[Genabel-commits] r1139 - pkg/ProbABEL/src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Mar 13 23:07:18 CET 2013
Author: maartenk
Date: 2013-03-13 23:07:17 +0100 (Wed, 13 Mar 2013)
New Revision: 1139
Modified:
pkg/ProbABEL/src/main.cpp
Log:
commented out unneeded code (+-230 lines) and removed some duplicated code by a function
Modified: pkg/ProbABEL/src/main.cpp
===================================================================
--- pkg/ProbABEL/src/main.cpp 2013-03-13 19:56:54 UTC (rev 1138)
+++ pkg/ProbABEL/src/main.cpp 2013-03-13 22:07:17 UTC (rev 1139)
@@ -330,6 +330,44 @@
}
}
+int get_start_position(const cmdvars& input_var, int model, int start_pos,
+ int number_of_rows_or_columns)
+{
+ if (!input_var.getAllcov() && model == 0 && input_var.getInteraction() == 0)
+ {
+ if (input_var.getNgpreds() == 2)
+ {
+ start_pos = number_of_rows_or_columns - 2;
+ } else
+ {
+ start_pos = number_of_rows_or_columns - 1;
+ }
+ } else if (!input_var.getAllcov() && model == 0
+ && input_var.getInteraction() != 0)
+ {
+ if (input_var.getNgpreds() == 2)
+ {
+ start_pos = number_of_rows_or_columns - 4;
+ } else
+ {
+ start_pos = number_of_rows_or_columns - 2;
+ }
+ } else if (!input_var.getAllcov() && model != 0
+ && input_var.getInteraction() == 0)
+ {
+ start_pos = number_of_rows_or_columns - 1;
+ } else if (!input_var.getAllcov() && model != 0
+ && input_var.getInteraction() != 0)
+ {
+ start_pos = number_of_rows_or_columns - 2;
+ } else
+ {
+ start_pos = 0;
+ }
+
+ return start_pos;
+}
+
int main(int argc, char * argv[])
{
cmdvars input_var;
@@ -593,323 +631,20 @@
{
write_mlinfo(outfile, file, mli, csnp, input_var, gcount, freq);
}
+ } else
+ {
- for (int model = 0; model < maxmod; model++)
- {
- if (poly) //allel freq is not to rare
- {
+ int file = 0;
+ write_mlinfo(outfile, file, mli, csnp, input_var, gcount, freq);
+ maxmod = 1;
-#if LOGISTIC
- logistic_reg rd(rgd);
- if (input_var.getScore())
- rd.score(nrd.residuals, rgd, 0, CHOLTOL, model,
- input_var.getInteraction(),
- input_var.getNgpreds(),
- invvarmatrix);
- else
- rd.estimate(rgd, 0, MAXITER, EPS, CHOLTOL, model,
- input_var.getInteraction(),
- input_var.getNgpreds(),
- invvarmatrix,
- input_var.getRobust());
-#elif LINEAR
- linear_reg rd(rgd);
- if (input_var.getScore())
- rd.score(nrd.residuals, rgd, 0, CHOLTOL, model,
- input_var.getInteraction(),
- input_var.getNgpreds(), invvarmatrix);
- else
- {
- // rd.mmscore(rgd,0,CHOLTOL,model,input_var.getInteraction(), input_var.getNgpreds(), invvarmatrix);
- rd.estimate(rgd, 0, CHOLTOL, model,
- input_var.getInteraction(),
- input_var.getNgpreds(), invvarmatrix,
- input_var.getRobust());
- }
-#elif COXPH
- coxph_reg rd(rgd);
- rd.estimate(rgd, 0, MAXITER, EPS, CHOLTOL, model,
- input_var.getInteraction(), true,
