inline double calc_probability_of_sequence(
NucleotideSequence * seq,
const ShortReadSequence& short_read,
double mean_number_of_errors_per_site) const {
TREESHREW_ASSERT(seq);
CharacterStateVectorType::const_iterator long_read_start_pos = seq->cbegin();
CharacterStateVectorType::const_iterator long_read_stop_pos = long_read_start_pos + this->num_active_sites_ - short_read.size() + 1;
CharacterStateVectorType::const_iterator short_read_begin = short_read.cbegin();
CharacterStateVectorType::const_iterator short_read_end = short_read.cend();
unsigned long short_read_size = short_read.size();
TREESHREW_ASSERT(long_read_stop_pos >= long_read_start_pos);
unsigned long num_mismatches = 0;
double prob = 0.0;
while (long_read_start_pos < long_read_stop_pos) {
num_mismatches = std::inner_product(
short_read_begin,
short_read_end,
long_read_start_pos,
0,
std::plus<unsigned int>(),
std::not2(std::equal_to<CharacterStateVectorType::value_type>()));
prob += gsl_ran_binomial_pdf(num_mismatches, mean_number_of_errors_per_site, short_read_size);
// prob += gsl_ran_poisson_pdf(num_mismatches, (mean_number_of_errors_per_site * short_read_size));
++long_read_start_pos;
}
return prob;
}
/*
* This does the pearson above, but computes histogram occupation using a
* binomial distribution. This is useful to compute e.g. the pvalue for a
* vector of tally results from flipping 100 coins, performed 100 times.
* It automatically cuts off the tails where bin membership isn't large
* enough to give a good result.
*/
double chisq_binomial(double *observed,double prob,unsigned int kmax,unsigned int nsamp)
{
unsigned int n,nmax,ndof;
double expected,delchisq,chisq,pvalue,obstotal,exptotal;
chisq = 0.0;
obstotal = 0.0;
exptotal = 0.0;
ndof = 0;
nmax = kmax;
if(verbose){
printf("# %7s %3s %3s %10s %10s %9s\n",
"bit/bin","DoF","X","Y","del-chisq","chisq");
printf("#==================================================================\n");
}
for(n = 0;n <= nmax;n++){
if(observed[n] > 10.0){
expected = nsamp*gsl_ran_binomial_pdf(n,prob,nmax);
obstotal += observed[n];
exptotal += expected;
delchisq = (observed[n] - expected)*(observed[n] - expected)/expected;
chisq += delchisq;
if(verbose){
printf("# %5u %3u %10.4f %10.4f %10.4f %10.4f\n",
n,ndof,observed[n],expected,delchisq,chisq);
}
ndof++;
}
}
if(verbose){
printf("Total: %10.4f %10.4f\n",obstotal,exptotal);
printf("#==================================================================\n");
printf("Evaluated chisq = %f for %u degrees of freedom\n",chisq,ndof);
}
/*
* Now evaluate the corresponding pvalue. The only real question
* is what is the correct number of degrees of freedom. I'd argue we
* did use a constraint when we set expected = binomial*nsamp, so we'll
* go for ndof (count of bins tallied) - 1.
