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git-svn-id: https://svn.code.sf.net/p/lazarus-ccr/svn@7897 8e941d3f-bd1b-0410-a28a-d453659cc2b4
657 lines
16 KiB
ObjectPascal
657 lines
16 KiB
ObjectPascal
unit CoxRegUnit;
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{$mode objfpc}{$H+}
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interface
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uses
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Classes, SysUtils, FileUtil, Forms, Controls, Graphics, Dialogs,
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StdCtrls, Buttons, ExtCtrls,
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Globals, MainUnit, BasicStatsReportFormUnit;
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type
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{ TCoxRegForm }
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TCoxRegForm = class(TBasicStatsReportForm)
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InBtn: TBitBtn;
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OutBtn: TBitBtn;
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DepInBtn: TBitBtn;
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DepOutBtn: TBitBtn;
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StatusInBtn: TBitBtn;
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StatusOutBtn: TBitBtn;
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DescChk: TCheckBox;
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MaxItsEdit: TEdit;
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Label5: TLabel;
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ProbsChk: TCheckBox;
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ItersChk: TCheckBox;
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DepVar: TEdit;
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GroupBox1: TGroupBox;
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StatusEdit: TEdit;
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Label1: TLabel;
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Label2: TLabel;
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BlockList: TListBox;
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Label3: TLabel;
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Label4: TLabel;
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VarList: TListBox;
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procedure BlockListDblClick(Sender: TObject);
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procedure DepInBtnClick(Sender: TObject);
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procedure DepOutBtnClick(Sender: TObject);
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procedure InBtnClick(Sender: TObject);
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procedure OutBtnClick(Sender: TObject);
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procedure StatusInBtnClick(Sender: TObject);
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procedure StatusOutBtnClick(Sender: TObject);
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function ChiSq(x : double; n : integer) : double;
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function Norm(z : double): double;
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function ix(j, k, nCols : integer): integer;
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procedure VarListDblClick(Sender: TObject);
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procedure VarListSelectionChange(Sender: TObject; {%H-}User: boolean);
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private
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{ private declarations }
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protected
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procedure AdjustConstraints; override;
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procedure Compute; override;
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procedure UpdateBtnStates; override;
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public
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procedure Reset; override;
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end;
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var
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CoxRegForm: TCoxRegForm;
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implementation
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{$R *.lfm}
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uses
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Math,
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Utils;
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{ TCoxRegForm }
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procedure TCoxRegForm.AdjustConstraints;
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begin
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inherited;
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ParamsPanel.Constraints.MinWidth := Max(
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4*CloseBtn.Width + 3*CloseBtn.BorderSpacing.Left,
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GroupBox1.Width);
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ParamsPanel.Constraints.MinHeight := InBtn.Top + 6*InBtn.Height + 7*OutBtn.BorderSpacing.Top +
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VarList.BorderSpacing.Bottom + MaxItsEdit.Height + MaxItsEdit.BorderSpacing.Bottom +
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GroupBox1.Height + ButtonBevel.Height + CloseBtn.BorderSpacing.Top + CloseBtn.Height;
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end;
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procedure TCoxRegForm.BlockListDblClick(Sender: TObject);
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var
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index: Integer;
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begin
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index := BlockList.ItemIndex;
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if index > -1 then
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begin
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VarList.Items.Add(BlockList.Items[index]);
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BlockList.Items.Delete(index);
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UpdateBtnStates;
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end;
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end;
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function TCoxRegForm.ChiSq(x: double; n: integer): double;
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var
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p, t, a: double;
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k: integer;
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begin
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p := exp(-0.5 * x);
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if n mod 2 = 1 then
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p := p * sqrt(2 * x / Pi);
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k := n;
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while K >= 2 do
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begin
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p := p * x / k;
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k := k - 2;
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end;
