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

 Package: CoGAPS

-Version: 2.6.0

+Version: 2.5.10

 Date: 2014-08-23

 Title: Coordinated Gene Activity in Pattern Sets

 Author: Wai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey, Genevieve

@@ -118,7 +118,7 @@ gapsRun <- function(D, S, ABins = data.frame(), PBins = data.frame(),

   names(cogapResult)[13] = "meanChi2";

   if (messages)

-    message(paste("Chi-Squared of Mean:",calcChiSq))

+    message(paste("Chi-Squared of Mean:", calcChiSq))

   return(cogapResult);

 }

@@ -1,8 +1,12 @@

 library(CoGAPS)

+print(packageVersion('CoGAPS'))

+

 data(SimpSim)

 nIter <- 1000

-eat <- gapsRun(SimpSim.D, SimpSim.S, nFactor=3, messages=FALSE, seed=12345)

+nFactor <- 7

+eat <- gapsRun(D=SimpSim.D, S=SimpSim.S, nEquil=nIter, nSample=nIter,

+    nFactor=nFactor, seed=12345)

 #data(GIST_TS_20084)

 #nIter <- 3000

@@ -1,6 +1,7 @@

 #!/bin/bash

 rm -f callgrind.out.*

-R -d "valgrind --tool=callgrind" -f profile_standard.R > valgrind_out.txt

+rm -f vgcore.*

+R -d "valgrind --tool=callgrind" -f profile_standard.R

 kcachegrind callgrind.out.*

deleted file mode 100644

@@ -1,20 +0,0 @@

-

-R version 3.4.1 (2017-06-30) -- "Single Candle"

-Copyright (C) 2017 The R Foundation for Statistical Computing

-Platform: x86_64-pc-linux-gnu (64-bit)

-

-R is free software and comes with ABSOLUTELY NO WARRANTY.

-You are welcome to redistribute it under certain conditions.

-Type 'license()' or 'licence()' for distribution details.

-

-  Natural language support but running in an English locale

-

-R is a collaborative project with many contributors.

-Type 'contributors()' for more information and

-'citation()' on how to cite R or R packages in publications.

-

-Type 'demo()' for some demos, 'help()' for on-line help, or

-'help.start()' for an HTML browser interface to help.

-Type 'q()' to quit R.

-

-> library(CoGAPS)

@@ -41,7 +41,7 @@ uint64_t AtomicSupport::randomFreePosition() const

     do

     {

         pos = gaps::random::uniform64();

-    } while (mAtomicDomain.count(pos));

+    } while (mAtomicDomain.count(pos) > 0);

     return pos;

 }

@@ -56,15 +56,15 @@ uint64_t AtomicSupport::randomAtomPosition() const

 AtomicProposal AtomicSupport::proposeDeath() const

 {

     uint64_t location = randomAtomPosition();

-    uint64_t mass = mAtomicDomain.at(location);

+    double mass = mAtomicDomain.at(location);

     return AtomicProposal(mLabel, 'D', location, -mass);

 }

 AtomicProposal AtomicSupport::proposeBirth() const

 {

     uint64_t location = randomFreePosition();

-    uint64_t mass = gaps::random::exponential(mLambda);

-    return AtomicProposal(mLabel, 'B', location, mass);

+    double mass = gaps::random::exponential(mLambda);

+    return AtomicProposal(mLabel, 'B', location, std::max(mass, EPSILON));

 }

 // move atom between adjacent atoms

@@ -72,7 +72,7 @@ AtomicProposal AtomicSupport::proposeMove() const

 {

     // get random atom

     uint64_t location = randomAtomPosition();

-    uint64_t mass = mAtomicDomain.at(location);

+    double mass = mAtomicDomain.at(location);

     // get an iterator to this atom

     std::map<uint64_t, double>::const_iterator it;

@@ -130,7 +130,7 @@ void AtomicSupport::updateAtomMass(uint64_t pos, double delta)

         mTotalMass += delta;

         mNumAtoms++;

     }

-    if (mAtomicDomain.at(pos) <= EPSILON) // check if atom is too small

+    if (mAtomicDomain.at(pos) < EPSILON) // check if atom is too small

     {

         mTotalMass -= mAtomicDomain.at(pos);

         mAtomicDomain.erase(pos);

@@ -138,8 +138,6 @@ void AtomicSupport::updateAtomMass(uint64_t pos, double delta)

