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3cce1cd
adding test OBDP back
azwaans Mar 28, 2022
083cb7c
minor corrections on old tests + data upload
azwaans Mar 30, 2022
3778061
expected outputs updated
azwaans Mar 30, 2022
6c76fc6
minor edits, updated expected outputs for macro skyline test
azwaans Mar 30, 2022
9e99db0
Delete .DS_Store
azwaans Mar 31, 2022
7d3c0a7
Delete .DS_Store
azwaans Mar 31, 2022
e91efde
updating outputs for latest changes in OBDP dist
azwaans Apr 29, 2022
5363e37
Merge branch 'development' of github.com:azwaans/tests into development
azwaans Apr 29, 2022
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1 change: 1 addition & 0 deletions data/data_OBDP/epidemio_occurrences.csv
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0.02800000000010261; 0.05400000000010263; 0.2370000000001028; 0.42100000000010296; 0.509000000000103; 1.3890000000000606; 2.6419999999999226; 4.768000000000029
23 changes: 23 additions & 0 deletions data/data_OBDP/epidemio_seq.nex
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16 changes: 16 additions & 0 deletions data/data_OBDP/epidemio_taxa.csv
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taxon min max
f107 1.6200000000000352 1.6200000000000352
f98 1.0620000000000966 1.0620000000000966
f67 0 0
f17 0 0
f84 0.15500000000010272 0.15500000000010272
f51 0 0
f44 0 0
f80 0 0
f106 1.3890000000000606 1.3890000000000606
f13 0 0
f15 0 0
f49 0 0
f114 2.110999999999981 2.110999999999981
f54 0 0
f95 0.8290000000001033 0.8290000000001033
18 changes: 18 additions & 0 deletions data/data_OBDP/macroevol_morpho.nex
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#NEXUS

Begin data;
Dimensions ntax=10 nchar=60;
Format datatype=standard gap=- missing=? symbols="01";
Matrix
f53 001110100101000000001001000010111011110001010110101100110110
f54 011110100101001000001001000010111011110001000110101100110110
f51 011010100101011000001010000010101111110001000110101100110110
f52 011110100101000000001010000010111111110001000110101101110110
f50 011110100100000000001010000010110111110001000110101100110110
f2 001110000001000000001001000110111011110001011111101100110110
f1 001100000001000010001001000110111111110001011111101100110110
f0 001110000001000000001001000110111011110001011111101100110110
f4 011110100101001000001010010110101111110001100111101101110110
f3 011110101101000000001010000010101111110001110010001101110110
;
End;
1 change: 1 addition & 0 deletions data/data_OBDP/macroevol_occurrences.csv
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1.1470000000000873; 1.441000000000055; 2.5529999999999324; 4.124999999999814; 5.2800000000002
13 changes: 13 additions & 0 deletions data/data_OBDP/macroevol_seq_extant.nex
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11 changes: 11 additions & 0 deletions data/data_OBDP/macroevol_taxa.csv
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taxon min max
f53 4.199999999999839 4.199999999999839
f54 5.16100000000016 5.16100000000016
f51 3.8029999999997948 3.8029999999997948
f52 3.947999999999779 3.947999999999779
f50 3.1139999999998706 3.1139999999998706
f2 0 0
f1 0 0
f0 0 0
f4 0 0
f3 0 0
1 change: 1 addition & 0 deletions data/simulations/epidemio_occurrences.csv
