@@ -1,3 +1,4 @@

+// Copyright [2014] <Fred Hutchinson Cancer Research Center>

 // This file was automatically generated by Kmisc::registerFunctions()

 #include <R.h>

@@ -1,14 +1,14 @@

+// Copyright [2014] <Fred Hutchinson Cancer Research Center>

 // [[Rcpp::interfaces(r)]]

 #include <Rcpp.h>

 using namespace Rcpp;

 template <typename T>

-T my_abs( const T& x){

-	return ::abs(x) ;

+T my_abs(const T& x) {

+  return ::abs(x);

 }

-

 #define rownames(x) as<CharacterVector>(VECTOR_ELT(x.attr("dimnames"), 0))

 #define colnames(x) as<CharacterVector>(VECTOR_ELT(x.attr("dimnames"), 1))

@@ -28,7 +28,6 @@ T my_abs( const T& x){

 // [[Rcpp::export(.CellCounts)]]

 IntegerMatrix CellCounts(List x, List combos) {

-

   int x_n = x.size();

   int combos_n = combos.size();

   IntegerMatrix output(x_n, combos_n);

@@ -38,22 +37,20 @@ IntegerMatrix CellCounts(List x, List combos) {

     LogicalMatrix mat = as<LogicalMatrix>(x[i]);

     int nrows = mat.nrow();

     for (int k = 0; k < combos_n; ++k) {

-

       int num = 0;

       IntegerVector c_combo = as<IntegerVector>(combos[k]);

       int n_c = c_combo.size();

-      IntegerVector c_combo_abs = sapply(c_combo,my_abs<int>);

+      IntegerVector c_combo_abs = sapply(c_combo, my_abs<int>);

       for (int j = 0; j < nrows; ++j) {

-

         LogicalMatrix::Row row = mat(j, _);

-// checking algorithm:

-// we loop through each entry in 'c_combo' => p

-// we check the element in 'row' at 'abs(c_combo[p])'

-// if 'abs(c_combo[p])' is > 0 and row[ c_combo[p] ] is true; continue

-// if 'abs(c_combo[p])' is <= 0 and row[ c_combo[p] ] is false; continue

-// else, 'false_case'

+        // checking algorithm:

+        // we loop through each entry in 'c_combo' => p

+        // we check the element in 'row' at 'abs(c_combo[p])'

+        // if 'abs(c_combo[p])' is > 0 and row[ c_combo[p] ] is true; continue

+        // if 'abs(c_combo[p])' is <= 0 and row[ c_combo[p] ] is false; continue

+        // else, 'false_case'

 #define c (c_combo[p])

 #define abs_c (c_combo_abs[p])

@@ -86,8 +83,8 @@ IntegerMatrix CellCounts(List x, List combos) {

   }

   if (!Rf_isNull(combos.attr("names"))) {

-    SET_VECTOR_ELT(

-        output.attr("dimnames"), 1, Rf_duplicate(combos.attr("names")));

+    SET_VECTOR_ELT(output.attr("dimnames"), 1,

+                   Rf_duplicate(combos.attr("names")));

   }

   return output;

@@ -1,13 +1,12 @@

+// Copyright [2014] <Fred Hutchinson Cancer Research Center>

 // [[Rcpp::interfaces(r)]]

 #include <Rcpp.h>

 using namespace Rcpp;

-

 extern "C" SEXP mat2vec(SEXP);

 // [[Rcpp::export]]

 IntegerMatrix CellCounts_character(List data, List combinations) {

-

   Function list2env("list2env");

   int m = data.size();          // rows

@@ -16,7 +15,6 @@ IntegerMatrix CellCounts_character(List data, List combinations) {

   // loop over data

   for (int i = 0; i < m; ++i) {

-

     SEXP m = PROTECT(mat2vec(as<LogicalMatrix>(data[i])));

     Environment env = list2env(m);

@@ -1,3 +1,5 @@

+// Copyright [2014] <Fred Hutchinson Cancer Research Center>

+

 // Generated by using Rcpp::compileAttributes() -> do not edit by hand

 // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

@@ -8,24 +10,25 @@ using namespace Rcpp;

 // CellCounts

 IntegerMatrix CellCounts(List x, List combos);

 RcppExport SEXP _COMPASS_CellCounts(SEXP xSEXP, SEXP combosSEXP) {

-BEGIN_RCPP

-    Rcpp::RObject rcpp_result_gen;

-    Rcpp::RNGScope rcpp_rngScope_gen;

-    Rcpp::traits::input_parameter< List >::type x(xSEXP);

