Bug fixes, code comments, and minor changes

3 files changed, 960 insertions, 919 deletions

diff --git a/sourcecodes/data/example_time_series/TEbmap.txt b/sourcecodes/data/example_time_series/TEbmap.txt
index a9e0ef24..20f9b470 100644
--- a/sourcecodes/data/example_time_series/TEbmap.txt
+++ b/sourcecodes/data/example_time_series/TEbmap.txt
@@ -1,10 +1,10 @@
-Genotype	1	0.499053	1.462000
-TraitA_T1	1	1.306059	0.037189
-TraitA_T2	1	1.304164	-0.061147
-TraitA_T3	1	1.174305	-0.083449
-TraitB_T1	2	0.929161	-0.056347
-TraitB_T2	1	1.021691	-0.045299
-TraitB_T3	1	0.940946	0.012204
-TraitC_T1	1	0.907725	-0.001607
-TraitC_T2	1	0.923711	0.091657
-TraitC_T3	1	1.015189	0.017718
+Genotype	0.499053	1.462000
+TraitA_T1	1.306059	0.037189
+TraitA_T2	1.304164	-0.061147
+TraitA_T3	1.174305	-0.083449
+TraitB_T1	0.929161	-0.056347
+TraitB_T2	1.021691	-0.045299
+TraitB_T3	0.940946	0.012204
+TraitC_T1	0.907725	-0.001607
+TraitC_T2	0.923711	0.091657
+TraitC_T3	1.015189	0.017718
diff --git a/sourcecodes/data/example_time_series/TEbnet_figure.txt b/sourcecodes/data/example_time_series/TEbnet_figure.txt
index 7b46ba95..1cceadd2 100644
--- a/sourcecodes/data/example_time_series/TEbnet_figure.txt
+++ b/sourcecodes/data/example_time_series/TEbnet_figure.txt
@@ -14,422 +14,422 @@ TraitC_T2	1
 250	150
 0
 0
--4.0699	0.0001
--3.9911	0.0002
--3.9123	0.0002
--3.8335	0.0003
--3.7548	0.0004
--3.6760	0.0005
--3.5972	0.0007
--3.5185	0.0009
--3.4397	0.0012
--3.3609	0.0015
--3.2821	0.0020
--3.2034	0.0025
--3.1246	0.0032
--3.0458	0.0041
--2.9670	0.0052
--2.8883	0.0065
--2.8095	0.0081
--2.7307	0.0101
--2.6520	0.0124
--2.5732	0.0152
--2.4944	0.0185
--2.4156	0.0224
--2.3369	0.0269
--2.2581	0.0322
--2.1793	0.0382
--2.1006	0.0451
--2.0218	0.0529
--1.9430	0.0617
--1.8642	0.0716
--1.7855	0.0824
--1.7067	0.0944
--1.6279	0.1074
--1.5492	0.1215
--1.4704	0.1366
--1.3916	0.1526
--1.3128	0.1695
--1.2341	0.1871
--1.1553	0.2052
--1.0765	0.2238
--0.9978	0.2425
--0.9190	0.2612
--0.8402	0.2796
--0.7614	0.2975
--0.6827	0.3147
--0.6039	0.3308
--0.5251	0.3456
--0.4464	0.3588
--0.3676	0.3703
--0.2888	0.3799
--0.2100	0.3873
--0.1313	0.3924
--0.0525	0.3952
-0.0263	0.3956
-0.1050	0.3936
-0.1838	0.3892
-0.2626	0.3826
-0.3414	0.3737
-0.4201	0.3629
-0.4989	0.3502
-0.5777	0.3358
-0.6564	0.3202
-0.7352	0.3033
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-1.0503	0.2300
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 TraitC_T1	1
 250	150
 0
 0
--3.8413	0.0003
--3.7581	0.0004
--3.6749	0.0005
--3.5917	0.0007
--3.5086	0.0009
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--3.0927	0.0036
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 TraitB_T3	1
 250	150
 0
 0
--3.8488	0.0003
--3.7734	0.0004
--3.6979	0.0005
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 TraitB_T1	1
 250	150
 0
 0
--3.7153	0.0004
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--1.8895	0.0683
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--1.7307	0.0906
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+-4.0697	0.0030
+-3.9700	0.0039
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+-3.5709	0.0093
+-3.4712	0.0114
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+-0.4784	0.3666
+-0.3786	0.3765
+-0.2788	0.3845
+-0.1791	0.3905
+-0.0793	0.3942