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t := p;
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a := n;
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while t > 0.000001 * p do
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begin
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a := a + 2;
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t := t * x / a;
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p := p + t;
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end;
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Result := (1 - p);
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end;
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procedure TCoxRegForm.Compute;
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var
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i, j, k : integer;
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indx : integer;
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cellstring : string;
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outline : string;
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nR : integer; // no. independent variables
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ColNoSelected : IntDyneVec = nil;
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nC : integer; // no. cases
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nP : integer; // survival time variable
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nS : integer; // survival status variable
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zX : double;
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v : double;
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Eps : double;
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iBig : integer;
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LLp, LL : double;
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LLn : double;
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s0 : double;
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StatI : double;
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Sf : double;
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CSq : double; // chi square statistic
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prob : double; // probability of chi square
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SurvT : DblDyneVec = nil;
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Stat : DblDyneVec = nil;
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Alpha : DblDyneVec = nil;
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a : DblDyneVec = nil;
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b : DblDyneVec = nil;
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s1 : DblDyneVec = nil;
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s2 : DblDyneVec = nil;
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s : DblDyneVec = nil;
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Av : DblDyneVec = nil;
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SD : DblDyneVec = nil;
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SE : DblDyneVec = nil;
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x : DblDyneVec = nil; // data matrix for independent variables
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RowLabels : StrDyneVec = nil;
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ColLabels : StrDyneVec;
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Lo95 : double;
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Hi95 : double;
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d : double;
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iters : integer;
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lReport: TStrings;
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begin
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if MaxItsEdit.Text = '' then
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begin
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MaxItsEdit.Setfocus;
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MessageDlg('Maximum iterations not specified.', mtError, [mbOK], 0);
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exit;
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end;
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if not TryStrToInt(MaxItsEdit.Text, iters) then
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begin
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MaxItsEdit.SetFocus;
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MessageDlg('Valid number required.', mtError, [mbOK], 0);
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exit;
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end;
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{ get independent item columns }
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nR := BlockList.Items.Count;
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nC := NoCases;
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SetLength(ColNoSelected,nR + 2);
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SetLength(RowLabels,nR + 2);
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SetLength(ColLabels,nR + 2);
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if nR < 1 then
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begin
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MessageDlg('No independent variables selected.', mtError, [mbOK], 0);
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exit;
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end;
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for i := 1 to nR do
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begin
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cellstring := BlockList.Items.Strings[i-1];
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for j := 1 to NoVariables do
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begin
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if cellstring = OS3MainFrm.DataGrid.Cells[j,0] then
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begin
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ColNoSelected[i-1] := j;
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RowLabels[i-1] := cellstring;
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ColLabels[i-1] := cellstring;
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end;
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end;
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end;
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{ get survival time variable column and survival status var. column }
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if DepVar.Text = '' then
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begin
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MessageDlg('No Survival time variable selected.', mtError, [mbOK], 0);
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exit;
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end;
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if StatusEdit.Text = '' then
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begin
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MessageDlg('No Survival Status variable selected.', mtError, [mbOK], 0);
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exit;
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end;
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nP := nR + 1;
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nS := nP + 1;
