Bug fixes, code comments, and minor changes

3 files changed, 430 insertions, 409 deletions

diff --git a/sourcecodes/data/example_sci/Llumap.txt b/sourcecodes/data/example_sci/Llumap.txt
index 958281d5..dfe8ca75 100644
--- a/sourcecodes/data/example_sci/Llumap.txt
+++ b/sourcecodes/data/example_sci/Llumap.txt
@@ -1,5 +1,5 @@
-Genotype	2	0.500305	1.514000
-Gene3	1	1.027261	-0.015284
-Gene2	1	1.160583	0.138097
-Phenotype	1	1.554104	0.069005
-Gene1	1	1.515414	0.174451
+Genotype	0.500305	1.514000
+Gene3	1.027261	-0.015284
+Gene2	1.160583	0.138097
+Phenotype	1.554104	0.069005
+Gene1	1.515414	0.174451
diff --git a/sourcecodes/data/example_sci/Llunet_figure.txt b/sourcecodes/data/example_sci/Llunet_figure.txt
index bdc07cbd..2f383b1a 100644
--- a/sourcecodes/data/example_sci/Llunet_figure.txt
+++ b/sourcecodes/data/example_sci/Llunet_figure.txt
@@ -15,419 +15,419 @@ Gene1	1
 250	150
 1	1
 1	3
--3.5013	0.0009
--3.4313	0.0012
--3.3613	0.0015
--3.2912	0.0019
--3.2212	0.0024
--3.1512	0.0030
--3.0811	0.0037
--3.0111	0.0046
--2.9411	0.0056
--2.8710	0.0069
--2.8010	0.0083
--2.7310	0.0101
--2.6609	0.0121
--2.5909	0.0145
--2.5209	0.0174
--2.4508	0.0206
--2.3808	0.0243
--2.3108	0.0286
--2.2407	0.0335
--2.1707	0.0389
--2.1007	0.0451
--2.0306	0.0520
--1.9606	0.0597
--1.8906	0.0682
--1.8205	0.0775
--1.7505	0.0876
--1.6805	0.0986
--1.6104	0.1105
--1.5404	0.1231
--1.4704	0.1366
--1.4003	0.1508
--1.3303	0.1657
--1.2603	0.1811
--1.1902	0.1971
--1.1202	0.2134
--1.0502	0.2300
--0.9801	0.2467
--0.9101	0.2633
--0.8401	0.2797
--0.7700	0.2956
--0.7000	0.3110
--0.6300	0.3256
--0.5599	0.3392
--0.4899	0.3517
--0.4199	0.3629
--0.3498	0.3726
--0.2798	0.3808
--0.2098	0.3873
--0.1397	0.3920
--0.0697	0.3948
-0.0003	0.3958
-0.0704	0.3948
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-0.2104	0.3872
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 Gene2	1
 250	150
 1	2
 2	4	5
--3.5862	0.0008
--3.5124	0.0010
--3.4385	0.0013
--3.3647	0.0016
--3.2909	0.0020
--3.2171	0.0026
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--2.1097	0.0453
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--1.9620	0.0607
--1.8882	0.0696
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--1.7405	0.0903
--1.6667	0.1021
--1.5929	0.1147
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 Gene3	1
 250	150
 2	1	3
 1	5
--4.3571	0.0001
--4.2762	0.0001
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--4.1145	0.0001
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 Phenotype	1
 250	150
 2	3	4
 0
--3.5574	0.0010
--3.4806	0.0013
--3.4037	0.0016
--3.3268	0.0021
--3.2499	0.0026
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--0.0213	0.3877
-0.0555	0.3872
-0.1324	0.3846
-0.2093	0.3798
-0.2861	0.3731
-0.3630	0.3644
-0.4399	0.3539
