Doc changes and tridiagonal determinant test.

dcwuser · dcwuser · commit 29f1b8771d3c · 2018-05-02T00:11:53.000-07:00
diff --git a/Examples/.vscode/launch.json b/Examples/.vscode/launch.json
@@ -11,7 +11,7 @@
             "preLaunchTask": "build",
             // If you have changed target frameworks, make sure to update the program path.
             "program": "${workspaceFolder}/bin/Debug/netcoreapp2.0/Examples.dll",
-            "args": ["FitToDistribution"],
+            "args": [],
             "cwd": "${workspaceFolder}",
             // For more information about the 'console' field, see https://github.com/OmniSharp/omnisharp-vscode/blob/master/debugger-launchjson.md#console-terminal-window
             "console": "internalConsole",
diff --git a/Examples/Data.cs b/Examples/Data.cs
@@ -9,10 +9,79 @@
 using Meta.Numerics.Statistics;
 using Meta.Numerics.Statistics.Distributions;
 
+using Newtonsoft.Json;
+
 namespace Examples {
     
     public static class Data {
 
+        public static void ConstructTestCsv () {
+
+            using (TextWriter writer = new StreamWriter(File.OpenWrite("test.csv"))) {
+                writer.WriteLine("Id, Name, Sex, Birthdate, Height, Weight, Result");
+                writer.WriteLine("1, John, M, 1970-01-02, 190.0, 75.0, True");
+                writer.WriteLine("2, Mary, F, 1980-02-03, 155.0, 40.0, True");
+                writer.WriteLine("3, Luke, M, 1990-03-04, 180.0, 60.0, False");
+            }
+
+        }
+
+        [ExampleMethod]
+        public static void ImportingData () {
+
+            FrameTable data;
+            using (TextReader reader = File.OpenText("test.csv")) {
+                data = FrameTable.FromCsv(reader);
+            }
+
+            Console.WriteLine($"Imported CSV file with {data.Rows.Count} rows.");
+            Console.WriteLine("The names and types of the columns are:");
+            foreach (FrameColumn column in data.Columns) {
+                Console.WriteLine($"  {column.Name} of type {column.StorageType}");
+            }
+
+            FrameTable titanic;
+            Uri url = new Uri("https://raw.githubusercontent.com/datasciencedojo/datasets/master/titanic.csv");
+            WebRequest request = WebRequest.Create(url);
+            using (WebResponse response = request.GetResponse()) {
+                using (StreamReader reader = new StreamReader(response.GetResponseStream())) {
+                    titanic = FrameTable.FromCsv(reader);
+                }
+            }
+
+            Uri jsonUrl = new Uri("https://raw.githubusercontent.com/dcwuser/metanumerics/master/Examples/Data/example.json");
+            WebClient client = new WebClient();
+            string input = client.DownloadString(jsonUrl);
+            List<Dictionary<string,object>> output = JsonConvert.DeserializeObject<List<Dictionary<string,object>>>(input);
+            FrameTable jsonExample = FrameTable.FromDictionaries(output);
+
+            // Define the schema.
+            FrameTable table = new FrameTable();
+            table.AddColumn<int>("Id");
+            table.AddColumn<string>("Name");
+            table.AddColumn<string>("Sex");
+            table.AddColumn<DateTime>("Birthdate");
+            table.AddColumn<double>("Height");
+            table.AddColumn<double?>("Weight");
+            table.AddColumn<bool>("Result");
+            
+            // Add rows using as arrays of objects.
+            table.AddRow(1, "John", "M", DateTime.Parse("1970-01-02"), 190.0, 75.0, true);
+            table.AddRow(2, "Mary", "F", DateTime.Parse("1980-02-03"), 155.0, null, true);
+
+            // Add a row using a dictionary. This is more verbose, but very clear.
+            table.AddRow(new Dictionary<string,object>(){
+                {"Id", 3},
+                {"Name", null},
+                {"Sex", "M"},
+                {"Birthdate", DateTime.Parse("1990-03-04")},
+                {"Height", 180.0},
+                {"Weight", 60.0},
+                {"Result", false}
+            });            
+
+        }        
+
         [ExampleMethod]
         public static void ManipulatingData () {
 