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for j := 1 to NoVariables do
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begin
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if DepVar.Text = OS3MainFrm.DataGrid.Cells[j,0] then
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begin
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ColNoSelected[nP-1] := j;
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RowLabels[nP-1] := OS3MainFrm.DataGrid.Cells[j,0];
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ColLabels[nP-1] := RowLabels[nP-1];
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end;
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if StatusEdit.Text = OS3MainFrm.DataGrid.Cells[j,0] then
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begin
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ColNoSelected[nS-1] := j;
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RowLabels[nS-1] := OS3MainFrm.DataGrid.Cells[j,0];
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ColLabels[nS-1] := RowLabels[nS-1];
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end;
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end;
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SetLength(SurvT,nC + 1);
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SetLength(Stat,nC + 1);
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SetLength(Alpha,nC + 1);
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SetLength(x,(nC + 1) * (nR + 1));
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SetLength(b,nC + 1);
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SetLength(a,(nR + 1) * (nR + 1));
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SetLength(s1,nR + 1);
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SetLength(s2,(nR + 1) * (nR + 1));
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SetLength(s,nR + 1);
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SetLength(Av,nR + 1);
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SetLength(SD,nR + 1);
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SetLength(SE,nR + 1);
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// get data
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for i := 0 to nC - 1 do
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begin
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indx := ix(i,0,nR+1);
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X[indx] := 1;
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for j := 0 to nR-1 do
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begin
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indx := ColNoSelected[j];
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zX := StrToFloat(Trim(OS3MainFrm.DataGrid.Cells[indx,i+1]));
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indx := ix(i,j,nR);
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x[indx] := zX;
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Av[j] := Av[j] + zX;
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SD[j] := SD[j] + (zX * zX);
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end;
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// get survival time
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indx := ColNoSelected[nP-1];
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zX := StrToFloat(Trim(OS3MainFrm.DataGrid.Cells[indx,i+1]));
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SurvT[i] := zX;
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// get survival status
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indx := ColNoSelected[nS-1];
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zX := StrToFloat(Trim(OS3MainFrm.DataGrid.Cells[indx,i+1]));
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Stat[i] := zX;
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end; // next case i
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// print descriptive statistics
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lReport := TStringList.Create;
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try
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lReport.Add('COX PROPORTIONAL HARARDS SURVIVAL REGRESSION adapted from John C. Pezzullo');
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lReport.Add('Java program at http://members.aol.com/johnp71/prophaz.html');
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lReport.Add('');
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if DescChk.Checked then
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begin
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lReport.Add('Descriptive Statistics');
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lReport.Add('Variable Label Average Std.Dev.');
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end;
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for j := 0 to nR-1 do
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begin
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Av[j] := Av[j] / nC;
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SD[j] := SD[j] / nC;
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SD[j] := sqrt( abs(SD[j] - Av[j] * Av[j]));
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if DescChk.Checked then
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lReport.Add(' %3d %15s %11.4f %11.4f', [j+1, RowLabels[j], Av[j], SD[j]]);
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end;
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lReport.Add('');
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d := 0.0;
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Eps := 1.0 / 1024.0;
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for i := 0 to nC-2 do
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begin
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iBig := i;
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for j := i+1 to nC-1 do
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if (SurvT[j] - Eps * Stat[j]) > (SurvT[iBig]-Eps * Stat[iBig]) then
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iBig := j;
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if iBig <> i then
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begin
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v := SurvT[i];
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SurvT[i] := SurvT[iBig];
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SurvT[iBig] := v;
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v := Stat[i];
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Stat[i] := Stat[iBig];
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Stat[iBig] := v;
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for j := 0 to nR-1 do
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begin
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v := x[ix(i,j,nR)];
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x[ix(i,j,nR)] := x[ix(iBig,j,nR)];
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x[ix(iBig,j,nR)] := v;
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end;
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end;
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end;
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if Stat[0] > 0 then
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Stat[0] := Stat[0] + 2;
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for i := 1 to nC-1 do
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begin
