After Installation, the program can be run simply by typing shiba
in a terminal window, while in the same directory it was compiled in. If you have not set your PATH
environmental variable to include β.
β, you will need to type ./shiba
. The options are:
-d NUM Use this value as the prob. of dispersal (probDispA) -f FILE Use this file as input. Default file: shibaInput.xml -h Print this help list -l Print input data summary -p INT Use this phylogeny (0...n). Default: 0 -s NUM Use this value as the prob. of survival (probSurvA) -v Print highly verbose event descriptions
## Successes : 102 (in 34000 runs) ## Number of runs in which the base of each lineage was in each space: (*= extant distrib) Space | 0 1 2 ------------+----------------- Lineage 0 | 51 46 5 --> l1 l2 Lineage 1 | 66* 31 5 --> Sp1 Lineage 2 | 36 60 6 --> l3 l4 Lineage 3 | 22 71* 9* --> Sp2 Lineage 4 | 28 66* 8* --> Sp3
βThe base of Lineage 0
(the basal lineage, in the first time period) occurred in 51 of the 102 successful runs in Area 0
, and in only 5 of the runs in Area 2
, hence indicating that it was more likely that the whole clade originated in the first and second areas than in the third. Lineage 0
splits to form lineages 1 and 2
. Lineage 1
is that which ends in extant taxon Sp1
and started predominantly in the first area. The *
indicates the extant distribution of Sp1
, which shows that runs in which the base of lineage 1
began in the second and third areas must have included the extinction of that taxon in those areas before the present.β