version 1.4.6

DESCRIPTION

@@ -1,16 +1,16 @@
 Package: bifactorial
-Version: 1.4.5
-Date: 2010-11-22
+Version: 1.4.6
+Date: 2010-12-21
 Author: Peter Frommolt
 Maintainer: Peter Frommolt <peter.frommolt@uni-koeln.de>
 Title: Inferences for bi- and trifactorial trial designs
-Depends: mvtnorm,multcomp,lattice,graphics,methods,Rcpp (>= 0.7.4)
+Depends: mvtnorm,multcomp,lattice,graphics,methods,Rcpp (>= 0.8.8)
 LinkingTo: Rcpp
 Description: This package makes global and multiple inferences for
         given bi- and trifactorial clinical trial designs using
         bootstrap methods and a classical approach.
 URL: http://portal.ccg.uni-koeln.de
 License: GPL
-Packaged: 2010-11-22 08:20:52 UTC; frommolt
+Packaged: 2010-12-21 12:18:00 UTC; frommolt
 Repository: CRAN
-Date/Publication: 2010-11-22 10:40:41
+Date/Publication: 2010-12-21 17:03:09

src/Makevars

@@ -1,2 +1,2 @@
-PKG_CPPFLAGS = -I. `${R_HOME}/bin/Rscript -e "Rcpp:::CxxFlags()"`
+PKG_CPPFLAGS = -I.
 PKG_LIBS = `${R_HOME}/bin/Rscript -e "Rcpp:::LdFlags()"`

src/Makevars.win

@@ -1,2 +1,2 @@
-PKG_LIBS = `$(R_HOME)/bin$(R_ARCH_BIN)/Rscript -e 'Rcpp:::LdFlags()'`
-PKG_CXXFLAGS = `$(R_HOME)/bin$(R_ARCH_BIN)/Rscript -e 'Rcpp:::CxxFlags()'` -I.
+PKG_LIBS = $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "Rcpp:::LdFlags()")
+PKG_CXXFLAGS =  -I.