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if (Stat[i] > 0) and ((Stat[i-1] = 0) or (SurvT[i-1] <> SurvT[i])) then
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Stat[i] := Stat[i] + 2;
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end;
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if Stat[nC-1] > 0 then
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Stat[nC-1] := Stat[nC-1] + 4;
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for i := nC-2 downto 0 do
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begin
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if (Stat[i] > 0) and ((Stat[i+1] = 0) or (SurvT[i+1] <> Survt[i])) then
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Stat[i] := Stat[i] + 4;
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end;
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for i := 0 to nC-1 do
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begin
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for j := 0 to nR-1 do
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begin
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x[ix(i,j,nR)] := (x[ix(i,j,nR)] - Av[j]) / SD[j];
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end;
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end;
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if ItersChk.Checked then
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lReport.Add('Iteration History...');
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for j := 0 to nR-1 do b[j] := 0;
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LLp := 2.0e30;
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LL := 1.0e30;
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// start iterations
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iters := 0;
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while (Abs(LLp-LL) > 0.0001) do
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begin
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iters := iters + 1;
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if iters > StrToInt(MaxItsEdit.Text) then break;
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LLp := LL;
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LL := 0.0;
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s0 := 0.0;
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for j := 0 to nR-1 do
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begin
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s1[j] := 0.0;
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a[ix(j,nR,nR+1)] := 0.0;
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for k := 0 to nR-1 do
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begin
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s2[ix(j,k,nR)] := 0.0;
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a[ix(j,k,nR+1)] := 0.0;
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end;
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end;
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for i := 0 to nC-1 do
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begin
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Alpha[i] := 1.0;
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v := 0.0;
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for j := 0 to nR-1 do v := v + b[j] * x[ix(i,j,nR)];
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v := exp(v);
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s0 := s0 + v;
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for j := 0 to nR-1 do
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begin
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s1[j] := s1[j] + x[ix(i,j,nR)] * v;
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for k := 0 to nR-1 do
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s2[ix(j,k,nR)] := s2[ix(j,k,nR)] + x[ix(i,j,nR)] * x[ix(i,k,nR)] * v;
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end;
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StatI := Stat[i];
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if (StatI = 2) or (StatI = 3) or (StatI = 6) or (StatI = 7) then
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begin
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d := 0.0;
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for j := 0 to nR-1 do s[j] := 0.0;
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end;
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if (StatI = 1) or (StatI = 3) or (StatI = 5) or (StatI = 7) then
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begin
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d := d + 1;
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for j := 0 to nR-1 do s[j] := s[j] + x[ix(i,j,nR)];
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end;
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if (StatI = 4) or (StatI = 5) or (StatI = 6) or (StatI = 7) then
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begin
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for j := 0 to nR-1 do
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begin
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LL := LL + s[j] * b[j];
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a[ix(j,nR,nR+1)] := a[ix(j,nR,nR+1)] + s[j] - d * s1[j] / s0;
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for k := 0 to nR-1 do
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begin
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a[ix(j,k,nR+1)] := a[ix(j,k,nR+1)] + d * (s2[ix(j,k,nR)] / s0 -
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s1[j] * s1[k] / (s0 * s0));
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end;
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end;
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LL := LL - d * Ln(s0);
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if d = 1 then Alpha[i] := Power((1.0 - v / s0),(1.0 / v))
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else Alpha[i] := exp(-d / s0);
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end;
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end;
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LL := -2.0 * LL;
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outline := format('-2 Log Likelihood: %.4f',[LL]);
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if iters = 1 then
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begin
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LLn := LL;
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if ItersChk.Checked then
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outline := outline + ' (Null Model)';
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end;
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if ItersChk.Checked then
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lReport.Add(outline);
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for i := 0 to nR-1 do
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begin
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v := a[ix(i,i,nR+1)];
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a[ix(i,i,nR+1)] := 1.0;
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for k := 0 to nR do
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a[ix(i,k,nR+1)] := a[ix(i,k,nR+1)] / v;
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for j := 0 to nR-1 do
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begin
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if i <> j then
