From 053ef5f0778201bae2628379a9ea6f375df8d0d1 Mon Sep 17 00:00:00 2001
From: "N. Brouard" <brouard@ined.fr>
Date: Tue, 4 Aug 2015 07:17:42 +0000
Subject: [PATCH] Summary: 0.98q4

---
 html/index.htm | 37 +++++++++++----------
 src/Makefile   | 88 ++++++++++++++++++++++++++++++++++----------------
 src/imach.c    | 41 +++++++++++++++++------
 3 files changed, 111 insertions(+), 55 deletions(-)

diff --git a/html/index.htm b/html/index.htm
index ca4d8a0..0c4d7d6 100644
--- a/html/index.htm
+++ b/html/index.htm
@@ -25,7 +25,7 @@ src="doc/euroreves2.gif" width="151" height="75"></p>
 color="#00006A">INED</font></a><font color="#00006A"> and </font><a
 href="http://euroreves.ined.fr"><font color="#00006A">EUROREVES</font></a></h3>
 
-<p align="center"><font color="#00006A" size="4"><strong>March 2015</strong></font></p>
+<p align="center"><font color="#00006A" size="4"><strong>August 2015</strong></font></p>
 
 <hr size="3" color="#EC5E5E">
 
@@ -54,10 +54,10 @@ from Cross-longitudinal surveys. <em>Mathematical Population Studies</em>.- 10(4
 
 <h2><font color="#EC5E5E"><strong>Download and instructions for installation</strong></font></h2>
 
-<h3> Current versions March 2015 </h3>
+<h3> Current versions August 2015 </h3>
 <ul>
-<li>On Windows (XP, Vista, Windows 7, Windows 8): 0.98p0 and 0.98q0</li>
-<li>On MacOS/X Leopard: 0.98p0 and 0.98q0</li>
+<li>On Windows (XP, Vista, Windows 7, Windows 8, Windows 10): 0.98q4</li>
+<li>On MacOS/X Leopard: 0.98q4</li>
 <li>On Linux, ask for the CVS version </li>
 </ul>
 The grapher that IMaCh uses is gnuplot
@@ -93,7 +93,7 @@ temporarly, to Administrator privileges (usally by right clicking the
 
 <ul>
     <li>Download latest <font size="2" face="Courier
-        New"><strong>imach-0.98p0-ilc-setup.exe</strong></font> and
+        New"><strong>imach-0.98q4-ilc-setup.exe</strong></font> and
       execute it .</li>
     <li> Gnuplot is installed by default on Windows. But if you are using another Operating system:
       <ul>
@@ -141,7 +141,7 @@ temporarly, to Administrator privileges (usally by right clicking the
 </ul>
 
 <br>
-Imach version 0.98p0 and 0.98q0 of March 2015 can
+Imach version 0.98q4 of August 2015 can
 be <a href="#Download">downloaded below</a> as a setup.exe file
 imach-0.98?-#-setup.exe. The ? corresponds to a version number while
 the # corresponds to same program but compiled differently.
@@ -178,7 +178,7 @@ like workpad but which have the advantage to be installed on any Windows).
 
 <p><a href="oldversions.html">Old Windows versions are accessible here.</a>
 
-<h3>On Mac OS/X Lion and higher (March 2015)</h3>
+<h3>On Mac OS/X Lion and higher (August 2015)</h3>
 
 IMaCh can be easily compiled with gcc on MacIntosh as soon as
 XCode (free download from Apple) is intalled on your MaCIntosh.<p>
@@ -227,11 +227,11 @@ a rpm yet, just ask us for the CVS tree location (not completely GPL
 today), and compile the sources. Remarks concerning the Linux versions
 are similar to the Mac OS/X version.
 <p>
-<font color="#FF0000" size="3"><tt>New (March 2015)</tt></font> You
+<font color="#FF0000" size="3"><tt>New (August 2015)</tt></font> You
 can <a href="#Download">download below</a> a binary tar file for
 respectively a 32 bits or 64 bits Linux bo, for example:
-imach-Linux-0.98p0-linux-i586-bin.tar.bz2 and
-imach-Linux-0.98p0-linux-x86-64-bin.tar.bz2
+imach-Linux-0.98q4-linux-i586-bin.tar.bz2 and
+imach-Linux-0.98q4-linux-x86-64-bin.tar.bz2
 
