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603 lines
17 KiB
ObjectPascal
603 lines
17 KiB
ObjectPascal
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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, LResources, Forms, Controls, Graphics, Dialogs,
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StdCtrls, Buttons, ExtCtrls,
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Globals, MainUnit, OutputUnit;
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type
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{ TCoxRegFrm }
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TCoxRegFrm = class(TForm)
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Bevel1: TBevel;
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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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ResetBtn: TButton;
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CancelBtn: TButton;
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ComputeBtn: TButton;
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ReturnBtn: TButton;
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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 ComputeBtnClick(Sender: TObject);
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procedure DepInBtnClick(Sender: TObject);
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procedure DepOutBtnClick(Sender: TObject);
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procedure FormActivate(Sender: TObject);
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procedure FormCreate(Sender: TObject);
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procedure FormShow(Sender: TObject);
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procedure InBtnClick(Sender: TObject);
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procedure OutBtnClick(Sender: TObject);
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procedure ResetBtnClick(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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private
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{ private declarations }
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FAutoSized: Boolean;
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public
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{ public declarations }
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end;
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var
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CoxRegFrm: TCoxRegFrm;
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implementation
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uses
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Math;
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{ TCoxRegFrm }
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procedure TCoxRegFrm.ResetBtnClick(Sender: TObject);
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VAR i : integer;
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begin
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BlockList.Clear;
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VarList.Clear;
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for i := 1 to NoVariables do
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begin
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VarList.Items.Add(OS3MainFrm.DataGrid.Cells[i,0]);
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end;
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InBtn.Enabled := true;
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OutBtn.Enabled := false;
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DepInBtn.Enabled := true;
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DepOutBtn.Enabled := false;
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ProbsChk.Checked := true;
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DescChk.Checked := true;
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DepVar.Text := '';
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StatusEdit.Text := '';
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StatusInBtn.Enabled := true;
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StatusOutBtn.Enabled := false;
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MaxItsEdit.Text := '20';
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end;
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procedure TCoxRegFrm.StatusInBtnClick(Sender: TObject);
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VAR index : integer;
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begin
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index := VarList.ItemIndex;
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StatusEdit.Text := VarList.Items.Strings[index];
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VarList.Items.Delete(index);
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StatusOutBtn.Enabled := true;
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StatusInBtn.Enabled := false;
