public static void Log(string clientName, string accountID, string accountName, Significance significance, String message)
{
string printLine, fileLine;
fileLine = DateTime.Now.ToString();
fileLine += "\t" + significance;
fileLine += "\t" + clientName;
fileLine += "\t" + accountID + "\t" + accountName;
{
fileLine += "\t" + "\t" + "\t";
printLine = System.String.Format("[{1}]<{0}> {2}({3}): {4}", significance, DateTime.Now.ToShortTimeString(), clientName, accountName, message);
}
fileLine += "\t" + message;
if (logger != null)
logger.SendEvent(fileLine);
//if (significance >= Significance.Unusual)
{
lock (logLock)
System.IO.File.AppendAllText("execution.log", fileLine + "\n");
Console.WriteLine(printLine);
}
}
public override string GetCommandLineArguments()
{
ArgumentFormatter argFormatter = new ArgumentFormatter();
StringBuilder arguments = new StringBuilder();
arguments.Append(" " + argFormatter.GetFormattedArgument(Responses)); //4
//get transforms
arguments.Append(" " + argFormatter.GetFormattedArgument(Transformation, false)); //5
//1st cat factor
arguments.Append(" " + argFormatter.GetFormattedArgument(FirstCatFactor, true)); //6
//2nd cat factor
arguments.Append(" " + argFormatter.GetFormattedArgument(SecondCatFactor, true)); //7
//3rd cat factor
arguments.Append(" " + argFormatter.GetFormattedArgument(ThirdCatFactor, true)); //8
//4th cat factor
arguments.Append(" " + argFormatter.GetFormattedArgument(FourthCatFactor, true)); //9
//Mean
arguments.Append(" " + argFormatter.GetFormattedArgument(Mean)); //10
//N
arguments.Append(" " + argFormatter.GetFormattedArgument(N)); //11
//St Dev
arguments.Append(" " + argFormatter.GetFormattedArgument(StandardDeviation)); //12
//Variances
arguments.Append(" " + argFormatter.GetFormattedArgument(Variance)); //13
//St Err
arguments.Append(" " + argFormatter.GetFormattedArgument(StandardErrorOfMean)); //14
//Min and Max
arguments.Append(" " + argFormatter.GetFormattedArgument(MinAndMax)); //15
//Median Quartile
arguments.Append(" " + argFormatter.GetFormattedArgument(MedianAndQuartiles)); //16
//Coefficient Variation
arguments.Append(" " + argFormatter.GetFormattedArgument(CoefficientOfVariation)); //17
//Confidence Limits
arguments.Append(" " + argFormatter.GetFormattedArgument(ConfidenceInterval)); //18
//Confidence Limits
arguments.Append(" " + argFormatter.GetFormattedArgument(Significance.ToString(), false)); //19
//Normal Probability Plots
arguments.Append(" " + argFormatter.GetFormattedArgument(NormalProbabilityPlot));
//By Categories and Overall
arguments.Append(" " + argFormatter.GetFormattedArgument(ByCategoriesAndOverall)); //20
return(arguments.ToString().Trim());
}
public void Add(Significance significance, string name)
{
Significances.Add(new ComparatorSignificance
{
Id = significance,
Name = name
});
}
public static string GetSignificanceTextWithAsterisks(Significance significance)
{
switch (significance)
{
case Significance.Better:
return "*, better than the average for England.";
case Significance.Worse:
return "*, worse than the average for England.";
default:
return "*.";
}
}
protected Significance AdjustForPolarity(Significance significance)
{
if (PolarityId == PolarityIds.RagLowIsGood)
{
switch (significance)
{
case Significance.Worse:
return Significance.Better;
case Significance.Better:
return Significance.Worse;
}
}
return significance;
}
/// <summary>
/// calculates the hash code for this object
/// </summary>
// ReSharper disable once FunctionComplexityOverflow
private int CalculateHashCode()
{
var hashCode = Start.GetHashCode();
if (Chromosome != null)
{
hashCode ^= Chromosome.GetHashCode();
}
if (ID != null)
{
hashCode ^= ID.GetHashCode();
}
if (AlleleOrigins != null)
{
hashCode ^= AlleleOrigins.GetHashCode();
}
if (AltAllele != null)
{
hashCode ^= AltAllele.GetHashCode();
}
if (MedGenIDs != null)
{
hashCode ^= MedGenIDs.GetHashCode();
}
if (OmimIDs != null)
{
hashCode ^= OmimIDs.GetHashCode();
}
if (OrphanetIDs != null)
{
