fix: resample score doesn't map to the tre

This commit is contained in:
kuoi 2023-09-12 17:51:41 +08:00
parent d4c7afd20c
commit 5a7faee66e

View file

@ -1,19 +1,15 @@
log tnt.log;
macro=;
taxname+1000;
taxname=;
mxram 10240;
nstates 32;
nstates NOGAPS;
macro=; taxname+1000; taxname=; mxram 10240; nstates 32; nstates NOGAPS;
/*Arguments*/
if ( argnumber != 1 )
silent -console;
quote - /-----------------------------------------------\;
quote - | GUOYI TNT SCRIPT 2022-2023 MIT |;
quote - | You need to give your filename |;
quote - | tnt*> guoyi filename |;
quote - \-----------------------------------------------/;
quote - /--------------------------------------------------\;
quote - | GUOYI TNT SCRIPT 2022-2023 MIT |;
quote - | You need to give your filename |;
quote - | shell> tnt run guoyi.tnt filename, (Linux & Mac) |;
quote - | shell> tnt run guoyi.run filename; (Windows) |;
quote - \--------------------------------------------------/;
proc/;
end
@ -22,8 +18,8 @@ quote - /-----------------------------------------------\;
quote - | Implied weighting will be estimated. |;
quote - | TBR Mult and Xmult will be performed. |;
quote - | Strict consensus will be used. |;
quote - | Relative bremer support, jackknifing and |;
quote - | boot will be shown on the resample.svg. |;
quote - | Jackknifing, bootstrap and relative bremer |;
quote - | will be shown on the resample.svg. |;
quote - | Apomorphic characters mapping will be shown |;
quote - | on the apo.svg and saved to apo*.tre. |;
quote - | TL, CI and RI will be calculated finally. |;
@ -37,13 +33,15 @@ piwe=12;
procedure %1;
hold 10000;
/*Search trees*/
/*Implied weighting settings*/
xpiwe(*;
piwe&;
/*Search trees*/
mult=replic 1000 tbr hold 1000;
bbreak=tbr;
bbreak=tbr fill;
sect: slack 1000;
xmult=hit 1000 noupdate replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
piwe&;
/*Export trees*/
export= trees.tre;
@ -56,16 +54,36 @@ tsave *= trees.tnt.tre;
/*Consensus tree*/
nelsen *;
/*Tree vault store*/
hold /+0;
tvault >/;
/*Export consensus tree*/
tchoose/;
tchoose /;
export - original.tre;
taxname-;
export - original_no.tre;
tsave = original.ctf;
tsave *= original.tnt.tre;
/*Caulculate TL/CI/RI score*/
report-;
var-;
var =
0 themin
1 themax
2 CI
3 RI
4 TL
;
set themin minsteps;
set themax maxsteps;
set TL length[0];
set CI 'themin'/'TL'; /*CI=1 means no homoplasy*/
set RI ('themax'-'TL')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
report=;
/*Apomorphic characters*/
tchoose/;
export = winclada.tre;
taxname =;
ttags=;
@ -81,20 +99,19 @@ taxname-;
export - apo_no.tre;
ttags-;
/*Get Bremer/jak/boot support*/
/*Get jak/boot/relative-bremer support*/
tchoose/;
ttags=;
ttags]; /*in one line*/
resample jak replications 1000 from 0;
resample boot replications 1000 from 0;
sub 1; hold +1000; bbreak=fill;
sub 2; hold +2000; bbreak=fill;
sub 3; hold +3000; bbreak=fill;
sub 4; hold +4000; bbreak=fill;
sub 5; hold +5000; bbreak=fill;
sub 6; hold +6000; bbreak=fill;
sub 7; hold +7000; bbreak=fill;
sub 8; hold +8000; bbreak=fill;
bsupport[;
resample jak replications 1000;
resample boot replications 1000;
/*Export consensus tree with supports*/
ttags & resample.svg thickness 7 italics fontsize 15;
@ -108,30 +125,11 @@ taxname-;
export - resample_no.tre;
ttags-;
/*Caulculate TL/CI/RI score*/
length *;
report-;
var-;
var =
0 themin
1 themax
+ CIs [ ( ntrees + 1 ) ]
+ RIs [ ( ntrees + 1 ) ]
+ this
;
set themin minsteps;
set themax maxsteps;
loop 0 ntrees
progress #1 (ntrees+1) Calculating indices...;
set this length[#1];
set CIs[#1] 'themin'/'this'; /*CI=1 means no homoplasy*/
set RIs[#1] ('themax'-'this')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
stop
progress/;
report=;
/*Report CI/RI/TL */
macfloat 3;
maketable CIs Consistency index;
maketable RIs Retention index;
quote Consistency Index (CI) is 'CI';
quote Retention Index (RI) is 'RI';
quote Tree Length (TL) is 'TL';
/*Report*/
quote - /----------------------------------------------\;
@ -154,7 +152,7 @@ quote - | The file `*.tnt.tre` contain |;
quote - | is the ctf file with taxname |;
quote - | The file `resample.svg` contain |;
quote - | strict consensus tree with |;
quote - | relative bremer, jak and boot |;
quote - | relative jak, boot and bremer |;
quote - | support on the tree |;
quote - | The file `apo.svg` contain the |;
quote - | tree with apomorphy mapping |;