src/ave.cpp

@@ -1,17 +1,21 @@
 #include <iostream>
 #include <math.h>
 #include <time.h>
-#include "Rcpp.h"
-#include "misc.h"
+#include <Rcpp.h>
+#include <misc.h>
 #include <vector>
+
+using namespace Rcpp ;
+
 //Implementations of bootstrap algorithms for the AVE-test (Hung, 2000)
 //AVE-test based on Student's t-test in bifactorial designs
 RcppExport SEXP avestudent2(SEXP Yr,SEXP nr,SEXP sonstNr,SEXP sonstRr){
-  RcppResultSet rs; RcppVector<int> sonstN(sonstNr); RcppMatrix<int> n(nr);
-  int a,b,i,j,k=1,l,m,nsim=sonstN(0),A=sonstN(1),B=sonstN(2),count=0;
+  IntegerVector sonstN(sonstNr); 
+  NumericMatrix n(nr);
+  int a,b,i,j,k=1,m,nsim=sonstN(0),A=sonstN(1),B=sonstN(2),count=0;
   int ** anfang; double ** mx; double ** vx; double ** oldmean; double ** delta;
   anfang=new int *[A+1]; for(i=0;i<A+1;++i){anfang[i]=new int[B+1];}
-  RcppVector<double> sonstR(sonstRr),Y(Yr); vector<double> X(0),Z(0),tminst(A*B);
+  NumericVector sonstR(sonstRr),Y(Yr); vector<double> X(0),Z(0),tminst(A*B);
   double taveSc=sonstR(0),simerror=sonstR(1);
   mx=new double *[A+1]; for(i=0;i<A+1;++i){mx[i]=new double[B+1];}
   vx=new double *[A+1]; for(i=0;i<A+1;++i){vx[i]=new double[B+1];}
@@ -47,12 +51,16 @@ RcppExport SEXP avestudent2(SEXP Yr,SEXP nr,SEXP sonstNr,SEXP sonstRr){
     }}
     ++k;
   }
-  rs.add("count",count); rs.add("nsim",nsim); return rs.getReturnList();
+  return List::create( 
+      _["count"] = count, 
+      _["nsim"]  = nsim 
+  ) ;
 }
+
 //AVE-test based on Student's t-test in trifactorial designs
 RcppExport SEXP avestudent3(SEXP Yr,SEXP nr,SEXP sonstNr,SEXP sonstRr){
-  RcppResultSet rs; RcppVector<int> sonstN(sonstNr), n(nr); RcppVector<double> sonstR(sonstRr),Y(Yr);
-  int a,b,c,i,j,k=1,l,m,nsim=sonstN(0),A=sonstN(1),B=sonstN(2),C=sonstN(3);
+  IntegerVector sonstN(sonstNr), n(nr); NumericVector sonstR(sonstRr),Y(Yr);
+  int a,b,c,i,j,k=1,m,nsim=sonstN(0),A=sonstN(1),B=sonstN(2),C=sonstN(3);
   int *** anfang; anfang=new int **[A+1];
   for(i=0;i<A+1;++i){anfang[i]=new int *[B+1]; for(j=0;j<B+1;++j){anfang[i][j]=new int[C+1];}}
   double taveSc=sonstR(0),simerror=sonstR(1); int count=0;
@@ -100,13 +108,19 @@ RcppExport SEXP avestudent3(SEXP Yr,SEXP nr,SEXP sonstNr,SEXP sonstRr){
     }}
     ++k;
   }
-  rs.add("count",count); rs.add("nsim",nsim); return rs.getReturnList();
+  return List::create( 
+      _["count"] = count, 
+      _["nsim"] = nsim 
+      ); 
 }
+
 //AVE-test based on a Z statistic in bifactorial designs
 RcppExport SEXP avebinomial2(SEXP nr,SEXP pr,SEXP sonstNr,SEXP sonstRr){
-  RcppResultSet rs; RcppVector<int> sonstN(sonstNr); RcppMatrix<int> n(nr);
-  RcppVector<double> sonstR(sonstRr); RcppMatrix<double> p(pr); 
-  int a,b,i,j,k=1,l,m,nsim=sonstN(0),A=sonstN(1),B=sonstN(2);
+  IntegerVector sonstN(sonstNr); 
+  IntegerMatrix n(nr);
+  NumericVector sonstR(sonstRr); 
+  NumericMatrix p(pr); 
+  int a,b,k=1,nsim=sonstN(0),A=sonstN(1),B=sonstN(2);
   double zave=sonstR(0),simerror=sonstR(1),count=0,p1,p2;
   vector<double> zminst(A*B); vector<int> Z1(0),Z2(0);
   while(k<=nsim){
@@ -130,12 +144,17 @@ RcppExport SEXP avebinomial2(SEXP nr,SEXP pr,SEXP sonstNr,SEXP sonstRr){
     }}
     ++k;
   }
-  rs.add("count",count); rs.add("nsim",nsim); return rs.getReturnList();
+  return List::create( 
+      _["count"] = count, 
+      _["nsim"] = nsim
+  ); 
 }
+
 //AVE-test based on a Z statistic in trifactorial designs
 RcppExport SEXP avebinomial3(SEXP nr,SEXP pr,SEXP sonstNr,SEXP sonstRr){
-  RcppResultSet rs; RcppVector<int> sonstN(sonstNr), n(nr); RcppVector<double> sonstR(sonstRr), p(pr); 
-  int a,b,c,i,j,k=1,l,m,nsim=sonstN(0),A=sonstN(1),B=sonstN(2),C=sonstN(3);
+  IntegerVector sonstN(sonstNr), n(nr); 
+  NumericVector sonstR(sonstRr), p(pr); 
+  int a,b,c,k=1,nsim=sonstN(0),A=sonstN(1),B=sonstN(2),C=sonstN(3);
   double zave=sonstR(0),simerror=sonstR(1),count=0,p1,p2,pi;
   vector<double> zminst(A*B*C); vector<int> Z1(0),Z2(0);
   while(k<=nsim){
@@ -166,5 +185,7 @@ RcppExport SEXP avebinomial3(SEXP nr,SEXP pr,SEXP sonstNr,SEXP sonstRr){
     }}
     ++k;
   }
-  rs.add("count",count); rs.add("nsim",nsim); return rs.getReturnList();
+  return List::create(
+      _["count"] = count, 
+      _["nsim"] = nsim ) ;
 }