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end;
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procedure TCoxRegFrm.StatusOutBtnClick(Sender: TObject);
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begin
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VarList.Items.Add(StatusEdit.Text);
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StatusEdit.Text := '';
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StatusInBtn.Enabled := true;
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end;
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procedure TCoxRegFrm.FormActivate(Sender: TObject);
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var
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w: Integer;
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begin
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if FAutoSized then
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exit;
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w := MaxValue([ResetBtn.Width, CancelBtn.Width, ComputeBtn.Width, ReturnBtn.Width]);
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ResetBtn.Constraints.MinWidth := w;
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CancelBtn.Constraints.MinWidth := w;
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ComputeBtn.Constraints.MinWidth := w;
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ReturnBtn.Constraints.MinWidth := w;
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Constraints.MinWidth := Width;
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Constraints.MinHeight := Height;
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FAutoSized := true;
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end;
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procedure TCoxRegFrm.FormCreate(Sender: TObject);
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begin
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Assert(OS3MainFrm <> nil);
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if OutputFrm = nil then Application.CreateForm(TOutputFrm, OutputFrm);
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end;
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procedure TCoxRegFrm.FormShow(Sender: TObject);
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begin
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ResetBtnClick(Self);
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end;
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procedure TCoxRegFrm.DepInBtnClick(Sender: TObject);
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VAR index : integer;
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begin
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index := VarList.ItemIndex;
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DepVar.Text := VarList.Items.Strings[index];
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VarList.Items.Delete(index);
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DepOutBtn.Enabled := true;
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DepInBtn.Enabled := false;
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end;
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procedure TCoxRegFrm.ComputeBtnClick(Sender: TObject);
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Label CleanUp;
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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;
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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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RowLabels, ColLabels : StrDyneVec;
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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;
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Stat : DblDyneVec;
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Dupl : DblDyneVec;
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Alpha : DblDyneVec;
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a : DblDyneVec;
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b : DblDyneVec;
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s1 : DblDyneVec;
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s2 : DblDyneVec;
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s : DblDyneVec;
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Av : DblDyneVec;
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SD : DblDyneVec;
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SE : DblDyneVec;
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x : DblDyneVec; // data matrix for independent variables
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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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begin
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OutputFrm.RichEdit.Clear;
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// OutputFrm.RichEdit.ParaGraph.Alignment := taLeftJustify;
