[R-sig-Geo] error in readShapePoly

Wed Jun 10 20:18:40 CEST 2009

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

> Is there an equivalent argument in readOGR() to read in a shapefile with
> a NULL geometry, or can this only be done with readShapePoly?

No, readOGR() uses drivers for multiple vector formats, and as it is now 
written, it stops when a NULL geometry is found. This isn't likely to 
change very soon, but will go on the TODO list.

Roger

>
> Thanks,
> Allen
>
> -----Original Message-----
> From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
> Sent: Wednesday, June 10, 2009 12:44 PM
> 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:
>
>> Thanks Roger!
>>
>> Are there any instances in which one would want delete_null_obj=FALSE?
>
> Well, they shouldn't be there, really. When I release maptools, with
> default delete_null_obj=FALSE, it will report which one, and then:
>
> library(foreign)
> tip <- read.dbf("trin_inca_pl.dbf")
> tip[134,]
>
> would show the contents of the DBF for the offending NULL geometry.
> Setting it to TRUE by default wouldn't warn the user that there was
> anything untoward. In this case, the file originator might want to know
> that a geometry has gone away, perhaps. In an earlier case, Statistics
> Australia was squirrelling data with no spatial position away in a NULL
> geometry, which is OK for the DBF, but not OK if the files are (as they
> are) intended to contain geometries with attributes.
>
> Roger
>
>>
>> -----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