protected override string CreateReportLine(
ModelScorer modelScorer,
PhyloTree phyloTree,
RowData rowAndTargetData,
UniversalWorkList workList,
int rowIndex, int workListCount, int workIndex)
{
Dictionary <string, string> row = rowAndTargetData.Row;
string predictorVariable = row[PhyloTree.PredictorVariableColumnName]; // e.g. hla
string targetVariable = row[PhyloTree.TargetVariableColumnName]; // e.g. A@182 (amino acid "A" at position 182)
int nullIndex = int.Parse(row[PhyloTree.NullIndexColumnName]);
//Dictionary<string, bool> caseIdToNonMissingPredictorValue = workList.NullIndexToPredictorToCaseIdToNonMissingValue[nullIndex][predictorVariable];
Dictionary <string, SufficientStatistics> caseIdToNonMissingPredictorValue = rowAndTargetData.PredictorData; //workList.GetCaseIdToNonMissingValueForNullIndexAndPredictorVariable(nullIndex, predictorVariable);
Dictionary <string, SufficientStatistics> caseIdToNonMissingTargetValue = rowAndTargetData.TargetData;
TwoByTwo fishers2by2 = TwoByTwo.GetInstance(
SufficientStatisticsMapToIntMap(caseIdToNonMissingPredictorValue),
SufficientStatisticsMapToIntMap(caseIdToNonMissingTargetValue));
double pValue = fishers2by2.FisherExactTest;
string reportLine = SpecialFunctions.CreateTabString(this, rowIndex, workListCount, workIndex, nullIndex,
predictorVariable,
targetVariable,
fishers2by2.CountsString(),
fishers2by2.FisherExactTest);
return(reportLine);
}
public override EvaluationResults EvaluateModelOnDataGivenParams(Converter <Leaf, SufficientStatistics> v1, Converter <Leaf, SufficientStatistics> v2, EvaluationResults previousResults)
{
TwoByTwo fishers2by2 = TwoByTwo.GetInstance(
SufficientStatisticsMapToIntDictionaryMap(v1, _fullLeafCollection),
SufficientStatisticsMapToIntDictionaryMap(v2, _fullLeafCollection));
int[] fisherCounts = fishers2by2.ToOneDArray();
List <Score> nullScores;
Score altScore;
ComputeIidScoresGivenParams(fisherCounts,
previousResults.NullScores[0].OptimizationParameters, previousResults.NullScores[1].OptimizationParameters,
previousResults.AltScore.OptimizationParameters,
out nullScores, out altScore);
//int tt = fisherCounts[(int)TwoByTwo.ParameterIndex.TT];
//int tf = fisherCounts[(int)TwoByTwo.ParameterIndex.TF];
//int ft = fisherCounts[(int)TwoByTwo.ParameterIndex.FT];
//int ff = fisherCounts[(int)TwoByTwo.ParameterIndex.FF];
//int sum = SpecialFunctions.Sum(fisherCounts);
//double pi0 = (double)(tt + tf) / sum;
//double pi1 = (double)(tt + ft) / sum;
//double ptt = (double)tt / sum;
//double ptf = (double)tf / sum;
//double pft = (double)ft / sum;
//double pff = 1 - ptt - ptf - pft;
//double predicted_pi0 = previousResults.NullScores[0].OptimizationParameters[0].Value;
//double predicted_pi1 = previousResults.NullScores[1].OptimizationParameters[0].Value;
//double predicted_ptt = previousResults.AltScore.OptimizationParameters[0].Value;
//double predicted_ptf = previousResults.AltScore.OptimizationParameters[1].Value;
//double predicted_pft = previousResults.AltScore.OptimizationParameters[2].Value;
//double predicted_pff = 1 - predicted_ptt - predicted_ptf - predicted_pft;
//double nullLLLeft = pi0 * Math.Log(predicted_pi0);
//double nullLLRight = pi1 * Math.Log(predicted_pi1);
//double altLL = predicted_ptt * Math.Log(ptt) + predicted_ptf * Math.Log(ptf) + predicted_pft * Math.Log(pft) + predicted_pff * Math.Log(pff);
//Score nullScoreLeft = Score.GetInstance(nullLLLeft, previousResults.NullScores[0].OptimizationParameters, null);
//Score nullScoreRight = Score.GetInstance(nullLLRight, previousResults.NullScores[1].OptimizationParameters, null);
//Score altScore = Score.GetInstance(altLL, previousResults.AltScore.OptimizationParameters, null);
//List<Score> nullScores = new List<Score>(2);
//nullScores.Add(nullScoreLeft);
//nullScores.Add(nullScoreRight);
EvaluationResults results = EvaluationResultsFisher.GetInstance(this, nullScores, altScore, fishers2by2);
return(results);
}
public override string ToHeaderString()
{
//EvaluationResults dummyResults = EvaluationResultsFisher.GetInstance(this, TwoByTwo.GetInstance(new int[] { 1, 1, 1, 1 }));
List <Score> nullScores;
Score altScore;
TwoByTwo fishers2by2 = TwoByTwo.GetInstance(new int[] { 1, 1, 1, 1 });
ComputeIidScores(fishers2by2.ToOneDArray(), out nullScores, out altScore);
EvaluationResults dummyResults = EvaluationResultsFisher.GetInstance(this, nullScores, altScore, fishers2by2);
return(dummyResults.ToHeaderString());
}
public override EvaluationResults EvaluateModelOnData(Converter <Leaf, SufficientStatistics> predMap, Converter <Leaf, SufficientStatistics> targMap)
{
TwoByTwo fishers2by2 = TwoByTwo.GetInstance(
SufficientStatisticsMapToIntDictionaryMap(predMap, _fullLeafCollection),
SufficientStatisticsMapToIntDictionaryMap(targMap, _fullLeafCollection));
int[] fisherCounts = fishers2by2.ToOneDArray();
List <Score> nullScores;
Score altScore;
ComputeIidScores(fisherCounts, out nullScores, out altScore);
EvaluationResultsFisher results = EvaluationResultsFisher.GetInstance(this, nullScores, altScore, fishers2by2);
#if DEBUG
EvaluationResults results2 = EvaluateModelOnDataGivenParams(predMap, targMap, results);
double eps = 1E-14;
Debug.Assert(ComplexNumber.ApproxEqual(results.AltLL, results2.AltLL, eps));
Debug.Assert(ComplexNumber.ApproxEqual(results.NullLL, results2.NullLL, eps));
Debug.Assert(ComplexNumber.ApproxEqual(results.ComputePValue(), results2.ComputePValue(), eps));
#endif
return(results);
}