@@ -82,8 +151,18 @@ public static void AnalyzingData () {
                     table = FrameTable.FromCsv(reader);
                 }
             }
+            FrameView view = table.WhereNotNull();
+
+            // Get the column with (zero-based) index 4.
+            FrameColumn column4 = view.Columns[4];
+            // Get the column named "Height".
+            FrameColumn heightsColumn = view.Columns["Height"];
+            // Even easier way to get the column named "Height".
+            FrameColumn alsoHeightsColumn = view["Height"];
 
-            SummaryStatistics summary = new SummaryStatistics(table["Height"].As<double>());
+            IReadOnlyList<double> heights = view["Height"].As<double>();
+
+            SummaryStatistics summary = new SummaryStatistics(view["Height"].As<double>());
             Console.WriteLine($"Count = {summary.Count}");
             Console.WriteLine($"Mean = {summary.Mean}");
             Console.WriteLine($"Standard Deviation = {summary.StandardDeviation}");
@@ -92,74 +171,77 @@ public static void AnalyzingData () {
             Console.WriteLine($"Estimated population standard deviation = {summary.PopulationStandardDeviation}");
 
             IReadOnlyList<double> maleHeights =
-                table.Where<string>("Sex", s => s == "M").Columns["Height"].As<double>();
+                view.Where<string>("Sex", s => s == "M").Columns["Height"].As<double>();
             IReadOnlyList<double> femaleHeights =
-                table.Where<string>("Sex", s => s == "F").Columns["Height"].As<double>();
+                view.Where<string>("Sex", s => s == "F").Columns["Height"].As<double>();
             TestResult test = Univariate.StudentTTest(maleHeights, femaleHeights);
-            Console.WriteLine($"{test.Statistic.Name} = {test.Statistic.Value}, P = {test.Probability}");
+            Console.WriteLine($"{test.Statistic.Name} = {test.Statistic.Value}");
+            Console.WriteLine($"P = {test.Probability}");
 
             TestResult maleHeightNormality = maleHeights.ShapiroFranciaTest();
-            TestResult totalHeightNormality = table["Height"].As<double>().ShapiroFranciaTest();
+            TestResult totalHeightNormality = view["Height"].As<double>().ShapiroFranciaTest();
             TestResult heightCompatibility = Univariate.KolmogorovSmirnovTest(maleHeights, femaleHeights);
 
             LinearRegressionResult fit =
-                table["Weight"].As<double>().LinearRegression(table["Height"].As<double>());
+                view["Weight"].As<double>().LinearRegression(view["Height"].As<double>());
             Console.WriteLine($"Model weight = ({fit.Slope}) * height + ({fit.Intercept}).");
             Console.WriteLine($"Model explains {fit.RSquared * 100.0}% of variation.");
 
             ContingencyTable<string, bool> contingency =
-                Bivariate.Crosstabs(table["Sex"].As<string>(), table["Result"].As<bool>());
+                Bivariate.Crosstabs(view["Sex"].As<string>(), view["Result"].As<bool>());
             Console.WriteLine($"Male incidence: {contingency.ProbabilityOfColumnConditionalOnRow(true, "M")}");
-            Console.WriteLine($"Female incidence: {contingency.ProbabilityOfColumnConditionalOnRow(false, "F")}");
+            Console.WriteLine($"Female incidence: {contingency.ProbabilityOfColumnConditionalOnRow(true, "F")}");
             Console.WriteLine($"Log odds ratio = {contingency.Binary.LogOddsRatio}");
 
-            table.AddComputedColumn("Bmi", r => ((double) r["Weight"])/MoreMath.Sqr((double) r["Height"] / 100.0));
-            table.AddComputedColumn("Age", r=> (DateTime.Now - (DateTime) r["Birthdate"]).TotalDays / 365.24);
+            view.AddComputedColumn("Bmi", r => ((double) r["Weight"])/MoreMath.Sqr((double) r["Height"] / 100.0));
+            view.AddComputedColumn("Age", r=> (DateTime.Now - (DateTime) r["Birthdate"]).TotalDays / 365.24);
 