-    Rcpp::traits::input_parameter< List >::type combos(combosSEXP);

-    rcpp_result_gen = Rcpp::wrap(CellCounts(x, combos));

-    return rcpp_result_gen;

-END_RCPP

+  BEGIN_RCPP

+  Rcpp::RObject rcpp_result_gen;

+  Rcpp::RNGScope rcpp_rngScope_gen;

+  Rcpp::traits::input_parameter<List>::type x(xSEXP);

+  Rcpp::traits::input_parameter<List>::type combos(combosSEXP);

+  rcpp_result_gen = Rcpp::wrap(CellCounts(x, combos));

+  return rcpp_result_gen;

+  END_RCPP

 }

 // CellCounts_character

 IntegerMatrix CellCounts_character(List data, List combinations);

-RcppExport SEXP _COMPASS_CellCounts_character(SEXP dataSEXP, SEXP combinationsSEXP) {

-BEGIN_RCPP

-    Rcpp::RObject rcpp_result_gen;

-    Rcpp::RNGScope rcpp_rngScope_gen;

-    Rcpp::traits::input_parameter< List >::type data(dataSEXP);

-    Rcpp::traits::input_parameter< List >::type combinations(combinationsSEXP);

-    rcpp_result_gen = Rcpp::wrap(CellCounts_character(data, combinations));

-    return rcpp_result_gen;

-END_RCPP

+RcppExport SEXP _COMPASS_CellCounts_character(SEXP dataSEXP,

+                                              SEXP combinationsSEXP) {

+  BEGIN_RCPP

+  Rcpp::RObject rcpp_result_gen;

+  Rcpp::RNGScope rcpp_rngScope_gen;

+  Rcpp::traits::input_parameter<List>::type data(dataSEXP);

+  Rcpp::traits::input_parameter<List>::type combinations(combinationsSEXP);

+  rcpp_result_gen = Rcpp::wrap(CellCounts_character(data, combinations));

+  return rcpp_result_gen;

+  END_RCPP

 }

@@ -1,3 +1,4 @@

+// Copyright [2014] <Fred Hutchinson Cancer Research Center>

 #include <math.h>

 double digamma(double x) {

@@ -1,3 +1,4 @@

+// Copyright [2014] <Fred Hutchinson Cancer Research Center>

 #define USE_RINTERNALS

 #include <R.h>

@@ -1,3 +1,4 @@

+// Copyright [2014] <Fred Hutchinson Cancer Research Center>

 #define USE_RINTERNALS

 #include <R.h>

@@ -1,24 +1,19 @@

+// Copyright [2014] <Fred Hutchinson Cancer Research Center>

+

 #include <Rcpp.h>

 using namespace Rcpp;

 // [[register]]

-RcppExport SEXP samplePuPs(SEXP alphau,

-                           SEXP alphas,

-                           SEXP gammat,

-                           SEXP T,

-                           SEXP K,

-                           SEXP nsi,

-                           SEXP nui,

-                           SEXP d,

-                           SEXP M) {

+RcppExport SEXP samplePuPs(SEXP alphau, SEXP alphas, SEXP gammat, SEXP T,

+                           SEXP K, SEXP nsi, SEXP nui, SEXP d, SEXP M) {

   BEGIN_RCPP

-  IntegerVector xnsi(nsi);        // n_s[i,]

-  IntegerVector xnui(nui);        // n_u[i,]

-  NumericMatrix xalphau(alphau);  // posterior samples for alpha_u

-  NumericMatrix xalphas(alphas);  // posterior samples for alpha_s

-  IntegerMatrix xgammat(gammat);  // posterior samples for gamma_i

-  IntegerMatrix xd(d);            // cytokine combination indicator matrix

+  IntegerVector xnsi(nsi);        //  n_s[i,]

+  IntegerVector xnui(nui);        //  n_u[i,]

+  NumericMatrix xalphau(alphau);  //  posterior samples for alpha_u

+  NumericMatrix xalphas(alphas);  //  posterior samples for alpha_s

+  IntegerMatrix xgammat(gammat);  //  posterior samples for gamma_i

+  IntegerMatrix xd(d);            //  cytokine combination indicator matrix

   // int xM = as<int>(M); // # markers

   int xT = as<int>(T);  // # MCMC iterations used

@@ -94,7 +89,6 @@ RcppExport SEXP samplePuPs(SEXP alphau,

       std::vector<double> as(sum);

       sass = 0.;

       for (int j = 0; j < sum; j++) {

-

         as[j] = alpha_s[place1[j]];

         sass += as[j];