 <p> The binaries have been crosscompiled with gcc on my OS/X Mac.
 Each binary contains two directories <tt>bin</tt>
@@ -245,14 +245,10 @@ is <tt>./bin/imach ./html/doc/biaspar.imach</tt> <p>
       today most efficient hardwares) the command <tt>gnuplot
       biaspar.gp</tt> will fail. If successful, typing <tt>e</tt> will
       open <tt>biaspar.htm</tt> with your browser and all the results
-      including graphs generated by gnuplot will appear. Please
-      subscribe to the mailing
-      list <tt>imach-users@listes.ined.fr</tt> for comments and
-      reports on the performance (see the Performance section of
-      the <a href="http://euroreves.ined.fr/imach/wiki">wiki</a>).
+      including graphs generated by gnuplot will appear.
 
 <p>
-  <h3>Downloads<a name="Download"></a></h3> Version 0.98p0 is similar
+  <h3>Downloads (see Download page for recent binaries)<a name="Download"></a></h3> Version 0.98p0 is similar
   to earlier versions with, hopefully, less bugs. Version 0.98q0 has
   one main advantage and one main disadvantage:
   <ul>
@@ -351,7 +347,7 @@ is <tt>./bin/imach ./html/doc/biaspar.imach</tt> <p>
 		</TR>
 	</TBODY>
 </TABLE>
-<p><a href="Download"><font color="#FF0000" size="3">Other downloads</font></a>
+<p><a href="Download"><font color="#FF0000" size="6">Downloads</font></a>
       and <a href="wiki/#Bugs"><font color="#FF0000" size="3">bugs reported</font></a> <p>
 
 <p><a href="http://euroreves.ined.fr/imach/wiki/index.php/Documentation"><font color="#FF0000" size="6">Click
@@ -392,8 +388,11 @@ href="http://euroreves.ined.fr/imach/wiki/index.php/Documentation">http://eurore
 subscribe by sending a mail to <a
 href=mailto:imach-users-subscribe@listes.ined.fr>imach-users-subscribe@listes.ined.fr</a>
 (and unsubscribe with <a
-href=mailto:imach-users-unsubscribe@listes.ined.fr>imach-users-unsubscribe@listes.ined.fr</a>
-</p>
+href=mailto:imach-users-unsubscribe@listes.ined.fr>imach-users-unsubscribe@listes.ined.fr</a>)
+ for help, comments and
+      reports on the performance (see the Performance section of
+  the <a href="http://euroreves.ined.fr/imach/wiki">wiki</a>). Archives can be accessed at <a href="https://listes.ined.fr/arc/imach-users">https://listes.ined.fr/arc/imach-users</a>
+  <p> If you ask for help, it is usually easier to send the parameter file, the .log file as well as some records of the datafile.
 
 <h2>IMaCh Wiki</h2> As discussed at the REVES meeting
 in <a href="http://www.prw.le.ac.uk/cgi-bin/reves/2005.cgi">Beijing</a>,
diff --git a/src/Makefile b/src/Makefile
index d70833f..7e20338 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -1,13 +1,13 @@
-VERSION=0.98q2
+VERSION=0.98q4
 COPYRIGHT=Copyright (C)  2002-2015 INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121) - Intel Software 2015
-IMACHSETUPVERSION=ilc
+IMACHSETUPVERSION=icl
 # This is for Windows only
 #IMACHSETUPVERSION=mvc
 
 #       Linux
 # make _linux=1 imachopt
 # make _linux=1 imach
-#
+# cpack -D CPACK_RPM_PACKAGE_DEBUG=1 -D CPACK_RPM_SPEC_INSTALL_POST="/bin/true" -G RPM
 # make _linux32onosx=1 imachopt
 # make _linux64onosx=1 imachopt
 
@@ -21,7 +21,7 @@ IMACHSETUPVERSION=ilc
 #  valgrind  --dsymutil=yes --leak-check=full --show-leak-kinds=all --track-origins=yes ~/Documents/imachcvs/imach/src/imach-1.129cvsmac radlc-1.129.imach
 
