diff --git a/guoyi.run b/guoyi.run index b81d8c2..d5a5782 100644 --- a/guoyi.run +++ b/guoyi.run @@ -319,9 +319,9 @@ end export= %7.trees.tre; taxname-; export= %7.trees_no.tre; +tsave *= %7.trees.tnt.tre; taxname=; tsave = %7.trees.ctf; -tsave *= %7.trees.tnt.tre; /*Get npars number*/ var: npars; @@ -341,35 +341,32 @@ ttags]; /*in one line*/ if (argnumber<=5) - /*bremer search*/ - sub 1; hold +1000; bbreak=fill; - sub 3; hold +3000; bbreak=fill; - sub 5; hold +5000; bbreak=fill; - sub 7; hold +7000; bbreak=fill; - - /*adjust to zero following Goloboff*/ - sub 0; - - /*get the consensus tree number*/ - var: nsubpars; - set nsubpars ntrees; + /*set value of suboptimal from most parsimony tree */ + sub: 0; /*save strict consensus tree for bremer*/ hold+1; - bs * 0.'nsubpars'; + nelsen * 0.'npars'; + + /*get the consensus tree number*/ + var: contree; + set contree ntrees; /*calculate relative bremer support*/ - bs [ 0.'nsubpars' ; + bs ]!! 'contree' ; /*set the br value float*/ - macfloat 2; + macfloat 1; /*calculate bremer support*/ - bsupport 0.'nsubpars'; + bsupport !! 'contree'; /*choose final tree*/ tchoose/; + /*adjust to zero following Pablo Goloboff*/ + sub 0; + /*jakknifing*/ resample jak replications 1000 from 0; /*from 0 will orphan other trees*/ /*bootstrap*/ @@ -380,40 +377,37 @@ else if(( %6 == 0.1 )||( %6 == 0.2 )||( %6 == 0.3 )||( %6==1.1 )||( %6 ==1.2 )||( %6 ==1.3 )||( %6 == 2.1 )||( %6 == 2.2 )||( %6 == 2.3 )||( %6 == 3.1 )||( %6 == 3.2 )||( %6 == 3.3 )||( %6 == 4.1 )||( %6 == 4.2 )||( %6 == 4.3 )||( %6 == 5.1 )||( %6 == 5.2 )||( %6 == 5.3 )||( %6 == 6.1 )||( %6 == 6.2 )||( %6 == 6.3 )||( %6 == 7.1 )||( %6 == 7.2 )||( %6 == 7.3 )) /*bremer support related can only use strict consensus*/ - /*bremer search*/ - sub 1; hold +1000; bbreak=fill; - sub 3; hold +3000; bbreak=fill; - sub 5; hold +5000; bbreak=fill; - sub 7; hold +7000; bbreak=fill; - - /*adjust to zero following Goloboff*/ - sub 0; - - /*get the consensus tree number*/ - var: nsubpars; - set nsubpars ntrees; + /*set value of suboptimal from most parsimony tree*/ + sub: 0; /*save strict consensus tree for bremer*/ hold+1; - bs * 0.'nsubpars'; + nelsen * 0.'npars'; + + /*get the consensus tree number*/ + var: contree; + set contree ntrees; if(( %6 == 0.1 )||( %6 == 0.3 )||( %6==1.1 )||( %6 ==1.3 )||( %6 == 2.1 )||( %6 == 2.3 )||( %6 == 3.1 )||( %6 == 3.3 )||( %6 == 4.1 )||( %6 == 4.3 )||( %6 == 5.1 )||( %6 == 5.3 )||( %6 == 6.1 )||( %6 == 6.3 )||( %6 == 7.1 )||( %6 == 7.3 )) /*calculate relative bremer support*/ - bs [ 0.'nsubpars'; + bs ]!! 'contree'; end if(( %6 == 0.2 )||( %6 == 0.3 )||( %6==1.2 )||( %6 ==1.3 )||( %6 == 2.2 )||( %6 == 2.3 )||( %6 == 3.2 )||( %6 == 3.3 )||( %6 == 4.2 )||( %6 == 4.3 )||( %6 == 5.2 )||( %6 == 5.3 )||( %6 == 6.2 )||( %6 == 6.3 )||( %6 == 7.2 )||( %6 == 7.3 )) /*set the br value float*/ - macfloat 2; + macfloat 1; /*calculate bremer support*/ - bsupport 0.'nsubpars'; + bsupport !! 'contree'; end /*choose final tree*/ tchoose/; + /*adjust to zero following Pablo Goloboff*/ + sub 0; + /*jackknifing*/ if((%6 == 1.1) || (%6 == 1.2) || (%6 == 1.3) || (%6 == 3.1) || (%6 == 3.2) || (%6 == 3.3) || (%6 == 5.1) || (%6 == 5.2) || (%6 == 5.3) || (%6 == 7.1) || (%6 == 7.2) || (%6 == 7.3)) resample jak replications 1000 from 0;