       }

@@ -119,8 +113,8 @@ RcppExport SEXP samplePuPs(SEXP alphau,

   p_s = p_s[seq(0, p_s.size() - 2)];

   p_u = p_u[seq(0, p_u.size() - 2)];

-  return List::create(

-      _["p_s"] = p_s, _["p_u"] = p_u, _["diff"] = DIFF, _["logd"] = LogD);

+  return List::create(_["p_s"] = p_s, _["p_u"] = p_u, _["diff"] = DIFF,

+                      _["logd"] = LogD);

   END_RCPP

 }

@@ -1,18 +1,12 @@

+// Copyright [2014] <Fred Hutchinson Cancer Research Center>

 #include <Rcpp.h>

 extern "C" double digamma(double);

 // [[register]]

-RcppExport SEXP updatealphas_Exp(SEXP alphast,

-                                 SEXP n_s,

-                                 SEXP K,

-                                 SEXP I,

-                                 SEXP lambda_s,

-                                 SEXP gammat,

-                                 SEXP var_1,

-                                 SEXP var_2,

-                                 SEXP p_var,

-                                 SEXP ttt) {

+RcppExport SEXP updatealphas_Exp(SEXP alphast, SEXP n_s, SEXP K, SEXP I,

+                                 SEXP lambda_s, SEXP gammat, SEXP var_1,

+                                 SEXP var_2, SEXP p_var, SEXP ttt) {

   BEGIN_RCPP

   Rcpp::NumericVector xalphast(alphast);

@@ -1,16 +1,11 @@

+// Copyright [2014] <Fred Hutchinson Cancer Research Center>

 #include <Rcpp.h>

 extern "C" double digamma(double);

 // [[register]]

-RcppExport SEXP updatealphau_noPu_Exp(SEXP alphaut,

-                                      SEXP n_s,

-                                      SEXP n_u,

-                                      SEXP I,

-                                      SEXP K,

-                                      SEXP lambda_u,

-                                      SEXP var_p,

-                                      SEXP ttt,

-                                      SEXP gammat) {

+RcppExport SEXP updatealphau_noPu_Exp(SEXP alphaut, SEXP n_s, SEXP n_u, SEXP I,

+                                      SEXP K, SEXP lambda_u, SEXP var_p,

+                                      SEXP ttt, SEXP gammat) {

   BEGIN_RCPP

   Rcpp::IntegerMatrix xgammat(gammat);

   Rcpp::NumericVector xalphaut(alphaut);

@@ -1,25 +1,14 @@

-#include <Rcpp.h>

+// Copyright [2014] <Fred Hutchinson Cancer Research Center>

 #include <R_ext/Utils.h>

+#include <Rcpp.h>

 #include <stdlib.h>

 // [[register]]

-RcppExport SEXP updategammak_noPu(SEXP n_s,

-                                  SEXP n_u,

-                                  SEXP gammat,

-                                  SEXP I,

-                                  SEXP K,

-                                  SEXP SS,

-                                  SEXP alphau,

-                                  SEXP alphas,

-                                  SEXP alpha,

-                                  SEXP mk,

-                                  SEXP Istar,

-                                  SEXP mKstar,

-                                  SEXP pp,

-                                  SEXP pb1,

-                                  SEXP pb2,

-                                  SEXP indi) {

+RcppExport SEXP updategammak_noPu(SEXP n_s, SEXP n_u, SEXP gammat, SEXP I,

+                                  SEXP K, SEXP SS, SEXP alphau, SEXP alphas,

+                                  SEXP alpha, SEXP mk, SEXP Istar, SEXP mKstar,

+                                  SEXP pp, SEXP pb1, SEXP pb2, SEXP indi) {

   BEGIN_RCPP

   Rcpp::IntegerMatrix xn_s(n_s);

@@ -358,11 +347,10 @@ RcppExport SEXP updategammak_noPu(SEXP n_s,

     }

   }

-  return Rcpp::List::create(Rcpp::Named("gamma_tt") = gamma_tt,

-                            Rcpp::Named("Ag") = xAg,

-                            Rcpp::Named("mKstar") = xmKstar,

-                            Rcpp::Named("xmk") = xmk,

-                            Rcpp::Named("xIstar") = xIstar);

+  return Rcpp::List::create(

+      Rcpp::Named("gamma_tt") = gamma_tt, Rcpp::Named("Ag") = xAg,

+      Rcpp::Named("mKstar") = xmKstar, Rcpp::Named("xmk") = xmk,

+      Rcpp::Named("xIstar") = xIstar);

   END_RCPP

 }