 #        Windows
-# make _windowsonosx=1 imachILC-setup (touch setup.iss.in) #binary should have been compiled on Windows with Intel
+# make _windowsonosx=1 imachICL-setup (touch setup.iss.in) #binary should have been compiled on Windows with Intel
 # make _windowsonosx=1 imachMVC-setup (touch setup.iss.in) #binary should have been compiled on Windows with cl
 # make _windowsonosx=1 imachMVC-noreg-setup
 #
@@ -299,35 +299,68 @@ imachcyg-noreg-setup: imachcygopt.exe noreg-setup.iss
 	$(CP) imachcygopt.exe imach$(VERSION)-$(BINVERSION).exe
 	$(SETUPCOMP) /cc $(TMPNOREGSETUPSCRIPT)
 	cp Output/$(TMPNOREGSETUPEXE) imachcyg-noreg-setup
-
+# ICL compiler 64
+imachICL-build: imach.c
+	icl /GS /W3 /Zc:wchar_t /O2  /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "UNICODE" /Qipo /Zc:forScope  /MT imach.c 
+#/GS /W3 /Gy /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope /Oi /MT /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh-icl-x64-0.98q2.pch"
+#  /Users/nbrouard/Documents/imach/imach-gui/build/icl64/Release/imach.exe
 # both 32 and 64 executables should have been built on Windows with Intel compiler.
-imachILC-setup: IMaCh-ilc64-$(VERSION).exe IMaCh-ilc32-$(VERSION).exe setup.iss
+imachICL-setup: ../build/icl64/Release/IMaCh-$(VERSION).exe ../build/icl32/Release/IMaCh-$(VERSION).exe setup.iss mybuildicl64.bat mybuildicl32.bat
 	pwd
 	$(SETUPCOMP) /cc setup.iss
-	$(CP) Output/$(TMPSETUPEXE) imachILC-setup
+	$(CP) Output/$(TMPSETUPEXE) imachICL-setup
 
-imachILC64-setup: IMaCh-ilc64-$(VERSION).exe setup.iss
-	pwd
-	$(CP) IMaCh-ilc64-$(VERSION).exe imach.exe
-	$(SETUPCOMP) /cc setup.iss
-	$(CP) Output/$(TMPSETUPEXE) imachILC64-setup
+# imachICL64-setup: IMaCh-icl64-$(VERSION).exe setup.iss
+# 	pwd
+# 	$(CP) IMaCh-icl64-$(VERSION).exe imach.exe
+# 	$(SETUPCOMP) /cc setup.iss
+# 	$(CP) Output/$(TMPSETUPEXE) imachICL64-setup
 