     }

 }

-#define GEOM_F(x) (((double) (x)) / ((double) (x + 1)))

-#define POISS_F(x,y) ((double)((x) * (y)) / (double)((x) - (y)))

 AtomicProposal AtomicSupport::makeProposal() const

 {

     if (mNumAtoms == 0)

@@ -148,7 +146,7 @@ AtomicProposal AtomicSupport::makeProposal() const

     }

     double unif = gaps::random::uniform();

-    if (mNumAtoms < 2 && unif <= 0.6667 || unif <= 0.5) // birth/death

+    if ((mNumAtoms < 2 && unif <= 0.6667) || unif <= 0.5) // birth/death

     {

         if (mNumAtoms >= mMaxNumAtoms)

         {

@@ -158,15 +156,20 @@ AtomicProposal AtomicSupport::makeProposal() const

         double pDelete = 0.5; // default uniform prior for mAlpha == 0

         if (mAlpha > 0) // poisson prior

         {

-            pDelete = 1 + POISS_F(mMaxNumAtoms, mNumAtoms) / (mAlpha * mNumBins);

+            double dMax = (double)mMaxNumAtoms;

+            double dNum = (double)mNumAtoms;

+            double maxTerm = (dMax - dNum) / dMax;

+

+            pDelete = dNum / (dNum + mAlpha * (double)mNumBins * maxTerm);

         }

         else if (mAlpha < 0) // geometric prior

         {

-            pDelete = 1 + GEOM_F(mNumAtoms) / GEOM_F(-mAlpha * mNumBins);

+            double c = -mAlpha * mNumBins / (-mAlpha * mNumBins + 1.0);

+            pDelete = (double)mNumAtoms / ((mNumAtoms + 1) * c + (double)mNumAtoms);

         }

         return gaps::random::uniform() < pDelete ? proposeDeath() : proposeBirth();

     }

-    return mNumAtoms < 2 || unif <= 0.75 ? proposeMove() : proposeExchange();

+    return (mNumAtoms < 2 || unif >= 0.75) ? proposeMove() : proposeExchange();

 }

 void AtomicSupport::acceptProposal(const AtomicProposal &prop)

@@ -100,7 +100,7 @@ public:

     // setters

     void setAlpha(double alpha) {mAlpha = alpha;}

     void setLambda(double lambda) {mLambda = lambda;}

-    void setMaxNumAtoms(uint64_t max) {mMaxNumAtoms = max;}

+    //void setMaxNumAtoms(uint64_t max) {mMaxNumAtoms = max;}

 };

 #endif

@@ -40,8 +40,6 @@ double maxGibbsMassP, int seed=-1, bool messages=false, bool singleCellRNASeq=fa

     chi2Vec.concat(chi2VecSample);

-    // compute statistics

-

     //Just leave the snapshots as empty lists

     return Rcpp::List::create(

         Rcpp::Named("Amean") = sampler.AMeanRMatrix(),

@@ -2,6 +2,7 @@

 #include "Algorithms.h"

 #include <Rcpp.h>

+#include <iostream>

 #define EPSILON 1E-10

@@ -25,6 +26,11 @@ mStatUpdates(0)

     mADomain.setLambda(alphaA * sqrt(nFactor / meanD));

     mPDomain.setAlpha(alphaP);

     mPDomain.setLambda(alphaP * sqrt(nFactor / meanD));

+

+    std::cout << "A lambda: " << mADomain.lambda() << "\n";

+    std::cout << "A alpha: " << mADomain.alpha() << "\n";

+    std::cout << "P lambda: " << mPDomain.lambda() << "\n";

+    std::cout << "P alpha: " << mPDomain.alpha() << "\n";

 }

 double GibbsSampler::getGibbsMass(const MatrixChange &change)

@@ -130,7 +136,7 @@ const AtomicProposal &proposal, double rejectProb)

 {

     MatrixChange change = domain.getMatrixChange(proposal);

     double delLL = computeDeltaLL(change);

-    if (delLL * mAnnealingTemp > rejectProb)

+    if (delLL * mAnnealingTemp >= rejectProb)

     {

         domain.acceptProposal(proposal);

         change.label == 'A' ? mAMatrix.update(change) : mPMatrix.update(change);

@@ -323,6 +329,10 @@ void GibbsSampler::updateStatistics()

     for (unsigned r = 0; r < mPMatrix.nRow(); ++r)

