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Add tricky event series unit test
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Updated code to deal with tricky event series without breaking simpler event series (all with 4 regions). Then added unit test for tricky event series. Everything seems to check out at the moment. Note that 666 m_d values I had to hardcode to force certain dispersal events to happen along the tricky event series!
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binho authored and binho committed Apr 5, 2024
1 parent 2dd502b commit d158808
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3 changes: 3 additions & 0 deletions examples/feature_files/feature_set_event_series_AB/age1/cb1_1.csv
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reg1,reg2
0,1
1,0
3 changes: 3 additions & 0 deletions examples/feature_files/feature_set_event_series_AB/age2/cb2_1.csv
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reg1,reg2
0,0
0,0
3 changes: 3 additions & 0 deletions examples/feature_files/feature_set_event_series_AB/age3/cb3_1.csv
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reg1,reg2
0,1
1,0
3 changes: 3 additions & 0 deletions examples/feature_files/feature_set_event_series_AB/age_summary.csv
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index,age_end
1,1.5
2,4.25
3 changes: 3 additions & 0 deletions examples/feature_files/feature_set_event_series_AB/epoch_age_1_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[1][1][1] m_d[1][1][2] m_d[1][2][1] m_d[1][2][2]
1 -10.0 -5.0 -1.0 1.0 2.0 0.1 1.0
10 -10.0 -5.0 -1.0 1.0 4.0 0.5 1.0
3 changes: 3 additions & 0 deletions examples/feature_files/feature_set_event_series_AB/epoch_age_2_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[2][1][1] m_d[2][1][2] m_d[2][2][1] m_d[2][2][2]
1 -10.0 -5.0 -1.0 1.0 0.1 0.1 1.0
10 -10.0 -5.0 -1.0 1.0 0.2 0.2 1.0
3 changes: 3 additions & 0 deletions examples/feature_files/feature_set_event_series_AB/epoch_age_3_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[3][1][1] m_d[3][1][2] m_d[3][2][1] m_d[3][2][2]
1 -10.0 -5.0 -1.0 1.0 0.1 2.1 1.0
10 -10.0 -5.0 -1.0 1.0 0.2 2.2 1.0
4 changes: 4 additions & 0 deletions examples/feature_files/feature_set_event_series_AB/feature_summary.csv
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time_index,feature_index,feature_relationship,feature_type,feature_path,name
1,1,between,categorical,examples/feature_files/feature_set_event_series_AB/age1/cb1_1.csv,cb_1
2,1,between,categorical,examples/feature_files/feature_set_event_series_AB/age2/cb2_1.csv,cb_1
3,1,between,categorical,examples/feature_files/feature_set_event_series_AB/age3/cb3_1.csv,cb_1
0 ...s_feature_set_event_series/age1/cb1_1.csv → ...ture_set_event_series_ABCD/age1/cb1_1.csv
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0 ...s_feature_set_event_series/age2/cb2_1.csv → ...ture_set_event_series_ABCD/age2/cb2_1.csv
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0 ...s_feature_set_event_series/age3/cb3_1.csv → ...ture_set_event_series_ABCD/age3/cb3_1.csv
