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I have a a big feature class in geodatabase (~1.3 million rows and 234 columns; you could download it using this link) in ArcGIS 10.4.1.

I want to import the feature class from the geodatabase to R and plot specific variables (using ggplot2).

I tried importing it into R, using the answer of this question, as below 

require(rgdal)
# The input file geodatabase
fgdb = "C:/Question_Online/union_question.gdb"
# List all feature classes in a file geodatabase
subset(ogrDrivers(), grepl("GDB", name))
fc_list = ogrListLayers(fgdb)
print(fc_list)
# Read the feature class
fc = readOGR(dsn=fgdb,layer="union_thirdtrial")

However, it took more than an hour, so I had to close RStudio to terminate the process.

Can anyone point out what I am missing for a better (faster) way to import this feature class to R?

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shiny
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1 Answers1

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You can use st_read from the sf package. It reads the GeoDatabase as a SimpleFeatures object, which you can convert to SpatialPolygonsDataFrame using the as() method. One caveat: the conversion does not allow for a Z-dimension, so you have to drop it.

I read your union_question.gdb in ~ 15 minutes with st_read(). The conversion to SPDF took 11 minutes.

library(sf)
library(sp)

x <- st_read(dsn="union_question.gdb")
y <- st_drop_zm(x)
z <- as(y, "Spatial")
eivindhammers
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  • Thanks for your time and help. I got this error after running z <- as(y, "Spatial") Error: cannot allocate vector of size 14 Kb. I will appreciate any help how to fix it. – shiny Jan 11 '17 at 22:42
  • That sounds like a memory issue. Either you need more physical RAM, or you can try to increase R's memory by observing the output of memory.limit(), and then increasing it with memory.limit(size = x). – eivindhammers Jan 11 '17 at 23:19
  • Thanks for your help. I'm using Windows 7 64-bit and my PC has 16 GB RAM. I checked memory.limit() [1] 16264 I think this means it is 16264 Mb which is higher than the actual memory of my PC. I think this means I don't need to increase it. Any feedback will be appreciated. – shiny Jan 12 '17 at 00:56
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    Then unfortunately I'm not sure what the problem is. Consider saving a copy of the GDB containing only the fields you need to plot in R. – eivindhammers Jan 16 '17 at 16:10
  • Thanks. I tried to delete specific columns from the attribute table in the feature class in the GDB but I couldn't. Any suggestions will be much appreciated. Also, could you please let me know how many RAMs your PC have and what was the memory.size() when you imported the GDB? – shiny Jan 16 '17 at 20:51
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    I have 8 GB memory, so that's not your problem. I'm not sure how to help you further. I would suggest figuring out how to make a copy of your GDB with only necessary fields, but it's hard to provide help for that (at least without further information). – eivindhammers Jan 16 '17 at 22:00
  • st_drom_zm is now st_zm in latest sf package – Chris Wilson Dec 01 '20 at 22:31