Cleanup legacy code

juliangehring · Oct 16, 2015 · d9bc118 · d9bc118
1 parent 97ec03b
commit d9bc118
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: HighSpeedStats
 Type: Package
 Title: High Speed Stats
-Version: 1.0.0
+Version: 1.1.0
 Author: Julian Gehring
 Maintainer: Julian Gehring <[email protected]>
 Imports: Rcpp (>= 0.11.0)

diff --git a/R/fisher-exact-test-functions.R b/R/fisher-exact-test-functions.R
@@ -3,21 +3,11 @@ fisherExactTest <- function(a, b, c, d) {
 }
 
 
-.fastfet <- function(a, b, c, d) {
-    .Call('HighSpeedStats_fastfet', PACKAGE = 'HighSpeedStats', a, b, c, d)
-}
-
-
 ultrafastfet <- function(a, b, c, d) {
     .Call('HighSpeedStats_ultrafastfet', PACKAGE = 'HighSpeedStats', a, b, c, d)
 }
 
 
-.jltrafastfet <- function(a, b, c, d) {
-    .Call('HighSpeedStats_jltrafastfet', PACKAGE = 'HighSpeedStats', a, b, c, d)
-}
-
-
 feTestR <- function (a, b, c, d, relErr = 1 + 1e-07)  {
 
     pval = mapply(function(x1, x2, n1, n2) {

diff --git a/README.org b/README.org
@@ -7,9 +7,6 @@
 [[https://codecov.io/github/julian-gehring/HighSpeedStats?branch=master][file:https://codecov.io/github/julian-gehring/HighSpeedStats/coverage.svg?branch=master]]
 
 
-[[file:https:/codecov.io/github/julian-gehring/HighSpeedStats/coverage.svg?branch=master][https://codecov.io]]
-
-
 ** Motivation
 
 The amount of data in the field of computational biology increases at a fast

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -39,26 +39,6 @@ END_RCPP
 }
 
 
-// fastfet
-SEXP fastfet(SEXP a, SEXP b, SEXP c, SEXP d);
-RcppExport SEXP HighSpeedStats_fastfet(SEXP aSEXP, SEXP bSEXP, SEXP cSEXP, SEXP dSEXP) {
-BEGIN_RCPP
-    SEXP __sexp_result;
-    {
-        Rcpp::RNGScope __rngScope;
-        Rcpp::traits::input_parameter< SEXP >::type a(aSEXP );
-        Rcpp::traits::input_parameter< SEXP >::type b(bSEXP );
-        Rcpp::traits::input_parameter< SEXP >::type c(cSEXP );
-        Rcpp::traits::input_parameter< SEXP >::type d(dSEXP );
-        SEXP __result = fastfet(a, b, c, d);
-        PROTECT(__sexp_result = Rcpp::wrap(__result));
-    }
-    UNPROTECT(1);
-    return __sexp_result;
-END_RCPP
-}
-
-
 // ultrafastfet
 SEXP ultrafastfet(SEXP a, SEXP b, SEXP c, SEXP d);
 RcppExport SEXP HighSpeedStats_ultrafastfet(SEXP aSEXP, SEXP bSEXP, SEXP cSEXP, SEXP dSEXP) {
@@ -77,23 +57,3 @@ BEGIN_RCPP
     return __sexp_result;
 END_RCPP
 }
-
-
-// jltrafastfet
-SEXP jltrafastfet(SEXP a, SEXP b, SEXP c, SEXP d);
-RcppExport SEXP HighSpeedStats_jltrafastfet(SEXP aSEXP, SEXP bSEXP, SEXP cSEXP, SEXP dSEXP) {
-BEGIN_RCPP
-    SEXP __sexp_result;
-    {
-        Rcpp::RNGScope __rngScope;
-        Rcpp::traits::input_parameter< SEXP >::type a(aSEXP );
-        Rcpp::traits::input_parameter< SEXP >::type b(bSEXP );
-        Rcpp::traits::input_parameter< SEXP >::type c(cSEXP );
-        Rcpp::traits::input_parameter< SEXP >::type d(dSEXP );
-        SEXP __result = jltrafastfet(a, b, c, d);
-        PROTECT(__sexp_result = Rcpp::wrap(__result));
-    }
-    UNPROTECT(1);
-    return __sexp_result;
-END_RCPP
-}
diff --git a/src/fastFisherExactTest.cpp b/src/fastFisherExactTest.cpp
diff --git a/src/ultraFastFisherExactTest.cpp b/src/ultraFastFisherExactTest.cpp
@@ -58,48 +58,3 @@ SEXP ultrafastfet(SEXP a, SEXP b, SEXP c, SEXP d) {
 
   return wrap(pval);
 }
-
-
-double jfet(int a, int b, int c, int d, double* logFacs) {
-  double logpCutoff = ulogHypergeometricProb(logFacs, a, b, c, d);
-  double pFraction = 0;
-  int n = a + b + c + d;
-  for(int x=0; x <= n; ++x) {
-    if ( a+b-x >= 0 && a+c-x >= 0 && d-a+x >=0 ) {
-      double l = ulogHypergeometricProb(logFacs, x, a+b-x, a+c-x, d-a+x);
-      if ( l <= logpCutoff ) {
-        pFraction += exp(l - logpCutoff);
-      }
-    }
-  }
-  double logpValue = logpCutoff + log(pFraction); // normalization: p_i = p_i / sum_i(p_i)
-  double pval = exp(logpValue);
-
-  return pval;
-}
-
-
-
-// [[Rcpp::export]]
-SEXP jltrafastfet(SEXP a, SEXP b, SEXP c, SEXP d) {
-
-  Rcpp::IntegerVector a_(a), b_(b), c_(c), d_(d);
-  Rcpp::NumericVector pval(a);
-  int n = a_.size();
-
-  int m = 0;
-  for(int i = 0; i < n; i++) {
-    m = fmax(m, a_(i) + b_(i) + c_(i) + d_(i));
-  }
-
-  double* ulogFacs = new double[m+1];
-  uinitLogFacs(ulogFacs, m);
-
-  for(int i = 0; i < n; i++) {
-    pval(i) = jfet(a_(i), b_(i), c_(i), d_(i), ulogFacs);
-  }
-
-  delete [] ulogFacs;
-
-  return wrap(pval);
-}