[R-sig-Geo] How to efficiently generate data of neighboring points

[Lom Navanyo]

Thank you very much for your support. This gives me what I need and I must
say listw2sn() is really great.

Why do I need the data in the format as in dataout? I am trying to test
spatial dependence (or neighborhood effect) by running a regression model
that entails pop_size_it = beta_1*sum of pop_size of point i's neighbors
within a specified radius. So my plan is to get the neighbors for each
focal point
as per the specified bands and their attributes (eg pop_size) so I can can
add them (attribute) by the bands.

I am totally new to the area of spatial econometrics, so I am taking things
one step at a time. Some readings suggest I may need distance matrix or
weight matrix but for now I think I should try the current approach.

Thank you.

-------------
Lom

On Wed, Jun 3, 2020 at 8:18 AM Roger Bivand <Roger.Bivand using nhh.no> wrote:

> On Wed, 3 Jun 2020, Lom Navanyo wrote:
>
> > I had the errors with rtree using R 3.6.3. I have since changed to R
> 4.0.0
> > but I got the same error.
> >
> > And  yes, for Roger's example, I have the objects wd1, ... wd4, all with
> > length 101. I think my difficulty is my inability to output the list
> > detailing the point IDs t50_fid.
>
> library(spData)
> library(sf)
> projdata<-st_transform(nz_height, 32759)
> pts <- st_coordinates(projdata)
> library(spdep)
> bufferR <- c(402.336, 1609.34, 3218.69, 4828.03, 6437.38)
> bds <- c(0, bufferR)
> wd1 <- dnearneigh(pts, bds[1], bds[2])
> wd2 <- dnearneigh(pts, bds[2], bds[3])
> wd3 <- dnearneigh(pts, bds[3], bds[4])
> wd4 <- dnearneigh(pts, bds[4], bds[5])
> sn_band1 <- listw2sn(nb2listw(wd1, style="B", zero.policy=TRUE))
> sn_band1$band <- paste(attr(wd1, "distances"), collapse="-")
> sn_band2 <- listw2sn(nb2listw(wd2, style="B", zero.policy=TRUE))
> sn_band2$band <- paste(attr(wd2, "distances"), collapse="-")
> sn_band3 <- listw2sn(nb2listw(wd3, style="B", zero.policy=TRUE))
> sn_band3$band <- paste(attr(wd3, "distances"), collapse="-")
> sn_band4 <- listw2sn(nb2listw(wd4, style="B", zero.policy=TRUE))
> sn_band4$band <- paste(attr(wd4, "distances"), collapse="-")
> data_out <- do.call("rbind", list(sn_band1, sn_band2, sn_band3, sn_band4))
> class(data_out) <- "data.frame"
> table(data_out$band)
> data_out$ID_from <- projdata$t50_fid[data_out$from]
> data_out$ID_to <- projdata$t50_fid[data_out$to]
> data_out$elev_from <- projdata$elevation[data_out$from]
> data_out$elev_to <- projdata$elevation[data_out$to]
> str(data_out)
>
> The "spatial.neighbour" representation was that used in the S-Plus
> SpatialStats module, with "from" and "to" columns, and here drops
> no-neighbour cases gracefully. So listw2sn() comes in useful
> for creating the output, and from there, just look-up in the
> input data.frame. Observations here cannot be their own neighbours.
>
> It would be relevant to know why you need these, are you looking at
> variogram clouds?
>
> Hope this clarifies,
>
> Roger
>
> >
> > ---------
> > Lom
> >
> > On Tue, Jun 2, 2020 at 8:02 PM Kent Johnson <kent3737 using gmail.com> wrote:
> >
> >> Roger's example works for me and gives a list of length 101. I did have
> >> some issues that were resolved by updating packages. I'm using R 3.6.3
> on
> >> macOS 10.15.4. I also use rtree successfully on Windows 10 with R 3.6.3.
> >>
