double calcR2(int N, int i, int q, int q2, MatrixT b)
{
double arg = -calcZ2(N, i, q, q2, b)*M_SQRT1_2;
double lnerfc;
if(arg>0.0)
lnerfc = log(0.5*derfcx(arg)) - arg*arg;
else
lnerfc = log(0.5*derfc(arg));
return(s[i][q]*(delta2B[i][q]-SQR(deltaB[i][q]))/(((double)N)-3.0) - 2.0*lnerfc);
}
void
d_scalar_scalar_1(void)
{
// d(x,x)?
if (equal(p1, p2)) {
push(one);
return;
}
// d(a,x)?
if (!iscons(p1)) {
push(zero);
return;
}
if (isadd(p1)) {
dsum();
return;
}
if (car(p1) == symbol(MULTIPLY)) {
dproduct();
return;
}
if (car(p1) == symbol(POWER)) {
dpower();
return;
}
if (car(p1) == symbol(DERIVATIVE)) {
dd();
return;
}
if (car(p1) == symbol(LOG)) {
dlog();
return;
}
if (car(p1) == symbol(SIN)) {
dsin();
return;
}
if (car(p1) == symbol(COS)) {
dcos();
return;
}
if (car(p1) == symbol(TAN)) {
dtan();
return;
}
if (car(p1) == symbol(ARCSIN)) {
darcsin();
return;
}
if (car(p1) == symbol(ARCCOS)) {
darccos();
return;
}
if (car(p1) == symbol(ARCTAN)) {
darctan();
return;
}
if (car(p1) == symbol(SINH)) {
dsinh();
return;
}
if (car(p1) == symbol(COSH)) {
dcosh();
return;
}
if (car(p1) == symbol(TANH)) {
dtanh();
return;
}
if (car(p1) == symbol(ARCSINH)) {
darcsinh();
return;
}
if (car(p1) == symbol(ARCCOSH)) {
darccosh();
return;
}
if (car(p1) == symbol(ARCTANH)) {
darctanh();
return;
}
if (car(p1) == symbol(ABS)) {
dabs();
return;
}
if (car(p1) == symbol(SGN)) {
dsgn();
return;
}
if (car(p1) == symbol(HERMITE)) {
dhermite();
return;
}
if (car(p1) == symbol(ERF)) {
derf();
return;
}
if (car(p1) == symbol(ERFC)) {
derfc();
return;
}
/*if (car(p1) == symbol(BESSELJ)) {
if (iszero(caddr(p1)))
dbesselj0();
else
dbesseljn();
return;
}*/
/*if (car(p1) == symbol(BESSELY)) {
if (iszero(caddr(p1)))
dbessely0();
else
dbesselyn();
return;
}*/
if (car(p1) == symbol(INTEGRAL) && caddr(p1) == p2) {
derivative_of_integral();
return;
}
dfunction();
}
double
calcR(int N, int i, int j, int jp)
{
/* modifications by billb for 0.2.8.5 */
double lnerfcj, lnerfcjp;
double argj, argjp;
double Dbpp_jjp, Dbpp_jpj;
double Dbpp_ijp, Dbpp_ij;
double Dbpp_jjpB, Dbpp_jpjB; /*B at end means "bar" or $\overline x$*/
double spp_jjp, spp_jpj;
double spp_ijp,spp_ij;
double sijpjBB, sijjpBB;
double sijpjB, sijjpB, sjjpiB;
double norm;
double normj, normjp;
double dijpB,dijB;
double bi, bj, bjp;
#define SIGMA23P(x,y,z) (sigma2_3p(x,y,z,oldDeltaB[x][z]))
if(recalcB)
{
norm = 1.0/(SIGMA23P(j,i,jp)+SIGMA23P(jp,i,j)+EPSILON);
normj = 1.0/(SIGMA23P(i,j,jp)+SIGMA23P(jp,j,i)+EPSILON);
normjp = 1.0/(SIGMA23P(i,jp,j)+SIGMA23P(j,jp,i)+EPSILON);
