Hi list,
One more go at this and I'll stop for other ideas. Below is a
slightly modified example using dbplyr::sql_render() to construct the
query, which works and to me feels a little cleaner, though maybe is
ill-advised. Then I try to construct a spatial filter (for points in
a polygon) this way with ST_Contains, but my effort comes back empty.
Not sure where I went wrong. Any ideas?
## boilerplate setup
library(duckdb)
conn <- DBI::dbConnect(duckdb::duckdb())
status <- DBI::dbExecute(conn, "INSTALL 'spatial';")
status <- DBI::dbExecute(conn, "LOAD 'spatial';")
test <- data.frame(site = letters[1:10], latitude = 1:10, longitude = 1:10)
DBI::dbWriteTable(conn, "test", test)
## Here we go, works!
sql <- tbl(con, "test") |>
mutate(geom = ST_AsHEXWKB(ST_Point(longitude, latitude))) |>
dbplyr::sql_render()
ex <- st_read(conn, query=sql, geometry_column = "geom", EWKB=FALSE)
ex
## a trivial search polygon to filter:
p2 <- rbind(c(1,1), c(1,2), c(2,2), c(1,1))
pol <-st_polygon(list(p2))
txt <- st_as_text(pol)
## Can we use this to filter duckdb?
sql <- tbl(conn, "test") |>
mutate(geometry = ST_Point(longitude, latitude),
geom = ST_AsHEXWKB(geometry)) |>
filter(ST_Contains(geometry, ST_GeomFromText({txt}))) |>
dbplyr::sql_render()
sql
ex <- st_read(conn, query=sql, geometry_column = "geom", EWKB=FALSE)
ex
## oh no! our result comes back empty? did I need CRS on this? Or do
I missunderstand "ST_Contains()"?
## Here's what the desired result would be from pure sf:
sf <- st_as_sf(test, coords = c(3,2))
filter <- st_as_sf(tibble(sites = "A", geometry = list(pol)))
sf |> st_filter(filter)
---
Carl Boettiger
http://carlboettiger.info/
On Tue, Aug 15, 2023 at 4:42 PM Carl Boettiger <cboet...@gmail.com> wrote:
>
> Ah ha. if we ask duckdb to coerce it's geometry format to hex, it
> appears sf can understand it just fine!
>
> replacing the above query with the following we are good to go.
>
>
>
> query <- paste(
> 'SELECT *, ST_AsHEXWKB(ST_Point(longitude, latitude)) AS geom',
> 'FROM "test"'
> )
> ex <- st_read(con, query=query, geometry_column = "geom", EWKB=FALSE)
> ex
>
>
> I'll experiment further. I'm terrible at SQL, and to my eyes it looks
> needlessly verbose. I'm keen to understand how I can better leverage
> sf's notation to compose the sql queries to duckdb.... but it seems
> to work! I'm also still trying to determine if duckdb is using EWKB
> or vanilla WKB....
>
> ---
> Carl Boettiger
> http://carlboettiger.info/
>
> On Tue, Aug 15, 2023 at 4:02 PM Carl Boettiger <cboet...@gmail.com> wrote:
> >
> > Hi folks,
> >
> >
> > I'm curious if anyone has explored the relatively new spatial
> > extension in duckdb (https://duckdb.org/docs/extensions/spatial.html)
> > or has any pointers/tutorials regarding its use from R?
> >
> > Consider the following minimal example that seeks to use the sf
> > library to speak to duckdb:
> >
> > library(duckdb)
> > library(sf)
> > conn <- DBI::dbConnect(duckdb::duckdb())
> > status <- DBI::dbExecute(conn, "INSTALL 'spatial';")
> > status <- DBI::dbExecute(conn, "LOAD 'spatial';")
> >
> > test <- data.frame(site = letters[1:10], latitude = 1:10, longitude =
> > 1:10)
> > DBI::dbWriteTable(conn, "test", test)
> >
> > # Ok, let's try and make a geometry column
> > query <- paste(
> > 'SELECT *, ST_Point(longitude, latitude) AS geom',
> > 'FROM "test"'
> > )
> >
> > ex <- st_read(con, query=query, geometry_column = "geom")
> > ## error: reading wkb type 0 is not supported
> >
> >
> > ex <- st_read(con, query=query, geometry_column = "geom", EWKB = FALSE)
> > ## prints: wkbType: 1572864
> > ## Error in CPL_read_wkb(x, EWKB, spatialite) : unsupported wkbType
> > dim in switch
> >
> > We seem to get closer than I might have hoped (sf doesn't just insist
> > that conn isn't postgresgis), but is getting stuck on the encoding of
> > the wkb. Is this something we can work around? The queries seem to
> > run successfully, I just seem to be getting some unsupported ecoding
> > of the WKB geometry column....
> >
> > ---
> > Carl Boettiger
> > http://carlboettiger.info/
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