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0.02800000000010261; 0.05400000000010263; 0.2370000000001028; 0.42100000000010296; 0.509000000000103; 1.3890000000000606; 2.6419999999999226; 4.768000000000029
23 changes: 23 additions & 0 deletions data/simulations/epidemio_seq.nex
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16 changes: 16 additions & 0 deletions data/simulations/epidemio_taxa.csv
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taxon min max
f107 1.6200000000000352 1.6200000000000352
f98 1.0620000000000966 1.0620000000000966
f67 0 0
f17 0 0
f84 0.15500000000010272 0.15500000000010272
f51 0 0
f44 0 0
f80 0 0
f106 1.3890000000000606 1.3890000000000606
f13 0 0
f15 0 0
f49 0 0
f114 2.110999999999981 2.110999999999981
f54 0 0
f95 0.8290000000001033 0.8290000000001033
18 changes: 18 additions & 0 deletions data/simulations/macroevol_morpho.nex
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#NEXUS

Begin data;
Dimensions ntax=10 nchar=60;
Format datatype=standard gap=- missing=? symbols="01";
Matrix
f53 001110100101000000001001000010111011110001010110101100110110
f54 011110100101001000001001000010111011110001000110101100110110
f51 011010100101011000001010000010101111110001000110101100110110
f52 011110100101000000001010000010111111110001000110101101110110
f50 011110100100000000001010000010110111110001000110101100110110
f2 001110000001000000001001000110111011110001011111101100110110
f1 001100000001000010001001000110111111110001011111101100110110
f0 001110000001000000001001000110111011110001011111101100110110
f4 011110100101001000001010010110101111110001100111101101110110
f3 011110101101000000001010000010101111110001110010001101110110
;
End;
1 change: 1 addition & 0 deletions data/simulations/macroevol_occurrences.csv
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1.1470000000000873; 1.441000000000055; 2.5529999999999324; 4.124999999999814; 5.2800000000002
13 changes: 13 additions & 0 deletions data/simulations/macroevol_seq_extant.nex
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11 changes: 11 additions & 0 deletions data/simulations/macroevol_taxa.csv
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taxon min max
f53 4.199999999999839 4.199999999999839
f54 5.16100000000016 5.16100000000016
f51 3.8029999999997948 3.8029999999997948
f52 3.947999999999779 3.947999999999779
f50 3.1139999999998706 3.1139999999998706
f2 0 0
f1 0 0
f0 0 0
f4 0 0
f3 0 0
12 changes: 12 additions & 0 deletions test_OBDP/output_expected/mcmc_OBDP_epi_test_skyline.out
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Iteration branch_rates extinction obd_tree omega origin_time rho sampling speciation[1] speciation[2]
0 0.002266 0.01 ((((f114[&index=15]:20.223282,f44[&index=14]:22.334282)[&index=16]:3.898820,((f67[&index=13]:0.739858,f51[&index=12]:0.739858)[&index=17]:4.237017,f15[&index=11]:4.976875)[&index=18]:21.256227)[&index=19]:1.349051,(f84[&index=10]:20.923940,f107[&index=9]:19.458940)[&index=20]:6.503213)[&index=21]:2.383646,(f17[&index=8]:28.070609,(((f80[&index=7]:8.433098,(f98[&index=6]:1.792628,f13[&index=5]:2.854628)[&index=22]:5.578470)[&index=23]:12.440015,(f106[&index=4]:15.172728,f49[&index=3]:16.561728)[&index=24]:4.311384)[&index=25]:2.306568,(f95[&index=2]:8.088333,f54[&index=1]:8.917333)[&index=26]:14.262347)[&index=27]:4.890928)[&index=28]:1.895190)[&index=29]:0.000000; 0.1693261 51.17489 0.07038391 0.3224907 0.005 0.005