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0 ...s_feature_set_event_series/age4/cb4_1.csv → ...ture_set_event_series_ABCD/age4/cb4_1.csv
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0 ...s_feature_set_event_series/age5/cb5_1.csv → ...ture_set_event_series_ABCD/age5/cb5_1.csv
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0 ...s_feature_set_event_series/age6/cb6_1.csv → ...ture_set_event_series_ABCD/age6/cb6_1.csv
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0 ..._feature_set_event_series/age_summary.csv → ...ure_set_event_series_ABCD/age_summary.csv
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4 changes: 4 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD/epoch_age_1_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[1][1][1] m_d[1][1][2] m_d[1][1][3] m_d[1][1][4] m_d[1][2][1] m_d[1][2][2] m_d[1][2][3] m_d[1][2][4] m_d[1][3][1] m_d[1][3][2] m_d[1][3][3] m_d[1][3][4] m_d[1][4][1] m_d[1][4][2] m_d[1][4][3] m_d[1][4][4]
1 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 10.0 0.1 0.1 10.0 1.0
2 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 10.0 0.1 0.1 10.0 1.0
3 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 10.0 0.1 0.1 10.0 1.0
4 changes: 4 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD/epoch_age_2_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[2][1][1] m_d[2][1][2] m_d[2][1][3] m_d[2][1][4] m_d[2][2][1] m_d[2][2][2] m_d[2][2][3] m_d[2][2][4] m_d[2][3][1] m_d[2][3][2] m_d[2][3][3] m_d[2][3][4] m_d[2][4][1] m_d[2][4][2] m_d[2][4][3] m_d[2][4][4]
1 -10.0 -5.0 -5.0 1.0 10.0 666.0 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 10.0 0.1 0.1 10.0 1.0
2 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 10.0 0.1 0.1 10.0 1.0
3 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 10.0 0.1 0.1 10.0 1.0
4 changes: 4 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD/epoch_age_3_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[3][1][1] m_d[3][1][2] m_d[3][1][3] m_d[3][1][4] m_d[3][2][1] m_d[3][2][2] m_d[3][2][3] m_d[3][2][4] m_d[3][3][1] m_d[3][3][2] m_d[3][3][3] m_d[3][3][4] m_d[3][4][1] m_d[3][4][2] m_d[3][4][3] m_d[3][4][4]
1 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 10.0 0.1 10.0 1.0
2 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 10.0 0.1 10.0 1.0
3 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 10.0 0.1 10.0 1.0
4 changes: 4 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD/epoch_age_4_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[4][1][1] m_d[4][1][2] m_d[4][1][3] m_d[4][1][4] m_d[4][2][1] m_d[4][2][2] m_d[4][2][3] m_d[4][2][4] m_d[4][3][1] m_d[4][3][2] m_d[4][3][3] m_d[4][3][4] m_d[4][4][1] m_d[4][4][2] m_d[4][4][3] m_d[4][4][4]
1 -10.0 -5.0 -5.0 1.0 10.0 0.1 10.0 10.0 1.0 10.0 0.1 0.1 10.0 1.0 10.0 10.0 0.1 10.0 1.0
2 -10.0 -5.0 -5.0 1.0 10.0 0.1 10.0 10.0 1.0 10.0 0.1 0.1 10.0 1.0 10.0 10.0 0.1 10.0 1.0
3 -10.0 -5.0 -5.0 1.0 10.0 0.1 10.0 10.0 1.0 10.0 0.1 0.1 10.0 1.0 10.0 10.0 0.1 10.0 1.0
4 changes: 4 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD/epoch_age_5_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[5][1][1] m_d[5][1][2] m_d[5][1][3] m_d[5][1][4] m_d[5][2][1] m_d[5][2][2] m_d[5][2][3] m_d[5][2][4] m_d[5][3][1] m_d[5][3][2] m_d[5][3][3] m_d[5][3][4] m_d[5][4][1] m_d[5][4][2] m_d[5][4][3] m_d[5][4][4]