     {

         normVec(r) = gaps::algo::sum(mPMatrix.getRow(r));

+        if (normVec(r) == 0)

+        {

+            normVec(r) = 1.0;

+        }

     }

     for (unsigned c = 0; c < mAMeanMatrix.nCol(); ++c)

@@ -11,4 +11,4 @@ OBJECTS =   Algorithms.o \

             cpp_tests/testMatrix.o \

             cpp_tests/testAlgorithms.o \

             cpp_tests/testAtomicSupport.o \

-            cpp_tests/testGibbsSampler.o

+            cpp_tests/testGibbsSampler.o

\ No newline at end of file

@@ -21,7 +21,8 @@ struct MatrixChange

     matrix_data_t delta2;

     MatrixChange(char l, unsigned r, unsigned c, double d)

-        : label(l), nChanges(1), row1(r), col1(c), delta1(d)

+        : label(l), nChanges(1), row1(r), col1(c), delta1(d), row2(0),

+        col2(0), delta2(0.0)

     {}

     MatrixChange(char l, unsigned r1, unsigned c1, double d1, unsigned r2,

@@ -4,12 +4,10 @@

 TEST_CASE("Test AtomicSupport.h")

 {

     unsigned nrow = 100, ncol = 500;

-    uint64_t maxAtoms = 100;

     SECTION("Make and Convert proposals")

     {

         AtomicSupport domain('A', nrow, ncol, 1.0, 0.5);

-        domain.setMaxNumAtoms(maxAtoms);

         REQUIRE(domain.alpha() == 1.0);

         REQUIRE(domain.lambda() == 0.5);

@@ -19,8 +17,6 @@ TEST_CASE("Test AtomicSupport.h")

         REQUIRE(prop.label == 'A');

         REQUIRE(prop.type == 'B');

         REQUIRE(prop.nChanges == 1);

-        REQUIRE(prop.pos1 == 0xf21db672ab2f52a4);

-        REQUIRE(prop.delta1 == 1.0);

         REQUIRE(prop.pos2 == 0);

         REQUIRE(prop.delta2 == 0.0);

@@ -55,10 +51,51 @@ TEST_CASE("Test AtomicSupport.h")

             double oldMass = domain.totalMass();

+            uint64_t nOld = domain.numAtoms();

+

             domain.acceptProposal(prop);

+

+            if (prop.type == 'B')

+            {

+                REQUIRE(domain.numAtoms() == nOld + 1);

+            }

+            else if (prop.type == 'D')

+            {

+                REQUIRE(domain.numAtoms() == nOld - 1);

+            }

+            /*else

+            {

+                REQUIRE(domain.numAtoms() == nOld);

+            }*/

             REQUIRE(domain.totalMass() == oldMass + prop.delta1 + prop.delta2);

-            REQUIRE(domain.numAtoms() <= maxAtoms);

         }

     }

+

+    SECTION("Proposal Distribution")

+    {

+        AtomicSupport domain('A', nrow, ncol, 0.01, 0.05);

+        

+        gaps::random::setSeed(1);

+

+        unsigned nB = 0, nD = 0, nM = 0, nE = 0;

+        for (unsigned i = 0; i < 5000; ++i)

+        {

+            AtomicProposal prop = domain.makeProposal();

+            domain.acceptProposal(prop);

+

+            switch(prop.type)

+            {

+                case 'B': nB++; break;

+                case 'D': nD++; break;

+                case 'M': nM++; break;

+                case 'E': nE++; break;

+            }

+        }

+        REQUIRE(domain.numAtoms() > 100);

+        REQUIRE(nB > 500);

+        //REQUIRE(nD > 500);

+        REQUIRE(nM > 500);

+        REQUIRE(nE > 500);

+    }

 }

\ No newline at end of file

@@ -22,7 +22,7 @@ TEST_CASE("Test GibbsSampler.h")

     SECTION("Create GibbsSampler")

     {

-        GibbsSampler sampler(rD, rS, 10, 1, 1, 5.0, 5.0, false);

+        GibbsSampler sampler(rD, rS, 10, 0.01, 0.01, 1.0, 1.0, false);

         REQUIRE(sampler.chi2() == 0.0);

         REQUIRE(sampler.totalNumAtoms('A') == 0);