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OutputFrm.RichEdit.Lines.Add('Cox Proportional Hazards Survival Regression Adapted from John C. Pezzullo');
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OutputFrm.RichEdit.Lines.Add('Java program at http://members.aol.com/johnp71/prophaz.html');
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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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ShowMessage('ERROR! No independent variables selected.');
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goto CleanUp;
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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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ShowMessage('Error! No Survival time variable selected.');
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goto CleanUp;
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end;
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if StatusEdit.Text = '' then
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begin
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ShowMessage('Error! No Survival Status variable selected.');
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goto Cleanup;
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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(Dupl,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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OutputFrm.RichEdit.Lines.Add('');
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if DescChk.Checked then
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begin
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OutputFrm.RichEdit.Lines.Add('Descriptive Statistics');
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OutputFrm.RichEdit.Lines.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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begin
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outline := format(' %3d %15s %10.4f %10.4f',[j+1,RowLabels[j],Av[j],SD[j]]);
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OutputFrm.RichEdit.Lines.Add(outline);
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end;
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end;
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OutputFrm.RichEdit.Lines.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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begin
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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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end;
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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 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 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 OutputFrm.RichEdit.Lines.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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||
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|
for j := 0 to nR-1 do
|
||
|
|
begin
|
||
|
|
s1[j] := 0.0;
|
||
|
|
a[ix(j,nR,nR+1)] := 0.0;
|
||
|
|
for k := 0 to nR-1 do
|
||
|
|
begin
|
||
|
|
s2[ix(j,k,nR)] := 0.0;
|
||
|
|
a[ix(j,k,nR+1)] := 0.0;
|
||
|
|
end;
|
||
|
|
end;
|
||
|
|
for i := 0 to nC-1 do
|
||
|
|
begin
|
||
|
|
Alpha[i] := 1.0;
|
||
|
|
v := 0.0;
|
||
|
|
for j := 0 to nR-1 do v := v + b[j] * x[ix(i,j,nR)];
|
||
|
|
v := exp(v);
|
||
|
|
s0 := s0 + v;
|
||
|
|
for j := 0 to nR-1 do
|
||
|
|
begin
|
||
|
|
s1[j] := s1[j] + x[ix(i,j,nR)] * v;
|
||
|
|
for k := 0 to nR-1 do
|
||
|
|
s2[ix(j,k,nR)] := s2[ix(j,k,nR)] + x[ix(i,j,nR)] * x[ix(i,k,nR)] * v;
|
||
|
|
end;
|
||
|
|
StatI := Stat[i];
|
||
|
|
if (StatI = 2) or (StatI = 3) or (StatI = 6) or (StatI = 7) then
|
||
|
|
begin
|
||
|
|
d := 0.0;
|
||
|
|
for j := 0 to nR-1 do s[j] := 0.0;
|
||
|
|
end;
|
||
|
|
if (StatI = 1) or (StatI = 3) or (StatI = 5) or (StatI = 7) then
|
||
|
|
begin
|
||
|
|
d := d + 1;
|
||
|
|
for j := 0 to nR-1 do s[j] := s[j] + x[ix(i,j,nR)];
|
||
|
|
end;
|
||
|
|
if (StatI = 4) or (StatI = 5) or (StatI = 6) or (StatI = 7) then
|
||
|
|
begin
|
||
|
|
for j := 0 to nR-1 do
|
||
|
|
begin
|
||
|
|
LL := LL + s[j] * b[j];
|
||
|
|
a[ix(j,nR,nR+1)] := a[ix(j,nR,nR+1)] + s[j] - d * s1[j] / s0;
|
||
|
|
for k := 0 to nR-1 do
|
||
|
|
begin
|
||
|
|
a[ix(j,k,nR+1)] := a[ix(j,k,nR+1)] + d * (s2[ix(j,k,nR)] / s0 -
|
||
|
|
s1[j] * s1[k] / (s0 * s0));
|
||
|
|
end;
|
||
|
|
end;
|
||
|
|
LL := LL - d * Ln(s0);
|
||
|
|
if d = 1 then Alpha[i] := Power((1.0 - v / s0),(1.0 / v))
|
||
|
|
else Alpha[i] := exp(-d / s0);
|
||
|
|
end;
|
||
|
|
end;
|
||
|
|
LL := -2.0 * LL;
|
||
|
|
outline := format('-2 Log Likelihood = %10.4f',[LL]);
|
||
|
|
if iters = 1 then
|
||
|
|
begin
|
||
|
|
LLn := LL;
|
||
|
|
if ItersChk.Checked then
|
||
|
|
outline := outline + ' (Null Model)';
|
||
|
|
end;
|
||
|
|
if ItersChk.Checked then
|
||
|
|
OutputFrm.RichEdit.Lines.Add(outline);
|
||
|
|
for i := 0 to nR-1 do
|
||
|
|
begin
|
||
|
|
v := a[ix(i,i,nR+1)];
|
||
|
|
a[ix(i,i,nR+1)] := 1.0;
|
||
|
|
for k := 0 to nR do
|
||
|
|
