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Pedigrees Available from create_GSP()

Rachel Giglio

2024-02-27

The function create_GSP() allows the user to quickly create several different pedigree structures that are “saturated” in the sense of using all the genomic material of the founders. There are 15 different pedigrees, and they can be specified by the user according to whether the user wants to have any of the following four hybrid categories to be present amongst the simulated descendants:

The following images show the pedigrees created by create_GSP() with different inputs (TRUE or FALSE) for the four parameters, F1, F2, F1B, F1B2, to the function.

See the documentation ?create_GSP for more information.

F1 = TRUE,      F2 = FALSE,      F1B = FALSE,      F1B2 = FALSE,     

xxx   1a p1 1 1 1a->1 2a p2 2 2 2a->2 1b p1 1b->1 2b p2 2b->2 3 3 1->3 2 2->3 2 s3 s3 3->s3 2

F1 = FALSE,      F2 = TRUE,      F1B = FALSE,      F1B2 = FALSE,     

xxx   1a p1 1 1 1a->1 2a p1 2 2 2a->2 3a p2 3 3 3a->3 4a p2 4 4 4a->4 1b p1 1b->1 2b p1 2b->2 3b p2 3b->3 4b p2 4b->4 5 5 1->5 2 6 6 2->6 2 3->5 2 4->6 2 7 7 5->7 4 6->7 4 s7 s7 7->s7 4

F1 = TRUE,      F2 = TRUE,      F1B = FALSE,      F1B2 = FALSE,     

xxx   1a p1 1 1 1a->1 2a p2 2 2 2a->2 3a p1 3 3 3a->3 4a p2 4 4 4a->4 1b p1 1b->1 2b p2 2b->2 3b p1 3b->3 4b p2 4b->4 5 5 1->5 2 2->5 2 6 6 3->6 2 4->6 2 7 7 5->7 2 s5 s5 5->s5 1 6->7 2 s6 s6 6->s6 1 s7 s7 7->s7 2

F1 = FALSE,      F2 = FALSE,      F1B = TRUE,      F1B2 = FALSE,     

xxx   1a p1 1 1 1a->1 2a p2 2 2 2a->2 3a p1 3 3 3a->3 4a p1 4 4 4a->4 1b p1 1b->1 2b p2 2b->2 3b p1 3b->3 4b p1 4b->4 5 5 1->5 2 2->5 2 6 6 3->6 2 7 7 4->7 2 5->6 2 5->7 2 s6 s6 6->s6 2 s7 s7 7->s7 2

F1 = TRUE,      F2 = FALSE,      F1B = TRUE,      F1B2 = FALSE,     

xxx   1a p1 1 1 1a->1 2a p2 2 2 2a->2 3a p1 3 3 3a->3 1b p1 1b->1 2b p2 2b->2 3b p1 3b->3 4 4 1->4 2 2->4 2 5 5 3->5 2 4->5 2 s4 s4 4->s4 1 s5 s5 5->s5 2

F1 = FALSE,      F2 = TRUE,      F1B = TRUE,      F1B2 = FALSE,     

xxx   1a p1 1 1 1a->1 2a p1 2 2 2a->2 3a p1 3 3 3a->3 4a p1 4 4 4a->4 5a p2 5 5 5a->5 6a p2 6 6 6a->6 1b p1 1b->1 2b p1 2b->2 3b p1 3b->3 4b p1 4b->4 5b p2 5b->5 6b p2 6b->6 7 7 1->7 2 8 8 2->8 2 9 9 3->9 2 10 10 4->10 2 5->7 2 6->8 2 7->9 2 11 11 7->11 2 8->10 2 8->11 2 s9 s9 9->s9 2 s10 s10 10->s10 2 s11 s11 11->s11 2

F1 = TRUE,      F2 = TRUE,      F1B = TRUE,      F1B2 = FALSE,     

xxx   1a p1 1 1 1a->1 2a p1 2 2 2a->2 3a p1 3 3 3a->3 4a p2 4 4 4a->4 5a p2 5 5 5a->5 1b p1 1b->1 2b p1 2b->2 3b p1 3b->3 4b p2 4b->4 5b p2 5b->5 6 6 1->6 2 7 7 2->7 2 8 8 3->8 2 4->6 2 5->7 2 6->8 2 9 9 6->9 2 7->9 2 s7 s7 7->s7 1 s8 s8 8->s8 2 s9 s9 9->s9 2

F1 = FALSE,      F2 = FALSE,      F1B = FALSE,      F1B2 = TRUE,     

xxx   1a p1 1 1 1a->1 2a p2 2 2 2a->2 3a p1 3 3 3a->3 4a p1 4 4 4a->4 5a p1 5 5 5a->5 6a p1 6 6 6a->6 7a p1 7 7 7a->7 8a p1 8 8 8a->8 1b p1 1b->1 2b p2 2b->2 3b p1 3b->3 4b p1 4b->4 5b p1 5b->5 6b p1 6b->6 7b p1 7b->7 8b p1 8b->8 9 9 1->9 2 2->9 2 10 10 3->10 2 11 11 4->11 2 12 12 5->12 2 13 13 6->13 2 14 14 7->14 2 15 15 8->15 2 9->10 2 9->11 2 10->12 2 10->13 2 11->14 2 11->15 2 s12 s12 12->s12 2 s13 s13 13->s13 2 s14 s14 14->s14 2 s15 s15 15->s15 2

