Merge pull request #110 from lilyclements/moving_to_instatCalculation

Moving to instat calculation
IDEMSInternational · Feb 26, 2025 · bce7166 · bce7166
2 parents a0338d0 + bff1c0a
commit bce7166
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Showing 88 changed files with 1,741 additions and 17,729 deletions.
diff --git a/instat/Interface/IDataViewGrid.vb b/instat/Interface/IDataViewGrid.vb
@@ -48,6 +48,8 @@ Public Interface IDataViewGrid
 
     Sub Focus()
 
+    Sub RemoveAllBackgroundColors()
+
     Function GetSelectedColumns() As List(Of clsColumnHeaderDisplay)
 
     Function GetFirstRowHeader() As String

diff --git a/instat/Model/RCommand/clsPrepareFunctionsForGrids.vb b/instat/Model/RCommand/clsPrepareFunctionsForGrids.vb
@@ -124,6 +124,7 @@ Public Class clsPrepareFunctionsForGrids
         clsGetColumnsFromData.AddParameter("col_names", Chr(34) & strColumnName & Chr(34), iPosition:=1)
         clsGetColumnsFromData.AddParameter("use_current_filter", "FALSE", iPosition:=2)
 
+        clsNNonNumeric.SetPackageName("instatExtras")
         clsNNonNumeric.SetRCommand("n_non_numeric")
         clsNNonNumeric.AddParameter("x", clsRFunctionParameter:=clsGetColumnsFromData, iPosition:=0)
         expTemp = _RLink.RunInternalScriptGetValue(clsNNonNumeric.ToScript(), bSilent:=True)

diff --git a/instat/UserControls/DataGrid/Linux/ucrDataViewLinuxGrid.vb b/instat/UserControls/DataGrid/Linux/ucrDataViewLinuxGrid.vb
@@ -175,6 +175,10 @@ Public Class ucrDataViewLinuxGrid
         dataGrid.Rows(iRow).Cells(iColumn).Value = GetCurrentDataFrameFocus.DisplayedData(iRow, iColumn)
     End Sub
 
+    Private Sub RemoveAllBackgroundColors() Implements IDataViewGrid.RemoveAllBackgroundColors
+
+    End Sub
+
     Public Sub SearchRowInGrid(rowNumbers As List(Of Integer), strColumn As String, Optional iRow As Integer = 0,
                             Optional bApplyToRows As Boolean = False) Implements IDataViewGrid.SearchRowInGrid
     End Sub

diff --git a/instat/UserControls/DataGrid/ReoGrid/ucrDataViewReoGrid.vb b/instat/UserControls/DataGrid/ReoGrid/ucrDataViewReoGrid.vb
@@ -375,6 +375,15 @@ Public Class ucrDataViewReoGrid
         Next
     End Sub
 
+    Private Sub RemoveAllBackgroundColors() Implements IDataViewGrid.RemoveAllBackgroundColors
+        For rowNumber As Integer = 0 To grdData.CurrentWorksheet.RowCount - 1
+            For colIndex As Integer = 0 To grdData.CurrentWorksheet.ColumnCount - 1
+                grdData.CurrentWorksheet.Cells(rowNumber, colIndex).Style.BackColor = Color.Transparent
+            Next
+        Next
+        grdData.CurrentWorksheet.RequestInvalidate()
+    End Sub
+
     Public Sub SearchRowInGrid(rowNumbers As List(Of Integer), strColumn As String, Optional iRow As Integer = 0,
                             Optional bApplyToRows As Boolean = False) Implements IDataViewGrid.SearchRowInGrid
         Dim currSheet = grdData.CurrentWorksheet

diff --git a/instat/clsFileUrlUtilities.vb b/instat/clsFileUrlUtilities.vb
@@ -50,6 +50,7 @@ Public Class clsFileUrlUtilities
         If bVignette Then
             Dim clsGetVignetteFunction As New RFunction
 
+            clsGetVignetteFunction.SetPackageName("instatExtras")
             clsGetVignetteFunction.SetRCommand("get_vignette")
             clsGetVignetteFunction.AddParameter("package", Chr(34) & strPackageName & Chr(34), iPosition:=0)
             strURL = frmMain.clsRLink.RunInternalScriptGetValue(clsGetVignetteFunction.ToScript(), bSeparateThread:=False).AsCharacter(0)

diff --git a/instat/clsGridROperations.vb b/instat/clsGridROperations.vb
@@ -52,6 +52,7 @@ Public Class GridROperations
         clsGetColumnsFromData.SetRCommand(frmMain.clsRLink.strInstatDataObject & "$get_columns_from_data")
         clsGetColumnsFromData.AddParameter("data_name", Chr(34) & strDataFrame & Chr(34), iPosition:=0)
 