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+0.6190	0.3590
+0.7188	0.3461
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+0.9183	0.3164
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+2.8137	0.0428
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+3.6118	0.0099
+3.7116	0.0081
+3.8113	0.0065
+3.9111	0.0052
+4.0108	0.0042
+4.1106	0.0033
+4.2104	0.0026
 TraitB_T2	1
 250	150
 2	5	8
 1	10
--3.6634	0.0006
--3.5878	0.0008
--3.5122	0.0010
--3.4365	0.0013
--3.3609	0.0017
--3.2853	0.0021
--3.2097	0.0027
--3.1340	0.0034
--3.0584	0.0043
--2.9828	0.0053
--2.9072	0.0066
--2.8315	0.0081
--2.7559	0.0100
--2.6803	0.0122
--2.6046	0.0148
--2.5290	0.0178
--2.4534	0.0214
--2.3778	0.0255
--2.3021	0.0302
--2.2265	0.0357
--2.1509	0.0419
--2.0753	0.0489
--1.9996	0.0568
--1.9240	0.0655
--1.8484	0.0752
--1.7727	0.0858
--1.6971	0.0975
--1.6215	0.1100
--1.5459	0.1235
--1.4702	0.1379
--1.3946	0.1532
--1.3190	0.1692
--1.2434	0.1858
--1.1677	0.2029
--1.0921	0.2204
--1.0165	0.2381
--0.9408	0.2557
--0.8652	0.2732
--0.7896	0.2902
--0.7140	0.3066
--0.6383	0.3222
--0.5627	0.3366
--0.4871	0.3498
--0.4115	0.3615
--0.3358	0.3715
--0.2602	0.3797
--0.1846	0.3859
--0.1089	0.3901
--0.0333	0.3921
-0.0423	0.3920
-0.1179	0.3897
-0.1936	0.3853
-0.2692	0.3788
-0.3448	0.3704
-0.4205	0.3602
-0.4961	0.3483
-0.5717	0.3350
-0.6473	0.3204
-0.7230	0.3047
-0.7986	0.2882
-0.8742	0.2711
-0.9498	0.2536
-1.0255	0.2359
-1.1011	0.2183
-1.1767	0.2008
-1.2524	0.1838
-1.3280	0.1672
-1.4036	0.1513
-1.4792	0.1362
-1.5549	0.1219
-1.6305	0.1085
-1.7061	0.0960
-1.7817	0.0845
-1.8574	0.0740
-1.9330	0.0644
-2.0086	0.0558
-2.0843	0.0480
-2.1599	0.0411
-2.2355	0.0350
-2.3111	0.0296
-2.3868	0.0250
-2.4624	0.0209
-2.5380	0.0174
-2.6136	0.0144
-2.6893	0.0119
-2.7649	0.0097
-2.8405	0.0079
-2.9162	0.0064
-2.9918	0.0052
-3.0674	0.0041
-3.1430	0.0033
-3.2187	0.0026
-3.2943	0.0021
-3.3699	0.0016
-3.4455	0.0013
-3.5212	0.0010
-3.5968	0.0008
-3.6724	0.0006
-3.7481	0.0004
-3.8237	0.0003
-3.8993	0.0003
+-3.7882	0.0006
+-3.7109	0.0008
+-3.6337	0.0010
+-3.5564	0.0013
+-3.4791	0.0017
+-3.4019	0.0021
+-3.3246	0.0027
+-3.2473	0.0034
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+-3.0928	0.0053
+-3.0155	0.0066
+-2.9382	0.0081
+-2.8610	0.0100
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+-2.4746	0.0255
+-2.3974	0.0302
+-2.3201	0.0357
+-2.2428	0.0419
+-2.1656	0.0489
+-2.0883	0.0568
+-2.0110	0.0655
+-1.9338	0.0752
+-1.8565	0.0858
+-1.7792	0.0975
+-1.7020	0.1100
+-1.6247	0.1235
+-1.5474	0.1379
+-1.4702	0.1532
+-1.3929	0.1692
+-1.3156	0.1858
+-1.2384	0.2029
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+-1.0838	0.2381
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+-0.8520	0.2902
+-0.7747	0.3066
+-0.6975	0.3222
+-0.6202	0.3366
+-0.5429	0.3498
+-0.4657	0.3615
+-0.3884	0.3715
+-0.3111	0.3797
+-0.2339	0.3859
+-0.1566	0.3901
+-0.0793	0.3921
+-0.0021	0.3920
+0.0752	0.3897
+0.1525	0.3853
+0.2297	0.3788
+0.3070	0.3704
+0.3843	0.3602
+0.4615	0.3483
+0.5388	0.3350
+0.6161	0.3204
+0.6933	0.3047
+0.7706	0.2882
+0.8479	0.2711
+0.9251	0.2536
+1.0024	0.2359
+1.0797	0.2183
+1.1569	0.2008
+1.2342	0.1838
+1.3115	0.1672
+1.3888	0.1513
+1.4660	0.1362
+1.5433	0.1219
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+1.6978	0.0960
+1.7751	0.0845
+1.8524	0.0740
+1.9296	0.0644
+2.0069	0.0558
