Usage

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 ‘.’, 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

Output format

  ## 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

In words

“The 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.”