+        clsNNonNumeric.SetPackageName("instatExtras")
         clsNNonNumeric.SetRCommand("n_non_numeric")
 
         clsConvertToNumeric.AddParameter("to_type", Chr(34) & "numeric" & Chr(34), iPosition:=2)

diff --git a/instat/clsQualityControl.vb b/instat/clsQualityControl.vb
@@ -66,7 +66,7 @@ Public Class clsQCJumpRCode
         clsPmaxFunction.bToScriptAsRString = True
 
         strCalcName = strlargestJump
-        clsJumpCalcFunction.SetRCommand("instat_calculation$new")
+        clsJumpCalcFunction.SetRCommand("instatCalculations::instat_calculation$new")
         clsJumpCalcFunction.AddParameter("type", Chr(34) & "calculation" & Chr(34), iPosition:=0)
         clsJumpCalcFunction.AddParameter("function_exp", clsRFunctionParameter:=clsPmaxFunction, iPosition:=1)
         clsJumpCalcFunction.AddParameter("result_name", Chr(34) & strCalcName & Chr(34), iPosition:=4)
@@ -75,7 +75,7 @@ Public Class clsQCJumpRCode
         strTestName = strJumpTest
         clsJumpListFunc.SetRCommand("list")
         clsJumpListFunc.AddParameter("sub1", clsRFunctionParameter:=clsJumpCalcFunction, bIncludeArgumentName:=False)
-        clsJumpTestFunction.SetRCommand("instat_calculation$new")
+        clsJumpTestFunction.SetRCommand("instatCalculations::instat_calculation$new")
         clsJumpTestFunction.AddParameter("type", Chr(34) & "calculation" & Chr(34), iPosition:=0)
         clsJumpTestFunction.AddParameter("function_exp", clsROperatorParameter:=clsGreaterJumpOperator, iPosition:=1)
         clsJumpTestFunction.AddParameter("result_name", Chr(34) & strTestName & Chr(34), iPosition:=4)
@@ -131,7 +131,7 @@ Public Class clsQCSameRCode
         clsDollarOperator.AddParameter("right", strParameterValue:=strLengths, bIncludeArgumentName:=False, iPosition:=1)
 
         strCalcName = strlargestSame
-        clsSameCalcFunction.SetRCommand("instat_calculation$new")
+        clsSameCalcFunction.SetRCommand("instatCalculations::instat_calculation$new")
         clsSameCalcFunction.AddParameter("type", Chr(34) & "calculation" & Chr(34), iPosition:=0)
         clsSameCalcFunction.AddParameter("function_exp", clsRFunctionParameter:=clsRepFunc, iPosition:=1)
         clsSameCalcFunction.AddParameter("result_name", Chr(34) & strCalcName & Chr(34), iPosition:=4)
@@ -142,7 +142,7 @@ Public Class clsQCSameRCode
         clsSameListFunc.SetRCommand("list")
         clsSameListFunc.AddParameter("sub1", clsRFunctionParameter:=clsSameCalcFunction, bIncludeArgumentName:=False)
 
-        clsSameTestFunction.SetRCommand("instat_calculation$new")
+        clsSameTestFunction.SetRCommand("instatCalculations::instat_calculation$new")
         clsSameTestFunction.AddParameter("type", Chr(34) & "calculation" & Chr(34), iPosition:=0)
         clsSameTestFunction.AddParameter("function_exp", clsROperatorParameter:=clsSameGreaterOperator, iPosition:=1)
         clsSameTestFunction.AddParameter("result_name", Chr(34) & strTestName & Chr(34), iPosition:=4)
@@ -179,7 +179,7 @@ Public Class clsQCDifferenceRCode
         clsDiffOperator.SetOperation("-")
         clsDiffOperator.bToScriptAsRString = True
 