*/
ndof--;
pvalue = gsl_sf_gamma_inc_Q((double)(ndof)/2.0,chisq/2.0);
if(verbose){
printf("Evaluted pvalue = %6.4f in chisq_binomial.\n",pvalue);
}
return(pvalue);
}
/*
* Alpha is the cutoff for the pvalue
*
*/
void pvalue_alpha_beta(unsigned int n,unsigned int u,unsigned int v,
double *_alpha,double *_beta_score) {
unsigned int i,j,k;
unsigned int middle=n/2+n%2;
unsigned int rest=n%2;
double error0=u+v;
double alpha0=1.0;
double beta0=1.0;
double beta_score=1.0;
unsigned int k0=1;
double alpha,beta,error;
//printf("n = %i middle = %i\n",n,middle);
for(j=0;j<n/2;j++) {
int a=middle-j-rest;
int b=middle+j;
//printf("%i: ",j);
double sum=0.0;
for(k=a;k<=b;k++) {
double p=gsl_ran_binomial_pdf(k,0.5,n);
//printf("[%i,%f] ",k,p);
sum+=p;
}
//printf("\n");
alpha=1-sum;
k=(b-a+1);
beta=(b-a+1)*1.0/(n+1);
//printf("\n alpha = %lf + beta = %lf = %lf\n",alpha,beta,alpha+beta);
error=u*alpha+v*beta;
beta_score=1.0*k0/k;
k0=k;
if (error > error0) {
break;
}
//printf("%u %f\n",j,error);
error0=error;
alpha0=alpha;
beta0=beta;
}
if (_alpha != NULL)
*_alpha=alpha0;
if (_beta_score != NULL)
*_beta_score=beta_score;
}
int main(){
int i;
const int M = 5e7;
time_t t1, t2, t;
double mu= 1e-7;
int L=3e6, T, N;
/* INIT GSL RNG*/
t = time(NULL); // time in seconds, used to change the seed of the random generator
gsl_rng * rng;
const gsl_rng_type *typ;
gsl_rng_env_setup();
typ=gsl_rng_default;
rng=gsl_rng_alloc(typ);
gsl_rng_set(rng,t); // changes the seed of the random generator
printf("\n - performing %d computations of Bernoulli prob mass fct - ", M);
time(&t1);
for(i=0;i<M;i++){
T=gsl_rng_uniform_int(rng,100); /* time */
N=gsl_rng_uniform_int(rng, 20); /* nb of mutations*/
gsl_ran_binomial_pdf((unsigned int) N, mu, T*L);
}
time(&t2);
printf("\nTime ellapsed: %d ", (int) (t2-t1));
printf("\n - performing %d computations of Poisson prob mass fct- ", M);
time(&t1);
for(i=0;i<M;i++){
T=gsl_rng_uniform_int(rng,100); /* time */
N=gsl_rng_uniform_int(rng, 20); /* nb of mutations*/
gsl_ran_poisson_pdf((unsigned int) N, mu*T*L);
}
time(&t2);
printf("\nTime ellapsed: %d \n", (int) (t2-t1));
}
static double binomial_ll(gsl_vector *hits, void *paramv){
return log(gsl_ran_binomial_pdf(hits->data[1], ((gsl_vector*)paramv)->data[1], ((gsl_vector*)paramv)->data[0]));
}
void MainWindow::binom(){
frmSettings *dlg = new frmSettings();
QSettings settings(QSettings::IniFormat, QSettings::UserScope, "RJsoft", "ssconf");
settings.beginGroup("CIprms");
if(settings.contains("k")){
dlg->m_ui->spinBox->setValue(settings.value("k").toInt());
} else {
dlg->m_ui->spinBox->setValue(0);
}
if(settings.contains("n")){
dlg->m_ui->spinBox_2->setValue(settings.value("n").toInt());
} else {
dlg->m_ui->spinBox_2->setValue(0);
}
if(settings.contains("alpha")){
dlg->m_ui->doubleSpinBox_3->setValue(settings.value("alpha").toDouble());
} else {
