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polish: bremer from TBR instead of sub

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kuoi 2023-10-09 17:00:29 +08:00
parent 0332d175fd
commit 33dd36290d
1 changed files with 27 additions and 33 deletions
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60
guoyi.run
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@ -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;