}
else
{
norm = 1.0/(sigma2_3(j,i,jp)+sigma2_3(jp,i,j)+EPSILON);
normj = 1.0/(sigma2_3(i,j,jp)+sigma2_3(jp,j,i)+EPSILON);
normjp = 1.0/(sigma2_3(i,jp,j)+sigma2_3(j,jp,i)+EPSILON);
}
if(norm<0.0) {
fprintf(stderr, "%s::%d\n", __FILE__, __LINE__);
if(recalcB)
fprintf(stderr, "Norm < 0 i=%d j=%d jp=%d norm=%g sigs %g %g\n",
i,j,jp,norm,
SIGMA23P(i,j,jp),SIGMA23P(i,jp,j));
else
fprintf(stderr, "Norm < 0 i=%d j=%d jp=%d norm=%g sigs %g %g\n",
i,j,jp,norm,
sigma2_3(i,j,jp),sigma2_3(i,jp,j));
exit(1);
}
#ifdef DEBUG
if(recalcB)
fprintf(stdout, "i=%d j=%d jp=%d normj=%g sigs %g %g\n",
i,j,jp,normj,
SIGMA23P(j,i,jp),SIGMA23P(j,jp,i));
else
fprintf(stdout, "i=%d j=%d jp=%d normj=%g sigs %g %g\n",
i,j,jp,normj,
sigma2_3(j,i,jp),sigma2_3(j,jp,i));
#endif
spp_jjp = (s[j][jp] - norm) + EPSILON;
spp_jpj = (s[jp][j] - norm) + EPSILON;
spp_ijp = (s[i][jp] - normj) + EPSILON;
spp_ij = (s[i][j] - normjp) + EPSILON;
#ifdef DEBUG
fprintf(stdout, "spp_jjp=%g, spp_jpj=%g, spp_ijp=%g, spp_ij=%g\n",
spp_jjp, spp_jpj, spp_ijp, spp_ij);
fprintf(stdout, " spp_ijp=%g, s[i][jp]=%g, normj=%g\n",
spp_ijp, s[i][jp], normj);
#endif
Dbpp_jjp =
(s[j][jp]*deltaB[j][jp] - (D(i,j)-D(i,jp))*norm)/(spp_jjp/*+EPSILON*/);
Dbpp_jpj =
(s[jp][j]*deltaB[jp][j] - (D(i,jp)-D(i,j))*norm)/(spp_jpj/*+EPSILON*/);
Dbpp_ijp =
(s[i][jp]*deltaB[i][jp] - (D(i,j)-D(jp,j))*normj)/(spp_ijp/*+EPSILON*/);
Dbpp_ij =
(s[i][j]*deltaB[i][j] - (D(i,jp)-D(j,jp))*normjp)/(spp_ij/*+EPSILON*/);
if(useSigmaBar)
{
sijjpB = sigma2_3(i,j,jp);
sijpjB = sigma2_3(i,jp,j);
sjjpiB = sigma2_3(j,jp,i);
}
else
{
bj = DMAX( (D(j, jp)+Dbpp_jjp)/2.0, MINB );
bjp = DMAX( (D(j, jp)-Dbpp_jjp)/2.0, MINB );
bi =
(
DMAX(D(i,j)-bj, MINB)/(sigma2_3(i,j,jp)+EPSILON)
+
DMAX(D(i,jp)-bjp, MINB)/(sigma2_3(i,jp,j)+EPSILON)
)/(1.0/(sigma2_3(i,j,jp)+EPSILON)+1.0/(sigma2_3(i,jp,j)+EPSILON));
sijjpB = sigma_na(bi+C(i),bj+C(j));
sijpjB = sigma_na(bi+C(i),bjp+C(jp));
sjjpiB = sigma_na(bj+C(j),bjp+C(jp));
}
if(useBarValues)
{
sijpjBB = 1.0/(1.0/(sijpjB+1.0/spp_jjp)+1.0/(sjjpiB+1.0/spp_ijp));
sijjpBB = 1.0/(1.0/(sijjpB+1.0/spp_jjp)+1.0/(sjjpiB+1.0/spp_ij));
dijpB = (D(i,jp)/(sijpjB+1.0/spp_jjp)+D(j,jp)/(sjjpiB+1.0/spp_ijp))*
sijpjBB;
dijB = (D(i,j)/(sijjpB+1.0/spp_jpj)+D(j,jp)/(sjjpiB+1.0/spp_ij))*
sijjpBB;
Dbpp_jjpB = (Dbpp_jjp/(sijpjB+1.0/spp_jjp)+Dbpp_ijp/(sjjpiB+1.0/spp_ijp))*
sijpjBB;
Dbpp_jpjB = (Dbpp_jpj/(sijjpB+1.0/spp_jpj)+Dbpp_ij/(sjjpiB+1.0/spp_ij))*
sijjpBB;
}
else
{
sijpjBB = 1.0/spp_jjp + sijpjB;
sijjpBB = 1.0/spp_jpj + sijjpB;
dijpB = D(i,jp);