dlg->m_ui->doubleSpinBox_3->setValue(0.95);
}
if(settings.contains("Sp")){
dlg->m_ui->doubleSpinBox_2->setValue(settings.value("Sp").toDouble());
} else {
dlg->m_ui->doubleSpinBox_2->setValue(1.0);
}
if(settings.contains("Se")){
dlg->m_ui->doubleSpinBox->setValue(settings.value("Se").toDouble());
} else {
dlg->m_ui->doubleSpinBox->setValue(1.0);
}
if(settings.contains("method")){
dlg->m_ui->comboBox->setCurrentIndex(dlg->m_ui->comboBox->findText(settings.value("method").toString(), Qt::MatchExactly));
} else {
dlg->m_ui->comboBox->setCurrentIndex(dlg->m_ui->comboBox->findText("Blaker", Qt::MatchExactly));
}
settings.endGroup();
if (dlg->exec() == QDialog::Accepted ){
QApplication::setOverrideCursor( Qt::WaitCursor );
unsigned int k = dlg->m_ui->spinBox->value();
unsigned int n = dlg->m_ui->spinBox_2->value();
double conf = dlg->m_ui->doubleSpinBox_3->value();
double alpha = 1-conf;
double Se = dlg->m_ui->doubleSpinBox->value();
double Sp = dlg->m_ui->doubleSpinBox_2->value();
settings.beginGroup("CIprms");
settings.setValue("k", k);
settings.setValue("n", n);
settings.setValue("alpha", dlg->m_ui->doubleSpinBox_3->value());
settings.setValue("Sp", Sp);
settings.setValue("Se", Se);
settings.setValue("method",dlg->m_ui->comboBox->currentText());
settings.endGroup();
double pbal = 0, pjobb=1, sum=0;
double prev = (double)k/(double)n;
ui->plainTextEdit->appendPlainText(
QString("Number of test positives: %1 out of %2\nSensitivity: %3 Specificity: %4 Confidence level: %5 Method: %6\n")
.arg(k).arg(n).arg(Se).arg(Sp).arg(conf)
.arg(dlg->m_ui->comboBox->currentText())
);
if (dlg->m_ui->comboBox->currentText()=="Sterne"){
// ----------------------------------------------------------
// -------------------- S T E R N E -------------------------
// ----------------------------------------------------------
//bal
int z =0;
for(double p=0.0001; p<=0.9999; p = p+0.0001){
sum=0;
double kp = gsl_ran_binomial_pdf(k, p, n);
for(unsigned int x=0; x!=n+1; x++){
double xp = gsl_ran_binomial_pdf(x, p, n);
if (xp<=kp){
sum = sum+xp;
}
}
if (sum<alpha){
pbal = p;
// ui->plainTextEdit->appendPlainText(QString("sum: %1; p: %2").arg(sum).arg(p));
} else {
break;
}
z++;
}
//jobb
z =0;
for(double p=0.9999; p>=0.0001; p = p-0.0001){
sum=0;
double kp = gsl_ran_binomial_pdf(k, p, n);
for(unsigned int x=0; x!=n+1; x++){
double xp = gsl_ran_binomial_pdf(x, p, n);
if (xp<=kp){
sum = sum+xp;
}
}
if (sum<alpha){
pjobb = p;
} else {
break;
}
z++;
}
} else if (dlg->m_ui->comboBox->currentText()=="Blaker"){
// ----------------------------------------------------------
// -------------------- B L A K E R -------------------------
// ----------------------------------------------------------
//bal
int z =0;
for(double p=0.0001; p<=0.9999; p = p+0.0001){
sum=0;
double kp = gsl_cdf_binomial_P(k, p, n);
