE)
>           im <- spatstat.geom::as.im <http://as.im>(r) return(im)
> }
> 
>   # to generalise the spatstat.geom::as.im <http://as.im> to SpatRaster 
> and RasterLayer
> as.im.SpatRaster <- function(x){ .raster_to_im(x) } as.im.RasterLayer <- 
> function(x){ .raster_to_im(x) }
> 
> 
> I haven’t used it in a while so there might be a direct support in the 
> spatstat.geom now!
> 
> 
> Roozbeh Valavi,
> Biodiversity Modeller & Spatial Ecologist
> Senior Research Scientist | CSIRO Environment, VIC, Australia
> *Twitter*:@ValaviRoozbeh | ResearchGate 
> <https://www.researchgate.net/profile/Roozbeh-Valavi> | Google Scholar 
> <https://scholar.google.co.uk/citations?user=3m0jCHwAAAAJ&hl=en&oi=ao>
> 
> 
> On Wed, 8 May 2024 at 7:41 PM, Roger Bivand <Roger.Bivand using nhh.no 
> <mailto:Roger.Bivand using nhh.no>> wrote:
> 
>     as.im <http://as.im>() was in maptools, which was retired last year.
>     If you need to recreate old work, install maptools from source from
>     the CRAN package archive
>     https://cran.r-project.org/src/contrib/Archive/maptools/
>     <https://cran.r-project.org/src/contrib/Archive/maptools/>.
> 
>     For non-archival work, update the workflow. See also
>     https://github.com/r-spatial/evolution/issues/8
>     <https://github.com/r-spatial/evolution/issues/8>.
> 
>     Hope this clarifies,
> 
>     Roger
> 
>     ---
>     Roger Bivand
>     Emeritus Professor
>     Department of Economics
>     Norwegian School of Economics, Bergen, Norway
> 
>     ________________________________
>     Fra: R-sig-Geo <r-sig-geo-bounces using r-project.org
>     <mailto:r-sig-geo-bounces using r-project.org>> på vegne av Edzer Pebesma
>     <edzer.pebesma using uni-muenster.de <mailto:edzer.pebesma using uni-muenster.de>>
>     Sendt: onsdag, mai 8, 2024 9:28:54 a.m.
>     Til: r-sig-geo using r-project.org <mailto:r-sig-geo using r-project.org>
>     <r-sig-geo using r-project.org <mailto:r-sig-geo using r-project.org>>
>     Emne: Re: [R-sig-Geo] as.im <http://as.im> in spatstat::ppm not
>     working as before
> 
>     r.grid.world.SGDF.F[[1]] is a numerical vector, not even a matrix, so
>     clearly as.im.default doesn't know what it should do with it.
> 
>     Maybe there was once a method as.im <http://as.im> for
>     r.grid.world.SGDF.F, which is of
>     class SpatialGridDataFrame, but no longer - software evolves.
> 
>     A way you could approach this is converting that object to a stars
>     object:
> 
>       > library(stars)
>     Loading required package: abind
>     Loading required package: sf
>     Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.3.1; sf_use_s2() is TRUE
>       > as.im <http://as.im>(st_as_stars(r.grid.world.SGDF.F))
>     Error: Only projected coordinates may be converted to spatstat class
>     objects
> 
>     and that points you to another issue you have: spatstat works with data
>     in Cartesian coordiantes (R2), not with geodetic coordinates (S2). So
>     that's a helpful error message.
> 
> 
>     On 08/05/2024 01:49, Alexandre Santos via R-sig-Geo wrote:
>      > Dear Members,
>      >
>      > I'll calculate some old codes for a paper review, and I'm
>     astonished that as.im <http://as.im>() for fitting the Poisson model
>     is not working as before. In my example:
>      >
>      > library(raster)
>      > library(spatstat)
>      >
>      >
>      > # Elevation
>      > r.grid.world <-
>     raster('https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2FLeprechault%2Ftrash%2Fmain%2Fwc2.1_10m_elev.tif&data=05%7C02%7CRoger.Bivand%40nhh.no%7Cd2a2b64634a7462f860708dc6f3082d5%7C33a15b2f849941998d56f20b5aa91af2%7C0%7C0%7C638507501339842669%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=cyducyKF16yIdtfuykXUSifCR8clFtxDhiG1eY4waFU%3D&reserved=0 <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2FLeprechault%2Ftrash%2Fmain%2Fwc2.1_10m_elev.tif&data=05%7C02%7CRoger.Bivand%40nhh.no%7Cd2a2b64634a7462f860708dc6f3082d5%7C33a15b2f849941998d56f20b5aa91af2%7C0%7C0%7C638507501339842669%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=cyducyKF16yIdtfuykXUSifCR8clFtxDhiG1eY4waFU%3D&reserved=0><https://raw.githubusercontent.com/Leprechault/trash/main/wc2.1_10m_elev.tif <https://raw.githubusercontent.com/Leprechault/trash/main/wc2.1_10m_elev.tif>>')
>      > proj4string(r.grid.world) <- CRS("+proj=longlat +datum=WGS84
>     +no_defs +ellps=WGS84 +towgs84=0,0,0")
>      > r.grid.world.SGDF.F <- as(r.grid.world, "SpatialGridDataFrame")
>      >
>      >
>      > #Fitting Poisson model
>      > fit.c <- ppm(nztrees, ~ elev,
>      > covariates=list(elev=as.im <http://as.im>(r.grid.world.SGDF.F[[1]])))
>      > #
>      > # Error in as.im.default(r.grid.world.SGDF.F[[1]]) :
>      > #   Can't convert X to a pixel image
>      >
>      > I tried as matrix and rotate, and the final real-valued pixel
>     image didn't work as a covariate in the model.
>      >
>      > Please, any help with it?
>      >
>      > Thanks in advance
>      >
>      > Alexandre
>      >
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> 
>     --
>     Edzer Pebesma (he/him)
>     Universität Münster, Institute for Geoinforma
>     <https://www.google.com/maps/search/versit%C3%A4t+M%C3%BCnster,+Institute+for+Geoinforma?entry=gmail&source=g>tics
>     Heisenbergstrasse 2, 48149 Münster, Germany
>     Phone: +49 251 8333081
> 
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-- 
Edzer Pebesma (he/him)
Universität Münster, Institute for Geoinformatics
Heisenbergstrasse 2, 48149 Münster, Germany
Phone: +49 251 8333081