Don,
When I load this shapefile into QGis, the CRS dialog indicates that it is EPSG code 4326 :
(+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs ).

That is the default value set in QGis preferences for layers that don't have projection information, and not the same as the information in the .prj file. Apparently the .prj file is not being read??
Yes, a bug (that has recently been fixed in trunk) causes non-recognised CRS' to be ignored... so really, you have two options... to manually adjust the .prj of your shapefile to match one of the ones specified in the QGIS database, or two, find the correct CRS using fTools 'define current projection' tool to overwrite it automatically... Or you can wait for the new release where this probably won't be a problem...


When I load the shapefile into R using readOGR(), I get:

 proj4string(nycb)
[1] " +proj=lcc +lat_1=40.66666666666666 +lat_2=41.03333333333333 +lat_0=40.16666666666666 +lon_0=-74 +x_0=300000 +y_0=0 +ellps=GRS80 +datum=NAD83 +to_meter=0.3048006096012192 +no_defs +towgs84=0,0,0"
Which means R loads the .prj file properly...
Going back to QGis, after that little side trip to R:

I tried saving to EPSG code 4269 (+proj=longlat +ellps=GRS80 +datum=NAD83 +no_defs), but it had no effect that I can see. For example, I load the saved shapefile into QGis, and it overlays exactly on the original.
Wait, let me get this strait... after transforming the layer in R, you saved it to file, and loaded this is QGIS, and it did not recognise the projection? Is this correct? Perhaps you could describe your exact steps from within R onwards?

Carson

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