Fixed issue with creating leaf height parameters for multiple trees but the XML is not going to work. Probably need to disallow this in BEAUti.
0 lines of code changed in 2 files:
Leaf taxa are only added to a treeModel if it has them.
27 lines of code changed in 3 files:
Origin date needs its units set.
0 lines of code changed in 2 files:
Auto sets the size of the MarkovJump count register
28 lines of code changed in 4 files:
Added fasta (and fa and fas) as recognized extensions
2 lines of code changed in 2 files:
Fixed that BEAUti was putting stateTagName attribute into TreeLikelihood elements (even though they should only be there for ancestralStateTreeLikelihoods). Was giving a parser warning when run (no other consequences).
11 lines of code changed in 5 files:
Added tool tip for lambda tree signal parameter check box.
18 lines of code changed in 6 files:
BEAUti: added Pagel's Lambda transform of tree shape to measure phylogenetic signal in continuous traits. Check box in sites panel for continuous trait partition. Lambda appears in priors table and operators table.
101 lines of code changed in 7 files:
Added parsing and setting of date precisions in BEAUti plus generation of uniform sampling within these bounds. Also fixed the date calculations so Jan 1st (say 2013) is 2013.0.
260 lines of code changed in 17 files:
Improved tip date parsing - now can read variable precision dates.
17 lines of code changed in 1 file:
Added local root search to Pathogen.
140 lines of code changed in 4 files:
A couple of minor fixes to the main(). -version now works. -beagle_info on the command line doesn't throw up the options dialog but prints the info and quits.
2 lines of code changed in 2 files:
Finished tipdate precision for Pathogen. Now shows these as error bars (the points are given a date that is midpoint within the specified precision).
154 lines of code changed in 5 files:
Adding date precision to the BEAUti/Pathogen date guessing panel
107 lines of code changed in 3 files:
DiscreteTraitBranchRateModel parser tweaks.
62 lines of code changed in 3 files:
DiscreteTraitBranchRateModel parser tweaks.
2 lines of code changed in 1 file:
Caching of rates doesn't seem to work with multiple partitions so turning it off now. The lazy computation of these (which does work) should prevent large overheads of computing these repeatedly at operator time (which was considerable when using gamma distributions due to the numerical quantile finding).
32 lines of code changed in 2 files:
<trait> element in Tree Logger can now take a filter="XXX" attribute instead of specifying a particular name to log all traits that starts with a particular string. Also if the <trait> element has neither a name or a filter attribute then all traits are logged.
67 lines of code changed in 1 file:
Some serious effort to build a post-analysis tool for antigenic mapping.
1367 lines of code changed in 17 files:
Created an 'AttributeBranchRateModel' which exposes an attribute embedded in a tree as a branch rate model.
158 lines of code changed in 7 files:
(1194 more)