             MultiLinearLogisticRegressionResult result = 
-                table["Result"].As<bool>().MultiLinearLogisticRegression(
-                    table["Bmi"].As<double>(),
-                    table["Sex"].As<string, double>(s => s == "M" ? 1.0 : 0.0)
+                view["Result"].As<bool>().MultiLinearLogisticRegression(
+                    view["Bmi"].As<double>(),
+                    view["Sex"].As<string, double>(s => s == "M" ? 1.0 : 0.0)
                 );
             foreach (Parameter parameter in result.Parameters) {
                 Console.WriteLine($"{parameter.Name} = {parameter.Estimate}");
             }
 
-            //TestResult ageResultPearson = Bivariate.PearsonRTest(table["Age"].As<double>(), table["Result"].As<double>());
-            TestResult spearman = Bivariate.SpearmanRhoTest(table["Age"].As<double>(), table["Result"].As<double>());
+            TestResult spearman = Bivariate.SpearmanRhoTest(view["Age"].As<double>(), view["Result"].As<double>());
             Console.WriteLine($"{spearman.Statistic.Name} = {spearman.Statistic.Value} P = {spearman.Probability}");
 
         }        
 
-        public static void ConstructData () {
+        public static void ConstructExampleData () {
 
             FrameTable table = new FrameTable();
             table.AddColumn<int>("Id");
             table.AddColumn<string>("Name");
             table.AddColumn<string>("Sex");
             table.AddColumn<DateTime>("Birthdate");
-            table.AddColumns<double>("Height", "Weight");
+            table.AddColumn<double>("Height");
+            table.AddColumns<double?>("Weight");
             table.AddColumn<bool>("Result");
 
-            //Random rng = new Random(3);
-            //Random rng = new Random(314159);
-            // Random rng = new Random(271828);
             Random rng = new Random(1000001);
 
-            //string[] maleNames = new string[1024];
             string[] maleNames = new string[] {"Alex", "Chris", "David", "Eric", "Frederic", "George", "Hans", "Igor", "John", "Kevin", "Luke", "Mark", "Oscar", "Peter", "Richard", "Stephan", "Thomas", "Vincent" };
             AddRows(table, maleNames, "M", 175.0, 12.0, 24.0, 3.0, 1, rng);
 
-            //string[] femaleNames = new string[1024];
             string[] femaleNames = new string[] {"Anne", "Belle", "Dorothy", "Elizabeth", "Fiona", "Helen", "Julia", "Kate", "Louise", "Mary", "Natalie", "Olivia", "Ruth", "Sarah", "Theresa", "Viola" };
             AddRows(table, femaleNames, "F", 160.0, 10.0, 24.0, 3.0, 0, rng);
 
-            string path = @"C:\Users\dawright\Documents\example.csv";
+            // add rows with nulls
+            table.AddRow(table.Rows.Count, null, "M", DateTime.Parse("1970-07-27"), 183.0, 74.0, false);
+            table.AddRow(table.Rows.Count, "Zoey", "F", DateTime.Parse("2007-09-17"), 138.0, null, false);
+
+            string path = @"example.csv";
             using (StreamWriter writer = new StreamWriter(File.OpenWrite(path))) {
                 table.ToCsv(writer);
             }
             Console.WriteLine(File.Exists(path));
 
+            string json = JsonConvert.SerializeObject(table.ToDictionaries(), Formatting.Indented);
+            File.WriteAllText("example.json", json);
+
         }
 
        private static void AddRows(FrameTable table, IReadOnlyList<string> names, string sex, double meanHeight, double stddevHeight, double meanBmi, double stddevBmi, int flag, Random rng) {
diff --git a/Examples/Examples.csproj b/Examples/Examples.csproj
@@ -5,5 +5,6 @@
   </PropertyGroup>
   <ItemGroup>
     <PackageReference Include="Meta.Numerics" Version="4.0.5-alpha"/>
+    <PackageReference Include="Newtonsoft.Json" Version="11.0.2"/>
   </ItemGroup>
 </Project>
diff --git a/Examples/Program.cs b/Examples/Program.cs
@@ -23,7 +23,6 @@ private static MethodInfo[] GetExampleMethods () {
 
         static void Main(string[] args)
         {
-
             MethodInfo[] methods = GetExampleMethods();
             Dictionary<string, MethodInfo> index = new Dictionary<string, MethodInfo>();
             foreach (MethodInfo method in methods) {
diff --git a/Numerics/Analysis/EvaluationSettings.cs b/Numerics/Analysis/EvaluationSettings.cs
@@ -5,12 +5,24 @@
 namespace Meta.Numerics.Analysis {
 
