document the tracelog function parameters
@@ -245,7 +245,6 @@ class TreeTime(ClockTree):
niter+=1
-
if ndiff==0 and n_resolved==0 and Tc!='skyline':
self.logger("###TreeTime.run: CONVERGED",0)
break
@@ -793,8 +792,17 @@ class TreeTime(ClockTree):
----------
niter : int
The current iteration.
-
- tracelog : bool, str
+ ndiff : int
+ The number of sequence changes.
+ n_resolved : int
+ The number of polytomy changes
+ time_marginal : bool
+ True if marginal position estimation was requested, else False
+ sequence_marginal : bool
+ True if marginal sequence estimation was requested, else False
+ Tc : float, str
+ The coalescent model that was used for the current iteration.
+ tracelog : str
The output file to write the trace log to.
Returns