src/krit.cpp

@@ -1,17 +1,20 @@
 #include <iostream>
 #include <math.h>
 #include <time.h>
-#include "Rcpp.h"
-#include "misc.h"
-#include <vector>
+#include <Rcpp.h>
+#include <misc.h>
+
+using namespace Rcpp ;
+
 //Implementations of bootstrap algorithms for simultaneous confidence intervals
 //Confidence intervals based on Student's t-test in bifactorial designs
 RcppExport SEXP kritstudent2(SEXP Yr,SEXP nr,SEXP parNr){
-  int a,b,i,k=0,m; SEXP rl=0; RcppResultSet rs; RcppVector<int> parN(parNr),n(nr);
+  int a,b,i,k=0,m; 
+  IntegerVector parN(parNr),n(nr);
   int nsim=parN(0),A=parN(1),B=parN(2);
   int ** anfang; anfang=new int *[A+1];
   for(i=0;i<A+1;++i){anfang[i]=new int[B+1];}
-  RcppVector<double> Y(Yr),maxi(nsim),mini(nsim); 
+  NumericVector Y(Yr),maxi(nsim),mini(nsim); 
   vector<double> X(0),Z(0),tst(A*B);
   double ** mx; mx=new double *[A+1]; for(i=0;i<A+1;++i){mx[i]=new double[B+1];}
   double ** vx; vx=new double *[A+1]; for(i=0;i<A+1;++i){vx[i]=new double[B+1];}
@@ -30,17 +33,23 @@ RcppExport SEXP kritstudent2(SEXP Yr,SEXP nr,SEXP parNr){
       tst.push_back((mx[a][b]-mx[a][0])/sqrt((vx[a][b]/n(c2(a,b,B)))+(vx[a][0]/n(c2(a,0,B)))));
       tst.push_back((mx[a][b]-mx[0][b])/sqrt((vx[a][b]/n(c2(a,b,B)))+(vx[0][b]/n(c2(0,b,B)))));
     }}
-    mini(k)=minimalwert(tst); maxi(k)=maximalwert(tst); ++k;
+    mini[k]=minimalwert(tst); 
+    maxi[k]=maximalwert(tst); ++k;
   }
-  rs.add("mini",mini); rs.add("maxi",maxi); return rs.getReturnList();
+  return List::create( 
+      _["mini"] = mini,
+      _["maxi"] = maxi
+      ) ;
 }
+
 //Confidence intervals based on Student's t-test in trifactorial designs
 RcppExport SEXP kritstudent3(SEXP Yr,SEXP nr,SEXP parNr){
-  int a,b,c,i,j,k=0,m; SEXP rl=0; RcppResultSet rs; RcppVector<int> parN(parNr),n(nr);
+  int a,b,c,i,j,k=0,m; 
+  IntegerVector parN(parNr),n(nr);
   int nsim=parN(0),A=parN(1),B=parN(2),C=parN(3);
   int *** anfang; anfang=new int **[A+1];
   for(i=0;i<A+1;++i){anfang[i]=new int *[B+1]; for(j=0;j<B+1;++j){anfang[i][j]=new int[C+1];}}
-  RcppVector<double> Y(Yr),maxi(nsim),mini(nsim); 
+  NumericVector Y(Yr),maxi(nsim),mini(nsim); 
   vector<double> X(0),Z(0),tst(A*B);
   double *** mx; mx=new double **[A+1];
   for(i=0;i<A+1;++i){mx[i]=new double *[B+1]; for(j=0;j<B+1;++j){mx[i][j]=new double[C+1];}}
@@ -62,15 +71,20 @@ RcppExport SEXP kritstudent3(SEXP Yr,SEXP nr,SEXP parNr){
       tst.push_back((mx[a][b][c]-mx[a][0][c])/sqrt((vx[a][b][c]/n(c3(a,b,c,B,C)))+(vx[a][0][c]/n(c3(a,0,c,B,C)))));
       tst.push_back((mx[a][b][c]-mx[0][b][c])/sqrt((vx[a][b][c]/n(c3(a,b,c,B,C)))+(vx[0][b][c]/n(c3(0,b,c,B,C)))));
     }}}
-    mini(k)=minimalwert(tst); maxi(k)=maximalwert(tst); ++k;
+    mini[k]=minimalwert(tst); 
+    maxi[k]=maximalwert(tst); ++k;
   }
-  rs.add("mini",mini); rs.add("maxi",maxi); return rs.getReturnList();
+  return List::create( 
+      _["mini"] = mini, 
+      _["maxi"] = maxi
+  ) ;
 }
+
 //Confidence intervals based on a Z statistic in bifactorial designs
 RcppExport SEXP kritbinomial2(SEXP pr,SEXP nr,SEXP parNr){
-  int a,b,i,j,k=0,m; SEXP rl=0; RcppResultSet rs; RcppVector<int> parN(parNr),n(nr);
+  int a,b,i,k=0; IntegerVector parN(parNr),n(nr);
   int nsim=parN(0),A=parN(1),B=parN(2);
-  RcppVector<double> p(pr),maxi(nsim),mini(nsim); 
+  NumericVector p(pr),maxi(nsim),mini(nsim); 
   vector<int> X(0); vector<double> zst(A*B); double pm;
   double ** px; px=new double *[A+1]; for(i=0;i<A+1;++i){px[i]=new double[B+1];}
   double ** vx; vx=new double *[A+1]; for(i=0;i<A+1;++i){vx[i]=new double[B+1];}
@@ -86,15 +100,21 @@ RcppExport SEXP kritbinomial2(SEXP pr,SEXP nr,SEXP parNr){
       zst.push_back((px[a][b]-px[a][0])/sqrt((vx[a][b]/n(c2(a,b,B)))+(vx[a][0]/n(c2(a,0,B)))));
       zst.push_back((px[a][b]-px[0][b])/sqrt((vx[a][b]/n(c2(a,b,B)))+(vx[0][b]/n(c2(0,b,B)))));
     }}
-    mini(k)=minimalwert(zst); maxi(k)=maximalwert(zst); ++k;
+    mini[k]=minimalwert(zst); 
+    maxi[k]=maximalwert(zst); ++k;
   }
-  rs.add("mini",mini); rs.add("maxi",maxi); return rs.getReturnList();
-}
+  return List::create( 
+      _["mini"] = mini, 
+      _["maxi"] = maxi
+  ) ;
+}    
+
 //Confidence intervals based on a Z statistic in trifactorial designs
 RcppExport SEXP kritbinomial3(SEXP pr,SEXP nr,SEXP parNr){
-  int a,b,c,i,j,k=0,m; RcppResultSet rs; RcppVector<int> parN(parNr),n(nr);
+  int a,b,c,i,j,k=0; 
+  IntegerVector parN(parNr),n(nr);
   int nsim=parN(0),A=parN(1),B=parN(2),C=parN(3);
-  RcppVector<double> p(pr),maxi(nsim),mini(nsim); 
+  NumericVector p(pr),maxi(nsim),mini(nsim); 
   vector<int> X(0); vector<double> zst(A*B*C); 
   double *** px; px=new double **[A+1];
   for(i=0;i<A+1;++i){px[i]=new double *[B+1]; for(j=0;j<B+1;++j){px[i][j]=new double[C+1];}}
@@ -121,5 +141,8 @@ RcppExport SEXP kritbinomial3(SEXP pr,SEXP nr,SEXP parNr){
     }}}
     mini(k)=minimalwert(zst); maxi(k)=maximalwert(zst); ++k;
   }
-  rs.add("mini",mini); rs.add("maxi",maxi); return rs.getReturnList();
+  return List::create( 
+      _["mini"] = mini, 
+      _["maxi"] = maxi
+  ) ;
 }