dijB = D(i,j);
Dbpp_jjpB = Dbpp_jjp;
Dbpp_jpjB = Dbpp_jpj;
}
argj = (D(i,j)-Dbpp_jjpB-dijpB)
/sqrt(2.0*(sijpjBB+sijjpB));
argjp = (D(i,jp)-Dbpp_jpjB-dijB)
/sqrt(2.0*(sijjpBB+sijpjB));
#ifdef DEBUG
fprintf(stdout, "ijjp=%d%d%d, bi=%g, bj=%g, bjp=%g,\n\t"
"C(i)=%g, C(j)=%g, C(jp)=%g\n",
i,j,jp,bi, bj, bjp, C(i), C(j), C(jp));
fprintf(stdout, "sijjpB=%g, sijpjB=%g, sjjpiB=%g\n",sijjpB, sijpjB, sjjpiB);
fprintf(stdout, "sijpjBB=%g sijjpB=%g, sijjpBB=%g sijpjB=%g\n\n",
sijpjBB,sijjpB,sijjpBB,sijpjB);
#endif
#ifdef OFF
if(argjp!=-argj) {
fprintf(stderr, "%s::%d\n", __FILE__, __LINE__);
fprintf(stderr, "FATAL ERROR argjp!=-argj\n");
fprintf(stderr,"%d%d%d %.16g %.16g %.16g %.16g sig %g %g"
"bi %g bj %g bjp %g norm %g spp %g %g diff %g\n",
i,j,jp,argj, argjp,Dbpp_jjp,Dbpp_jpj ,
sigma2_3p(i,j,jp), sigma2_3p(i,jp,j), bi, bj, bjp, norm,
spp_jjp, spp_jpj, argjp+argj);
exit(0);
}
#endif
if(argj>0.0)
lnerfcj = log(derfcx(argj)) - argj*argj;
else
lnerfcj = log(derfc(argj));
if(argjp>0.0)
lnerfcjp = log(derfcx(argjp)) - argjp*argjp;
else
lnerfcjp = log(derfc(argjp));
#ifdef DEBUG
fprintf(stdout,">>>%lf, %lf || %lf %lf %g %g\n"
"===========================\n\n",
s[i][j]*(delta2B[i][j]-SQR(deltaB[i][j]))
-s[i][jp]*(delta2B[i][jp]-SQR(deltaB[i][jp])),
-2.0*(lnerfcj-lnerfcjp), lnerfcj, lnerfcjp, argj, argjp);
#endif
if(!n_Flag)
return( (s[i][j]*(delta2B[i][j]-SQR(deltaB[i][j]))
-s[i][jp]*(delta2B[i][jp]-SQR(deltaB[i][jp])))/(((double)N)-3.0)
-2.0*(lnerfcj-lnerfcjp));
else {
double Y;
Y = (sigma2_3(i,jp,j) + sigma2_3(j,jp,i) + 1.0/spp_ij)
/(sigma2_3(i,jp,j) + sigma2_3(j,jp,i)+(((double)N)-3.0)/spp_ij);
return(Y*(s[i][j]*(delta2B[i][j]-SQR(deltaB[i][j]))
-s[i][jp]*(delta2B[i][jp]-SQR(deltaB[i][jp])))
-2.0*(lnerfcj-lnerfcjp));
}
}
void
calc_q(int N, int *q, VectorT R, MatrixT b,
int* q2, VectorT LLR, VectorT Zscore)
{
int i, j, jwin;
double Rmin = -1.0; /* best R */
/* for best speed I think we could omit the following (test it first!)
2 variables. Without them different second best values are
printed with -v, but who cares? */
double R2ndmin = -1.0; /* 2ndbest R */
double R3rdmin = -1.0; /* 3rdbest R ; note first 2 might be the same */
VectorT z = vector(N); /* $z(i,q(i))$ */
/*
First compute $b_{i;j}$, $\Delta b_{ij}$, $\Delta^2b_{ij}$,
$s_{ij}$ */
calc_b(N, b, deltaB, delta2B, s);
if(recalcB)
{
/*
This is the original $\Delta b_{ij}$. The one before the
recalculation using the new sigma's. We need to save this for the
proper calculation of $s''_{ij}$ which also uses the new sigma's.
