Removed all occurrences of ceiling parameter

g6pd/__init__.py

@@ -27,25 +27,25 @@ def check_data(input):
         if np.any(input[pos]<0) or np.any(input[pos]>input[n]):
             raise ValueError, 'Some observations are negative.'
 
-def male_def(sp_sub, ceiling):
+def male_def(sp_sub):
     allele = sp_sub.copy('F')
-    allele = invlogit(allele)*ceiling
+    allele = invlogit(allele)
     return allele
 
-def fem_def_conservative(sp_sub, ceiling):
-    hom = male_def(sp_sub, ceiling)
+def fem_def_conservative(sp_sub):
+    hom = male_def(sp_sub)
     fast_inplace_mul(hom,hom)
     return hom
 
-def hw_hetero(sp_sub, ceiling):
-    p = male_def(sp_sub, ceiling)
+def hw_hetero(sp_sub):
+    p = male_def(sp_sub)
     q = fast_inplace_scalar_add(-p,1)
     fast_inplace_mul(p,q)
     return 2*p
 
-def fem_def(sp_sub, ceiling, a, b):
-    homo = male_def(sp_sub, ceiling)
-    hetero = hw_hetero(sp_sub, ceiling)
+def fem_def(sp_sub, a, b):
+    homo = male_def(sp_sub)
+    hetero = hw_hetero(sp_sub)
     het_def = pm.rbeta(a,b)
     hetero *= het_def
     return hetero+homo
@@ -55,15 +55,15 @@ def fem_def(sp_sub, ceiling, a, b):
 def validate_male(data):
     obs = data.male_pos
     n = data.n_male
-    def f(sp_sub, ceiling, n=n):
-        return pm.rbinomial(n=n,p=pm.invlogit(sp_sub)*ceiling)
+    def f(sp_sub, n=n):
+        return pm.rbinomial(n=n,p=pm.invlogit(sp_sub))
     return obs, n, f
 
 def validate_female(data):
     obs = data.fem_pos
     n = data.n_fem
-    def f(sp_sub, ceiling, a, b, n=n):
-        p = pm.invlogit(sp_sub)*ceiling
+    def f(sp_sub, a, b, n=n):
+        p = pm.invlogit(sp_sub)
         h = pm.rbeta(a,b,size=len(sp_sub))
         p_def = g6pd.p_fem_def(p,h)
         return pm.rbinomial(n=n, p=p)
@@ -81,8 +81,8 @@ def area_male(gc):
     def h(**region):
         return np.array(region.values()[0])
 
-    def f(sp_sub, x, ceiling):
-        p = pm.invlogit(sp_sub(x))*ceiling
+    def f(sp_sub, x):
+        p = pm.invlogit(sp_sub(x))
         return p
 
     g = {gc.keys()[0]: f}
@@ -96,8 +96,8 @@ def area_fem_def_conservative(gc):
     def h(**region):
         return np.array(region.values()[0])
 
-    def f(sp_sub, x, ceiling):
-        p = pm.invlogit(sp_sub(x))*ceiling
+    def f(sp_sub, x):
+        p = pm.invlogit(sp_sub(x))
         return p**2
 
     g = {gc.keys()[0]: f}
@@ -111,8 +111,8 @@ def area_fem_def(gc):
     def h(**region):
         return np.array(region.values()[0])
 
-    def f(sp_sub, x, ceiling, a, b):
-        p = pm.invlogit(sp_sub(x))*ceiling
+    def f(sp_sub, x, a, b):
+        p = pm.invlogit(sp_sub(x))
         h = pm.rbeta(a,b,size=len(p))
         return g6pd.p_fem_def(p,h)