- input_var.getNgpreds());
-#endif
-
- if (!input_var.getAllcov() && model == 0
- && input_var.getInteraction() == 0)
- {
- if (input_var.getNgpreds() == 2)
- {
- start_pos = rd.beta.nrow - 2;
- } else
- {
- start_pos = rd.beta.nrow - 1;
- }
- } else if (!input_var.getAllcov() && model == 0
- && input_var.getInteraction() != 0)
- {
- if (input_var.getNgpreds() == 2)
- {
- start_pos = rd.beta.nrow - 4;
- } else
- {
- start_pos = rd.beta.nrow - 2;
- }
- } else if (!input_var.getAllcov() && model != 0
- && input_var.getInteraction() == 0)
- {
- start_pos = rd.beta.nrow - 1;
- } else if (!input_var.getAllcov() && model != 0
- && input_var.getInteraction() != 0)
- {
- start_pos = rd.beta.nrow - 2;
- } else
- {
- start_pos = 0;
- }
-
- for (int pos = start_pos; pos < rd.beta.nrow; pos++)
- {
- *beta_sebeta[model] << input_var.getSep()
- << rd.beta[pos]
- << input_var.getSep()
- << rd.sebeta[pos];
- //Han Chen
-#if !COXPH
- if (input_var.getInverseFilename() == NULL
- && !input_var.getAllcov()
- && input_var.getInteraction() != 0)
- {
- if (pos > start_pos)
- {
- if (model == 0)
- {
- if (pos > start_pos + 2
- || input_var.getNgpreds() != 2)
- {
- *covvalue[model] << rd.covariance[pos
- - 3]
- << input_var.getSep()
- << rd.covariance[pos - 2];
- }
- } else
- {
- *covvalue[model] << rd.covariance[pos - 1];
- }
- }
- }
-#endif
- //Oct 26, 2009
- }
-
- //calculate chi2
- //________________________________
- //cout << rd.loglik<<" "<<input_var.getNgpreds() << "\n";
-
- if ((input_var.getInverseFilename() == NULL
- && input_var.getNgpreds() != 2)
- || input_var.getNgpreds() == 2)
- {
- cout << rd.loglik
- << " "
- << input_var.getNgpreds()
- << "\n";
- if (input_var.getScore() == 0)
- {
- //*chi2[model] << 2.*(rd.loglik-null_loglik);
- *chi2[model] << rd.loglik;
- } else
- {
- //*chi2[model] << rd.chi2_score;
- *chi2[model] << "nan";
- }
- }
- //________________________________
- } else //beta, sebeta = nan
- {
- if (!input_var.getAllcov() && model == 0
- && input_var.getInteraction() == 0)
- {
- if (input_var.getNgpreds() == 2)
- {
- start_pos = rgd.X.ncol - 2;
- } else
- {
- start_pos = rgd.X.ncol - 1;
- }
- } else if (!input_var.getAllcov() && model == 0
- && input_var.getInteraction() != 0)
- {
- if (input_var.getNgpreds() == 2)
- {
- start_pos = rgd.X.ncol - 4;
- } else
- {
- start_pos = rgd.X.ncol - 2;
- }
- } else if (!input_var.getAllcov() && model != 0
- && input_var.getInteraction() == 0)
- {
- start_pos = rgd.X.ncol - 1;
- } else if (!input_var.getAllcov() && model != 0
- && input_var.getInteraction() != 0)
- {
- start_pos = rgd.X.ncol - 2;
- } else
- {
- start_pos = 0;
- }
- if (input_var.getInteraction() != 0
- && !input_var.getAllcov()
- && input_var.getNgpreds() != 2)
- {
- start_pos++;
- }
-
- if (model == 0)
- {
- end_pos = rgd.X.ncol;
