ESRI / ArcGIS has moved beyond shapefiles too with the advent of geodatabases. In a GIS environment these are superior to shapefiles in many ways, and ESRI in its own training and help resources encourage geodatabases over shapefiles. As far as I've seen only SpaceStat has made itself compatible with geodatabases. But I think that it's a high priority for R, QGIS, etc to adopt the geodatabase as a common format, esp to facilitate interchange with ArcGIS.
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