Narrow param grid for serotypes

blab · Jan 27, 2019 · 388fe96 · 388fe96
1 parent c6f6c47
commit 388fe96
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/fitness_model/antigenic_fitness.py b/fitness_model/antigenic_fitness.py
@@ -54,7 +54,7 @@ def get_Dij(j, i):
             return af.titers[(j, i)]
         except KeyError:
             return af.titers[(serotype_of(j), serotype_of(i))]
-            
+
     def sum_over_j(i, past_timepoint):
         ''' Return a frequency-weighted sum of the probability of protection from i given prior exposure to j '''
         antigenic_distance = [ get_Dij(j, i) if i != j else 0. for j in af.clades] # Pull precomputed antigenic distance between virus i and serum j
@@ -540,9 +540,9 @@ def plot_trajectory(af, trajectory, ax=None):
 
     elif args.mode == 'fit':
 
-        d1_vals = np.linspace(0,7,8)
+        d1_vals = np.linspace(1,3,8)
-        d2_vals = np.linspace(0,7,8)
+        d2_vals = np.linspace(1,3,8)
-        d3_vals = np.linspace(0,7,8)
+        d3_vals = np.linspace(0,2,8)
 
         output = []
         for (d1,d2,d3) in product(d1_vals, d2_vals, d3_vals):

diff --git a/fitness_model/helper_scripts/sbatch_param_wrapper.py b/fitness_model/helper_scripts/sbatch_param_wrapper.py
@@ -14,9 +14,9 @@
 if not os.path.isdir(out_path):
 	os.mkdir(out_path)
 
-beta_vals = np.linspace(0,3,8)
+beta_vals = np.linspace(2,3,8)
-gamma_vals = np.linspace(0,3,8)
+gamma_vals = np.linspace(0.5,1.5,8)
-sigma_vals = np.linspace(0,3,8)
+sigma_vals = np.linspace(0,1,8)
 
 for (b,g,s) in product(beta_vals, gamma_vals, sigma_vals):
 	name = ''.join(random.choice('0123456789abcdef') for n in xrange(30))