- } else
- {
- end_pos = rgd.X.ncol - 1;
- }
-
- if (input_var.getInteraction() != 0)
- {
- end_pos++;
- }
-
- for (int pos = start_pos; pos < end_pos; pos++)
- {
- *beta_sebeta[model] << input_var.getSep()
- << "nan"
- << input_var.getSep()
- << "nan";
- }
-
- if (input_var.getNgpreds() == 2)
- {
- //Han Chen
-#if !COXPH
- if (!input_var.getAllcov()
- && input_var.getInteraction() != 0)
- {
- if (model == 0)
- {
- *covvalue[model] << "nan"
- << input_var.getSep()
- << "nan";
- } else
- {
- *covvalue[model] << "nan";
- }
- }
-#endif
- //Oct 26, 2009
- *chi2[model] << "nan";
- } else
- { //ngpreds=1
- if (input_var.getInverseFilename() == NULL)
- {
- // Han Chen
-#if !COXPH
- if (!input_var.getAllcov()
- && input_var.getInteraction() != 0)
- {
- *covvalue[model] << "nan";
- }
-#endif
- //Oct 26, 2009
- *chi2[model] << "nan";
- }
- }
-
- }
- }
- //end of model cycle
- if (input_var.getNgpreds() == 2)
- {
- cout << "ngpreds==2 model end" << "\n";
-
- //Han Chen
- *outfile[0] << beta_sebeta[0]->str() << input_var.getSep();
-#if !COXPH
- if (!input_var.getAllcov() && input_var.getInteraction() != 0)
- {
- *outfile[0] << covvalue[0]->str() << input_var.getSep();
- }
-#endif
- *outfile[0] << chi2[0]->str() << "\n";
-
- *outfile[1] << beta_sebeta[1]->str() << input_var.getSep();
-#if !COXPH
- if (!input_var.getAllcov() && input_var.getInteraction() != 0)
- {
- *outfile[1] << covvalue[1]->str() << input_var.getSep();
- }
-#endif
- *outfile[1] << chi2[1]->str() << "\n";
-
- *outfile[2] << beta_sebeta[2]->str() << input_var.getSep();
-#if !COXPH
- if (!input_var.getAllcov() && input_var.getInteraction() != 0)
- {
- *outfile[2] << covvalue[2]->str() << input_var.getSep();
- }
-#endif
- *outfile[2] << chi2[2]->str() << "\n";
-
- *outfile[3] << beta_sebeta[3]->str() << input_var.getSep();
-#if !COXPH
- if (!input_var.getAllcov() && input_var.getInteraction() != 0)
- {
- *outfile[3] << covvalue[3]->str() << input_var.getSep();
- }
-#endif
- *outfile[3] << chi2[3]->str() << "\n";
-
- *outfile[4] << beta_sebeta[4]->str() << input_var.getSep();
-#if !COXPH
- if (!input_var.getAllcov() && input_var.getInteraction() != 0)
- {
- *outfile[4] << covvalue[4]->str() << input_var.getSep();
- }
-#endif
- *outfile[4] << chi2[4]->str() << "\n";
- //Oct 26, 2009
-
- } else //ngpreds == 1
- {
-
- if (input_var.getInverseFilename() == NULL)
- {
- //Han Chen
- *outfile[0] << beta_sebeta[0]->str() << input_var.getSep();
-#if !COXPH
- if (!input_var.getAllcov()
- && input_var.getInteraction() != 0)
- {
- *outfile[0] << covvalue[0]->str() << input_var.getSep();
- }
-#endif
- *outfile[0] << chi2[0]->str() << "\n";
- //Oct 26, 2009
- } else
- {
- *outfile[0] << beta_sebeta[0]->str() << "\n";
- }
- } // end ngpreds ==1
-
}
-//
-//End of All models output.
