[R-sig-Geo] write/readOGR issue with date / time strings
Roger Bivand
Roger.Bivand at nhh.no
Sat Nov 12 21:17:11 CET 2011
On Fri, 11 Nov 2011, Corrie Curtice wrote:
>
>> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C/en_US.UTF-8/C/C/C/C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] rgdal_0.7-1 sp_0.9-84
OK, you have the most recent release.
>
> loaded via a namespace (and not attached):
> [1] grid_2.13.1 lattice_0.19-30 tools_2.13.1
>
> I installed rgdal and PROJ4 as follows:
>
> setRepositories(ind=1:2)
> install.packages("rgdal")
> install.packages("PROJ.4")
>
Quoting the loading messages would help, to confirm the version of the
underlying GDAL binary. The PROJ.4 package is not required or used by
rgdal. My rgdal version on Fedora reports:
> library(rgdal)
Loading required package: sp
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 1.8.1, released 2011/06/04
Path to GDAL shared files: /usr/local/share/gdal
Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009, [PJ_VERSION: 470]
Path to PROJ.4 shared files: (autodetected)
>
>
I do not see the problem in the R-forge development version, and cannot
reproduce the problem. This now works in (unreleased) 0.7-4:
library(rgdal)
dsn <- system.file("vectors", package = "rgdal")[1]
kiritimati_primary_roads <- readOGR(dsn=dsn,
layer="kiritimati_primary_roads")
summary(kiritimati_primary_roads)
kiritimati_primary_roads$dt <- as.POSIXct("2011-11-11 11:11:11")+(60*0:34)
summary(kiritimati_primary_roads)
td <- tempdir()
writeOGR(kiritimati_primary_roads, td, "kiri1", driver="ESRI Shapefile")
kiri1 <- readOGR(td, "kiri1")
summary(kiri1)
kiri1$dt <- as.POSIXct(as.character(kiri1$dt))
summary(kiri1)
This failed in 0.7-1 because the POSIXct column is not recognized as also
POSIXt; this is corrected in 0.7-4. However, this was not the original
problem. Had you reported the output of:
sapply(spdfUTM at data, class)
sapply(spdfUTM at data, storage.mode)
we would have known how krillGMTtime was stored - it does not seem to have
been detected as a column requiring conversion to character string, or as
a column that should trigger an error. In general, as Alex wrote, all date
time columns should be converted to character and converted back on
reading back from the shapefile. OGR drivers treat field types
differently, so writeOGR has to take a conservative view of possibilities.
Hope this clarifies,
Roger
> Thanks,
>
> Corrie
>
>
>
> On 11/11/11 5:31 PM, "Roger Bivand" <Roger.Bivand at nhh.no> wrote:
>
>> On Fri, 11 Nov 2011, Corrie Curtice wrote:
>>
>>> Hello,
>>>
>>> Apologies if this has already been addressed somewhere, I did a brief
>>> search
>>> of archives but didn't find quite this issue.
>>
>> Which versions of what are you using? You should provide the output of
>> sessionInfo(), the messages given when rgdal loads, and details of how
>> you
>> installed rgdal. In addition, a use case would be helpful, but only when
>> we know what version you are using. In current rgdal, data frame columns
>> of class POSIXt are converted to character strings before writing with
>> writeOGR().
>>
>> Roger
>>
>>>
>>> I'm writing out an ESRI shapefile. My spdf has a date/time field.
>>> Looks
>>> like this:
>>>
>>>> head(spdfUTM at data)
>>> krillGMTtime Lat Lon
>>> 1 2010-05-12 12:34:21 -64.67655969 -62.15040195
>>> 21 2010-05-12 12:35:12 -64.6771229 -62.1519511
>>> 38 2010-05-12 12:36:02 -64.67775863 -62.15340614
>>> 57 2010-05-12 12:36:53 -64.67838269 -62.15494829
>>> 78 2010-05-12 12:37:43 -64.67901497 -62.15647203
>>> 100 2010-05-12 12:38:37 -64.67973667 -62.15773224
>>>
>>> All three fields are reported to be "factors" by str. writeOGR appears
>>> happy:
>>>
>>>> writeOGR(spdfUTM,dd,layer="krillPoints-UTM",driver="ESRI
>>> Shapefile",verbose=TRUE,overwrite=TRUE)
>>> $object_type
>>> [1] "SpatialPointsDataFrame"
>>> $output_dsn
>>> [1] "/users/corriecurtice/documents/Data_2010/Shapefiles/"
>>> $output_layer
>>> [1] "krillPoints-UTM"
>>> $output_diver
>>> [1] "ESRI Shapefile"
>>> $output_n
>>> [1] 11179
>>> $output_nfields
>>> [1] 3
>>> $output_fields
>>> [1] "krillGMTtime" "Lat" "Lon"
>>> $output_fclasses
>>> [1] 4 4 4
>>> $dataset_options
>>> NULL
>>> $layer_options
>>> NULL
>>> Warning message:
>>> In writeOGR(spdfUTM, dd, layer = "krillPoints-UTM", driver = "ESRI
>>> Shapefile", :
>>> existing layer removed
>>>
>>> When I read it right back in again, the date/time field is NAs. This is
>>> also true if I load the shapefile into ArcMap.
>>>
>>>> foo <- readOGR(dd,layer="krillPoints-UTM",verbose=TRUE)
>>> OGR data source with driver: ESRI Shapefile
>>> Source: "/users/corriecurtice/documents/Data_2010/Shapefiles/", layer:
>>> "krillPoints-UTM"
>>> with 11179 features and 3 fields
>>> Feature type: wkbPoint with 2 dimensions
>>>
>>>> head(foo at data)
>>> krillGMTti Lat Lon
>>> 1 <NA> -64.67655969 -62.15040195
>>> 2 <NA> -64.6771229 -62.1519511
>>> 3 <NA> -64.67775863 -62.15340614
>>> 4 <NA> -64.67838269 -62.15494829
>>> 5 <NA> -64.67901497 -62.15647203
>>> 6 <NA> -64.67973667 -62.15773224
>>>
>>> Thoughts? Am I missing something obvious?
>>>
>>> I can break it up into separate date and time fields, but since the
>>> field is
>>> simply a factor anyways I'm not sure how that would help.
>>>
>>> Cheers,
>>>
>>> Corrie
>>>
>>> ---
>>> Corrie Curtice
>>> Research Analyst
>>> Marine Geospatial Ecology Lab
>>> Nicholas School of the Environment, Duke University
>>> http://mgel.env.duke.edu
>>> em: corrie.curtice at duke.edu
>>> ph: 252-504-7538
>>>
>>>
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> R-sig-Geo at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>
>> --
>> Roger Bivand
>> Department of Economics, NHH Norwegian School of Economics,
>> 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
>>
>
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--
Roger Bivand
Department of Economics, NHH Norwegian School of Economics,
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
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