a[ix(i,k,nR+1)] := a[ix(i,k,nR+1)] / v;
|
||
|
|
for j := 0 to nR-1 do
|
||
|
|
begin
|
||
|
|
if i <> j then
|
||
|
|
begin
|
||
|
|
v := a[ix(j,i,nR+1)];
|
||
|
|
a[ix(j,i,nR+1)] := 0.0;
|
||
|
|
for k := 0 to nR do
|
||
|
|
a[ix(j,k,nR+1)] := a[ix(j,k,nR+1)] - v * a[ix(i,k,nR+1)];
|
||
|
|
end;
|
||
|
|
end;
|
||
|
|
end;
|
||
|
|
for j := 0 to nR-1 do b[j] := b[j] + a[ix(j,nR,nR+1)];
|
||
|
|
end;
|
||
|
|
|
||
|
|
OutputFrm.RichEdit.Lines.Add('Converged');
|
||
|
|
Csq := LLn - LL;
|
||
|
|
OutputFrm.RichEdit.Lines.Add('');
|
||
|
|
OutputFrm.RichEdit.Lines.Add('Overall Model Fit...');
|
||
|
|
if Csq > 0.0 then prob := ChiSq(Csq,nR) else prob := 1.0;
|
||
|
|
outline := format('Chi Square = %8.4f with d.f. %d and probability = %8.4f',[Csq,nR,prob]);
|
||
|
|
OutputFrm.RichEdit.Lines.Add(outline);
|
||
|
|
OutputFrm.RichEdit.Lines.Add('');
|
||
|
|
OutputFrm.RichEdit.Lines.Add('Coefficients, Std Errs, Signif, and Confidence Intervals');
|
||
|
|
OutputFrm.RichEdit.Lines.Add('');
|
||
|
|
OutputFrm.RichEdit.Lines.Add('Var Coeff. StdErr p Lo95% Hi95%');
|
||
|
|
for j := 0 to nR-1 do
|
||
|
|
begin
|
||
|
|
b[j] := b[j] / SD[j];
|
||
|
|
SE[j] := sqrt(a[ix(j,j,nR+1)]) / SD[j];
|
||
|
|
prob := Norm(Abs(b[j] / SE[j]));
|
||
|
|
Lo95 := b[j] - 1.96 * SE[j];
|
||
|
|
Hi95 := b[j] + 1.96 * SE[j];
|
||
|
|
outline := format('%10s %10.4f %10.4f %8.4f %8.4f %8.4f',
|
||
|
|
[RowLabels[j],b[j],SE[j],prob,Lo95,Hi95]);
|
||
|
|
OutputFrm.RichEdit.Lines.Add(outline);
|
||
|
|
end;
|
||
|
|
OutputFrm.RichEdit.Lines.Add('');
|
||
|
|
OutputFrm.RichEdit.Lines.Add('Risk Ratios and Confidence Intervals');
|
||
|
|
OutputFrm.RichEdit.Lines.Add('');
|
||
|
|
OutputFrm.RichEdit.Lines.Add('Variable Risk Ratio Lo95% Hi95%');
|
||
|
|
for j := 0 to nR-1 do
|
||
|
|
begin
|
||
|
|
outline := format('%10s %10.4f %10.4f %10.4f',
|
||
|
|
[RowLabels[j],exp(b[j]),exp(b[j]-1.96*SE[j]),exp(b[j]+1.96*SE[j])]);
|
||
|
|
OutputFrm.RichEdit.Lines.Add(outline);
|
||
|
|
end;
|
||
|
|
OutputFrm.RichEdit.Lines.Add('');
|
||
|
|
if ProbsChk.Checked then
|
||
|
|
OutputFrm.RichEdit.Lines.Add('Baseline Survivor Function (at predictor means)...');
|
||
|
|
SF := 1.0;
|
||
|
|
for i := nC-1 downto 0 do
|
||
|
|
begin
|
||
|
|
Sf := Sf * Alpha[i];
|
||
|
|
if Alpha[i] < 1.0 then
|
||
|
|
begin
|
||
|
|
if ProbsChk.Checked then
|
||
|
|
begin
|
||
|
|
outline := format('%10.4f %10.4f',[SurvT[i],Sf]);
|
||
|
|
OutputFrm.RichEdit.Lines.Add(outline);
|
||
|
|
end;
|
||
|
|
end;
|
||
|
|
end;
|
||
|
|
OutputFrm.ShowModal;
|
||
|
|
|
||
|
|
cleanup:
|
||
|
|
SurvT := nil;
|
||
|
|
Stat := nil;
|
||
|
|
Dupl := nil;
|
||
|
|
Alpha := nil;
|
||
|
|
x := nil;
|
||
|
|
b := nil;
|
||
|
|
a := nil;
|
||
|
|
s1 := nil;
|
||
|
|
s2 := nil;
|
||
|
|
s := nil;
|
||
|
|
Av := nil;
|
||
|
|
SD := nil;
|
||
|
|
SE := nil;
|
||
|
|
RowLabels := nil;
|
||
|
|
ColLabels := nil;
|
||
|
|
ColNoSelected := nil;
|
||
|
|
end;
|
||
|
|
|
||
|
|
procedure TCoxRegFrm.DepOutBtnClick(Sender: TObject);
|
||
|
|
begin
|
||
|
|
VarList.Items.Add(DepVar.Text);
|
||
|
|
DepVar.Text := '';
|
||
|
|
DepInBtn.Enabled := true;
|
||
|
|
end;
|
||
|
|
|
||
|
|
procedure TCoxRegFrm.InBtnClick(Sender: TObject);
|
||
|
|
VAR i, index : integer;
|
||
|
|
begin
|
||
|
|
index := VarList.Items.Count;
|
||
|
|
i := 0;
|
||
|
|
while i < index do
|
||
|
|
begin
|
||
|
|
if (VarList.Selected[i]) then
|
||
|
|
begin
|
||
|
|
BlockList.Items.Add(VarList.Items.Strings[i]);
|
||
|
|
VarList.Items.Delete(i);
|
||
|
|
index := index - 1;
|
||
|
|
i := 0;
|
||
|
|
end
|
||
|
|
else i := i + 1;
|
||
|
|
end;
|
||
|
|
OutBtn.Enabled := true;
|
||
|
|
end;
|
||
|
|
|
||
|
|
procedure TCoxRegFrm.OutBtnClick(Sender: TObject);
|
||
|
|
VAR index : integer;
|
||
|
|
begin
|
||
|
|
index := BlockList.ItemIndex;
|
||
|
|
VarList.Items.Add(BlockList.Items.Strings[index]);
|
||
|
|
BlockList.Items.Delete(index);
|
||
|
|
InBtn.Enabled := true;
|
||
|
|
if BlockList.Items.Count = 0 then OutBtn.Enabled := false;
|
||
|
|
end;
|
||
|
|
|
||
|
|
function TCoxRegFrm.ChiSq(x : double; n : integer) : double;
|
||
|
|
var
|
||
|
|
p, t, a : double;
|
||
|
|
k : integer;
|
||
|
|
|
||
|
|
begin
|
||
|
|
p := exp(-0.5 * x);
|
||
|
|
if n mod 2 = 1 then p := p * sqrt(2 * x / Pi);
|
||
|
|
k := n;
|
||
|
|
while K >= 2 do
|
||
|
|
begin
|
||
|
|
p := p * x / k;
|
||
|
|
k := k - 2;
|
||
|
|
end;
|
||
|
|
t := p;
|
||
|
|
a := n;
|
||
|
|
while t > 0.000001 * p do
|
||
|
|
begin
|
||
|
|
a := a + 2;
|
||
|
|
t := t * x / a;
|
||
|
|
p := p + t;
|
||
|
|
end;
|
||
|
|
ChiSq := (1 - p);
|
||
|
|
end;
|
||
|
|
//-------------------------------------------------------------------
|
||
|
|
|
||
|
|
function TCoxRegFrm.Norm(z : double): double;
|
||
|
|
begin
|
||
|
|
Norm := ChiSq(z * z, 1);
|
||
|
|
end;
|
||
|
|
//-------------------------------------------------------------------
|
||
|
|
|
||
|
|
function TCoxRegFrm.ix(j, k, nCols : integer): integer;
|
||
|
|
begin
|
||
|
|
ix := j * nCols + k;
|
||
|
|
end;
|
||
|
|
|
||
|
|
initialization
|
||
|
|
{$I coxregunit.lrs}
|
||
|
|
|
||
|
|
end.
|
||
|
|
|