Thursday, 7 June 2018

Read a table from an ESRI file geodatabase (.gdb) using R


I am trying to read a table directly from an ESRI file geodatabase into R. An example data file can be downloaded here. The database contains a point feature class (Zone9_2014_01_Broadcast) and two linked tables (Zone9_2014_01_Vessel and Zone9_2014_01_Voyage). You can read the shapefile in R using readOGR from the rgeos package:


library(rgeos)
library(downloader)


download("https://coast.noaa.gov/htdata/CMSP/AISDataHandler/2014/01/Zone9_2014_01.zip", dest="Zone9_2014_01.zip", mode="wb")
unzip("Zone9_2014_01.zip", exdir = ".")

# Not Run (loads large point file)
# broadcast <- readOGR(dsn = "Zone9_2014_01.gdb", layer = "Zone9_2014_01_Broadcast")

The two linked tables also show when you use ogrListLayers or ogrInfo. However, ogrInfo gives a warning:



Warning message: In ogrInfo("Zone9_2014_01.gdb", layer = "Zone9_2014_01_Vessel") : ogrInfo: all features NULL




And if you try to use readOGR on the tables you get an error:


vessel <- readOGR(dsn = "Zone9_2014_01.gdb", layer = "Zone9_2014_01_Vessel")


Error in readOGR(dsn = "Zone9_2014_01.gdb", layer = "Zone9_2014_01_Vessel") : no features found In addition: Warning message: In ogrInfo(dsn = dsn, layer = layer, encoding = encoding, use_iconv = use_iconv, : ogrInfo: all features NULL



Thus, it appears that only geographical features can be read by readOGR. Is there any way to import the tables directly into R or is the only solution to first export them from ArcGIS as *.dbf (or *.txt) files as in this answer?


As an addition, if anyone can provide calls from R to a python script that automates the export of *csv (preferrably) or *.dbf files, that would be an acceptable work-around. The solution just needs to be scalable and automated.



Answer



I'm a little bit late to the party, but this can now be read by sf, with



vessel <- sf::st_read(dsn = "Zone9_2014_01.gdb", layer = "Zone9_2014_01_Vessel")

It returns a warning (no feature geometries present) but also a data.frame with the table. See the thread that started here: https://stat.ethz.ch/pipermail/r-sig-geo/2018-February/026344.html


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