// ui->plainTextEdit->appendPlainText(QString("k %1 p %2 n %3 kp %4\n").arg(k).arg(p).arg(n).arg(kp));
double kp2 = gsl_cdf_binomial_Q(k, p, n) + gsl_ran_binomial_pdf(k, p, n);
// ui->plainTextEdit->appendPlainText(QString("k %1 p %2 n %3 kp2 %4\n").arg(k).arg(p).arg(n).arg(kp2));
if (kp2 < kp) kp=kp2;
for(unsigned int x=0; x!=n+1; x++){
double xp = gsl_cdf_binomial_P(x, p, n);
// ui->plainTextEdit->appendPlainText(QString("x %1 p %2 n %3 kp %4\n").arg(x).arg(p).arg(n).arg(xp));
double xp2 = gsl_cdf_binomial_Q(x, p, n) + gsl_ran_binomial_pdf(x, p, n);
// ui->plainTextEdit->appendPlainText(QString("x %1 p %2 n %3 kp2 %4\n").arg(x).arg(p).arg(n).arg(xp2));
if (xp2 < xp) xp=xp2;
double xxp = gsl_ran_binomial_pdf(x, p, n);
// ui->plainTextEdit->appendPlainText(QString("x %1 p %2 n %3 xxp %4\n").arg(x).arg(p).arg(n).arg(xxp));
if (xp<=kp){
sum = sum+xxp;
}
// ui->plainTextEdit->appendPlainText(QString("p %1 sum %2\n").arg(p).arg(sum));
}
if (sum<alpha){
pbal = p;
// ui->plainTextEdit->appendPlainText(QString("sum: %1; p: %2").arg(sum).arg(p));
} else {
break;
}
z++;
}
//jobb
z =0;
for(double p=0.9999; p>=0.0001; p = p-0.0001){
sum=0;
double kp = gsl_cdf_binomial_P(k, p, n);
double kp2 = gsl_cdf_binomial_Q(k, p, n) + gsl_ran_binomial_pdf(k, p, n);
if (kp2 < kp) kp=kp2;
for(unsigned int x=0; x!=n+1; x++){
double xp = gsl_cdf_binomial_P(x, p, n);
double xp2 = gsl_cdf_binomial_Q(x, p, n) + gsl_ran_binomial_pdf(x, p, n);
if (xp2 < xp) xp=xp2;
double xxp = gsl_ran_binomial_pdf(x, p, n);
if (xp<=kp){
sum = sum+xxp;
}
}
// ui->plainTextEdit->appendPlainText(QString("p %1 sum %2\n").arg(p).arg(sum));
if (sum<alpha){
pjobb = p;
} else {
break;
}
z++;
}
} else if (dlg->m_ui->comboBox->currentText()=="Wilson"){
// ----------------------------------------------------------
// -------------------- W I L S O N -------------------------
// ----------------------------------------------------------
double zkrit = 1.96;
double plusminus = zkrit * pow(pow(zkrit, 2.) + 4. * k * (n-k) / n, .5);
double nevezo = 2.*(n + pow(zkrit, 2.));
pbal = (2.*k + pow(zkrit, 2) - plusminus)/nevezo;
pjobb = (2.*k + pow(zkrit, 2) + plusminus)/nevezo;
} else if (dlg->m_ui->comboBox->currentText()=="Clopper-Pearson"){
// ----------------------------------------------------------
// ------------- C L O P P E R P E A R S O N --------------
// ----------------------------------------------------------
//bal
int z =0;
for(double p=0.0001; p<=0.9999; p = p+0.0001){
double kp = gsl_cdf_binomial_Q(k, p, n) + gsl_ran_binomial_pdf(k, p, n);
// ui->plainTextEdit->appendPlainText(QString("kp: %1; p: %2").arg(kp).arg(p));
if (kp<0.5*alpha){
pbal = p;
} else {
break;
}
z++;
}
//jobb
z =0;
for(double p=0.9999; p>=0.0001; p = p-0.0001){
double kp = gsl_cdf_binomial_P(k, p, n);
if (kp<0.5*alpha){
pjobb = p;
} else {
break;
}
z++;
}
}
kiir(pbal, pjobb, prev, Sp, Se);