F1 = TRUE,      F2 = FALSE,      F1B = FALSE,      F1B2 = TRUE,     

xxx   1a p1 1 1 1a->1 2a p2 2 2 2a->2 3a p1 3 3 3a->3 4a p1 4 4 4a->4 5a p1 5 5 5a->5 1b p1 1b->1 2b p2 2b->2 3b p1 3b->3 4b p1 4b->4 5b p1 5b->5 6 6 1->6 2 2->6 2 7 7 3->7 2 8 8 4->8 2 9 9 5->9 2 6->7 2 s6 s6 6->s6 1 7->8 2 7->9 2 s8 s8 8->s8 2 s9 s9 9->s9 2

F1 = FALSE,      F2 = TRUE,      F1B = FALSE,      F1B2 = TRUE,     

xxx   1a p1 1 1 1a->1 2a p1 2 2 2a->2 3a p1 3 3 3a->3 4a p1 4 4 4a->4 5a p1 5 5 5a->5 6a p1 6 6 6a->6 7a p1 7 7 7a->7 8a p1 8 8 8a->8 9a p2 9 9 9a->9 10a p2 10 10 10a->10 1b p1 1b->1 2b p1 2b->2 3b p1 3b->3 4b p1 4b->4 5b p1 5b->5 6b p1 6b->6 7b p1 7b->7 8b p1 8b->8 9b p2 9b->9 10b p2 10b->10 11 11 1->11 2 12 12 2->12 2 14 14 3->14 2 15 15 4->15 2 16 16 5->16 2 17 17 6->17 2 18 18 7->18 2 19 19 8->19 2 9->11 2 10->12 2 13 13 11->13 2 11->14 2 12->13 2 12->15 2 s13 s13 13->s13 2 14->16 2 14->17 2 15->18 2 15->19 2 s16 s16 16->s16 2 s17 s17 17->s17 2 s18 s18 18->s18 2 s19 s19 19->s19 2

F1 = TRUE,      F2 = TRUE,      F1B = FALSE,      F1B2 = TRUE,     

xxx   1a p1 1 1 1a->1 2a p1 2 2 2a->2 3a p1 3 3 3a->3 4a p1 4 4 4a->4 5a p1 5 5 5a->5 6a p2 6 6 6a->6 7a p2 7 7 7a->7 1b p1 1b->1 2b p1 2b->2 3b p1 3b->3 4b p1 4b->4 5b p1 5b->5 6b p2 6b->6 7b p2 7b->7 8 8 1->8 2 9 9 2->9 2 10 10 3->10 2 11 11 4->11 2 12 12 5->12 2 6->8 2 7->9 2 8->10 2 13 13 8->13 2 9->13 2 s9 s9 9->s9 1 10->11 2 10->12 2 s11 s11 11->s11 2 s12 s12 12->s12 2 s13 s13 13->s13 2

F1 = FALSE,      F2 = FALSE,      F1B = TRUE,      F1B2 = TRUE,     

xxx   1a p1 1 1 1a->1 2a p1 2 2 2a->2 3a p1 3 3 3a->3 4a p1 4 4 4a->4 5a p1 5 5 5a->5 6a p2 6 6 6a->6 1b p1 1b->1 2b p1 2b->2 3b p1 3b->3 4b p1 4b->4 5b p1 5b->5 6b p2 6b->6 7 7 1->7 2 8 8 2->8 2 10 10 3->10 2 9 9 4->9 2 11 11 5->11 2 6->7 2 7->8 2 7->9 2 8->10 2 s8 s8 8->s8 1 9->11 2 s9 s9 9->s9 1 s10 s10 10->s10 2 s11 s11 11->s11 2

F1 = TRUE,      F2 = FALSE,      F1B = TRUE,      F1B2 = TRUE,     

xxx   1a p1 1 1 1a->1 2a p1 2 2 2a->2 3a p1 3 3 3a->3 4a p2 4 4 4a->4 1b p1 1b->1 2b p1 2b->2 3b p1 3b->3 4b p2 4b->4 5 5 1->5 2 6 6 2->6 2 7 7 3->7 2 4->5 2 5->6 2 s5 s5 5->s5 1 6->7 2 s6 s6 6->s6 1 s7 s7 7->s7 2

F1 = FALSE,      F2 = TRUE,      F1B = TRUE,      F1B2 = TRUE,     

xxx   1a p1 1 1 1a->1 2a p1 2 2 2a->2 3a p1 3 3 3a->3 4a p1 4 4 4a->4 5a p1 5 5 5a->5 6a p1 6 6 6a->6 7a p2 7 7 7a->7 8a p2 8 8 8a->8 1b p1 1b->1 2b p1 2b->2 3b p1 3b->3 4b p1 4b->4 5b p1 5b->5 6b p1 6b->6 7b p2 7b->7 8b p2 8b->8 9 9 1->9 2 10 10 2->10 2 11 11 3->11 2 12 12 4->12 2 13 13 5->13 2 14 14 6->14 2 7->9 2 8->10 2 9->11 2 15 15 9->15 2 10->12 2 10->15 2 11->13 2 s11 s11 11->s11 1 12->14 2 s12 s12 12->s12 1 s13 s13 13->s13 2 s14 s14 14->s14 2 s15 s15 15->s15 2

F1 = TRUE,      F2 = TRUE,      F1B = TRUE,      F1B2 = TRUE,     

xxx   1a p1 1 1 1a->1 2a p1 2 2 2a->2 3a p1 3 3 3a->3 4a p1 4 4 4a->4 5a p2 5 5 5a->5 6a p2 6 6 6a->6 1b p1 1b->1 2b p1 2b->2 3b p1 3b->3 4b p1 4b->4 5b p2 5b->5 6b p2 6b->6 7 7 1->7 2 8 8 2->8 2 9 9 3->9 2 10 10 4->10 2 5->7 2 6->8 2 11 11 7->11 2 s7 s7 7->s7 1 8->9 2 8->11 2 9->10 2 s9 s9 9->s9 1 s10 s10 10->s10 2 s11 s11 11->s11 2

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