*/
/*
Save the original value of \|deltaB| for use in calculating $s''$
and $\Delta b''$
*/
setMM(N,deltaB,oldDeltaB);
/*
Now recompute $b_{i;j}$, $\Delta b_{ij}$, $\Delta^2b_{ij}$,
$s_{ij}$ using the previously calculted values of $\Delta b_{ij}$
and the new noise function.
*/
recalc_b(N, b, deltaB, delta2B, s);
}
/*
First calculate the $q(i)$ array using equation 0.11 to run a
single elmination tournament among the $j$'s
*/
if(printLevel>3)
fprintf(outfile,"args:\n");
for(i=0;i<N;++i)
{
double minR=0, tmpR;
int j2win=-1;
if(i!=0)
jwin = 0;
else
jwin = 1;
for(j=0;j<N;++j)
if(j!=i && j!=jwin)
{
if(calcR(N,i,j,jwin)<0.0)
jwin = j;
}
if(printLevel>3) {
fprintf(outfile,"basics:\n");
fprintf(outfile,"%f %f \n",calcR(N,0,2,1),calcR(N,0,2,3));
}
/*
Now make sure the \|jwin| is really the winner
*/
for(j=0;j<N;++j)
if(j!=i && j!=jwin && (((tmpR=calcR(N,i,j,jwin))<minR) || j2win==-1))
{
minR = tmpR;
j2win = j;
}
if(minR<0)
{
if(printLevel>1) {
fprintf(outfile, "WARNING: non-transitive R(i,j,j'); tree could depend on input order\n");
fprintf(outfile, "New winner %d (orig winner was %d)\n\n",
j2win, jwin);
}
if(!warnFlag) {
fprintf(stderr, "WARNING: non-transitive R(i,j,j'); tree could depend on input order\n");
warnFlag=True;
}
/* New winner swap, jwin and j2win */
q[i] = j2win;
q2[i] = jwin;
}
else
{
q[i] = jwin;
q2[i] = j2win;
if(minR==0.0) {
if(printLevel>1) {
fprintf(outfile, "WARNING: Tie in R(i,j,j'); tree likely to depend on input order\n");
fprintf(outfile, "Tie %d==%d\n\n", j2win, jwin);
}
if(!warnFlag) {
fprintf(stderr, "WARNING: Tie in R(i,j,j'); tree likely to depend on input order\n");
warnFlag=True;
}
}
}
if(printLevel>2)
fprintf(outfile, "i=%d q[i]=%d q2[i]=%d minR=%f\n",
i, q[i], q2[i], minR);
/*
The \|LLR| array holds the 3 index R values for the winning
pair and the second best taxon.
*/
LLR[i] = -0.5*calcR(N,i,q[i],q2[i]);
}
/*
now calculate $z(i,q(i))$ and then the full residule (eq 0.10)
Two different methods for calculating $z(i,j)$ choose the old one
if the \|oldZflag| is set else use the newer ($N^2$) method.
*/
for(i=0;i<N;++i)
{
double arg;
double lnerfc;
if(!x_Flag) {
R[i] =
s[i][q[i]]*(delta2B[i][q[i]]-SQR(deltaB[i][q[i]]))/(((double)N)-3.0) ;
} else {
R[i] =
2.0*s[i][q[i]]*(delta2B[i][q[i]]-SQR(deltaB[i][q[i]]))
/(((double)N)-2.0) ;
}
/* only do z if R looks ok so far */
if(R[i] < R3rdmin || R3rdmin==-1.0)
{
if(!oldZflag)
calc_z2(N, z, q, q2, b, i);
else
calc_z1(N, z, q, i);
/*
Finally calculate $R(i,q(i))$ eq 0.10
*/
arg = -z[i]*M_SQRT1_2;
/*
Save \|Zscore| for use in \|build.c|
*/
Zscore[i] = z[i];
if(arg>0.0)
lnerfc = log(0.5*derfcx(arg)) - arg*arg;
else
lnerfc = log(0.5*derfc(arg));
R[i] -=
2.0*lnerfc;
if(R[i] < R3rdmin || R3rdmin==-1.0) R3rdmin = R[i];
if(R[i] < R2ndmin || R2ndmin==-1.0) {R3rdmin = R2ndmin; R2ndmin = R[i];}
if(R[i] < Rmin || Rmin==-1.0) {R2ndmin = Rmin; Rmin=R[i];}
if(printLevel>2)
fprintf(outfile, "z(%d,%d)=%g\n", i, q[i], z[i]);
}
}
if(printLevel>0)
fprintf(outfile, "\n");
freeVector(z);
}