QApplication::restoreOverrideCursor();
}
}
double pdf_Binomial(double p, long n, long x) { return gsl_ran_binomial_pdf(x,p,n); }
double
test_binomial_large_pdf (unsigned int n)
{
return gsl_ran_binomial_pdf (n, 0.3, 55);
}
double calcLoonIndex(t_Data *ptSeqData, t_Data *ptRefData, int nI, int nP1, int nP2, int* pnSplit, int* pnParentD, t_Params *ptParams)
{
int i = 0, nLenI = ptSeqData->anLen[nI], nLenP1 = ptRefData->anLen[nP1], nLenP2 = ptRefData->anLen[nP2];
FILE *ofp = NULL;
char szCommand[MAX_LINE_LENGTH];
t_Data tAlign;
int nDiff1 = 0, anDiff1[MAX_DIFF + 1];
int nDiff2 = 0, anDiff2[MAX_DIFF + 1];
int anSplits[2*MAX_DIFF], s = 0, s1 = 0, s2 = 0;
int nSplit = -1, sMin = 0, nMinD = BIG_INT;
int anD[2*MAX_DIFF];
int nMaxLen = 0, nTLen = 0;
char* acSequences = NULL;
double dRet = 0;
char szTempFasta[MAX_LINE_LENGTH], szTempAlign[MAX_LINE_LENGTH];
int nTGap1 = 0, nTGap2 = 0, nTGap3 = 0,nMaxTGap = -1;
int nParentD = 0;
/*create sequence filenames*/
if(ptParams->bOutputAlignments == FALSE){
sprintf(szTempFasta, "Temp%s",FASTA_SUFFIX);
sprintf(szTempAlign, "Temp%s",ALIGN_SUFFIX);
}
else{
sprintf(szTempFasta, "Temp%d%s",nI,FASTA_SUFFIX);
sprintf(szTempAlign, "Temp%d%s",nI,ALIGN_SUFFIX);
}
/*write sequences*/
ofp = fopen(szTempFasta, "w");
if(ofp){
writeSequenceI(ofp, ptSeqData, nI);
writeSequenceI(ofp, ptRefData, nP1);
writeSequenceI(ofp, ptRefData, nP2);
fclose(ofp);
}
else{
fprintf(stderr, "Failed to open %s for writing ... abort\n",szTempFasta);
exit(EXIT_FAILURE);
}
/*run mafft remotely*/
sprintf(szCommand,"mafft-linsi %s > %s 2> %s",szTempFasta,szTempAlign, TEMP_ERROR_FILE);
system(szCommand);
/*read in mafft output - three sequence alignment*/
readData(szTempAlign, &tAlign);
acSequences = tAlign.acSequences; nMaxLen = tAlign.nMaxLen;
/*alignment length*/
nTLen = tAlign.nMaxLen;
/*find largest terminal gap*/
while(acSequences[nTLen - 1 - nTGap1] == GAP && nTLen - nTGap1> 1){
nTGap1++;
}
while(acSequences[nMaxLen + nTLen - 1 - nTGap2] == GAP && nTLen - nTGap2> 1){
nTGap2++;
}
while(acSequences[2*nMaxLen + nTLen - 1 - nTGap3] == GAP && nTLen - nTGap3> 1){
nTGap3++;
}
nMaxTGap = nTGap1 > nTGap2 ? nTGap1 : nTGap2;
nMaxTGap = nTGap3 > nMaxTGap ? nTGap3 : nMaxTGap;
/*remove from alignment*/
nTLen -= nMaxTGap;
/*find all differences between chimera and parents and positions*/
for(i = 0; i < nTLen; i++){
if(acSequences[i] != acSequences[nMaxLen + i]){
if(nDiff1 < MAX_DIFF){
anDiff1[nDiff1] = i;
nDiff1++;
}
else{
fprintf(stderr,"Max diff reached in calcLoon\n");
}
}
if(acSequences[i] != acSequences[2*nMaxLen + i]){
if(nDiff2 < MAX_DIFF){
anDiff2[nDiff2] = i;
nDiff2++;
}
else{
fprintf(stderr,"Max diff reached in calcLoon\n");
}
}
}
for(i = 0; i < nTLen; i++){
if(acSequences[nMaxLen + i] != acSequences[2*nMaxLen + i]){
nParentD++;
}
}
anDiff1[nDiff1] = nTLen;
anDiff2[nDiff2] = nTLen;
s = 0; s1 = 0; s2 = 0;
