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Output of the second example

 

----------------------- Logger -----------------------

Iteration;    Posterior;  ESS;    Likelihood;    Prior;  ESS;    #Reticulation

0;    -32.31804;    0.00000;    -26.31804;   -6.00000;    0.00000;    0;

(C:1.0,(F:1.0,(G:1.0,K:1.0):1.0):1.0);

1;    -30.67945;    0.00000;    -24.36941;   -6.31004;    0.00000;    0;

(((F:1.100296825380626,G:3.091462635493304):0.0672071335563177,C:1.2631834608546109):0.022439620222693815,K:0.7654486703017418);

......

9;    -39.23243;    5.00000;    -24.51469;   -14.71774;    5.00000;    0;

(C:1.303229359865713,(G:1.184262389767834,(F:9.355326885355721,K:1.9913949707859038)I0:0.8785013943118355)I3:0.005027219859507291)I2;

10;    -47.01271;    6.00000;    -23.75691;   -23.25580;    6.00000;    1;

((((G:0.6775006643112376)I1#H1:0.10254403746151251::0.6222138281679854,(K:0.40305290671104776,F:11.774054935191478)I3:1.0127444936379693)I4:0.11119651081773953,C:0.6245266587065907)I2:0.24534630112752273,I1#H1:0.6332472675472998::0.3777861718320146)I0;

----------------------- Summarization: -----------------------

Burn-in = 5000, Chain length = 10000, Sample size = 5 Acceptance rate = 0.62080 

         --------------- Operations ---------------

Operation:Move-Head; Used:196; Accepted:35 ACrate:0.17857142857142858

Operation:Change-Length; Used:5782; Accepted:5628 ACrate:0.9733656174334141

Operation:Add-Reticulation; Used:92; Accepted:1 ACrate:0.010869565217391304

Operation:Flip-Reticulation; Used:191; Accepted:44 ACrate:0.23036649214659685

Operation:Change-Probability; Used:172; Accepted:165 ACrate:0.9593023255813954

Operation:Move-Tail; Used:3564; Accepted:332 ACrate:0.0931537598204265

Operation:Delete-Reticulation; Used:3; Accepted:3 ACrate:1.0

 

Overall MAP = -39.13178296704008

(((G:1.8467353971326255,F:3.669429912707025)I4:0.72972613976057,C:0.7672463997220461)I0:0.14233512944191162,K:7.34631035390478)I3;

         -------------- 95% credible set of topologies: --------------

Rank = 0; Size = 2; Percent = 40.00; MAP = -39.23243337560144:(C:1.303229359865713,(G:1.184262389767834,(F:9.355326885355721,K:1.9913949707859038)I0:0.8785013943118355)I3:0.005027219859507291)I2; Ave=-39.25394715434493; (C:1.20916762172346,(G:2.057607023787008,(K:4.61838854181666,F:6.605842763421295)I0:0.5911795016873735)I4:0.1657841343330578)I3;

Rank = 1; Size = 1; Percent = 20.00; MAP = -47.01271365298103:((((G:0.6775006643112376)I1#H1:0.10254403746151251::0.6222138281679854,(K:0.40305290671104776,F:11.774054935191478)I3:1.0127444936379693)I4:0.11119651081773953,C:0.6245266587065907)I2:0.24534630112752273,I1#H1:0.6332472675472998::0.3777861718320146)I0; Ave=-47.01271365298103; ((G:0.6775006643112376)I1#H1:0.6332472675472998::0.3777861718320146,(C:0.6245266587065907,((F:11.774054935191478,K:0.40305290671104776)I3:1.0127444936379693,I1#H1:0.10254403746151251::0.6222138281679854)I4:0.11119651081773953)I2:0.24534630112752273)I0;

Rank = 2; Size = 1; Percent = 20.00; MAP = -39.13178296704008:(((G:1.8467353971326255,F:3.669429912707025)I4:0.72972613976057,C:0.7672463997220461)I0:0.14233512944191162,K:7.34631035390478)I3; Ave=-39.13178296704008; (K:7.34631035390478,(C:0.7672463997220461,(F:3.669429912707025,G:1.8467353971326255)I4:0.72972613976057)I0:0.14233512944191162)I3;

Rank = 3; Size = 1; Percent = 20.00; MAP = -40.2382981193348:(((F:7.823288510084807,K:6.50888387662072)I0:0.32861454580215427,C:0.8862007905628368)I4:0.1556168196177095,G:1.218111399301718)I3; Ave=-40.2382981193348; (G:1.218111399301718,(C:0.8862007905628368,(K:6.50888387662072,F:7.823288510084807)I0:0.32861454580215427)I4:0.1556168196177095)I3; 