     /// <summary>
-    /// Contains settings controling the evaluation of a function.
+    /// Contains settings governing the evaluation of a function.
     /// </summary>
+    /// <remarks>
+    /// <para>Negative values of <see cref="EvaluationBudget"/>,
+    /// <see cref="RelativePrecision"/>, and <see cref="AbsolutePrecision"/>
+    /// indicate that the analysis method should use its defaults for
+    /// that property. Override the default for a property by
+    /// setting it explicitly. If you set values for some properties
+    /// but not others, your setting will be applied to the property
+    /// you set and the others will use defaults.</para>
+    /// <para>When an analysis method returns an <see cref="EvaluationResult"/>
+    /// object, its evaluation setting object will contain the specific
+    /// settings used, so you can see which default values were applied.</para>
+    /// </remarks>
     public class EvaluationSettings {
 
         /// <summary>
-        /// Initializes a new set of default evaulation settings.
+        /// Initializes a new set of default evaluation settings.
         /// </summary>
         public EvaluationSettings () {
             evaluationBudget = -1;
diff --git a/Numerics/Data/FrameTable.cs b/Numerics/Data/FrameTable.cs
@@ -13,15 +13,15 @@ namespace Meta.Numerics.Data
     // Additional flags could include: iid, series, circular
 
     /// <summary>
-    /// A modify-able array of data.
+    /// Represents a modify-able array of data.
     /// </summary>
     /// <remarks>
     /// <para>This is the central class for storing data in our data frame system.</para>
     /// <para>Use the <see cref="FromCsv"/> method to create a frame table from a comma-separated values
     /// file or the <see cref="FromDictionaries"/> method to create a frame table from JSON or another
     /// collection-of-dictionaries representation. Or create one programmatically by using the
     /// <see cref="FrameTable()"/> constructor to instantiate an empty data frame and
-    /// <see cref="AddColumn{T}(string)"/> and <see cref="AddRow(object[])"/> to add columns and rows.</para>
+    /// <see cref="AddColumn{T}(string)" autoUpgrade="true"/> and <see cref="AddRow(object[])" autoUpgrade="true"/> to add columns and rows.</para>
     /// <para>Using the methods inherited from the <see cref="FrameView"/> class, you can filter, re-order,
     /// manipulate, and analyze data without incurring the space or time costs of copying the stored data.</para>
     /// </remarks>
@@ -165,7 +165,7 @@ public void AddColumn<T>(string name, List<T> storage) {
         }
 
         /// <summary>
-        /// Adds the new columns with the given names.
+        /// Adds new columns with the given names.
         /// </summary>
         /// <typeparam name="T">The type of the columns.</typeparam>
         /// <param name="names">The names of the columns.</param>
diff --git a/Numerics/Data/FrameView.cs b/Numerics/Data/FrameView.cs
@@ -29,7 +29,7 @@ public enum SortOrder {
 
 
     /// <summary>
-    /// A read-only view of an array of data.
+    /// Represents a read-only view of an array of data.
     /// </summary>
     /// <remarks>
     /// <para>This is the central class for viewing data in our data frame system.</para>
@@ -50,10 +50,14 @@ public enum SortOrder {
     /// <see cref="this[string]"/> accessor to get a column, together with the <see cref="FrameColumn.As{T}"/>
     /// caster to expose it as a collection of the required type.
     /// For example, to obtain a estimate of the mean of the population from the sample in the
-    /// column named "heights", write <tt>view["height"].As&lt;double&gt;().PopulationMean()</tt>.</para>
+    /// column named "heights", write <tt>view["height"].As&lt;double&gt;().PopulationMean()</tt>.
+    /// Note that, for this to succeed, the underlying storage type of the heights column need not be double. As
+    /// long as the data are convertible to the target type, no problems will arise. For example,
+    /// the underlying storage type might be int, or double? as long as no null values are present in the view.</para>
     /// <para>To create the original array of data that will be manipulated, use the <see cref="FrameTable"/>
     /// class. Note that, because the underlying data is not copied when a new view is generated, changes
-    /// to the original table may not be reflected in the views that have been generated from it.</para>
+    /// to the original table may have unexpected consequences for the views linked to it. Best practice
+    /// is not to change the underlying data after generating views based on it.</para>
     /// <para>You can export a view to CSV or JSON formats using the <see cref="ToCsv(TextWriter)"/>
     /// and <see cref="ToDictionaries"/> methods.</para>
     /// </remarks>
diff --git a/Numerics/Properties/AssemblyInfo.cs b/Numerics/Properties/AssemblyInfo.cs
@@ -46,6 +46,6 @@
 //
 // You can specify all the values or you can default the Revision and Build Numbers 
 // by using the '*' as shown below:
-[assembly: AssemblyVersion("4.0.5.0")]
-[assembly: AssemblyFileVersion("4.0.5.0")]
+[assembly: AssemblyVersion("4.0.7.0")]
+[assembly: AssemblyFileVersion("4.0.7.0")]
 