anSplits[s] = -1;
anD[s] = nDiff2;
s++;
/*loop differences to find optimal split point*/
while(s1 < nDiff1 || s2 < nDiff2){
if(anDiff1[s1] <= anDiff2[s2]){
anD[s] = anD[s - 1] + 1;
anSplits[s] = anDiff1[s1];
s++;
s1++;
}
else if(anDiff1[s1] > anDiff2[s2]){
anD[s] = anD[s - 1] - 1;
anSplits[s] = anDiff2[s2];
s++;
s2++;
}
}
for(i = 0; i < s; i++){
if(anD[i] < nMinD){
nMinD = anD[i];
sMin = i;
}
}
if(sMin < s - 1){
nSplit = (anSplits[sMin] + anSplits[sMin + 1])/2;
}
else{
nSplit = nTLen - 1;
}
/*dummy if, as we always do this*/
if(TRUE){
int nA = -1, nB = -1;
int nDLP1 = 0, nDRP1 = 0, nDLP2 = 0, nDRP2 = 0;
int nX = 0, nY = 0, nZ = 0, nXZ = 0;
int nXA = 0, nXB = 0, nYA = 0, nYB = 0;
char cC = '\0';
double pA = 0.0, pB = 0.0;
double dP = 0.0;
for(i = 0; i < nTLen; i++){
char cI = acSequences[i], cP1 = acSequences[nMaxLen + i], cP2 = acSequences[2*nMaxLen + i];
/*get consenus base*/
cC = getC(cI, cP1, cP2);
/*count number of differences between chimera and consensus*/
if(cI != cC){
nZ++;
}
/*count number of differences between chimera and parent 1*/
if(cP1 != cC){
/*count number to left*/
if(i <= nSplit){
nDLP1++;
}
/*count number to right*/
else{
nDRP1++;
}
}
/*count number of differences between chimera and parent 2*/
if(cP2 != cC){
if(i <= nSplit){
nDLP2++;
}
else{
nDRP2++;
}
}
}
/*if Parent1 is left*/
if(nDiff1 <= nDiff2){
nA = nP1;
nB = nP2;
nX = nDLP1 + nDRP1;
nXA = nDLP1; nXB = nDRP1;
nY = nDLP2 + nDRP2;
nYA = nDLP2; nYB = nDRP2;
pA = ((double) nSplit + 1)/((double) nTLen); /*probability of change to left*/
pB = ((double) nTLen - nSplit - 1)/((double) nTLen);/*prob. to right*/
}
else{
/*if parent 1 is right*/
nA = nP2;
nB = nP1;
nX = nDLP2 + nDRP2;
nXA = nDRP2; nXB = nDLP2;
nY = nDLP1 + nDRP1;
nYA = nDRP1; nYB = nDLP1;
pB = ((double) nSplit + 1)/((double) nTLen);
pA = ((double) nTLen - nSplit - 1)/((double) nTLen);
}
nXZ = nX + nZ;
dRet = 0.0;
dP = 0.0;
/*adds extra factor for tree imbalance - not generally used*/
if(ptParams->bImbalance){
if(nXZ > 0){
for(i = nX; i <= nXZ; i++){
dP += gsl_ran_binomial_pdf (i, 0.5, nXZ);
}
dRet += -log(dP);
}
}
/*contribution from right parent*/
if(nY > 0){
dP = 0.0;
for(i = nYA; i <= nY; i++){
dP += gsl_ran_binomial_pdf(i, pA, nY);
}
dRet += -log(dP);
}
/*contribution from left*/
if(nX > 0){
dP = 0.0;
for(i = nXB; i <= nX; i++){
dP += gsl_ran_binomial_pdf(i, pB, nX);
}
dRet += -log(dP);
}
}
(*pnSplit) = nSplit;
(*pnParentD) = nParentD;
/*free up memory*/
destroyData(&tAlign);
return dRet;
}
double
test_binomial_huge_knuth_pdf (unsigned int n)
{
return gsl_ran_binomial_pdf (n, 0.3, 5500);
}
double
test_binomial1_pdf (unsigned int n)
{
return gsl_ran_binomial_pdf (n, 1, 8);
}
int main(int argc, char **argv){
distlist distribution = Normal;
char msg[10000], c;
int pval = 0, qval = 0;
double param1 = GSL_NAN, param2 =GSL_NAN, findme = GSL_NAN;
char number[1000];