-imachILC64-noreg-setup: IMaCh-ilc64-$(VERSION).exe noreg-setup.iss
+imachICL64-noreg-setup: IMaCh-icl64-$(VERSION).exe noreg-setup.iss
 	touch setup.iss.in
 	$(SETUPCOMP) /cc $(TMPNOREGSETUPSCRIPT)
-	$(CP) Output/$(TMPSETUPEXE) imachILC64-noreg-setup
-
-imachILC32-setup: IMaCh-ilc32-$(VERSION).exe setup.iss
-	touch setup.iss.in
-	$(CP) IMaCh-ilc32-$(VERSION).exe imach.exe
-	$(SETUPCOMP) /cc setup.iss
-	$(CP) Output/$(TMPSETUPEXE) imachILC32-setup
-
-imachILC32-noreg-setup: IMaCh-ilc32.exe noreg-setup.iss
+	$(CP) Output/$(TMPSETUPEXE) imachICL64-noreg-setup
+
+../build/icl64/Release/IMaCh-$(VERSION).exe: imach.c mybuildicl64.bat
+	rm -rf ../build/icl64  && mkdir ../build/icl64
+	cp mybuildicl64.bat ../build/icl64/
+	cd ../build/icl64
+	VBoxManage --nologo guestcontrol "Windows7-64" execute --image "C:\Windows\SysWOW64\cmd.exe" \
+	--username brouard  --verbose --wait-exit --wait-stdout  --wait-stderr -- "/c" "g:\imachcvs\NetBeans\imach\build\icl64\mybuildicl64.bat" "$(VERSION)"
+
+../build/icl32/Release/IMaCh-$(VERSION).exe: imach.c mybuildicl32.bat
+	rm -rf ../build/icl32 && mkdir -p ../build/icl32
+	cp mybuildicl32.bat ../build/icl32/
+	cd ../build/icl32
+	VBoxManage --nologo guestcontrol "Windows7-64" execute --image "C:\Windows\SysWOW64\cmd.exe" \
+	--username brouard  --verbose --wait-exit --wait-stdout -- "/c" "g:\imachcvs\NetBeans\imach\build\icl32\mybuildicl32.bat" "$(VERSION)"
+
+../build/vs32/Release/IMaCh-$(VERSION).exe: imach.c mybuildvs32.bat
+	rm -rf ../build/vs32 && mkdir -p ../build/vs32
+	cp mybuildvs32.bat ../build/vs32/
+	cd ../build/vs32
+	VBoxManage --nologo guestcontrol "Windows7-64" execute --image "C:\Windows\SysWOW64\cmd.exe" \
+	--username brouard  --verbose --wait-exit --wait-stdout -- "/c" "g:\imach\imach-gui\build\vs32\mybuildvs32.bat" "$(VERSION)"
+# C:\Windows\SysWOW64\cmd.exe /E:ON /V:ON /K "g:\imach\imach-gui\build\icl32\mybuild.bat"
+#WORK	--username brouard  --verbose --wait-exit --wait-stdout -- "/c" "c:\users\brouard\mybuild.bat"
+#	--username brouard  --verbose --wait-exit --wait-stdout -- "/c" "g: && cd \imach\imach-gui\build\icl32 && mybuild.bat"
+#	--username brouard  --verbose --wait-exit --wait-stdout -- "/c" "g: && cd \imach\imach-gui\build\icl32-xp  &&" "C:\Program Files (x86)\Microsoft Visual Studio 12.0\Common7\Tools\VsDevCmd.bat" "&&" "C:\Program Files (x86)\Intel\Composer XE 2015\bin\ipsxe-comp-vars.bat" "ia32" "vs2013" "&&" "msbuild imach-0.98q3.vcxproj /t:Build /p:Configuration=Release"
+#	--username brouard --wait-exit --wait-stdout -- "/c" "g: && cd \imach\imach-gui\build\icl32-xp\ &&C:\Windows\SysWOW64\cmd.exe /E:ON /V:ON /K ""C:\Program Files (x86)\Intel\Composer XE 2015\bin\ipsxe-comp-vars.bat" ia32 vs2013"&& msbuild imach.vcxproj >c:\users\brouard\totog.txt"
+#		--username brouard --wait-exit --wait-stdout -- "/c" "g: && dir >c:\users\brouard\totog.txt"
+#C:\Windows\SysWOW64\cmd.exe /E:ON /V:ON /K ""C:\Program Files (x86)\Intel\Composer XE 2015\bin\ipsxe-comp-vars.bat" ia32 vs2013"
+#C:\Windows\SysWOW64\cmd.exe /E:ON /V:ON /K ""C:\Program Files (x86)\Intel\Composer XE 2015\bin\ipsxe-comp-vars.bat" intel64 vs2013"
+
+imachICL64-setup: ../build/icl64/Release/IMaCh-$(VERSION).exe setup.iss mybuildicl64.bat
+
+imachICL32-setup: ../build/icl32/Release/IMaCh-$(VERSION).exe setup.iss mybuildicl32.bat
+
+imachVS32-setup: ../build/vs32/Release/IMaCh-$(VERSION).exe setup.iss mybuildvs32.bat
+
+imachICL32-noreg-setup: IMaCh-icl32.exe noreg-setup.iss
 	touch setup.iss.in
-	$(CP) IMaCh-ilc32.exe imach.exe
+	$(CP) IMaCh-icl32.exe imach.exe
 	$(SETUPCOMP) /cc $(TMPNOREGSETUPSCRIPT)
-	$(CP) Output/$(TMPSETUPEXE) imachILC32-noreg-setup
+	$(CP) Output/$(TMPSETUPEXE) imachICL32-noreg-setup
 
 imachMVC-setup: imachMVC.exe setup.iss
 	touch setup.iss.in
@@ -401,7 +434,7 @@ imachBOBYQAopt.o : imach.c
 