1 0.002266 0.01 ((((f114[&index=15]:20.223282,f44[&index=14]:22.334282)[&index=16]:3.898820,((f67[&index=13]:0.739858,f51[&index=12]:0.739858)[&index=17]:4.237017,f15[&index=11]:4.976875)[&index=18]:21.256227)[&index=19]:1.349051,(f84[&index=10]:20.923940,f107[&index=9]:19.458940)[&index=20]:6.503213)[&index=21]:2.383646,(f17[&index=8]:28.070609,(((f80[&index=7]:8.433098,(f98[&index=6]:1.792628,f13[&index=5]:2.854628)[&index=22]:5.578470)[&index=23]:12.440015,(f106[&index=4]:15.172728,f49[&index=3]:16.561728)[&index=24]:4.311384)[&index=25]:2.306568,(f95[&index=2]:8.088333,f54[&index=1]:8.917333)[&index=26]:14.262347)[&index=27]:4.890928)[&index=28]:1.895190)[&index=29]:0.000000; 0.1693261 51.17604 0.07038391 0.3224907 0.005 0.005
2 0.002266 0.01 ((((f114[&index=15]:20.223282,f44[&index=14]:22.334282)[&index=16]:3.898820,((f67[&index=13]:0.739858,f51[&index=12]:0.739858)[&index=17]:4.237017,f15[&index=11]:4.976875)[&index=18]:21.256227)[&index=19]:1.349051,(f84[&index=10]:20.923940,f107[&index=9]:19.458940)[&index=20]:6.503213)[&index=21]:2.383646,(f17[&index=8]:28.070609,(((f80[&index=7]:8.433098,(f98[&index=6]:1.792628,f13[&index=5]:2.854628)[&index=22]:5.578470)[&index=23]:12.440015,(f106[&index=4]:15.172728,f49[&index=3]:16.561728)[&index=24]:4.311384)[&index=25]:2.306568,(f95[&index=2]:8.088333,f54[&index=1]:8.917333)[&index=26]:14.262347)[&index=27]:4.890928)[&index=28]:1.895190)[&index=29]:0.000000; 0.1693261 51.18046 0.07038391 0.3224907 0.005 0.005
3 0.002266 0.01 ((((f114[&index=15]:20.223282,f44[&index=14]:22.334282)[&index=16]:3.898820,((f67[&index=13]:0.739858,f51[&index=12]:0.739858)[&index=17]:4.237017,f15[&index=11]:4.976875)[&index=18]:21.256227)[&index=19]:1.349051,(f84[&index=10]:20.923940,f107[&index=9]:19.458940)[&index=20]:6.503213)[&index=21]:2.383646,(f17[&index=8]:28.070609,(((f80[&index=7]:8.433098,(f98[&index=6]:1.792628,f13[&index=5]:2.854628)[&index=22]:5.578470)[&index=23]:12.440015,(f106[&index=4]:15.172728,f49[&index=3]:16.561728)[&index=24]:4.311384)[&index=25]:2.306568,(f95[&index=2]:8.088333,f54[&index=1]:8.917333)[&index=26]:14.262347)[&index=27]:4.890928)[&index=28]:1.895190)[&index=29]:0.000000; 0.1693261 51.17961 0.07038391 0.3224907 0.005 0.005
4 0.002266 0.01 ((((f114[&index=15]:20.223282,f44[&index=14]:22.334282)[&index=16]:3.898820,((f67[&index=13]:0.739858,f51[&index=12]:0.739858)[&index=17]:4.237017,f15[&index=11]:4.976875)[&index=18]:21.256227)[&index=19]:1.349051,(f84[&index=10]:20.923940,f107[&index=9]:19.458940)[&index=20]:6.503213)[&index=21]:2.383646,(f17[&index=8]:28.070609,(((f80[&index=7]:8.433098,(f98[&index=6]:1.792628,f13[&index=5]:2.854628)[&index=22]:5.578470)[&index=23]:12.440015,(f106[&index=4]:15.172728,f49[&index=3]:16.561728)[&index=24]:4.311384)[&index=25]:2.306568,(f95[&index=2]:8.088333,f54[&index=1]:8.917333)[&index=26]:14.262347)[&index=27]:4.890928)[&index=28]:1.895190)[&index=29]:0.000000; 0.1693261 51.17726 0.07038391 0.3224907 0.005 0.005