1 -10.0 -5.0 -5.0 1.0 10.0 1.0 10.0 10.0 1.0 10.0 10.0 1.0 10.0 1.0 10.0 10.0 10.0 10.0 1.0
2 -10.0 -5.0 -5.0 1.0 10.0 1.0 10.0 10.0 1.0 10.0 10.0 1.0 10.0 1.0 10.0 10.0 10.0 10.0 1.0
3 -10.0 -5.0 -5.0 1.0 10.0 1.0 10.0 10.0 1.0 10.0 10.0 1.0 10.0 1.0 10.0 10.0 10.0 10.0 1.0
4 changes: 4 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD/epoch_age_6_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[6][1][1] m_d[6][1][2] m_d[6][1][3] m_d[6][1][4] m_d[6][2][1] m_d[6][2][2] m_d[6][2][3] m_d[6][2][4] m_d[6][3][1] m_d[6][3][2] m_d[6][3][3] m_d[6][3][4] m_d[6][4][1] m_d[6][4][2] m_d[6][4][3] m_d[6][4][4]
1 -10.0 -5.0 -5.0 1.0 10.0 10.0 10.0 10.0 1.0 10.0 10.0 10.0 10.0 1.0 10.0 10.0 10.0 10.0 1.0
2 -10.0 -5.0 -5.0 1.0 10.0 10.0 10.0 10.0 1.0 10.0 10.0 10.0 10.0 1.0 10.0 10.0 10.0 10.0 1.0
3 -10.0 -5.0 -5.0 1.0 10.0 10.0 10.0 10.0 1.0 10.0 10.0 10.0 10.0 1.0 10.0 10.0 10.0 10.0 1.0
7 changes: 7 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD/feature_summary.csv
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time_index,feature_index,feature_relationship,feature_type,feature_path,name
1,1,between,categorical,examples/feature_files/feature_set_event_series_ABCD/age1/cb1_1.csv,cb_1
2,1,between,categorical,examples/feature_files/feature_set_event_series_ABCD/age2/cb2_1.csv,cb_1
3,1,between,categorical,examples/feature_files/feature_set_event_series_ABCD/age3/cb3_1.csv,cb_1
4,1,between,categorical,examples/feature_files/feature_set_event_series_ABCD/age4/cb4_1.csv,cb_1
5,1,between,categorical,examples/feature_files/feature_set_event_series_ABCD/age5/cb5_1.csv,cb_1
6,1,between,categorical,examples/feature_files/feature_set_event_series_ABCD/age6/cb6_1.csv,cb_1
5 changes: 5 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD_tricky/age1/cb1_1.csv
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reg1,reg2,reg3,reg4
1,1,0,0
1,1,0,0
0,0,1,1
0,0,1,1
5 changes: 5 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD_tricky/age2/cb2_1.csv
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@@ -0,0 +1,5 @@
reg1,reg2,reg3,reg4
1,1,0,0
1,1,0,0
0,0,1,1
0,0,1,1
5 changes: 5 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD_tricky/age3/cb3_1.csv
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@@ -0,0 +1,5 @@
reg1,reg2,reg3,reg4
1,0,0,0
0,1,0,0
0,0,1,1
0,0,1,1
5 changes: 5 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD_tricky/age4/cb4_1.csv
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@@ -0,0 +1,5 @@
reg1,reg2,reg3,reg4
1,1,0,0
1,1,0,0
0,0,1,0
0,0,0,1
5 changes: 5 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD_tricky/age5/cb5_1.csv
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@@ -0,0 +1,5 @@
reg1,reg2,reg3,reg4
1,1,0,0
1,1,0,0
0,0,1,0
0,0,0,1
5 changes: 5 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD_tricky/age6/cb6_1.csv
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reg1,reg2,reg3,reg4
1,1,0,1
1,1,0,0
0,0,1,0
1,0,0,1
6 changes: 6 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD_tricky/age_summary.csv