 imachopt : imachopt.o 
 	$(CC) $(LFLAGSOPT) -o imachopt imachopt.o
-#	ln -f imachopt imach
+	ln -f imachopt imach
 	$(CP) imachopt Output/imachopt$(VERSION)-$(BINVERSION)
 	$(CP) -f imach ../bin
 ifdef _intel64onosx
@@ -460,8 +493,9 @@ imachdmg : imachopt.o create-dmg applet IMaChInfo.plist.in IMaChPkgInfo.in IMaCh
 md5:
 	ls Output/* | xargs md5sum
 upload:
-	rsync -v Output/imach-0.98q2-ilc-setup.exe brouard@henry.ined.fr:/home/euroreves/html/imach/
-#rsync -v Output/* brouard@henry.ined.fr:/home/euroreves/html/imach/
+	rsync -v Output/IMaCh-0.98q4-icl-setup.exe brouard@henry.ined.fr:/home/euroreves/html/imach/Download
+	rsync -v Output/imach0.98q4.dmg brouard@henry.ined.fr:/home/euroreves/html/imach/Download
+#	rsync -v Output/* brouard@henry.ined.fr:/home/euroreves/html/imach/Download
 
 imachcyg : imachcyg.o
 	$(CC) $(LFLAGS) -o imach imachcyg.o
diff --git a/src/imach.c b/src/imach.c
index 09cffdd..c1d4866 100644
--- a/src/imach.c
+++ b/src/imach.c
@@ -1,6 +1,9 @@
 /* $Id$
   $State$
   $Log$
+  Revision 1.192  2015/07/16 16:49:02  brouard
+  Summary: Fixing some outputs
+
   Revision 1.191  2015/07/14 10:00:33  brouard
   Summary: Some fixes
 
@@ -693,7 +696,7 @@ typedef struct {
 /* $Id$ */
 /* $State$ */
 
-char version[]="Imach version 0.98q3, July 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
+char version[]="Imach version 0.98q4, July 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
 char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
@@ -4533,12 +4536,12 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
  }/* End k1 */
  fprintf(fichtm,"</ul>");
 
-
  fprintf(fichtm,"\
 \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
- - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+ - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
+ - 95%% confidence intervals and T statistics are in the log file.<br>\n", rfileres,rfileres);
 
- fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+ fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
 	 subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
  fprintf(fichtm,"\
  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
@@ -6558,7 +6561,7 @@ int main(int argc, char *argv[])
 	if(jj==i) continue;
 	j++;
 	fscanf(ficpar,"%1d%1d",&i1,&j1);
-	if ((i1 != i) && (j1 != j)){
+	if ((i1 != i) || (j1 != jj)){
 	  printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
 It might be a problem of design; if ncovcol and the model are correct\n \
 run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
@@ -6566,8 +6569,8 @@ run imach with mle=-1 to get a correct template of the parameter file.\n",numlin
 	}
 	fprintf(ficparo,"%1d%1d",i1,j1);
 	if(mle==1)
-	  printf("%1d%1d",i,j);
-	fprintf(ficlog,"%1d%1d",i,j);
+	  printf("%1d%1d",i,jj);
+	fprintf(ficlog,"%1d%1d",i,jj);
 	for(k=1; k<=ncovmodel;k++){
 	  fscanf(ficpar," %lf",&param[i][j][k]);
 	  if(mle==1){
@@ -7108,9 +7111,10 @@ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
     }
     
     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
-    for (i=1;i<=NDIM;i++) 
+    for (i=1;i<=NDIM;i++) {
       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-
+      fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+    }
     lsurv=vector(1,AGESUP);
     lpop=vector(1,AGESUP);
     tpop=vector(1,AGESUP);
@@ -7207,6 +7211,24 @@ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
+    printf("Parameters and 95%% confidence intervals\n");
+    fprintf(ficlog, "Parameters, T and confidence intervals\n");
+    for(i=1,jk=1; i <=nlstate; i++){
+      for(k=1; k <=(nlstate+ndeath); k++){
+	if (k != i) {
+	  printf("%d%d ",i,k);
+	  fprintf(ficlog,"%d%d ",i,k);
+	  for(j=1; j <=ncovmodel; j++){
+	    printf("%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
+	    fprintf(ficlog,"%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
+	    jk++; 
+	  }
+	  printf("\n");
+	  fprintf(ficlog,"\n");
+	}
+      }
+    }
+
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
@@ -7363,6 +7385,7 @@ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
     
     fscanf(ficpar,"pop_based=%d\n",&popbased);
+    fprintf(ficlog,"pop_based=%d\n",popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
-- 
2.43.0