+2.0842	0.0480
+2.1614	0.0411
+2.2387	0.0350
+2.3160	0.0296
+2.3932	0.0250
+2.4705	0.0209
+2.5478	0.0174
+2.6250	0.0144
+2.7023	0.0119
+2.7796	0.0097
+2.8568	0.0079
+2.9341	0.0064
+3.0114	0.0052
+3.0886	0.0041
+3.1659	0.0033
+3.2432	0.0026
+3.3204	0.0021
+3.3977	0.0016
+3.4750	0.0013
+3.5523	0.0010
+3.6295	0.0008
+3.7068	0.0006
+3.7841	0.0004
+3.8613	0.0003
+3.9386	0.0003
 TraitC_T3	1
 250	150
 2	8	9
 0
--4.6954	0.0000
--4.6103	0.0000
--4.5253	0.0000
--4.4402	0.0000
--4.3551	0.0000
--4.2701	0.0001
--4.1850	0.0001
--4.1000	0.0001
--4.0149	0.0002
--3.9298	0.0002
--3.8448	0.0003
--3.7597	0.0005
--3.6746	0.0006
--3.5896	0.0008
--3.5045	0.0011
--3.4195	0.0015
--3.3344	0.0019
--3.2493	0.0025
--3.1643	0.0033
--3.0792	0.0042
--2.9942	0.0054
--2.9091	0.0069
--2.8240	0.0087
--2.7390	0.0109
--2.6539	0.0135
--2.5688	0.0167
--2.4838	0.0205
--2.3987	0.0250
--2.3137	0.0303
--2.2286	0.0364
--2.1435	0.0435
--2.0585	0.0516
--1.9734	0.0608
--1.8884	0.0711
--1.8033	0.0826
--1.7182	0.0953
--1.6332	0.1091
--1.5481	0.1242
--1.4630	0.1403
--1.3780	0.1575
--1.2929	0.1755
--1.2079	0.1943
--1.1228	0.2136
--1.0377	0.2331
--0.9527	0.2527
--0.8676	0.2721
--0.7825	0.2910
--0.6975	0.3090
--0.6124	0.3259
--0.5274	0.3413
--0.4423	0.3550
--0.3572	0.3667
--0.2722	0.3762
--0.1871	0.3833
--0.1021	0.3878
--0.0170	0.3897
-0.0681	0.3889
-0.1531	0.3854
-0.2382	0.3793
-0.3233	0.3708
-0.4083	0.3599
-0.4934	0.3470
-0.5784	0.3322
-0.6635	0.3159
-0.7486	0.2983
-0.8336	0.2797
-0.9187	0.2605
-1.0038	0.2410
-1.0888	0.2214
-1.1739	0.2019
-1.2589	0.1829
-1.3440	0.1646
-1.4291	0.1471
-1.5141	0.1305
-1.5992	0.1150
-1.6842	0.1007
-1.7693	0.0875
-1.8544	0.0755
-1.9394	0.0648
-2.0245	0.0551
-2.1096	0.0466
-2.1946	0.0391
-2.2797	0.0326
-2.3647	0.0270
-2.4498	0.0222
-2.5349	0.0182
-2.6199	0.0147
-2.7050	0.0119
-2.7900	0.0095
-2.8751	0.0075
-2.9602	0.0060
-3.0452	0.0047
-3.1303	0.0036
-3.2154	0.0028
-3.3004	0.0022
-3.3855	0.0016
-3.4705	0.0012
-3.5556	0.0009
-3.6407	0.0007
-3.7257	0.0005
-3.8108	0.0004
+-4.7490	0.0000
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+-1.1221	0.2136
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+-0.9494	0.2527
+-0.8631	0.2721
+-0.7767	0.2910
+-0.6904	0.3090
+-0.6040	0.3259
+-0.5177	0.3413
+-0.4313	0.3550
+-0.3449	0.3667
+-0.2586	0.3762
+-0.1722	0.3833
+-0.0859	0.3878
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+2.3320	0.0326
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+3.1092	0.0047
+3.1956	0.0036
+3.2819	0.0028
+3.3683	0.0022
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diff --git a/sourcecodes/data/example_time_series/TEbparameters.txt b/sourcecodes/data/example_time_series/TEbparameters.txt
new file mode 100644
index 00000000..14ddb1ac
--- /dev/null
+++ b/sourcecodes/data/example_time_series/TEbparameters.txt
@@ -0,0 +1,41 @@
+Genotype
+Discrete node with 2 states
+1	0.5380
+2	0.4620
+
+TraitA_T1
+Continuous node
+0.0372	1.3165
+
+TraitA_T2
+Continuous node
+-0.0611	1.3146
+
+TraitA_T3
+Continuous node
+-0.0834	1.1837
+
+TraitB_T1
+Continuous node
+-0.0563	0.9366
+
+TraitB_T2
+Continuous node
+-0.0453	1.0389
+
+TraitB_T3
+Continuous node
+0.0122	0.9485
+
+TraitC_T1
+Continuous node
+-0.0016	0.9150
+
+TraitC_T2
+Continuous node
+0.0917	0.9311
+
+TraitC_T3
+Continuous node
+0.0177	1.0392
+