-//
- else //Only additive model. Only one output file
+
+ for (int model = 0; model < maxmod; model++)
{
- //Write mlinfo to output:
- int file = 0;
- write_mlinfo(outfile, file, mli, csnp, input_var, gcount, freq);
- int model = 0;
- if (poly) //allel freq is not to rare
+ if (poly) //allel freq is not to rare
{
+
#if LOGISTIC
logistic_reg rd(rgd);
if (input_var.getScore())
@@ -924,88 +659,17 @@
invvarmatrix,
input_var.getRobust());
#elif LINEAR
- //cout << (rgd.get_unmasked_data()).nids << " 1\n";
-#if DEBUG
- rgd.X.print();
- rgd.Y.print();
-#endif
linear_reg rd(rgd);
-#if DEBUG
- rgd.X.print();
- rgd.Y.print();
-#endif
- //cout << (rgd.get_unmasked_data()).nids << " 2\n";
if (input_var.getScore())
- {
-#if DEBUG
- cout << "input_var.getScore/n";
- nrd.residuals.print();
- cout << CHOLTOL << " <-CHOLTOL\n";
- cout << model << " <-model\n";
- cout << input_var.getInteraction()
- << " <-input_var.getInteraction()\n";
- cout << input_var.getNgpreds()
- << " <-input_var.getNgpreds()\n";
- invvarmatrix.print();
-#endif
rd.score(nrd.residuals, rgd, 0, CHOLTOL, model,
input_var.getInteraction(), input_var.getNgpreds(),
invvarmatrix);
-#if DEBUG
- rd.beta.print();
- cout << rd.chi2_score << " <-chi2_scoren\n";
- rd.covariance.print();
- rd.residuals.print();
- rd.sebeta.print();
- cout << rd.loglik << " <-logliken\n";
- cout << rd.sigma2 << " <-sigma2\n";
-#endif
- } else
+ else
{
- // if(input_var.getInverseFilename()== NULL)
- // {
- // cout << (rgd.get_unmasked_data()).nids << " 3\n";
-#if DEBUG
- cout << "rd.estimate\n";
- cout << CHOLTOL << " <-CHOLTOL\n";
- cout << model << " <-model\n";
- cout << input_var.getInteraction()
- << " <-input_var.getInteraction()\n";
- cout << input_var.getNgpreds()
- << " <-input_var.getNgpreds()\n";
- cout << input_var.getRobust()
- << " <-input_var.getRobust()\n";
- cout << "start invarmatrix\n";
- invvarmatrix.print();
- cout << "end invarmatrix\n";
- cout << rgd.is_interaction_excluded
- << " <-rgd.is_interaction_excluded\n";
-#endif
+ // rd.mmscore(rgd,0,CHOLTOL,model,input_var.getInteraction(), input_var.getNgpreds(), invvarmatrix);
rd.estimate(rgd, 0, CHOLTOL, model,
input_var.getInteraction(), input_var.getNgpreds(),
invvarmatrix, input_var.getRobust());
-
-#if DEBUG
- cout << "rd.beta\n";
- rd.beta.print();
- cout << rd.chi2_score << " <-chi2_scoren\n";
- cout << "rd.covariance\n";
- rd.covariance.print();
- cout << "rd.residuals\n";
- rd.residuals.print();
- cout << "rd.sebeta\n";
- rd.sebeta.print();
- cout << rd.loglik << " <-logliken\n";
- cout << rd.sigma2 << " <-sigma2\n";
-#endif
- //cout << (rgd.get_unmasked_data()).nids << " 4\n";
- //}
- //else
- //{
- // rd.mmscore(rgd, 0, CHOLTOL, model,
- // input_var.getInteraction(),
