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Short version: how can I get into R the dataset available at this link? (you need to log in to download, but registration is free)

The dataset that is downloadable at that link expands to a directory; as pointed out in the comments, this is an ESRI file geodatabase, and the important stuff is in a subdirectory. The format was reverse engineered and is readable by GDAL:

$ ogrinfo eschscholzia_minutiflora_twisselmannii/data/v93/tempgdb.gdb
Had to open data source read-only.
INFO: Open of `eschscholzia_minutiflora_twisselmannii/data/v93/tempgdb.gdb'
  using driver `OpenFileGDB' successful.
1: Eschscholzia_minutiflora_ssp_twisselmannii (Multi Polygon)

However, reading this into R results in:

x <-readOGR('eschscholzia_minutiflora_twisselmannii/data/v93/tempgdb.gdb', 'Eschscholzia_minutiflora_ssp_twisselmannii')

Error in readOGR("eschscholzia_minutiflora_twisselmannii/data/v93/tempgdb.gdb",  :
Unsupported field type: Binary

Another tack, using ogr2ogr, produces a shapefile:

$ ogr2ogr --mapFieldType Binary=Integer test_output eschscholzia_minutiflora_twisselmannii/data/v93/tempgdb.gdb/
Warning 6: Normalized/laundered field name: 'FOOTPRINT_Length' to 'FOOTPRINT_'
Warning 6: Normalized/laundered field name: 'FOOTPRINT_Area' to 'FOOTPRIN_1'
Warning 1: Value 121687920 of field FOOTPRINT_ of feature 0 not successfully written. Possibly due to too larger number with respect to field width
Warning 1: Value 925496867120400 of field FOOTPRIN_1 of feature 0 not successfully written. Possibly due to too larger number with respect to field width

but the resulting shapefile doesn't seem to have the information in it. Or, maybe I don't know the right way to read it into R?

petrelharp
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  • You can read it directly into R with rgdal::readOGR, try "x <- readOGR('eschscholzia_minutiflora_twisselmannii/data/v93/tempgdb.gdb', 'Eschscholzia_minutiflora_ssp_twisselmannii')" but no idea about the .lyr file specifically. See ?ogrListLayers to discover information about the layer/s in the data set. – mdsumner Dec 21 '15 at 04:48
  • That doesn't work (see revised post): maybe this has to do with the new mapFieldType option? – petrelharp Dec 21 '15 at 05:10
  • The main file you're downloading is an Esri File Geodatabase, so you could check the R documentation to see whether they explain how to work with this (the *.lyr layer file is used within Esri software to provide ready-made symbols, labels, etc and doesn't contain any actual content) – Stephen Lead Dec 21 '15 at 05:24
  • This may also help: http://gis.stackexchange.com/a/151622/3112 – Stephen Lead Dec 21 '15 at 05:27
  • @stephen-lead Thanks. It seems the problem is the Binary format of the fields? – petrelharp Dec 21 '15 at 05:50
  • Try "drop_unsupported_fields=TRUE" see ?readOGR – mdsumner Dec 21 '15 at 10:25
  • Scratch that, I believe your data is a raster. R can't read the geodatabase raster (neither can GDAL). Get them to provide a useable format is the only option I'm afraid. When you read it as vector (or convert to shapefile) I think you just get the bounding box polygon. – mdsumner Dec 21 '15 at 10:39

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Those data are rasters, and sadly (as of December 2015) it seems there's no way to read file geodatabase rasters with open source tools. The nice folk(s) who reverse-engineered the format haven't done rasters, and as described in this question, ESRI isn't helping. =(

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petrelharp
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