[Genabel-commits] r1673 - in branches/ProbABEL-0.50: checks checks/R-tests doc src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Apr 3 11:19:29 CEST 2014
Author: maartenk
Date: 2014-04-03 11:19:29 +0200 (Thu, 03 Apr 2014)
New Revision: 1673
Modified:
branches/ProbABEL-0.50/checks/R-tests/Makefile.am
branches/ProbABEL-0.50/checks/test_mms.sh
branches/ProbABEL-0.50/doc/ChangeLog
branches/ProbABEL-0.50/doc/ProbABEL_manual.tex
branches/ProbABEL-0.50/doc/pacoxph.1
branches/ProbABEL-0.50/doc/palinear.1
branches/ProbABEL-0.50/doc/palogist.1
branches/ProbABEL-0.50/doc/probabel.1
branches/ProbABEL-0.50/src/reg1.cpp
Log:
merged trunk to branch
Modified: branches/ProbABEL-0.50/checks/R-tests/Makefile.am
===================================================================
--- branches/ProbABEL-0.50/checks/R-tests/Makefile.am 2014-04-02 20:54:11 UTC (rev 1672)
+++ branches/ProbABEL-0.50/checks/R-tests/Makefile.am 2014-04-03 09:19:29 UTC (rev 1673)
@@ -30,6 +30,11 @@
## The palogist R test still doesn't run correctly.
XFAIL_TESTS = run_R_test_palogist.sh
+## The pacoxph R test fails on SNP 6 when EIGEN is not enabled.
+if !WITH_EIGEN
+XFAIL_TESTS += run_R_test_pacox.sh
+endif
+
EXTRA_DIST = $(check_SCRIPTS) $(R_test_files)
Modified: branches/ProbABEL-0.50/checks/test_mms.sh
===================================================================
--- branches/ProbABEL-0.50/checks/test_mms.sh 2014-04-02 20:54:11 UTC (rev 1672)
+++ branches/ProbABEL-0.50/checks/test_mms.sh 2014-04-03 09:19:29 UTC (rev 1673)
@@ -1,7 +1,6 @@
#!/bin/bash
# This script runs checks on ProbABEL's palinear module for
# quantitative traits combined with the mmscore option.
-
echo "Analysis using MMScore..."
scriptdir=$(dirname $0)
Modified: branches/ProbABEL-0.50/doc/ChangeLog
===================================================================
--- branches/ProbABEL-0.50/doc/ChangeLog 2014-04-02 20:54:11 UTC (rev 1672)
+++ branches/ProbABEL-0.50/doc/ChangeLog 2014-04-03 09:19:29 UTC (rev 1673)
@@ -1,11 +1,12 @@
-***** v.0.4.3 (2014.03)
-* Speed up of a factor of X after simplifying the way filevector data is
- read in.
+***** v.0.4.3 (2014.04.01)
+* Speed-up of a factor of ~ 2 for linear, logistic and Cox regression when
+ using filevector input files.
* Fixed bug #5404: "ProbABEL's R check for Cox regression doesn't check if
the survival package is installed".
* Fixed bug #5403: "The ProbABEL manual doesn't contain any information on
how to install ProbABEL"
+
***** v.0.4.2 (2014.01.02)
* The 'probabel.pl' script is now simply renamed to 'probabel' (a user
shouldn't care what scripting language we use). For at least several
@@ -34,6 +35,7 @@
* For developers: a start has been made on documenting the internal
functions using Doxygen.
+
***** v.0.4.1 (2013.08.29)
* Fix bug #4854: When using mmscore, there is one (nan) column missing in
the output for low-frequency SNPs. Also includes a simplification of the
Modified: branches/ProbABEL-0.50/doc/ProbABEL_manual.tex
===================================================================
--- branches/ProbABEL-0.50/doc/ProbABEL_manual.tex 2014-04-02 20:54:11 UTC (rev 1672)
+++ branches/ProbABEL-0.50/doc/ProbABEL_manual.tex 2014-04-03 09:19:29 UTC (rev 1673)
@@ -11,11 +11,10 @@
$^{2}${\small Erasmus MC, Rotterdam}\\
$^{3}${\small Institute of Cytology and Genetics SD RAS, Novosibirsk}
}
-\date{March 19, 2014}
+\date{April 1, 2014}
\usepackage[utf8]{inputenc}
-\usepackage{eurosym} % Makes the Euro symbol available.