- // input_var.getNgpreds(), invvarmatrix);
- //}
}
#elif COXPH
coxph_reg rd(rgd);
@@ -1014,23 +678,13 @@
input_var.getNgpreds());
#endif
- if (!input_var.getAllcov() && input_var.getInteraction() == 0)
- {
- start_pos = rd.beta.nrow - 1;
- } else if (!input_var.getAllcov()
- && input_var.getInteraction() != 0)
- {
- start_pos = rd.beta.nrow - 2;
- } else
- {
- start_pos = 0;
- }
-#if DEBUG
- cout << " start_pos;" << start_pos << "\n";
-#endif
+ int number_of_rows_or_columns = rd.beta.nrow;
+ start_pos = get_start_position(input_var, model, start_pos,
+ number_of_rows_or_columns);
+ cout << "start_pos" << start_pos << "\n";
for (int pos = start_pos; pos < rd.beta.nrow; pos++)
{
- *beta_sebeta[0] << input_var.getSep()
+ *beta_sebeta[model] << input_var.getSep()
<< rd.beta[pos]
<< input_var.getSep()
<< rd.sebeta[pos];
@@ -1042,7 +696,29 @@
{
if (pos > start_pos)
{
- *covvalue[0] << rd.covariance[pos - 1];
+ if (model == 0)
+ {
+ if (input_var.getNgpreds() == 2)
+ {
+ if (pos > start_pos + 2)
+ {
+ *covvalue[model] << rd.covariance[pos
+ - 3]
+ << input_var.getSep()
+ << rd.covariance[pos - 2];
+ }
+
+ } //end ngpred=2
+ else
+ {
+ *covvalue[model] << rd.covariance[pos - 1];
+ }
+
+ } //end model
+ else
+ {
+ *covvalue[model] << rd.covariance[pos - 1];
+ } //end ngpred==1
}
}
#endif
@@ -1051,62 +727,150 @@
//calculate chi2
//________________________________
- if (input_var.getInverseFilename() == NULL)
+ //cout << rd.loglik<<" "<<input_var.getNgpreds() << "\n";
+
+ if ((input_var.getInverseFilename() == NULL
+ && input_var.getNgpreds() != 2)
+ || input_var.getNgpreds() == 2)
{
-#if DEBUG
- cout << " inverse_filename == NULL" << "\n";
-#endif
+
if (input_var.getScore() == 0)
{
- *chi2[0] << rd.loglik; //2.*(rd.loglik-null_loglik);
+ //*chi2[model] << 2.*(rd.loglik-null_loglik);
+ *chi2[model] << rd.loglik;
} else
{
- *chi2[0] << "nan"; //rd.chi2_score;
+ //*chi2[model] << rd.chi2_score;
+ *chi2[model] << "nan";
}
}
//________________________________
} else //beta, sebeta = nan
{
- if (!input_var.getAllcov() && input_var.getInteraction() == 0)
- start_pos = rgd.X.ncol - 1;
- else if (!input_var.getAllcov()
- && input_var.getInteraction() != 0)
- start_pos = rgd.X.ncol - 2;
- else
- start_pos = 0;
+ int number_of_rows_or_columns = rgd.X.ncol;
+ start_pos = get_start_position(input_var, model, start_pos,
+ number_of_rows_or_columns);
- end_pos = rgd.X.ncol;
- if (input_var.getInteraction() != 0)
+ if (input_var.getInteraction() != 0 && !input_var.getAllcov()
+ && input_var.getNgpreds() != 2)
{
- end_pos++;
+ start_pos++;
}
- if (input_var.getInteraction() != 0 && !input_var.getAllcov())
+
+ if (model == 0)
{
- start_pos++;
+ end_pos = rgd.X.ncol;
+ } else
+ {
+ end_pos = rgd.X.ncol - 1;
}