-0.5168	0.3418
-0.5936	0.3283
-0.6705	0.3136
-0.7474	0.2979
-0.8242	0.2813
-0.9011	0.2643
-0.9780	0.2468
-1.0549	0.2293
-1.1317	0.2118
-1.2086	0.1945
-1.2855	0.1777
-1.3623	0.1614
-1.4392	0.1458
-1.5161	0.1310
-1.5930	0.1170
-1.6698	0.1039
-1.7467	0.0918
-1.8236	0.0806
-1.9004	0.0704
-1.9773	0.0612
-2.0542	0.0529
-2.1311	0.0454
-2.2079	0.0388
-2.2848	0.0329
-2.3617	0.0278
-2.4385	0.0234
-2.5154	0.0195
-2.5923	0.0162
-2.6692	0.0134
-2.7460	0.0110
-2.8229	0.0090
-2.8998	0.0073
-2.9766	0.0059
-3.0535	0.0047
-3.1304	0.0038
-3.2073	0.0030
-3.2841	0.0024
-3.3610	0.0019
-3.4379	0.0015
-3.5147	0.0011
-3.5916	0.0009
-3.6685	0.0007
-3.7454	0.0005
-3.8222	0.0004
-3.8991	0.0003
-3.9760	0.0002
-4.0528	0.0002
-4.1297	0.0001
+-5.4596	0.0010
+-5.3401	0.0013
+-5.2207	0.0016
+-5.1012	0.0021
+-4.9817	0.0026
+-4.8623	0.0033
+-4.7428	0.0042
+-4.6233	0.0052
+-4.5039	0.0065
+-4.3844	0.0080
+-4.2649	0.0098
+-4.1455	0.0120
+-4.0260	0.0146
+-3.9065	0.0176
+-3.7871	0.0212
+-3.6676	0.0253
+-3.5481	0.0300
+-3.4287	0.0354
+-3.3092	0.0416
+-3.1897	0.0486
+-3.0703	0.0564
+-2.9508	0.0651
+-2.8314	0.0748
+-2.7119	0.0854
+-2.5924	0.0970
+-2.4730	0.1096
+-2.3535	0.1230
+-2.2340	0.1374
+-2.1146	0.1526
+-1.9951	0.1685
+-1.8756	0.1850
+-1.7562	0.2021
+-1.6367	0.2195
+-1.5172	0.2370
+-1.3978	0.2545
+-1.2783	0.2718
+-1.1588	0.2887
+-1.0394	0.3049
+-0.9199	0.3202
+-0.8004	0.3344
+-0.6810	0.3473
+-0.5615	0.3587
+-0.4420	0.3684
+-0.3226	0.3763
+-0.2031	0.3822
+-0.0836	0.3860
+0.0358	0.3877
+0.1553	0.3872
+0.2748	0.3846
+0.3942	0.3798
+0.5137	0.3731
+0.6332	0.3644
+0.7526	0.3539
+0.8721	0.3418
+0.9916	0.3283
+1.1110	0.3136
+1.2305	0.2979
+1.3500	0.2813
+1.4694	0.2643
+1.5889	0.2468
+1.7084	0.2293
+1.8278	0.2118
+1.9473	0.1945
+2.0668	0.1777
+2.1862	0.1614
+2.3057	0.1458
+2.4252	0.1310
+2.5446	0.1170
+2.6641	0.1039
+2.7836	0.0918
+2.9030	0.0806
+3.0225	0.0704
+3.1420	0.0612
+3.2614	0.0529
+3.3809	0.0454
+3.5004	0.0388
+3.6198	0.0329
+3.7393	0.0278
+3.8588	0.0234
+3.9782	0.0195
+4.0977	0.0162
+4.2171	0.0134
+4.3366	0.0110
+4.4561	0.0090
+4.5755	0.0073
+4.6950	0.0059
+4.8145	0.0047
+4.9339	0.0038
+5.0534	0.0030
+5.1729	0.0024
+5.2923	0.0019
+5.4118	0.0015
+5.5313	0.0011
+5.6507	0.0009
+5.7702	0.0007
+5.8897	0.0005
+6.0091	0.0004
+6.1286	0.0003
+6.2481	0.0002
+6.3675	0.0002
+6.4870	0.0001
diff --git a/sourcecodes/data/example_sci/Lluparameters.txt b/sourcecodes/data/example_sci/Lluparameters.txt
new file mode 100644
index 00000000..11583baa
--- /dev/null
+++ b/sourcecodes/data/example_sci/Lluparameters.txt
@@ -0,0 +1,21 @@
+Genotype
+Discrete node with 2 states
+1	0.4860
+2	0.5140
+
+Gene3
+Continuous node
+-0.0150	1.0589
+
+Gene2
+Continuous node
+0.1381	1.1779
+
+Phenotype
+Continuous node
+0.0693	1.5989
+
+Gene1
+Continuous node
+0.1745	1.5275
+