diff --git a/Numerics/Statistics/Distributions/PearsonRDistribution.cs b/Numerics/Statistics/Distributions/PearsonRDistribution.cs
@@ -25,7 +25,7 @@ public override double ProbabilityDensity (double x) {
             if (Math.Abs(x) > 1.0) {
                 return (0.0);
             } else {
-                return (Math.Pow(1.0 - x * x, (n - 4) / 2.0) / AdvancedMath.Beta(0.5, (n - 2) / 2.0));
+                return (Math.Pow((1.0 - x) * (1.0 + x), (n - 4) / 2.0) / AdvancedMath.Beta(0.5, (n - 2) / 2.0));
             }
         }
 
@@ -89,7 +89,7 @@ public override double LeftProbability (double x) {
             if (x <= -1.0) {
                 return (0.0);
             } else if (x < 0.0) {
-                return (AdvancedMath.Beta((n - 2) / 2.0, 0.5, 1.0 - x * x) / AdvancedMath.Beta((n-2) / 2.0, 0.5) / 2.0);
+                return (AdvancedMath.Beta((n - 2) / 2.0, 0.5, (1.0 - x) * (1.0 + x)) / AdvancedMath.Beta((n-2) / 2.0, 0.5) / 2.0);
             } else if (x < 1.0) {
                 return ((1.0 + AdvancedMath.Beta(0.5, (n - 2) / 2.0, x * x) / AdvancedMath.Beta(0.5, (n-2) / 2.0)) / 2.0);
             } else {
diff --git a/Test/BivariateSampleTest.cs b/Test/BivariateSampleTest.cs
@@ -371,7 +371,7 @@ public void BivariateLinearRegressionNullDistribution () {
 
                 Assert.IsTrue(TestUtilities.IsNearlyEqual(
                     result.R.Probability, result.F.Probability,
-                    new EvaluationSettings() { RelativePrecision = 1.0E-14, AbsolutePrecision = 1.0E-16 }
+                    new EvaluationSettings() { RelativePrecision = 1.0E-13, AbsolutePrecision = 1.0E-16 }
                 ));
 
             }
diff --git a/Test/TridiagonalMatrixTest.cs b/Test/TridiagonalMatrixTest.cs

Original file line number	Diff line number	Diff line change
`@@ -23,7 +23,6 @@ private static MethodInfo[] GetExampleMethods () {`
`23`	`23`
`24`	`24`	`static void Main(string[] args)`
`25`	`25`	`{`
`26`		`-`
`27`	`26`	`MethodInfo[] methods = GetExampleMethods();`
`28`	`27`	`Dictionary<string, MethodInfo> index = new Dictionary<string, MethodInfo>();`
`29`	`28`	`foreach (MethodInfo method in methods) {`
Original file line number	Diff line number	Diff line change
`@@ -371,7 +371,7 @@ public void BivariateLinearRegressionNullDistribution () {`
`371`	`371`
`372`	`372`	`Assert.IsTrue(TestUtilities.IsNearlyEqual(`
`373`	`373`	`result.R.Probability, result.F.Probability,`
`374`		`- new EvaluationSettings() { RelativePrecision = 1.0E-14, AbsolutePrecision = 1.0E-16 }`
	`374`	`+ new EvaluationSettings() { RelativePrecision = 1.0E-13, AbsolutePrecision = 1.0E-16 }`
`375`	`375`	`));`
`376`	`376`
`377`	`377`	`}`