-        clsDiffCalcFunction.SetRCommand("instat_calculation$new")
+        clsDiffCalcFunction.SetRCommand("instatCalculations::instat_calculation$new")
         clsDiffCalcFunction.AddParameter("type", Chr(34) & "calculation" & Chr(34), iPosition:=0)
         clsDiffCalcFunction.AddParameter("function_exp", clsROperatorParameter:=clsDiffOperator, iPosition:=1)
         clsDiffCalcFunction.AddParameter("result_name", Chr(34) & strDiffCalc & Chr(34), iPosition:=4)
@@ -188,7 +188,7 @@ Public Class clsQCDifferenceRCode
         strTestName = strDiffTest
         clsListFunc.SetRCommand("list")
         clsListFunc.AddParameter("sub1", bIncludeArgumentName:=False, clsRFunctionParameter:=clsDiffCalcFunction, iPosition:=0)
-        clsDiffTestFunction.SetRCommand("instat_calculation$new")
+        clsDiffTestFunction.SetRCommand("instatCalculations::instat_calculation$new")
         clsDiffTestFunction.AddParameter("type", Chr(34) & "calculation" & Chr(34), iPosition:=0)
         clsDiffTestFunction.AddParameter("function_exp", clsROperatorParameter:=clsLessDiffOperator, iPosition:=1)
         clsDiffTestFunction.AddParameter("result_name", Chr(34) & strTestName & Chr(34), iPosition:=4)
@@ -223,7 +223,7 @@ Public Class clsQCAcceptableRange
         clsRangeOrOperator.AddParameter("left", clsROperatorParameter:=clsLessEqualToOperator, iPosition:=0, bIncludeArgumentName:=False)
         clsRangeOrOperator.AddParameter("right", clsROperatorParameter:=clsGreaterEqualToOperator, iPosition:=1, bIncludeArgumentName:=False)
 
-        clsAcceptableRangeTestFunc.SetRCommand("instat_calculation$new")
+        clsAcceptableRangeTestFunc.SetRCommand("instatCalculations::instat_calculation$new")
         clsAcceptableRangeTestFunc.AddParameter("type", Chr(34) & "calculation" & Chr(34), iPosition:=0)
         clsAcceptableRangeTestFunc.AddParameter("function_exp", clsROperatorParameter:=clsRangeOrOperator, iPosition:=1)
         clsAcceptableRangeTestFunc.AddParameter("result_name", Chr(34) & strRangeName & Chr(34), iPosition:=4)
@@ -265,7 +265,7 @@ Public Class clsQcOutliers
         strUpperTestName = strOutlierUpperTestCalcName
         strLowerTestName = strOutlierLowerTestCalcName
 
-        clsOutlierUpperLimitCalc.SetRCommand("instat_calculation$new")
+        clsOutlierUpperLimitCalc.SetRCommand("instatCalculations::instat_calculation$new")
         clsOutlierUpperLimitCalc.AddParameter("type", Chr(34) & "calculation" & Chr(34), iPosition:=0)
         clsOutlierUpperLimitCalc.AddParameter("function_exp", clsRFunctionParameter:=clsOutlierUpperLimitFunc, iPosition:=1)
         clsOutlierUpperLimitCalc.AddParameter("result_name", Chr(34) & strUpperCalcName & Chr(34), iPosition:=4)
@@ -275,7 +275,7 @@ Public Class clsQcOutliers
         clsOutlierUpperLimitFunc.AddParameter("bupperlimit", "TRUE")
         clsOutlierUpperLimitFunc.bToScriptAsRString = True
 
-        clsOutlierLowerLimitCalc.SetRCommand("instat_calculation$new")
+        clsOutlierLowerLimitCalc.SetRCommand("instatCalculations::instat_calculation$new")
         clsOutlierLowerLimitCalc.AddParameter("type", Chr(34) & "calculation" & Chr(34), iPosition:=0)
         clsOutlierLowerLimitCalc.AddParameter("function_exp", clsRFunctionParameter:=clsOutlierLowerLimitFunc, iPosition:=1)
         clsOutlierLowerLimitCalc.AddParameter("result_name", Chr(34) & strLowerCalcName & Chr(34), iPosition:=4)
@@ -285,7 +285,7 @@ Public Class clsQcOutliers
         clsOutlierLowerLimitFunc.AddParameter("bupperlimit", "FALSE")
         clsOutlierLowerLimitFunc.bToScriptAsRString = True
 
-        clsOutlierLowerLimitTestCalc.SetRCommand("instat_calculation$new")
+        clsOutlierLowerLimitTestCalc.SetRCommand("instatCalculations::instat_calculation$new")
         clsOutlierLowerLimitTestCalc.AddParameter("type", Chr(34) & "calculation" & Chr(34), iPosition:=0)
         clsOutlierLowerLimitTestCalc.AddParameter("function_exp", clsROperatorParameter:=clsOutlierLowerOperator, iPosition:=1)
         clsOutlierLowerLimitTestCalc.AddParameter("sub_calculations", clsRFunctionParameter:=clsOutlierLowerList, iPosition:=2)
@@ -299,7 +299,7 @@ Public Class clsQcOutliers
         clsOutlierLowerOperator.bToScriptAsRString = True
         clsOutlierLowerOperator.AddParameter("right", strLowerCalcName, iPosition:=1)
 