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begin
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v := a[ix(j,i,nR+1)];
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a[ix(j,i,nR+1)] := 0.0;
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for k := 0 to nR do
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a[ix(j,k,nR+1)] := a[ix(j,k,nR+1)] - v * a[ix(i,k,nR+1)];
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end;
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end;
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end;
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for j := 0 to nR-1 do b[j] := b[j] + a[ix(j,nR,nR+1)];
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end;
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lReport.Add('Converged');
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Csq := LLn - LL;
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lReport.Add('');
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lReport.Add('Overall Model Fit...');
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if Csq > 0.0 then prob := ChiSq(Csq,nR) else prob := 1.0;
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lReport.Add('Chi Square: %8.4f', [csq]);
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lReport.Add(' with d.f. %8d', [nR]);
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lReport.Add(' and probability: %8.4f', [prob]);
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lReport.Add('');
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lReport.Add('Coefficients, Std Errs, Signif, and Confidence Intervals');
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lReport.Add('');
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lReport.Add('Var Coeff. StdErr p Lo95% Hi95%');
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for j := 0 to nR-1 do
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begin
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b[j] := b[j] / SD[j];
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SE[j] := sqrt(a[ix(j,j,nR+1)]) / SD[j];
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prob := Norm(Abs(b[j] / SE[j]));
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Lo95 := b[j] - 1.96 * SE[j];
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Hi95 := b[j] + 1.96 * SE[j];
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lReport.Add('%10s %10.4f %10.4f %8.4f %8.4f %8.4f',
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[RowLabels[j], b[j], SE[j], prob, Lo95, Hi95]);
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end;
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lReport.Add('');
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lReport.Add('Risk Ratios and Confidence Intervals');
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lReport.Add('');
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lReport.Add('Variable Risk Ratio Lo95% Hi95%');
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for j := 0 to nR-1 do
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lReport.Add('%10s %10.4f %10.4f %10.4f',
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[RowLabels[j], exp(b[j]), exp(b[j]-1.96*SE[j]), exp(b[j]+1.96*SE[j])]);
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lReport.Add('');
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if ProbsChk.Checked then
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lReport.Add('Baseline Survivor Function (at predictor means)...');
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SF := 1.0;
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for i := nC-1 downto 0 do
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begin
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Sf := Sf * Alpha[i];
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if Alpha[i] < 1.0 then
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begin
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if ProbsChk.Checked then
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lReport.Add('%10.4f %10.4f', [SurvT[i], Sf]);
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|
end;
|
|
end;
|
|
|
|
FReportFrame.DisplayReport(lReport);
|
|
|
|
finally
|
|
lReport.Free;
|
|
end;
|
|
end;
|
|
|
|
|
|
procedure TCoxRegForm.DepInBtnClick(Sender: TObject);
|
|
var
|
|
index: integer;
|
|
begin
|
|
index := VarList.ItemIndex;
|
|
if (index > -1) and (DepVar.Text = '') then
|
|
begin
|
|
DepVar.Text := VarList.Items[index];
|
|
VarList.Items.Delete(index);
|
|
end;
|
|
UpdateBtnStates;
|
|
end;
|
|
|
|
|
|
procedure TCoxRegForm.DepOutBtnClick(Sender: TObject);
|
|
begin
|
|
if DepVar.Text <> '' then
|
|
begin
|
|
VarList.Items.Add(DepVar.Text);
|
|
DepVar.Text := '';
|
|
end;
|
|
UpdateBtnStates;
|
|
end;
|
|
|
|
|
|
procedure TCoxRegForm.InBtnClick(Sender: TObject);
|
|
var
|
|
i: integer;
|
|
begin
|
|
i := 0;
|
|
while i < VarList.Items.Count do
|
|
begin
|
|
if VarList.Selected[i] then
|
|
begin
|
|
BlockList.Items.Add(VarList.Items[i]);
|
|
VarList.Items.Delete(i);
|
|
i := 0;
|
|
end else
|
|
i := i + 1;
|
|
end;
|
|
UpdateBtnStates;
|
|
end;
|
|
|
|
|
|
function TCoxRegForm.ix(j, k, nCols : integer): integer;
|
|
begin
|
|
Result := j*nCols + k;
|
|
end;
|
|
|
|
|
|
function TCoxRegForm.Norm(z: double): double;
|
|
begin
|
|
Result := ChiSq(z*z, 1);
|
|
end;
|
|
|
|
|
|
procedure TCoxRegForm.OutBtnClick(Sender: TObject);
|
|
var
|
|
i: integer;
|
|
begin
|
|
i := 0;
|
|
while i < BlockList.Items.Count do
|
|
begin
|
|
if BlockList.Selected[i] then
|
|
begin
|
|
VarList.Items.Add(BlockList.Items[i]);
|
|
BlockList.Items.Delete(i);
|
|
i := 0;
|
|
end else
|
|
i := i + 1;
|
|
UpdateBtnStates;
|
|
end;
|
|
end;
|
|
|
|
|
|
procedure TCoxRegForm.Reset;
|
|
var
|
|
i: integer;
|
|
begin
|
|
inherited;
|
|
|
|
BlockList.Clear;
|
|
VarList.Clear;
|
|
for i := 1 to NoVariables do
|
|
VarList.Items.Add(OS3MainFrm.DataGrid.Cells[i,0]);
|
|
ProbsChk.Checked := true;
|
|
DescChk.Checked := true;
|
|
DepVar.Text := '';
|
|
StatusEdit.Text := '';
|
|
MaxItsEdit.Text := '20';
|
|
end;
|
|
|
|
|
|
procedure TCoxRegForm.StatusInBtnClick(Sender: TObject);
|
|
var
|
|
index: integer;
|
|
begin
|
|
index := VarList.ItemIndex;
|
|
if (index > -1) and (StatusEdit.Text = '') then
|
|
begin
|
|
StatusEdit.Text := VarList.Items[index];
|
|
VarList.Items.Delete(index);
|
|
end;
|
|
UpdateBtnStates;
|
|
end;
|
|
|
|
|
|
procedure TCoxRegForm.StatusOutBtnClick(Sender: TObject);
|
|
begin
|
|
if (StatusEdit.Text <> '') then
|
|
begin
|
|
VarList.Items.Add(StatusEdit.Text);
|
|
StatusEdit.Text := '';
|
|
end;
|
|
UpdateBtnStates;
|
|
end;
|
|
|
|
|
|
procedure TCoxRegForm.UpdateBtnStates;
|
|
var
|
|
lSelected: Boolean;
|
|
begin
|
|
inherited;
|
|
|
|
lSelected := AnySelected(VarList);
|
|
InBtn.Enabled := lSelected;
|
|
DepInBtn.Enabled := lSelected and (DepVar.Text = '');
|
|
StatusInBtn.Enabled := lSelected and (StatusEdit.Text = '');
|
|
|
|
OutBtn.Enabled := AnySelected(BlockList);
|
|
DepOutBtn.Enabled := DepVar.Text <> '';
|
|
StatusOutBtn.Enabled := StatusEdit.Text <> '';
|
|
end;
|
|
|
|
|
|
procedure TCoxRegForm.VarListDblClick(Sender: TObject);
|
|
var
|
|
index: Integer;
|
|
begin
|
|
index := VarList.ItemIndex;
|
|
if index > -1 then
|
|
begin
|
|
BlockList.Items.Add(VarList.Items[index]);
|
|
VarList.Items.Delete(index);
|
|
UpdateBtnStates;
|
|
end;
|
|
end;
|
|
|
|
|
|
procedure TCoxRegForm.VarListSelectionChange(Sender: TObject; User: boolean);
|
|
begin
|
|
UpdateBtnStates;
|
|
end;
|
|
|
|
|
|
|
|
end.
|
|
|