src/misc.cpp

@@ -6,7 +6,7 @@ using namespace std;
 #include <valarray> 
 using std::valarray;
 #include <time.h>
-#include "Rcpp.h"
+#include <Rcpp.h>
 //Determine largest integer smaller than x///////////////////////////
 int gaussklammer(double x){
   int k=0;
@@ -78,12 +78,12 @@ double summe(vector<int>& X){
 //Determine the minimum of x and y///////////////////////////////////
 double min(double x, double y){
   if(x<=y){ return x; }
-  if(y<=x){ return y; }
+  return y;
 }
 //Determine the maximum of x and y///////////////////////////////////
 double max(double x, double y){
   if(x>=y){ return x; }
-  if(y>=x){ return y; }
+  return y;
 }
 //Determine the minimum of the data X////////////////////////////////
 double minimalwert(vector<double>& X){
@@ -109,8 +109,9 @@ double betrag(double x){
   else{return -x;}
 }
 //Calculate number of simulations according to prespecified standard error
-int newnsim(RcppVector<int>& count,int k, int nsim,double simerror,int D){
-  vector<double> abst(D); int l,lmax;
+int newnsim(Rcpp::IntegerVector& count,int k, int nsim,double simerror,int D){
+  vector<double> abst(D);
+  int l,lmax=0;
   if(simerror!=9 & k==900){
     for(l=0;l<=D-1;++l){abst[l]=betrag(double(count(l))-double(450));}
     for(l=0;l<=D-1;++l){if(abst[l]==minimalwert(abst)){lmax=l;}}//Der Fehler wird für p=.5 maximal

src/misc.h

@@ -12,7 +12,7 @@ double max(double x, double y);
 double maximalwert(vector<double>& X);
 double minimalwert(vector<double>& X);
 double betrag(double x);
-int newnsim(RcppVector<int>& count, int k, int nsim,double simerror,int D);
+int newnsim(Rcpp::IntegerVector& count, int k, int nsim,double simerror,int D);
 int c2(int a,int b,int B);
 int c20(int a,int b,int B);
 int c3(int a,int b,int c,int B,int C);