-        clsOutlierUpperLimitTestCalc.SetRCommand("instat_calculation$new")
+        clsOutlierUpperLimitTestCalc.SetRCommand("instatCalculations::instat_calculation$new")
         clsOutlierUpperLimitTestCalc.AddParameter("type", Chr(34) & "calculation" & Chr(34), iPosition:=0)
         clsOutlierUpperLimitTestCalc.AddParameter("function_exp", clsROperatorParameter:=clsOutlierUpperOperator, iPosition:=1)
         clsOutlierUpperLimitTestCalc.AddParameter("sub_calculations", clsRFunctionParameter:=clsOutlierUpperList, iPosition:=2)

diff --git a/instat/clsRCodeStructure.vb b/instat/clsRCodeStructure.vb
@@ -530,6 +530,7 @@ Public Class RCodeStructure
 
                 If _strAssignToObjectTypeLabel = RObjectTypeLabel.Graph Then
                     Dim clsCheckGraphRFunction As New RFunction
+                    clsCheckGraphRFunction.SetPackageName("instatExtras")
                     clsCheckGraphRFunction.SetRCommand("check_graph")
                     clsCheckGraphRFunction.AddParameter("graph_object", _strAssignToObject)
                     clsAddRObject.AddParameter("object", clsRFunctionParameter:=clsCheckGraphRFunction)

diff --git a/instat/clsRLink.vb b/instat/clsRLink.vb
@@ -669,6 +669,7 @@ Public Class RLink
         Dim strExistingNames As String
         Dim expPrefix As SymbolicExpression
 
+        clsGetDefault.SetPackageName("instatExtras")
         clsGetDefault.SetRCommand("next_default_item")
         clsGetDefault.AddParameter("prefix", Chr(34) & strPrefix & Chr(34))
         strExistingNames = GetListAsRString(lstItems)
@@ -784,7 +785,7 @@ Public Class RLink
                                       bSeparateThread:=False, bShowWaitDialogOverride:=Nothing)
             ElseIf Not clsRStatement.IsAssignment _
                 AndAlso Not String.IsNullOrWhiteSpace(clsRStatement.TextNoFormatting) Then
-                strOutput = GetFileOutput("view_object_data(object = " _
+                strOutput = GetFileOutput("instatExtras::view_object_data(object = " _
                                           & clsRStatement.TextNoFormatting _
                                           & " , object_format = 'text' )", bSilent:=False,
                                           bSeparateThread:=False, bShowWaitDialogOverride:=Nothing)
@@ -795,7 +796,7 @@ Public Class RLink
 
             ' Add output to logger
             clsOutputLogger.AddOutput(clsRStatement.Text, strOutput, bAsFile:=True,
-                        bDisplayOutputInExternalViewer:=clsRStatement.TextNoFormatting.StartsWith("view_object_data"))
+                        bDisplayOutputInExternalViewer:=clsRStatement.TextNoFormatting.StartsWith("instatExtras::view_object_data"))
 
             ' Log the script
             LogScript(clsRStatement.Text.TrimEnd(vbCr, vbLf))
@@ -894,7 +895,7 @@ Public Class RLink
                     Dim strRStatementAsSingleLine As String = strRStatement.Replace(vbCr, String.Empty)
                     strRStatementAsSingleLine = strRStatementAsSingleLine.Replace(vbLf, String.Empty)
                     'wrap final command inside view_object_data just in case there is an output object
-                    strOutput = GetFileOutput("view_object_data(object = " & strRStatementAsSingleLine & " , object_format = 'text' )", False, False, Nothing)
+                    strOutput = GetFileOutput("instatExtras::view_object_data(object = " & strRStatementAsSingleLine & " , object_format = 'text' )", False, False, Nothing)
                 Else
                     Evaluate(strRStatement, bSilent:=False, bSeparateThread:=False, bShowWaitDialogOverride:=Nothing)
                 End If
@@ -1037,7 +1038,7 @@ Public Class RLink
                         End If
 
                         If bSuccess Then
-                            strOutput = GetFileOutput("view_object_data(object = " & arrExecutableRScriptLines.Last() & " , object_format = 'text' )", bSilent, bSeparateThread, bShowWaitDialogOverride)
+                            strOutput = GetFileOutput("instatExtras::view_object_data(object = " & arrExecutableRScriptLines.Last() & " , object_format = 'text' )", bSilent, bSeparateThread, bShowWaitDialogOverride)
                         End If
                     End If
 