+ if (input_var.getInteraction() != 0)
+ {
+ end_pos++;
+ }
+
for (int pos = start_pos; pos < end_pos; pos++)
{
- *beta_sebeta[0] << input_var.getSep()
+ *beta_sebeta[model] << input_var.getSep()
<< "nan"
<< input_var.getSep()
<< "nan";
}
- if (input_var.getInverseFilename() == NULL)
+
+ if (input_var.getNgpreds() == 2)
{
//Han Chen
#if !COXPH
if (!input_var.getAllcov()
&& input_var.getInteraction() != 0)
{
- *covvalue[0] << "nan";
+ if (model == 0)
+ {
+ *covvalue[model] << "nan"
+ << input_var.getSep()
+ << "nan";
+ } else
+ {
+ *covvalue[model] << "nan";
+ }
}
#endif
//Oct 26, 2009
- *chi2[0] << "nan";
+ *chi2[model] << "nan";
+ } else
+ { //ngpreds=1
+ if (input_var.getInverseFilename() == NULL)
+ {
+ // Han Chen
+#if !COXPH
+ if (!input_var.getAllcov()
+ && input_var.getInteraction() != 0)
+ {
+ *covvalue[model] << "nan";
+ }
+#endif
+ //Oct 26, 2009
+ *chi2[model] << "nan";
+ }
}
+
}
+ }
+ //end of model cycle
+ if (input_var.getNgpreds() == 2)
+ {
+ //Han Chen
+ *outfile[0] << beta_sebeta[0]->str() << input_var.getSep();
+#if !COXPH
+ if (!input_var.getAllcov() && input_var.getInteraction() != 0)
+ {
+ *outfile[0] << covvalue[0]->str() << input_var.getSep();
+ }
+#endif
+ *outfile[0] << chi2[0]->str() << "\n";
+
+ *outfile[1] << beta_sebeta[1]->str() << input_var.getSep();
+#if !COXPH
+ if (!input_var.getAllcov() && input_var.getInteraction() != 0)
+ {
+ *outfile[1] << covvalue[1]->str() << input_var.getSep();
+ }
+#endif
+ *outfile[1] << chi2[1]->str() << "\n";
+
+ *outfile[2] << beta_sebeta[2]->str() << input_var.getSep();
+#if !COXPH
+ if (!input_var.getAllcov() && input_var.getInteraction() != 0)
+ {
+ *outfile[2] << covvalue[2]->str() << input_var.getSep();
+ }
+#endif
+ *outfile[2] << chi2[2]->str() << "\n";
+
+ *outfile[3] << beta_sebeta[3]->str() << input_var.getSep();
+#if !COXPH
+ if (!input_var.getAllcov() && input_var.getInteraction() != 0)
+ {
+ *outfile[3] << covvalue[3]->str() << input_var.getSep();
+ }
+#endif
+ *outfile[3] << chi2[3]->str() << "\n";
+
+ *outfile[4] << beta_sebeta[4]->str() << input_var.getSep();
+#if !COXPH
+ if (!input_var.getAllcov() && input_var.getInteraction() != 0)
+ {
+ *outfile[4] << covvalue[4]->str() << input_var.getSep();
+ }
+#endif
+ *outfile[4] << chi2[4]->str() << "\n";
+ //Oct 26, 2009
+
+ } else //ngpreds == 1
+ {
+
if (input_var.getInverseFilename() == NULL)
{
//Han Chen
@@ -1117,17 +881,244 @@
*outfile[0] << covvalue[0]->str() << input_var.getSep();
}
#endif
- *outfile[0] << chi2[model]->str() << "\n";
+ *outfile[0] << chi2[0]->str() << "\n";
//Oct 26, 2009
} else
{
*outfile[0] << beta_sebeta[0]->str() << "\n";
-#if DEBUG
- cout << "Se beta" << beta_sebeta[0] << "\n";
-#endif
}
+ //} // end ngpreds ==1
+
}
//
+//End of All models output.