sprintf(msg, "%s [opts] number_to_lookup\n\n"
"Look up a probability or p-value for a given standard distribution.\n"
"[This is still loosely written and counts as beta. Notably, negative numbers are hard to parse.]\n"
"E.g.:\n"
"%s -dbin 100 .5 34\n"
"sets the distribution to a Binomial(100, .5), and find the odds of 34 appearing.\n"
"%s -p 2 \n"
"find the area of the Normal(0,1) between -infty and 2. \n"
"\n"
"-pval Find the p-value: integral from -infinity to your value\n"
"-qval Find the q-value: integral from your value to infinity\n"
"\n"
"After giving an optional -p or -q, specify the distribution. \n"
"Default is Normal(0, 1). Other options:\n"
"\t\t-binom Binomial(n, p)\n"
"\t\t-beta Beta(a, b)\n"
"\t\t-f F distribution(df1, df2)\n"
"\t\t-norm Normal(mu, sigma)\n"
"\t\t-negative bin Negative binomial(n, p)\n"
"\t\t-poisson Poisson(L)\n"
"\t\t-t t distribution(df)\n"
"I just need enough letters to distinctly identify a distribution.\n"
, argv[0], argv[0], argv[0]);
opterr=0;
if(argc==1){
printf("%s", msg);
return 0;
}
while ((c = getopt (argc, argv, "B:b:F:f:N:n:pqT:t:")) != -1){
switch (c){
case 'B':
case 'b':
if (optarg[0]=='i')
distribution = Binomial;
else if (optarg[0]=='e')
distribution = Beta;
else {
printf("I can't parse the option -b%s\n", optarg);
exit(0);
}
param1 = atof(argv[optind]);
param2 = atof(argv[optind+1]);
findme = atof(argv[optind+2]);
break;
case 'F':
case 'f':
distribution = F;
param1 = atof(argv[optind]);
findme = atof(argv[optind+1]);
break;
case 'H':
case 'h':
printf("%s", msg);
return 0;
case 'n':
case 'N':
if (optarg[0]=='o'){ //normal
param1 = atof(argv[optind]);
param2 = atof(argv[optind+1]);
findme = atof(argv[optind+2]);
} else if (optarg[0]=='e'){
distribution = Negbinom;
param1 = atof(argv[optind]);
param2 = atof(argv[optind+1]);
findme = atof(argv[optind+2]);
} else {
printf("I can't parse the option -n%s\n", optarg);
exit(0);
}
break;
case 'p':
if (!optarg || optarg[0] == 'v')
pval++;
else if (optarg[0] == 'o'){
distribution = Poisson;
param1 = atof(argv[optind]);
findme = atof(argv[optind+1]);
} else {
printf("I can't parse the option -p%s\n", optarg);
exit(0);
}
break;
case 'q':
qval++;
break;
case 'T':
case 't':
distribution = T;
param1 = atof(argv[optind]);
findme = atof(argv[optind+1]);
break;
case '?'://probably a negative number
if (optarg)
snprintf(number, 1000, "%c%s", optopt, optarg);
else snprintf(number, 1000, "%c", optopt);
if (gsl_isnan(param1)) param1 = -atof(number);
else if (gsl_isnan(param2)) param2 = -atof(number);
else if (gsl_isnan(findme)) findme = -atof(number);
}
}
if (gsl_isnan(findme)) findme = atof(argv[optind]);
//defaults, as promised
if (gsl_isnan(param1)) param1 = 0;
if (gsl_isnan(param2)) param2 = 1;
if (!pval && !qval){
double val =
distribution == Beta ? gsl_ran_beta_pdf(findme, param1, param2)