hashCode ^= OrphanetIDs.GetHashCode();
}
if (Phenotypes != null)
{
hashCode ^= Phenotypes.GetHashCode();
}
if (ReferenceAllele != null)
{
hashCode ^= ReferenceAllele.GetHashCode();
}
if (Significance != null)
{
hashCode ^= Significance.GetHashCode();
}
return(hashCode);
}
private string ProcessSentance3And4(Significance sig)
{
var qualifiedItems = new List<string>();
if ((data.TeenagePregnancySig != sig) &&
(data.GcseAchievementSig != sig) &&
(data.BreastfeedingInitiationSig != sig) &&
(data.SmokingAtTimeOfDeliverySig != sig))
{
return string.Empty;
}
if (data.TeenagePregnancySig == sig)
{
qualifiedItems.Add("teenage pregnancy");
}
if (data.GcseAchievementSig == sig)
{
qualifiedItems.Add("GCSE attainment");
}
if (data.BreastfeedingInitiationSig == sig)
{
qualifiedItems.Add("breastfeeding initiation");
}
if (data.SmokingAtTimeOfDeliverySig == sig)
{
qualifiedItems.Add("smoking at time of delivery");
}
string options = PhraseJoiner.Join(qualifiedItems);
string betterOrWorse = HealthProfilesKeyMessage4Builder.GetBetterOrWorse(sig);
var sentenceData = new Dictionary<string, string> {
{"Options", options},
{"BetterOrWorse", betterOrWorse}
};
return Render.StringToString(Sentence3Template, sentenceData);
}
[Test] public void TestPValue()
{
var p = Significance.PValue(1046, 0.42, 0.5);
TestHelpers.AlmostEqual(1 / 9000000, p);
}
public static string GetBetterOrWorse(Significance sig)
{
return sig == Significance.Better ? "better" : "worse";
}
[Test] public void TestPValueTwoSided()
{
var p = Significance.PValue(1000, 0.576, 0.5, two_sided: true);
TestHelpers.AlmostEqual(1 / 663000, p);
}
public string GetSentence6(Significance sig)
{
var qualifiedItems = new List<string>();
if ((data.AdultHipFracturesSignificance != sig) &&
(data.AdultSTISignificance != sig) &&
(data.AdultKilledAndSeriouslyInjuredOnRoadsSignificance != sig) &&
(data.AdultIncidenceOfTBSignificance != sig))
{
return string.Empty;
}
if (data.AdultHipFracturesSignificance == sig)
qualifiedItems.Add("hip fractures");
if (data.AdultSTISignificance == sig)
qualifiedItems.Add("sexually transmitted infections");
if (data.AdultKilledAndSeriouslyInjuredOnRoadsSignificance == sig)
qualifiedItems.Add("people killed and seriously injured on roads");
if (data.AdultIncidenceOfTBSignificance == sig)
qualifiedItems.Add("TB");
string rate, isOrAre;
if (qualifiedItems.Count > 1)
{
rate = "Rates";
isOrAre = "are";
}
else
{
rate = "The rate";
isOrAre = "is";
}
string options = PhraseJoiner.Join(qualifiedItems);
var sentenceData = new Dictionary<string, string>
{
{"Rate", rate},
{"Options", options},
{"IsOrAre", isOrAre},
{"BetterOrWorse", GetBetterOrWorse(sig)}
};
return Render.StringToString(Sentence6And7Template, sentenceData);
}
public string GetSentence7(Significance sig)
{
var sigList = new List<Significance>
{
data.AdultStatutoryHomelessnessSig,
data.AdultViolentCrimeSig,
data.AdultLongTermUnemploymentSig,
data.AdultIncidenceOfMalignantMelanomaSig,
data.AdultDrugMisuseSig,
data.AdultExcessWinterDeathsSig,
data.AdultUnder75MortalityRateCvdSig,
data.AdultUnder75MortalityRateCancerSig
};
var significanceCounter = new SignificanceCounter(sigList);
if ((!(significanceCounter.ProportionGreen >= 0.5)) && (!(significanceCounter.ProportionAmber >= 0.5)))
{
return string.Empty;
}
var qualifiedItems = new List<string>();
if (data.AdultStatutoryHomelessnessSig == sig)
qualifiedItems.Add("statutory homelessness");
if (data.AdultViolentCrimeSig == sig)
qualifiedItems.Add("violent crime");
if (data.AdultLongTermUnemploymentSig == sig)
qualifiedItems.Add("long term unemployment");
if (data.AdultIncidenceOfMalignantMelanomaSig == sig)
qualifiedItems.Add("new cases of malignant melanoma");
if (data.AdultDrugMisuseSig == sig)
qualifiedItems.Add("deaths from drug misuse");
if (data.AdultExcessWinterDeathsSig == sig)
qualifiedItems.Add("excess winter deaths");
if (data.AdultUnder75MortalityRateCvdSig == sig)
qualifiedItems.Add("early deaths from cardiovascular diseases");