+//
+// else //Only additive model. Only one output file
+// {
+// //Write mlinfo to output:
+// int file = 0;
+// write_mlinfo(outfile, file, mli, csnp, input_var, gcount, freq);
+// int model = 0;
+// if (poly) //allel freq is not to rare
+// {
+//#if LOGISTIC
+// logistic_reg rd(rgd);
+// if (input_var.getScore())
+// rd.score(nrd.residuals, rgd, 0, CHOLTOL, model,
+// input_var.getInteraction(),
+// input_var.getNgpreds(),
+// invvarmatrix);
+// else
+// rd.estimate(rgd, 0, MAXITER, EPS, CHOLTOL, model,
+// input_var.getInteraction(),
+// input_var.getNgpreds(),
+// invvarmatrix,
+// input_var.getRobust());
+//#elif LINEAR
+// //cout << (rgd.get_unmasked_data()).nids << " 1\n";
+//#if DEBUG
+// rgd.X.print();
+// rgd.Y.print();
+//#endif
+// linear_reg rd(rgd);
+//#if DEBUG
+// rgd.X.print();
+// rgd.Y.print();
+//#endif
+// //cout << (rgd.get_unmasked_data()).nids << " 2\n";
+// if (input_var.getScore())
+// {
+//#if DEBUG
+// cout << "input_var.getScore/n";
+// nrd.residuals.print();
+// cout << CHOLTOL << " <-CHOLTOL\n";
+// cout << model << " <-model\n";
+// cout << input_var.getInteraction()
+// << " <-input_var.getInteraction()\n";
+// cout << input_var.getNgpreds()
+// << " <-input_var.getNgpreds()\n";
+// invvarmatrix.print();
+//#endif
+// rd.score(nrd.residuals, rgd, 0, CHOLTOL, model,
+// input_var.getInteraction(), input_var.getNgpreds(),
+// invvarmatrix);
+//#if DEBUG
+// rd.beta.print();
+// cout << rd.chi2_score << " <-chi2_scoren\n";
+// rd.covariance.print();
+// rd.residuals.print();
+// rd.sebeta.print();
+// cout << rd.loglik << " <-logliken\n";
+// cout << rd.sigma2 << " <-sigma2\n";
+//#endif
+// } else
+// {
+// // if(input_var.getInverseFilename()== NULL)
+// // {
+// // cout << (rgd.get_unmasked_data()).nids << " 3\n";
+//#if DEBUG
+// cout << "rd.estimate\n";
+// cout << CHOLTOL << " <-CHOLTOL\n";
+// cout << model << " <-model\n";
+// cout << input_var.getInteraction()
+// << " <-input_var.getInteraction()\n";
+// cout << input_var.getNgpreds()
+// << " <-input_var.getNgpreds()\n";
+// cout << input_var.getRobust()
+// << " <-input_var.getRobust()\n";
+// cout << "start invarmatrix\n";
+// invvarmatrix.print();
+// cout << "end invarmatrix\n";
+// cout << rgd.is_interaction_excluded
+// << " <-rgd.is_interaction_excluded\n";
+//#endif
+// rd.estimate(rgd, 0, CHOLTOL, model,
+// input_var.getInteraction(), input_var.getNgpreds(),
+// invvarmatrix, input_var.getRobust());
+//
+//#if DEBUG
+// cout << "rd.beta\n";
+// rd.beta.print();
+// cout << rd.chi2_score << " <-chi2_scoren\n";
+// cout << "rd.covariance\n";
+// rd.covariance.print();
+// cout << "rd.residuals\n";
+// rd.residuals.print();
+// cout << "rd.sebeta\n";
+// rd.sebeta.print();
+// cout << rd.loglik << " <-logliken\n";
+// cout << rd.sigma2 << " <-sigma2\n";
+//#endif
+// //cout << (rgd.get_unmasked_data()).nids << " 4\n";
+// //}
+// //else
+// //{
+// // rd.mmscore(rgd, 0, CHOLTOL, model,
+// // input_var.getInteraction(),
+// // input_var.getNgpreds(), invvarmatrix);
+// //}
+// }
+//#elif COXPH
+// coxph_reg rd(rgd);
+// rd.estimate(rgd, 0, MAXITER, EPS, CHOLTOL, model,
+// input_var.getInteraction(), true,
+// input_var.getNgpreds());
+//#endif
+//
+// if (!input_var.getAllcov() && input_var.getInteraction() == 0)
+// {
+// start_pos = rd.beta.nrow - 1;
+// } else if (!input_var.getAllcov()
+// && input_var.getInteraction() != 0)
+// {
+// start_pos = rd.beta.nrow - 2;
+// } else
+// {
+// start_pos = 0;
+// }
+//#if DEBUG
+// cout << " start_pos;" << start_pos << "\n";
+//#endif
+// for (int pos = start_pos; pos < rd.beta.nrow; pos++)
+// {
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/genabel -r 1139
More information about the Genabel-commits
mailing list