5 0.002266 0.01 ((((f114[&index=15]:20.223282,f44[&index=14]:22.334282)[&index=16]:3.898820,((f67[&index=13]:0.739858,f51[&index=12]:0.739858)[&index=17]:4.237017,f15[&index=11]:4.976875)[&index=18]:21.256227)[&index=19]:1.349051,(f84[&index=10]:20.923940,f107[&index=9]:19.458940)[&index=20]:6.503213)[&index=21]:2.383646,(f17[&index=8]:28.070609,(((f80[&index=7]:8.433098,(f98[&index=6]:1.792628,f13[&index=5]:2.854628)[&index=22]:5.578470)[&index=23]:12.440015,(f106[&index=4]:15.172728,f49[&index=3]:16.561728)[&index=24]:4.311384)[&index=25]:2.306568,(f95[&index=2]:8.088333,f54[&index=1]:8.917333)[&index=26]:14.262347)[&index=27]:4.890928)[&index=28]:1.895190)[&index=29]:0.000000; 0.1693261 51.17323 0.07038391 0.3224907 0.005 0.005
6 0.002266 0.01 ((((f114[&index=15]:20.223282,f44[&index=14]:22.334282)[&index=16]:3.898820,((f67[&index=13]:0.739858,f51[&index=12]:0.739858)[&index=17]:4.237017,f15[&index=11]:4.976875)[&index=18]:21.256227)[&index=19]:1.349051,(f84[&index=10]:20.923940,f107[&index=9]:19.458940)[&index=20]:6.503213)[&index=21]:2.383646,(f17[&index=8]:28.070609,(((f80[&index=7]:8.433098,(f98[&index=6]:1.792628,f13[&index=5]:2.854628)[&index=22]:5.578470)[&index=23]:12.440015,(f106[&index=4]:15.172728,f49[&index=3]:16.561728)[&index=24]:4.311384)[&index=25]:2.306568,(f95[&index=2]:8.088333,f54[&index=1]:8.917333)[&index=26]:14.262347)[&index=27]:4.890928)[&index=28]:1.895190)[&index=29]:0.000000; 0.1693261 51.17309 0.07038391 0.3224907 0.005 0.005
7 0.002266 0.01 ((((f114[&index=15]:20.223282,f44[&index=14]:22.334282)[&index=16]:3.898820,((f67[&index=13]:0.739858,f51[&index=12]:0.739858)[&index=17]:4.237017,f15[&index=11]:4.976875)[&index=18]:21.256227)[&index=19]:1.349051,(f84[&index=10]:20.923940,f107[&index=9]:19.458940)[&index=20]:6.503213)[&index=21]:2.383646,(f17[&index=8]:28.070609,(((f80[&index=7]:8.433098,(f98[&index=6]:1.792628,f13[&index=5]:2.854628)[&index=22]:5.578470)[&index=23]:12.440015,(f106[&index=4]:15.172728,f49[&index=3]:16.561728)[&index=24]:4.311384)[&index=25]:2.306568,(f95[&index=2]:8.088333,f54[&index=1]:8.917333)[&index=26]:14.262347)[&index=27]:4.890928)[&index=28]:1.895190)[&index=29]:0.000000; 0.1693261 51.17274 0.07038391 0.3224907 0.005 0.005
8 0.002266 0.01 ((((f114[&index=15]:20.223282,f44[&index=14]:22.334282)[&index=16]:3.898820,((f67[&index=13]:0.739858,f51[&index=12]:0.739858)[&index=17]:4.237017,f15[&index=11]:4.976875)[&index=18]:21.256227)[&index=19]:1.349051,(f84[&index=10]:20.923940,f107[&index=9]:19.458940)[&index=20]:6.503213)[&index=21]:2.383646,(f17[&index=8]:28.070609,(((f80[&index=7]:8.433098,(f98[&index=6]:1.792628,f13[&index=5]:2.854628)[&index=22]:5.578470)[&index=23]:12.440015,(f106[&index=4]:15.172728,f49[&index=3]:16.561728)[&index=24]:4.311384)[&index=25]:2.306568,(f95[&index=2]:8.088333,f54[&index=1]:8.917333)[&index=26]:14.262347)[&index=27]:4.890928)[&index=28]:1.895190)[&index=29]:0.000000; 0.1693261 51.16803 0.07038391 0.3224907 0.005 0.005
9 0.002266 0.01 ((((f114[&index=15]:20.223282,f44[&index=14]:22.334282)[&index=16]:3.898820,((f67[&index=13]:0.739858,f51[&index=12]:0.739858)[&index=17]:4.237017,f15[&index=11]:4.976875)[&index=18]:21.256227)[&index=19]:1.349051,(f84[&index=10]:20.923940,f107[&index=9]:19.458940)[&index=20]:6.503213)[&index=21]:2.383646,(f17[&index=8]:28.070609,(((f80[&index=7]:8.433098,(f98[&index=6]:1.792628,f13[&index=5]:2.854628)[&index=22]:5.578470)[&index=23]:12.440015,(f106[&index=4]:15.172728,f49[&index=3]:16.561728)[&index=24]:4.311384)[&index=25]:2.306568,(f95[&index=2]:8.088333,f54[&index=1]:8.917333)[&index=26]:14.262347)[&index=27]:4.890928)[&index=28]:1.895190)[&index=29]:0.000000; 0.1693261 51.16803 0.07038391 0.3224907 0.005 0.005098088