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index,age_end
1,1.0
2,2.0
3,3.0
4,4.0
5,5.0
4 changes: 4 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD_tricky/epoch_age_1_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[1][1][1] m_d[1][1][2] m_d[1][1][3] m_d[1][1][4] m_d[1][2][1] m_d[1][2][2] m_d[1][2][3] m_d[1][2][4] m_d[1][3][1] m_d[1][3][2] m_d[1][3][3] m_d[1][3][4] m_d[1][4][1] m_d[1][4][2] m_d[1][4][3] m_d[1][4][4]
1 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 10.0 0.1 0.1 10.0 1.0
2 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 10.0 0.1 0.1 10.0 1.0
3 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 10.0 0.1 0.1 10.0 1.0
4 changes: 4 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD_tricky/epoch_age_2_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[2][1][1] m_d[2][1][2] m_d[2][1][3] m_d[2][1][4] m_d[2][2][1] m_d[2][2][2] m_d[2][2][3] m_d[2][2][4] m_d[2][3][1] m_d[2][3][2] m_d[2][3][3] m_d[2][3][4] m_d[2][4][1] m_d[2][4][2] m_d[2][4][3] m_d[2][4][4]
1 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 10.0 0.1 0.1 10.0 1.0
2 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 10.0 0.1 0.1 10.0 1.0
3 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 10.0 0.1 0.1 10.0 1.0
4 changes: 4 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD_tricky/epoch_age_3_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[3][1][1] m_d[3][1][2] m_d[3][1][3] m_d[3][1][4] m_d[3][2][1] m_d[3][2][2] m_d[3][2][3] m_d[3][2][4] m_d[3][3][1] m_d[3][3][2] m_d[3][3][3] m_d[3][3][4] m_d[3][4][1] m_d[3][4][2] m_d[3][4][3] m_d[3][4][4]
1 -10.0 -5.0 -5.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 0.1 0.1 0.1 1.0 10.1 0.1 0.1 10.0 1.0
2 -10.0 -5.0 -5.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 0.1 0.1 0.1 1.0 10.1 0.1 0.1 10.0 1.0
3 -10.0 -5.0 -5.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 0.1 0.1 0.1 1.0 10.1 0.1 0.1 10.0 1.0
4 changes: 4 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD_tricky/epoch_age_4_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[4][1][1] m_d[4][1][2] m_d[4][1][3] m_d[4][1][4] m_d[4][2][1] m_d[4][2][2] m_d[4][2][3] m_d[4][2][4] m_d[4][3][1] m_d[4][3][2] m_d[4][3][3] m_d[4][3][4] m_d[4][4][1] m_d[4][4][2] m_d[4][4][3] m_d[4][4][4]
1 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 0.1 0.1 0.1 1.0
2 -10.0 -5.0 -5.0 1.0 10.0 666 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 0.1 0.1 0.1 1.0
3 -10.0 -5.0 -5.0 1.0 10.0 666 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 0.1 0.1 0.1 1.0
4 changes: 4 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD_tricky/epoch_age_5_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[5][1][1] m_d[5][1][2] m_d[5][1][3] m_d[5][1][4] m_d[5][2][1] m_d[5][2][2] m_d[5][2][3] m_d[5][2][4] m_d[5][3][1] m_d[5][3][2] m_d[5][3][3] m_d[5][3][4] m_d[5][4][1] m_d[5][4][2] m_d[5][4][3] m_d[5][4][4]
1 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 0.1 0.1 0.1 1.0
2 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 0.1 0.1 0.1 1.0
3 -10.0 -5.0 -5.0 1.0 10.0 0.1 0.1 10.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 0.1 0.1 0.1 1.0