@@ -2157,6 +2158,7 @@ Public Class RLink
         clsGetColumn.SetRCommand(strInstatDataObject & "$get_columns_from_data")
         clsGetColumn.AddParameter("data_name", Chr(34) & strDataName & Chr(34))
         clsGetColumn.AddParameter("col_names", Chr(34) & strColumn & Chr(34))
+        clsIsBinary.SetPackageName("instatExtras")
         clsIsBinary.SetRCommand("is.binary")
         clsIsBinary.AddParameter("x", clsRFunctionParameter:=clsGetColumn)
         expBinary = RunInternalScriptGetValue(clsIsBinary.ToScript())
@@ -2260,7 +2262,7 @@ Public Class RLink
         Dim strRStatementTrimmed As String = TrimStartRStatement(strRStatement)
         Return strRStatementTrimmed.StartsWith(strInstatDataObject & "$get_object_data") _
                OrElse strRStatementTrimmed.StartsWith(strInstatDataObject & "$get_last_object_data") _
-               OrElse strRStatementTrimmed.StartsWith("view_object_data")
+               OrElse strRStatementTrimmed.StartsWith("instatExtras::view_object_data")
     End Function
 
     Private Function TrimStartRStatement(strRStatement As String) As String

diff --git a/instat/dlgAnonymiseIDColumn.vb b/instat/dlgAnonymiseIDColumn.vb
@@ -72,6 +72,7 @@ Public Class dlgAnonymiseIDColumn
         ucrSelectorAnonymiseIDColumn.Reset()
         ucrSaveAnonymisedColumn.Reset()
 
+        clsHashFunction.SetPackageName("instatExtras")
         clsHashFunction.SetRCommand("hashed_id")
         clsHashFunction.AddParameter("algo", Chr(34) & "crc32" & Chr(34), iPosition:=2)
 

diff --git a/instat/dlgCalculationsSummary.vb b/instat/dlgCalculationsSummary.vb
@@ -61,7 +61,7 @@ Public Class dlgCalculationsSummary
         clsApplyCalculation.SetRCommand(frmMain.clsRLink.strInstatDataObject & "$run_instat_calculation")
         clsApplyCalculation.AddParameter("calc", clsRFunctionParameter:=clsNewCalculationFunction)
 
-        clsNewCalculationFunction.SetRCommand("instat_calculation$new")
+        clsNewCalculationFunction.SetRCommand("instatCalculations::instat_calculation$new")
         clsNewCalculationFunction.AddParameter("name", Chr(34) & strCalcName & Chr(34))
         clsNewCalculationFunction.AddParameter("type", Chr(34) & "calculation" & Chr(34))
         clsNewCalculationFunction.AddParameter("save", "2")

diff --git a/instat/dlgCanonicalCorrelationAnalysis.vb b/instat/dlgCanonicalCorrelationAnalysis.vb
@@ -93,6 +93,7 @@ Public Class dlgCanonicalCorrelationAnalysis
                                                   strRDataFrameNameToAddObjectTo:=ucrSelectorCCA.strCurrentDataFrame,
                                                   strObjectName:="last_model")
 
+        clsRFunctionCoef.SetPackageName("instatExtras")
         clsRFunctionCoef.SetRCommand("cancor_coef")
         clsRFunctionCoef.bExcludeAssignedFunctionOutput = False
         clsRFunctionCoef.SetAssignToOutputObject(strRObjectToAssignTo:="last_summary",

diff --git a/instat/dlgCircularDensityPlot.vb b/instat/dlgCircularDensityPlot.vb
@@ -150,6 +150,7 @@ Public Class dlgCircularDensityPlot
         clsScatterPlotFunction.AddParameter("sep", 0.0003, iPosition:=5)
         clsScatterPlotFunction.AddParameter("shrink", 1, iPosition:=9)
 
+        clsRecordGraphFunction.SetPackageName("instatExtras")
         clsRecordGraphFunction.SetRCommand("record_graph")
         clsRecordGraphFunction.AddParameter("x", clsRFunctionParameter:=clsDensityPlotFunction, iPosition:=0)
 

diff --git a/instat/dlgClimaticBoxPlot.vb b/instat/dlgClimaticBoxPlot.vb
@@ -269,6 +269,7 @@ Public Class dlgClimaticBoxPlot
         clsRaesFunction.SetRCommand("aes")
         clsRaesFunction.AddParameter("x", Chr(34) & Chr(34))
 
+        clsAsFactorFunction.SetPackageName("instatExtras")
         clsAsFactorFunction.SetRCommand("make_factor")
         clsAsFactorFunction.AddParameter("x", Chr(34) & Chr(34), bIncludeArgumentName:=False)