\usepackage[T1]{fontenc}
\usepackage{textcomp}
Modified: branches/ProbABEL-0.50/doc/pacoxph.1
===================================================================
--- branches/ProbABEL-0.50/doc/pacoxph.1 2014-04-02 20:54:11 UTC (rev 1672)
+++ branches/ProbABEL-0.50/doc/pacoxph.1 2014-04-03 09:19:29 UTC (rev 1673)
@@ -1,4 +1,4 @@
-.TH pacoxph 1 "2 January 2014" "ProbABEL 0.4.3"
+.TH pacoxph 1 "01 April 2014" "ProbABEL 0.4.3"
.SH NAME
pacoxph \- Perform Genome-Wide Association Analysis using a linear model
.SH SYNOPSIS
Modified: branches/ProbABEL-0.50/doc/palinear.1
===================================================================
--- branches/ProbABEL-0.50/doc/palinear.1 2014-04-02 20:54:11 UTC (rev 1672)
+++ branches/ProbABEL-0.50/doc/palinear.1 2014-04-03 09:19:29 UTC (rev 1673)
@@ -1,4 +1,4 @@
-.TH palinear 1 "2 January 2014" "ProbABEL 0.4.3"
+.TH palinear 1 "01 April 2014" "ProbABEL 0.4.3"
.SH NAME
palinear \- Perform Genome-Wide Association Analysis using a linear model
.SH SYNOPSIS
Modified: branches/ProbABEL-0.50/doc/palogist.1
===================================================================
--- branches/ProbABEL-0.50/doc/palogist.1 2014-04-02 20:54:11 UTC (rev 1672)
+++ branches/ProbABEL-0.50/doc/palogist.1 2014-04-03 09:19:29 UTC (rev 1673)
@@ -1,4 +1,4 @@
-.TH palogist 1 "2 January 2014" "ProbABEL 0.4.3"
+.TH palogist 1 "01 April 2014" "ProbABEL 0.4.3"
.SH NAME
palogist \- Perform Genome-Wide Association Analysis using a linear model
.SH SYNOPSIS
Modified: branches/ProbABEL-0.50/doc/probabel.1
===================================================================
--- branches/ProbABEL-0.50/doc/probabel.1 2014-04-02 20:54:11 UTC (rev 1672)
+++ branches/ProbABEL-0.50/doc/probabel.1 2014-04-03 09:19:29 UTC (rev 1673)
@@ -1,4 +1,4 @@
-.TH ProbABEL 1 "2 January 2014" "ProbABEL 0.4.3"
+.TH ProbABEL 1 "01 April 2014" "ProbABEL 0.4.3"
.SH NAME
probabel \- Wrapper around the three ProbABEL binaries, simplifying their use
.SH SYNOPSIS
Modified: branches/ProbABEL-0.50/src/reg1.cpp
===================================================================
--- branches/ProbABEL-0.50/src/reg1.cpp 2014-04-02 20:54:11 UTC (rev 1672)
+++ branches/ProbABEL-0.50/src/reg1.cpp 2014-04-03 09:19:29 UTC (rev 1673)
@@ -747,7 +747,8 @@
double emu = eMu.get(i, 0);
double value = emu;
double zval;
- value = exp(value) / (1. + exp(value));
+ double expval = exp(value);
+ value = expval / (1. + expval);
residuals[i] = (reg_data.Y).get(i, 0) - value;
eMu.put(value, i, 0);
W.put(value * (1. - value), i, 0);
@@ -806,11 +807,13 @@
beta.print();
}
// std::cout << "beta:\n"; beta.print();
- // compute likelihood
+
+ // Compute the likelihood.
double prevlik = loglik;
- loglik = 0.;
- for (int i = 0; i < eMu.nrow; i++)
+ loglik = 0;
+ for (int i = 0; i < eMu.nrow; i++) {
loglik += reg_data.Y[i] * eMu_us[i] - log(1. + exp(eMu_us[i]));
+ }
delta = fabs(1. - (prevlik / loglik));
niter++;
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