10 0.002266 0.01 ((((f114[&index=15]:20.223282,f44[&index=14]:22.334282)[&index=16]:3.898820,((f67[&index=13]:0.739858,f51[&index=12]:0.739858)[&index=17]:4.237017,f15[&index=11]:4.976875)[&index=18]:21.256227)[&index=19]:1.349051,(f84[&index=10]:20.923940,f107[&index=9]:19.458940)[&index=20]:6.503213)[&index=21]:2.383646,(f17[&index=8]:28.070609,(((f80[&index=7]:8.433098,(f98[&index=6]:1.792628,f13[&index=5]:2.854628)[&index=22]:5.578470)[&index=23]:12.440015,(f106[&index=4]:15.172728,f49[&index=3]:16.561728)[&index=24]:4.311384)[&index=25]:2.306568,(f95[&index=2]:8.088333,f54[&index=1]:8.917333)[&index=26]:14.262347)[&index=27]:4.890928)[&index=28]:1.895190)[&index=29]:0.000000; 0.1693261 51.1702 0.07038391 0.3224907 0.005 0.005098088
12 changes: 12 additions & 0 deletions test_OBDP/output_expected/mcmc_OBDP_epi_test_skyline.trees
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Iteration Posterior Likelihood Prior obd_tree
0 -170008.5 -169752.2 -256.3392 ((((f114[&index=15]:20.223282,f44[&index=14]:22.334282)[&index=16]:3.898820,((f67[&index=13]:0.739858,f51[&index=12]:0.739858)[&index=17]:4.237017,f15[&index=11]:4.976875)[&index=18]:21.256227)[&index=19]:1.349051,(f84[&index=10]:20.923940,f107[&index=9]:19.458940)[&index=20]:6.503213)[&index=21]:2.383646,(f17[&index=8]:28.070609,(((f80[&index=7]:8.433098,(f98[&index=6]:1.792628,f13[&index=5]:2.854628)[&index=22]:5.578470)[&index=23]:12.440015,(f106[&index=4]:15.172728,f49[&index=3]:16.561728)[&index=24]:4.311384)[&index=25]:2.306568,(f95[&index=2]:8.088333,f54[&index=1]:8.917333)[&index=26]:14.262347)[&index=27]:4.890928)[&index=28]:1.895190)[&index=29]:0.000000;
1 -170008.5 -169752.2 -256.3392 ((((f114[&index=15]:20.223282,f44[&index=14]:22.334282)[&index=16]:3.898820,((f67[&index=13]:0.739858,f51[&index=12]:0.739858)[&index=17]:4.237017,f15[&index=11]:4.976875)[&index=18]:21.256227)[&index=19]:1.349051,(f84[&index=10]:20.923940,f107[&index=9]:19.458940)[&index=20]:6.503213)[&index=21]:2.383646,(f17[&index=8]:28.070609,(((f80[&index=7]:8.433098,(f98[&index=6]:1.792628,f13[&index=5]:2.854628)[&index=22]:5.578470)[&index=23]:12.440015,(f106[&index=4]:15.172728,f49[&index=3]:16.561728)[&index=24]:4.311384)[&index=25]:2.306568,(f95[&index=2]:8.088333,f54[&index=1]:8.917333)[&index=26]:14.262347)[&index=27]:4.890928)[&index=28]:1.895190)[&index=29]:0.000000;
2 -170008.5 -169752.2 -256.3392 ((((f114[&index=15]:20.223282,f44[&index=14]:22.334282)[&index=16]:3.898820,((f67[&index=13]:0.739858,f51[&index=12]:0.739858)[&index=17]:4.237017,f15[&index=11]:4.976875)[&index=18]:21.256227)[&index=19]:1.349051,(f84[&index=10]:20.923940,f107[&index=9]:19.458940)[&index=20]:6.503213)[&index=21]:2.383646,(f17[&index=8]:28.070609,(((f80[&index=7]:8.433098,(f98[&index=6]:1.792628,f13[&index=5]:2.854628)[&index=22]:5.578470)[&index=23]:12.440015,(f106[&index=4]:15.172728,f49[&index=3]:16.561728)[&index=24]:4.311384)[&index=25]:2.306568,(f95[&index=2]:8.088333,f54[&index=1]:8.917333)[&index=26]:14.262347)[&index=27]:4.890928)[&index=28]:1.895190)[&index=29]:0.000000;
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