@@ -31,12 +31,63 @@ TEST_CASE("Test GibbsSampler.h")

     SECTION("Update GibbsSampler")

     {

-        GibbsSampler sampler(rD, rS, 10, 1, 1, 5.0, 5.0, false);

+        GibbsSampler sampler(rD, rS, 10, 0.01, 0.01, 1.0, 1.0, false);

-        for (unsigned i = 0; i < 1000; ++i)

+        for (unsigned i = 0; i < 5000; ++i)

         {

             REQUIRE_NOTHROW(sampler.update('A'));

             REQUIRE_NOTHROW(sampler.update('P'));

         }

+        REQUIRE(sampler.totalNumAtoms('A') > 10);

+        REQUIRE(sampler.totalNumAtoms('P') > 10);

+    }

+

+    SECTION("GibbsSampler Statistics")

+    {

+        GibbsSampler sampler(rD, rS, 10, 0.01, 0.01, 1.0, 1.0, false);

+

+        for (unsigned i = 0; i < 1000; ++i)

+        {

+            for (unsigned j = 0; j < 10; ++j)

+            {

+                sampler.update('A');

+                sampler.update('P');

+            }

+            sampler.updateStatistics();

+        }

+        Rcpp::NumericMatrix AMean = sampler.AMeanRMatrix();

+        Rcpp::NumericMatrix AStd = sampler.AStdRMatrix();

+        Rcpp::NumericMatrix PMean = sampler.PMeanRMatrix();

+        Rcpp::NumericMatrix PStd = sampler.PStdRMatrix();

+

+        REQUIRE(AMean.nrow() == rD.nrow());

+        REQUIRE(AMean.ncol() == 10);

+

+        REQUIRE(AStd.nrow() == rD.nrow());

+        REQUIRE(AStd.ncol() == 10);

+

+        REQUIRE(PMean.nrow() == 10);

+        REQUIRE(PMean.ncol() == rD.ncol());

+

+        REQUIRE(PStd.nrow() == 10);

+        REQUIRE(PStd.ncol() == rD.ncol());

+

+        for (unsigned r = 0; r < AMean.nrow(); ++r)

+        {

+            for (unsigned c = 0; c < AMean.ncol(); ++c)

+            {

+                REQUIRE(AMean(r,c) >= 0.0);

+                REQUIRE(AStd(r,c) >= 0.0);

+            }

+        }

+

+        for (unsigned r = 0; r < PMean.nrow(); ++r)

+        {

+            for (unsigned c = 0; c < PMean.ncol(); ++c)

+            {

+                REQUIRE(PMean(r,c) >= 0.0);

+                REQUIRE(PStd(r,c) >= 0.0);

+            }

+        }

     }

 }

\ No newline at end of file

@@ -13,13 +13,19 @@ TEST_CASE("Test Random.h - Random Number Generation")

     SECTION("Test uniform distribution over unit interval")

     {

         double min = 1, max = 0;

-        for (unsigned i = 0; i < 10000; ++i)

+        double sum = 0.0;

+        unsigned N = 10000;

+        for (unsigned i = 0; i < N; ++i)

         {

             min = std::min(gaps::random::uniform(), min);

             max = std::max(gaps::random::uniform(), max);

+            sum += gaps::random::uniform();

         }

+        REQUIRE(sum / N == Approx(0.5).epsilon(0.01));

         REQUIRE(min >= 0);

+        REQUIRE(min < 0.01);

         REQUIRE(max <= 1);

+        REQUIRE(max > 0.99);

     }

     SECTION("Test uniform distribution over general interval")

@@ -1,6 +1,6 @@

-context("lints")

+#context("lints")

-test_that("Package Style", {

-    skip("Don't lint for now")

-    lintr::expect_lint_free()

-})

+#test_that("Package Style", {

+#    skip("Don't lint for now")

+#    lintr::expect_lint_free()

+#})

@@ -4,7 +4,9 @@ test_that("GAPS Simple Simulation",

 {

     data(SimpSim)

     nIter <- 1000

-    expect_error(gapsRun(SimpSim.D, SimpSim.S, nFactor=3, messages=FALSE), NA)

+    res <- gapsRun(SimpSim.D, SimpSim.S, nFactor=3, messages=FALSE)

+

+    expect_true(!is.na(res$meanChi2))

 })

 #test_that("GAPSmap Simple Simulation",