: distribution == Binomial ? gsl_ran_binomial_pdf(findme, param2, param1)
: distribution == F ? gsl_ran_fdist_pdf(findme, param1, param2)
: distribution == Negbinom ? gsl_ran_negative_binomial_pdf(findme, param2, param1)
: distribution == Normal ? gsl_ran_gaussian_pdf(findme, param2)+param1
: distribution == Poisson ? gsl_ran_poisson_pdf(findme, param1)
: distribution == T ? gsl_ran_tdist_pdf(findme, param1) : GSL_NAN;
printf("%g\n", val);
return 0;
}
if (distribution == Binomial){
printf("Sorry, the GSL doesn't have a Binomial CDF.\n");
return 0; }
if (distribution == Negbinom){
printf("Sorry, the GSL doesn't have a Negative Binomial CDF.\n");
return 0; }
if (distribution == Poisson){
printf("Sorry, the GSL doesn't have a Poisson CDF.\n");
return 0; }
if (pval){
double val =
distribution == Beta ? gsl_cdf_beta_P(findme, param1, param2)
: distribution == F ? gsl_cdf_fdist_P(findme, param1, param2)
: distribution == Normal ? gsl_cdf_gaussian_P(findme-param1, param2)
: distribution == T ? gsl_cdf_tdist_P(findme, param1) : GSL_NAN;
printf("%g\n", val);
return 0;
}
if (qval){
double val =
distribution == Beta ? gsl_cdf_beta_Q(findme, param1, param2)
: distribution == F ? gsl_cdf_fdist_Q(findme, param1, param2)
: distribution == Normal ? gsl_cdf_gaussian_Q(findme-param1, param2)
: distribution == T ? gsl_cdf_tdist_Q(findme, param1) : GSL_NAN;
printf("%g\n", val);
}
}
void
sign_execute (const struct dataset *ds,
struct casereader *input,
enum mv_class exclude,
const struct npar_test *test,
bool exact UNUSED,
double timer UNUSED)
{
int i;
bool warn = true;
const struct dictionary *dict = dataset_dict (ds);
const struct two_sample_test *t2s = UP_CAST (test, const struct two_sample_test, parent);
struct ccase *c;
struct sign_test_params *stp = xcalloc (t2s->n_pairs, sizeof *stp);
struct casereader *r = input;
for (; (c = casereader_read (r)) != NULL; case_unref (c))
{
const double weight = dict_get_case_weight (dict, c, &warn);
for (i = 0 ; i < t2s->n_pairs; ++i )
{
variable_pair *vp = &t2s->pairs[i];
const union value *value0 = case_data (c, (*vp)[0]);
const union value *value1 = case_data (c, (*vp)[1]);
const double diff = value0->f - value1->f;
if (var_is_value_missing ((*vp)[0], value0, exclude))
continue;
if (var_is_value_missing ((*vp)[1], value1, exclude))
continue;
if ( diff > 0)
stp[i].pos += weight;
else if (diff < 0)
stp[i].neg += weight;
else
stp[i].ties += weight;
}
}
casereader_destroy (r);
for (i = 0 ; i < t2s->n_pairs; ++i )
{
int r = MIN (stp[i].pos, stp[i].neg);
stp[i].one_tailed_sig = gsl_cdf_binomial_P (r,
0.5,
stp[i].pos + stp[i].neg);
stp[i].point_prob = gsl_ran_binomial_pdf (r, 0.5,
stp[i].pos + stp[i].neg);
}
output_frequency_table (t2s, stp, dict);
output_statistics_table (t2s, stp);
free (stp);
}
double
test_binomial_max_pdf (unsigned int n)
{
return gsl_ran_binomial_pdf (n, 1e-8, 1<<31);
}