4 changes: 4 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD_tricky/epoch_age_6_rel_rates.log
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Iteration Posterior Likelihood Prior m_d[6][1][1] m_d[6][1][2] m_d[6][1][3] m_d[6][1][4] m_d[6][2][1] m_d[6][2][2] m_d[6][2][3] m_d[6][2][4] m_d[6][3][1] m_d[6][3][2] m_d[6][3][3] m_d[6][3][4] m_d[6][4][1] m_d[6][4][2] m_d[6][4][3] m_d[6][4][4]
1 -10.0 -5.0 -5.0 1.0 10.0 0.1 10.0 10.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 10.0 0.1 0.1 1.0
2 -10.0 -5.0 -5.0 1.0 10.0 0.1 10.0 10.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 10.0 0.1 0.1 1.0
3 -10.0 -5.0 -5.0 1.0 10.0 0.1 10.0 10.0 1.0 0.1 0.1 0.1 0.1 1.0 0.1 10.0 0.1 0.1 1.0
7 changes: 7 additions & 0 deletions examples/feature_files/feature_set_event_series_ABCD_tricky/feature_summary.csv
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time_index,feature_index,feature_relationship,feature_type,feature_path,name
1,1,between,categorical,examples/feature_files/feature_set_event_series_ABCD_tricky/age1/cb1_1.csv,cb_1
2,1,between,categorical,examples/feature_files/feature_set_event_series_ABCD_tricky/age2/cb2_1.csv,cb_1
3,1,between,categorical,examples/feature_files/feature_set_event_series_ABCD_tricky/age3/cb3_1.csv,cb_1
4,1,between,categorical,examples/feature_files/feature_set_event_series_ABCD_tricky/age4/cb4_1.csv,cb_1
5,1,between,categorical,examples/feature_files/feature_set_event_series_ABCD_tricky/age5/cb5_1.csv,cb_1
6,1,between,categorical,examples/feature_files/feature_set_event_series_ABCD_tricky/age6/cb6_1.csv,cb_1
7 changes: 0 additions & 7 deletions examples/feature_files/four_regions_feature_set_event_series/feature_summary.csv
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0 examples/test_event_series1.pj → examples/test_event_series_AB.pj
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0 examples/test_event_series2.pj → examples/test_event_series_ABCD.pj
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1 change: 1 addition & 0 deletions examples/trees_maps_files/geosse_dummy_tree3.tre
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(((A:[&index=1]0.25,B:[&index=2]0.25):[&index=5]3.0,(C:[&index=3]0.25,D:[&index=4]0.25):[&index=6]3.0):[&index=7]2.75):[&index=8]0.0;
47 changes: 47 additions & 0 deletions examples/trees_maps_files/geosse_dummy_tree3_maps.tsv
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iteration node_index branch_start_time branch_end_time start_state end_state transition_time transition_type parent_index child1_index child2_index
1 8 6.0 6.0 7 7 NA no_change 8 7 7
1 7 6.0 3.25 7 7 NA no_change 7 5 6
1 7 6.0 3.25 7 7 3.25 cladogenetic 7 5 6
1 5 3.25 0.25 7 11 2.5 anagenetic 5 1 2
1 5 3.25 0.25 11 14 0.75 anagenetic 5 1 2
1 6 3.25 0.25 7 12 1.5 anagenetic 6 3 4
1 6 3.25 0.25 12 14 0.75 anagenetic 6 3 4
1 1 0.25 0.0 4 4 NA no_change 5 NA NA
1 2 0.25 0.0 9 9 NA no_change 5 NA NA
1 3 0.25 0.0 4 4 NA no_change 6 NA NA
1 4 0.25 0.0 9 9 NA no_change 6 NA NA
1 5 3.25 0.5 14 4 0.25 cladogenetic 5 1 2
1 5 3.25 0.5 14 9 0.25 cladogenetic 5 1 2
1 6 3.25 0.5 14 4 0.25 cladogenetic 6 3 4