Total elapsed time : 31.53400 s

Summarization

  • Topologies: the samples (samples from burn-in period are excluded) from all the files are combined. The topologies are ranked on their posterior probabilities. Only the topologies in the 95% credible set are printed out. The first topology is MPP (maximum posterior probability) topology.
  • PSRF (Potential Scale Reduction Factor): The PSRF values of posterior, likelihood and prior are calculated respectively. A PSRF value indicates good mixing when it approaches 1.0. 
  • Sojourns: a method to evaluate convergence/mixing. 'Sojourn' is a consecutive series of samples in which only the topology of interest was found. For each file, we summarize the frequency, the posterior probability, the number of sojourns, and the max and average length of sojourns for each topology in the 95% credible set. Ideally the number of sojourns is large while the length of sojourns is small -- the ability to leave and then return quickly and repeatedly to the same topology suggests good mixing with respect to topologies. 
  • SRQ (Scaled Regeneration Quantile) Plot: a method to evaluate convergence/mixing via topologies. Let Ti be the number of sampled MPP topology in the first i iteration of the stationary phase. For each file, we extract <i/n, Ti/Tn> for every i in 1...n into <x,y>. The slope of <x,y> in an SRQ plot should ideally be close to the posterior probability of MPP. Departures from this indicate that at some points the chain was on a trajectory that should have led to a different final posterior probability. 
  • Trace Plot: a method to evaluate convergence/mixing via posterior values. For each file, we extract a list of posterior values from the sampling phase. The format is compatible with Matlab and Python. 
---------------- Topologies ----------------

PosteriorProbability Topology

0.4500 ((TaB:0.2658858620952823)I2#H1:0.7341141379047177::0.8708100650901477,(TaA:1.0,(TaD:0.32466899225557677,I2#H1:1.3465736635156926::0.1291899349098523)I3:2.4002600314073748)I1:0.19747493612759992)I0;
0.2500 ((TaD:1.0,TaA:1.0):1.0,TaB:1.0);
0.1500 (((TaD:1.57737312713865)I3#H1:0.7217516903113591::0.42596342801648157,TaB:0.3702926554366514)I2:0.5822736350667996,(I3#H1:0.8251033741688848::0.5740365719835184,TaA:0.5942441726893598)I1:0.6915888106669655)I0;
0.1500 ((((TaA:0.2655477426293258)I1#H1:0.11325339702702007::0.4241273916272569,TaD:1.935302259486147)I3:0.786549353980848,TaB:0.40541038525824113)I2:0.2974313193957629,I1#H1:1.0824385015100584::0.5758726083727431)I0;
---------------- PSRF ----------------
Posterior - 1.0498673507956626
Likelihood - 1.09497860895306455
Prior - 1.0576479101618842

---------------- Sojourn ----------------
Topology Frequency Posterior #sojourns max(sjs) ave(sjs)
1 & 4 & 0.4000 & 2 & 3 & 2.00 \\
2 & 4 & 0.4000 & 1 & 4 & 4.00 \\
3 & 1 & 0.1000 & 1 & 1 & 1.00 \\
4 & 1 & 0.1000 & 1 & 1 & 1.00 \\
Topology Frequency Posterior #sojourns max(sjs) ave(sjs)
1 & 8 & 0.8000 & 1 & 8 & 8.00 \\
2 & 2 & 0.2000 & 1 & 2 & 2.00 \\
3 & 0 & 0.0000 & 0 & 0 & NaN \\
4 & 0 & 0.0000 & 0 & 0 & NaN \\
Topology Frequency Posterior #sojourns max(sjs) ave(sjs)
1 & 4 & 0.4000 & 2 & 2 & 2.00 \\
2 & 2 & 0.2000 & 1 & 2 & 2.00 \\
3 & 1 & 0.1000 & 1 & 1 & 1.00 \\
4 & 3 & 0.3000 & 2 & 2 & 1.50 \\
Topology Frequency Posterior #sojourns max(sjs) ave(sjs)
1 & 2 & 0.2000 & 2 & 1 & 1.00 \\
2 & 2 & 0.2000 & 1 & 2 & 2.00 \\
3 & 4 & 0.4000 & 3 & 2 & 1.33 \\
4 & 2 & 0.2000 & 2 & 1 & 1.00 \\

---------------- SRQ Plot ----------------
y0 = [0.25,0.5,0.75,1.0];
x0 = [0.5,0.6,0.7,1.0];
y1 = [0.125,0.25,0.375,0.5,0.625,0.75,0.875,1.0];
x1 = [0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0];
y2 = [0.25,0.5,0.75,1.0];
x2 = [0.3,0.4,0.8,0.9];
y3 = [0.5,1.0];
x3 = [0.5,0.7];
---------------- Trace Plot ----------------

y0 = [-2736.2903,-2487.17354,-2464.78381,-2465.97101,-2452.65531,-2443.28357,-2439.46916,-2441.01877,-2439.93589,-2442.0554,];

y1 = [-2736.2903,-2469.68094,-2438.08212,-2438.52812,-2439.02494,-2438.4918,-2439.33072,-2438.70721,-2438.68125,-2438.68995,];
y2 = [-2736.2903,-2474.94649,-2446.39497,-2438.87233,-2440.56426,-2442.1411,-2438.8736,-2439.18374,-2438.65952,-2439.23713,];
y3 = [-2736.2903,-2466.11338,-2451.75728,-2439.36378,-2439.58731,-2437.75625,-2439.12275,-2438.99142,-2439.20819,-2440.1315,]; 

 

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