add: setk

README

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+# TNT Script used by Guoyi
+
+This scripts are followed MIT except for setk.run which belongs to Salvador Arias(Instituto Miguel Lillo, San Miguel de Tucumán, Argentina).
+
+## tnt.run
+
+- `file.tnt` must be changed to your own file;
+
+- `trees.tre`, `bt.tre` are trees with taxaname;
+
+- `trees_no.tre`, `bt_no.tre` are trees without taxaname which can be put into Winclada with the `file.tnt`;
+
+- `majority` can be replaced by `nelsen`;
+
+- `boot` can be replaced by `jack`;
+
+## setk_tnt.run
+
+- `file.tnt` must be changed to your own file;
+
+- You can find the recommended k from `setk.log` and then change in `piwe=` `tnt.run`;

setk.run

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+macro=
+
+var:
+ actK
+ minK
+ maxK
+ gVal
+ a
+ b
+ Nval
+ maxIts
+;
+
+if (ntax<0)
+  quote NO HAY DATOS!;
+  proc/;
+end
+
+set gVal 1;
+
+/* busca el valor de g */
+loop 0 nchar
+  if (!isinfo[#1]) continue; end
+  if (!isact[#1]) continue; end
+  set a=maxsteps[#1];
+  set b=minsteps[#1];
+  if (('a'-'b')>'gVal')
+    set gVal 'a'-'b';
+  end
+stop
+
+quote valor de g = 'gVal';
+
+set actK 10;
+set minK 0;
+set maxK 500; /* Asume 500 como el maximo posible valor de K */
+
+set maxIts 0;
+
+/* busca el mejor valor de K */
+loop 0 1
+  quote actual valor de k = 'actK';
+  set a 1-('actK'/('actK'+1));
+  quote 'a';
+  set b ('actK'/('actK'+'gVal'-1))-('actK'/('actK'+'gVal'));
+  quote 'b';
+  set Nval 'a'/'b';
+  quote valor de N = 'Nval';
+  if (('Nval'>14.8)&&('Nval'<15.2)) endloop; end /* N esta en el rango */
+  if ('Nval'>15.2)
+    set minK 'actK';
+  else
+    set maxK 'actK';
+  end
+  set a ('maxK'-'minK')/2;
+  set actK 'minK' + 'a';
+  set maxIts ++;
+  if ('maxIts'==100) endloop; end /* salida de emergencia */
+  setloop 0;
+stop
+
+/* Si salio de emergencia */
+if ('maxIts'==100)
+  quote NO SE TERMINARON LAS ITERACIONES;
+  quote mejor K encontrado: 'actK';
+  proc /;
+end
+
+quote Valor de K: 'actK' (N='Nval');
+piwe='actK';
+proc/;

setk_tnt.run

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+log setk.log;
+p file.tnt;
+setk.run;
+quit;

winclada.run

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-mxram 10240 ;
-nstates 32 ;
-nstates NOGAPS ;
-
-piwe=12;
-
-procedure mor.tnt ;
-log winclada.log ;
-
-hold 100000 ;
-xpiwe(*; mult=replic 1000 tbr hold 10;
-xpiwe&; piwe&;
-export= treeswc.tre ;
-
-bbreak=tbr ;
-majority * ;
-
-resample boot replications 1000;
-export= btwc.tre ;
-
-length * ;
-stats.run;
-
-quit ;