removed obsolete treereg setup
@@ -7,20 +7,6 @@ from scipy import stats
from scipy.ndimage import binary_dilation
from treetime import config as ttconf
-def setup_TreeRegr(tt, covariation=True):
- from .treeregression import TreeRegression
-
- tip_value = lambda x:np.mean(x.numdate_given) if (x.is_terminal() and x.bad_branch is False) else None
- branch_value = lambda x:x.mutation_length
- if covariation:
- om = tt.one_mutation
- branch_variance = lambda x:(x.mutation_length+(ttconf.OVER_DISPERSION*om if x.is_terminal() else 0.0))*om
- else:
- branch_variance = lambda x:1.0 if x.is_terminal() else 0.0
-
- return TreeRegression(tt.tree, tip_value=tip_value,
- branch_value=branch_value, branch_variance=branch_variance)
-
class DateConversion(object):
"""