if (data.AdultUnder75MortalityRateCancerSig == sig)
qualifiedItems.Add("early deaths from cancer");
if (!qualifiedItems.Any())
// check at least one of the indicator is red or green ( depending upon passed sig )
return string.Empty;
string rate, isOrAre;
if (qualifiedItems.Count > 1)
{
rate = "Rates";
isOrAre = "are";
}
else
{
rate = "The rate";
isOrAre = "is";
}
string options = PhraseJoiner.Join(qualifiedItems);
var sentenceData = new Dictionary<string, string>
{
{"Rate", rate},
{"Options", options},
{"IsOrAre", isOrAre},
{"BetterOrWorse", GetBetterOrWorse(sig)}
};
return Render.StringToString(Sentence6And7Template, sentenceData);
}
private KeyMessageData Sentence3Data(Significance maleLifeExpectancyAtBirth, Significance femaleLifeExpectancyAtBirth)
{
return new KeyMessageData()
{
MaleLifeExpectancyAtBirth = maleLifeExpectancyAtBirth,
FemaleLifeExpectancyAtBirth = femaleLifeExpectancyAtBirth
};
}
public string GetSentence5(Significance sig)
{
var qualifiedItems = new List<string>();
if ((data.AdultExcessWeightSignificance != sig) &&
(data.AdultSmokingPrevalenceSignificance != sig) &&
(data.AdultPhysicalActivitySignificance != sig))
{
return string.Empty;
}
if (data.AdultExcessWeightSignificance == sig)
qualifiedItems.Add("excess weight");
if (data.AdultSmokingPrevalenceSignificance == sig)
qualifiedItems.Add("smoking");
if (data.AdultPhysicalActivitySignificance == sig)
qualifiedItems.Add("physical activity");
string options = PhraseJoiner.Join(qualifiedItems);
var sentenceData = new Dictionary<string, string>
{
{"Options", options},
{"BetterOrWorse", GetBetterOrWorse(sig)}
};
return Render.StringToString(Sentence5Template, sentenceData);
}
public static void Log(Significance significance, String message)
{
Log("", "", "", significance, message);
}
[Test] public void TestMeanPValue()
{
var p = Significance.MeanPValue(60, 7.177, 2.948);
Assert.AreEqual(0, p);
}
private CoreDataSet GetCoreDataSet(Grouping grouping, out Significance significance)
{
IndicatorMetadata metadata = indicatorMetadataCollection.GetIndicatorMetadataById(grouping.IndicatorId);
CoreDataSet coreDataSet = coreDataSetProvider.GetData(grouping, TimePeriod.GetDataPoint(grouping), metadata);
CoreDataSet benchmarkData = benchmarkDataProvider.GetData(grouping, TimePeriod.GetDataPoint(grouping),
metadata);
significance = _indicatorComparerFactory.New(grouping).Compare(coreDataSet, benchmarkData, metadata);
return coreDataSet;
}
[Test] public void TestMeanPValue3()
{
var p = Significance.MeanPValue(130, 36.80513, 0.407324, two_sided: true);
Assert.AreEqual(1 / 4000000, p);
}
[Test] public void TestMeanPValue2()
{
var p = Significance.MeanPValue(400, -14.15, 14.13, two_sided: true);
Assert.AreEqual(0, p);
}
private static void AssertExpected(RangeTargetComparer comparer, Significance expected, double val)
{
var significance = comparer.CompareAgainstTarget(new CoreDataSet { Value = val });
Assert.AreEqual(expected, significance);
}
public static void Log(Significance significance, String message)
{
Log("", "", "", significance, message);
}
public static void Log(string clientName, string accountID, string accountName, Significance significance, String message)
{
string printLine, fileLine;
fileLine = DateTime.Now.ToString();
fileLine += "\t" + significance;
fileLine += "\t" + clientName;
fileLine += "\t" + accountID + "\t" + accountName;
{
fileLine += "\t" + "\t" + "\t";
printLine = System.String.Format("[{1}]<{0}> {2}({3}): {4}", significance, DateTime.Now.ToShortTimeString(), clientName, accountName, message);
}
fileLine += "\t" + message;
if (logger != null)
{
logger.SendEvent(fileLine);
}
//if (significance >= Significance.Unusual)
{
lock (logLock)
System.IO.File.AppendAllText("execution.log", fileLine + "\n");
Console.WriteLine(printLine);
}
}
public void AddSignificance(int comparatorId, Significance significance)
{
if (Significance.ContainsKey(comparatorId) == false)
{
Significance.Add(comparatorId, (int)significance);
}
}
