Python RateMatrix.get_likelihoodの例

コード例 #1

ファイル: 20080523a.py プロジェクト: argriffing/xgcode

 def __call__(self, rate):
     """
     Return the negative likelihood of a column.
     The negative likelihood is computed using
     the tree, matrix, and rate.
     @param rate: the rate of the rate matrix
     @return: the negative likelihood of the column
     """
     if not rate:
         inf = float('inf')
         neginf = float('-inf')
         states = [tip.state for tip in self.tree.gen_tips()]
         if len(set(states)) == 1:
             likelihood = 1
         else:
             likelihood = 0
     else:
         self.rate_matrix.set_rate(rate)
         likelihood = RateMatrix.get_likelihood(self.tree, self.rate_matrix)
     return -likelihood

コード例 #2

 def __call__(self, rate):
     """
     Return the negative likelihood of a column.
     The negative likelihood is computed using
     the tree, matrix, and rate.
     @param rate: the rate of the rate matrix
     @return: the negative likelihood of the column
     """
     if not rate:
         inf = float('inf')
         neginf = float('-inf')
         states = [tip.state for tip in self.tree.gen_tips()]
         if len(set(states)) == 1:
             likelihood = 1
         else:
             likelihood = 0
     else:
         self.rate_matrix.set_rate(rate)
         likelihood = RateMatrix.get_likelihood(self.tree, self.rate_matrix)
     return -likelihood