[R-sig-Geo] error in readShapePoly

[Hurlbert, Allen H. (Biology)]

Thanks Roger!

Are there any instances in which one would want delete_null_obj=FALSE?

-----Original Message-----
From: Roger Bivand [mailto:Roger.Bivand at nhh.no] 
Sent: Wednesday, June 10, 2009 10:36 AM
To: Hurlbert, Allen H. (Biology)
Subject: RE: [R-sig-Geo] error in readShapePoly

On Wed, 10 Jun 2009, Hurlbert, Allen H. (Biology) wrote:

> Hi Roger,
>
> Here is the result of the traceback():
>
> 4: .shp2srsI(shapes[[belongs[[i]][j]]],
> .nParts.shpI(shapes[[belongs[[i]][j]]]),
>       force_ring = force_ring)
> 3: .asSpatialPolygonsShapes(Map$Shapes, IDs, proj4string =
proj4string,
>       force_ring = force_ring)
> 2: .Map2PolyDF(Map, IDs = IDvar, proj4string = proj4string, force_ring
=
> force_ring,
>       delete_null_obj = delete_null_obj, retrieve_ABS_null =
> retrieve_ABS_null)
> 1:
>
readShapePoly(paste("\\\\Bioark.bio.unc.edu\\hurlbertallen\\GIS\\BirdRan
> geMaps\\NatureServe3.0\\",
>       as.character(families[f]), "\\", as.character(spp.list[s2,
>           1]), sep = ""), proj4string = CRS("+proj=latlong
> +datum=NAD83"))
>
> The shapefiles are bird range maps available online from NatureServe
> here: http://www.natureserve.org/getData/birdMaps.jsp. The problem
file
> is trin_inca_pl.shp which is included in the zipped 'Scolopacidae'
file
> on that page.
>
> Unfortunately, I am unfamiliar with the syntax of readOGR() and can't
> quite figure out how I'm supposed to use it to read in a shapefile.

It is a bit more revealing:

> trin_inca_pl <- readOGR("Scolopacidae", "trin_inca_pl")
Error in ogrInfo(dsn = dsn, layer = layer, input_field_name_encoding = 
input_field_name_encoding) :
   NULL geometry found

and suggests using the fix in:

> trin_inca_pl <- readShapePoly("Scolopacidae/trin_inca_pl.shp", 
+  delete_null_obj=TRUE)
Warning message:
In .Map2PolyDF(Map, IDs = IDvar, proj4string = proj4string, force_ring =

force_ring,  :
   Null objects with the following indices deleted: 134

So the data provider has inserted a NULL geometry into the data - they 
shouldn't do it, but it has been seen before. Could you summarise to the

list, please? I'll see if I can add a test in readShapePoly to point
users 
to the optional argument.

Roger

>
> Thanks!
> Allen
>
> -----Original Message-----
> From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
> Sent: Wednesday, June 10, 2009 9:38 AM
> To: Hurlbert, Allen H. (Biology)
> Cc: r-sig-geo at stat.math.ethz.ch
> Subject: Re: [R-sig-Geo] error in readShapePoly
>
> On Wed, 10 Jun 2009, Hurlbert, Allen H. (Biology) wrote:
>
>> Hello list,
>>
>>
>>
>> I'm new to GIS in R, so I appreciate any pointers with my problem.
>>
>>
>>
>> I have code that uses readShapePoly to read in shapefiles in a loop
> and
>> does some basic operations. This code appeared to be working great
for
>> twenty or so files, but then on one shapefile bonked with the
> following
>> error:   Error in from[j]:to[j] : NA/NaN argument.
>>
>>
>>
>> The problem shapefile opens fine in ArcGIS and there is nothing
> readily
>> different about its attribute table or source information that I can
> see
>> (and furthermore, all shapefiles are from the same standardized
> source,
>> although of course that doesn't mean one of them didn't get messed up
>> somewhere along the way). I am running 2.7.2 on Windows XP x64.
>>
>
> Could you 1) try readOGR() in rgdal instead of readShapePoly() in
> maptools
> if possible, and see if the problem is repeated; 2) post either the
> output
> of traceback() run immediately after the error occurs (will show
where,
> more or less, the problem is in code) here and/or the shapefile(s) all
> 3-4
> files in a zip archive on a website and post the URL here so that
others
>
> can debug this? The problem seems to be a shot Pstart vector putting
an
> invalid value into the range from which to extract ring coordinates,
but
>
> the question is why it is shot.
>
> If you can say something about the origin of the file, this may also
> help
> (what software wrote it), some have broken *.shx files.
>
> Roger
>
>>
>>
>> Thanks in advance,
>>
>> Allen
>>
>>
>> 	[[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> R-sig-Geo at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
>

-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no