Changeset 448 for trunk/src/stgen.py

Timestamp:

08/18/10 15:11:57 (21 months ago)

Author:

emuller

Message:

Added support for using rpy2 in stgen if present, without breaking support for older rpy.

Files:

• trunk/src/stgen.py (modified) (2 diffs)

trunk/src/stgen.py

@@ -86 +86 @@
     # support directly returning the log.
 
-    if not check_dependency('rpy'):
-        raise ImportError("gamma_hazard requires RPy (http://rpy.sourceforge.net/)")
-
-    from rpy import r
-
-    # scipy.special.gammaincc has numerical problems
-    #Hpre = -log(scipy.special.gammaincc(a,(x-dt)/b))
-    #Hpost = -log(scipy.special.gammaincc(a,(x+dt)/b))
-
-    # reverting to the good old r.pgamma
-    Hpre = -r.pgamma(x-dt,shape=a,scale=b,lower=False,log=True)
-    Hpost = -r.pgamma(x+dt,shape=a,scale=b,lower=False,log=True)
-    val =  0.5*(Hpost-Hpre)/dt
-
-    return val
+    if check_dependency('rpy'):
+        from rpy import r
+
+        # scipy.special.gammaincc has numerical problems
+        #Hpre = -log(scipy.special.gammaincc(a,(x-dt)/b))
+        #Hpost = -log(scipy.special.gammaincc(a,(x+dt)/b))
+
+        # reverting to the good old r.pgamma
+        Hpre = -r.pgamma(x-dt,shape=a,scale=b,lower=False,log=True)
+        Hpost = -r.pgamma(x+dt,shape=a,scale=b,lower=False,log=True)
+        val =  0.5*(Hpost-Hpre)/dt
+
+        return val
+
+    elif check_dependency('rpy2'):
+
+        from rpy2.robjects import r
+
+        # scipy.special.gammaincc has numerical problems
+        #Hpre = -log(scipy.special.gammaincc(a,(x-dt)/b))
+        #Hpost = -log(scipy.special.gammaincc(a,(x+dt)/b))
+
+        # reverting to the good old r.pgamma
+        Hpre = -r.pgamma(x-dt,shape=a,scale=b,lower=False,log=True)[0]
+        Hpost = -r.pgamma(x+dt,shape=a,scale=b,lower=False,log=True)[0]
+        val =  0.5*(Hpost-Hpre)/dt
+
+        return val
+    else:
+        raise ImportError("gamma_hazard requires RPy or RPy2 (http://rpy.sourceforge.net/)")
 
 
@@ -435 +450 @@
 
         if not self.rpy_checked:
-            self.have_rpy = check_dependency('rpy')
+            self.have_rpy = check_dependency('rpy') or check_dependency('rpy2')
             self.rpy_checked = True
         if self.have_rpy:
             return self._inh_gamma_generator_python(a, b, t, t_stop, array)
         else:
-            raise Exception("inh_gamma_generator is disabled as dependency RPy was not found.")
+            raise Exception("inh_gamma_generator is disabled as dependency RPy|RPy2 was not found.")