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I need to project a number of reef sites onto the coastline of southwest Madagascar. I was hoping to use R for this as I find ArcGIS too big and clunky. I need to create a basemap for both the reefs and coastline. Is there anyway to 'trace' an existing map and input the coordinates into R since reef are rarely shown on world maps. How would I do this?

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If you find ArcGIS big and clunky, if might be worth investigating SAGA-GIS or another GIS software –  mnel Sep 26 '12 at 11:38
Quantum GIS will do this and is Open Source and not clunky. Start it up, add a base layer (from Open Street Map, or other non-free sources such as google) and then create a new layer and start drawing. –  Spacedman Sep 26 '12 at 12:34
Hmm..I was hoping to do it in R as I want to automate the mapping process. I just realised that you can trace objects in google maps save it as a kml file and then open this in excel and tidy it up as a csv file which then goes into R. Fiddly but I just need to create a simple base map of the reefs. –  Elizabeth Sep 26 '12 at 12:50
Is this 'tracing' something done by hand (a user clicking outline points) or something you want to do automatically (which might be very hard depending on what your input map is). –  Spacedman Sep 26 '12 at 13:47
There is an R SIG list for spatial stats that might have a higher concentration of experts in this domain. They are probably going to want some sample data for reef locations and for you to tell them what map data you were planning to use. –  DWin Sep 26 '12 at 17:23
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For tracing/digitizing the maps, I think you're still better off using an open source GIS like @Spacedman has said. You'd still be manually tracing in R anyway, might as well do it in a GIS. Once you have the digitized layer, you can then automate the mapping process in R.

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