1 6 3.25 0.5 14 9 0.25 cladogenetic 6 3 4
2 8 6.0 6.0 11 11 NA no_change 8 7 7
2 7 6.0 3.25 11 11 NA no_change 7 5 6
2 7 6.0 3.25 11 11 3.25 cladogenetic 7 5 6
2 5 3.25 0.25 11 4 2.5 anagenetic 5 1 2
2 5 3.25 0.25 4 10 1.5 anagenetic 5 1 2
2 5 3.25 0.25 10 14 0.75 anagenetic 5 1 2
2 6 3.25 0.25 11 14 2.75 anagenetic 6 3 4
2 6 3.25 0.25 14 12 2.5 anagenetic 6 3 4
2 6 3.25 0.25 12 14 0.75 anagenetic 6 3 4
2 1 0.25 0.0 4 4 NA no_change 5 NA NA
2 2 0.25 0.0 9 9 NA no_change 5 NA NA
2 3 0.25 0.0 4 4 NA no_change 6 NA NA
2 4 0.25 0.0 9 9 NA no_change 6 NA NA
2 5 3.25 0.5 14 4 0.25 cladogenetic 5 1 2
2 5 3.25 0.5 14 9 0.25 cladogenetic 5 1 2
2 6 3.25 0.5 14 4 0.25 cladogenetic 6 3 4
2 6 3.25 0.5 14 9 0.25 cladogenetic 6 3 4
3 7 6.0 3.25 0 5 4.5 anagenetic 7 5 6
3 7 6.0 3.25 5 5 3.25 cladogenetic 7 5 6
3 5 3.25 0.25 5 10 2.5 anagenetic 5 1 2
3 5 3.25 0.25 10 14 0.75 anagenetic 5 1 2
3 6 3.25 0.25 5 10 1.5 anagenetic 5 1 2
3 6 3.25 0.25 10 14 0.75 anagenetic 5 1 2
3 1 0.25 0.0 4 4 NA no_change 5 NA NA
3 2 0.25 0.0 9 9 NA no_change 5 NA NA
3 3 0.25 0.0 4 4 NA no_change 6 NA NA
3 4 0.25 0.0 9 9 NA no_change 6 NA NA
3 5 3.25 0.5 14 4 0.25 cladogenetic 5 1 2
3 5 3.25 0.5 14 9 0.25 cladogenetic 5 1 2
3 6 3.25 0.5 14 4 0.25 cladogenetic 6 3 4
3 6 3.25 0.5 14 9 0.25 cladogenetic 6 3 4
4 changes: 4 additions & 0 deletions examples/trees_maps_files/geosse_dummy_tree3_tip_states.tsv
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nd1 4
nd2 9
nd3 4
nd4 9
1 change: 1 addition & 0 deletions examples/trees_maps_files/geosse_dummy_tree4.tre
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((A:[&index=1]0.25,B:[&index=2]0.25):[&index=3]5.75):[&index=4]0.0;
25 changes: 25 additions & 0 deletions examples/trees_maps_files/geosse_dummy_tree4_maps.tsv
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iteration node_index branch_start_time branch_end_time start_state end_state transition_time transition_type parent_index child1_index child2_index
1 4 6.0 6.0 4 4 NA no_change NA 3 3
1 3 6.0 0.25 4 10 3.5 anagenetic 3 1 2
1 3 6.0 0.25 10 14 2.5 anagenetic 3 1 2
1 3 6.0 0.25 14 11 1.5 anagenetic 3 1 2
1 3 6.0 0.25 11 14 0.5 anagenetic 3 1 2
1 1 0.25 0.0 4 4 NA no_change 3 NA NA
1 2 0.25 0.0 9 9 NA no_change 3 NA NA
1 3 6.0 0.25 14 4 0.25 cladogenetic 3 1 2
1 3 6.0 0.25 14 9 0.25 cladogenetic 3 1 2
2 4 6.0 6.0 11 11 NA no_change NA 3 3
2 3 6.0 0.25 11 14 3.5 anagenetic 3 1 2
2 3 6.0 0.25 14 11 2.5 anagenetic 3 1 2
2 3 6.0 0.25 11 14 1.5 anagenetic 3 1 2
2 1 0.25 0.0 4 4 NA no_change 3 NA NA
2 2 0.25 0.0 9 9 NA no_change 3 NA NA
2 3 6.0 0.25 14 4 0.25 cladogenetic 3 1 2
2 3 6.0 0.25 14 9 0.25 cladogenetic 3 1 2
3 4 6.0 6.0 7 7 NA no_change NA 3 3
3 3 6.0 0.25 7 12 3.5 anagenetic 3 1 2
3 3 6.0 0.25 12 14 1.5 anagenetic 3 1 2
3 1 0.25 0.0 4 4 NA no_change 3 NA NA
3 2 0.25 0.0 9 9 NA no_change 3 NA NA
3 3 6.0 0.25 14 4 0.25 cladogenetic 3 1 2
3 3 6.0 0.25 14 9 0.25 cladogenetic 3 1 2
2 changes: 2 additions & 0 deletions examples/trees_maps_files/geosse_dummy_tree4_tip_states.tsv
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nd1 4
nd2 9
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