> >> Kent
> >>
> >> On Tue, Jun 2, 2020 at 12:29 PM Roger Bivand <Roger.Bivand using nhh.no>
> wrote:
> >>
> >>> On Tue, 2 Jun 2020, Kent Johnson wrote:
> >>>
> >>>> rtree uses Euclidean distance so the points should be in a coordinate
> >>>> system where this makes sense at least as a reasonable approximation.
> >>>
> >>> I tried the original example:
> >>>
> >>> remotes::install_github("hunzikp/rtree")
> >>> library(spData)
> >>> library(sf)
> >>> projdata<-st_transform(nz_height, 32759)
> >>> library(rtree)
> >>> pts <- st_coordinates(projdata)
> >>> rt <- RTree(st_coordinates(projdata))
> >>> bufferR <- c(402.336, 1609.34, 3218.69, 4828.03, 6437.38)
> >>> wd1 <- withinDistance(rt, pts, bufferR[1])
> >>>
> >>> but unfortunately failed (maybe newer Boost headers than yours?):
> >>>
> >>> Error in UseMethod("withinDistance", rTree) :
> >>>    no applicable method for 'withinDistance' applied to an object of
> >>> class
> >>> "c('list', 'RTree')"
> >>>
> >>>>
> >>>> Kent
> >>>>
> >>>> On Tue, Jun 2, 2020 at 9:59 AM Roger Bivand <Roger.Bivand using nhh.no>
> >>> wrote:
> >>>>
> >>>>> On Tue, 2 Jun 2020, Kent Johnson wrote:
> >>>>>
> >>>>>>> Date: Tue, 2 Jun 2020 02:44:17 -0500
> >>>>>>> From: Lom Navanyo <lomnavasia using gmail.com>
> >>>>>>> To: r-sig-geo using r-project.org
> >>>>>>> Subject: [R-sig-Geo] How to efficiently generate data of
> neighboring
> >>>>>>>         points within specified radii (distances) for each point
> in a
> >>>>> given
> >>>>>>>         points data set.
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>>> Hello,
> >>>>>>> I have data set of about 3400 location points with which I am
> trying
> >>> to
> >>>>>>> generate data of each point and their neighbors within defined
> radii
> >>>>> (eg,
> >>>>>>> 0.25, 1, and 3 miles).
> >>>>>>>
> >>>>>>
> >>>>>> The rtree package is very fast and memory-efficient for
> >>> within-distance
> >>>>>> calculations.
> >>>>>> https://github.com/hunzikp/rtree
> >>>>>
> >>>>> Thanks! Does this also apply when the input points are in
> geographical
> >>>>> coordinates?
> >>>>>
> >>>>> Roger
> >>>>>
> >>>>>>
> >>>>>> Kent Johnson
> >>>>>> Cambridge, MA
> >>>>>>
> >>>>>>       [[alternative HTML version deleted]]
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> R-sig-Geo mailing list
> >>>>>> R-sig-Geo using r-project.org
> >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>>>>>
> >>>>>
> >>>>> --
> >>>>> Roger Bivand
> >>>>> Department of Economics, Norwegian School of Economics,
> >>>>> Helleveien 30, N-5045 Bergen, Norway.
> >>>>> voice: +47 55 95 93 55; e-mail: Roger.Bivand using nhh.no
> >>>>> https://orcid.org/0000-0003-2392-6140
> >>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
> >>>>>
> >>>>
> >>>
> >>> --
> >>> Roger Bivand
> >>> Department of Economics, Norwegian School of Economics,
> >>> Helleveien 30, N-5045 Bergen, Norway.
> >>> voice: +47 55 95 93 55; e-mail: Roger.Bivand using nhh.no
> >>> https://orcid.org/0000-0003-2392-6140
> >>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
> >>>
> >>
> >
>
> --
> Roger Bivand
> Department of Economics, Norwegian School of Economics,
> Helleveien 30, N-5045 Bergen, Norway.
> voice: +47 55 95 93 55; e-mail: Roger.Bivand using nhh.no
> https://orcid.org/0000-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>

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