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- SURVIVAL Version 6.0.3
- (COX'S PROPORTIONAL HAZARDS REGRESSION MODEL)
- © M. URRUTIA AVISRROR (1995).
- UNIVERSITY OF SALAMANCA - DEPARTAMENT OF UROLOGY
- SALAMANCA - SPAIN
-
- =====================================================
-
- WELCOME TO SURVIVAL:
-
- To run the application you need at least a LC Mac or a higher model with a FPU
- (or the Pseudo-FP INIT) with a gray or Color Monitor. We firmly recommend to
- use System 7.xx and a minimum of 4 megabytes of RAM.
- This module allows the user to easily estimate survival functions from censored
- data and to assess the relationship between survival and a set of both continuous
- and categorical variables, known as covariates or prognostic factors.
- Main features of Survival include:
- -Use of both fixed covariates and time dependent covariates.
- -A Text Editor with all the possibilities of edition found in commercial modules
- -A Macro Option which permits the on-line transformation of data and the on-line
- computation of the value of Time Dependent covariates. It also includes different
- statistical macros to compute descriptive statistics, to perform chi-square
- and Student T Tests and to estimate exact probabilities for the Normal, F,
- T and Chi-Square distributions.
- -Internal transformation of categorical variables into Indicator Variables or
- Deviation Contrast Variables.
- -Graph plots for all functions, which may be saved as Pict files or Printed
- -A powerfull macro-language for on-line transformation of DataArray in
- memory and to perform fully automated Survival Analysis.
- -A survival chart option to estimate the probability of survival of a given
- patient as a function of a user-defined covariate pattern.
-
- • If the Option key is pressed while launching the application, a macro file is loaded
- in memory and the macro located in second position in the macro menu is
- automatically executed. The first position is left to allow the user to define a
- function for time-dependent survival analysis. The file should be named 'Survival
- Macros' and must be located in the same folder than the application. If you don't
- press the Option key the file is just loaded to be used from the Macros Menu
- This option allows to link Survival with your current database for fully automated
- survival analysis.
- • Now the full manual is included in a Help file which is accessed with the Help
- item from the Apple Menu. You can make a Hardcopy with the Print option of
- the File Menu.
- • To see the latest changes read the file named 'SurvivalLastChanges.txt'
-
-
- THE OUTPUT OF THE PROGRAM INCLUDES
-
- • PARAMETERS FOR THE SURVIVAL MODEL •
- - Estimated maximum likelihood coefficients for the variables in the model
- - Estimated standardized coefficients.
- - Chi-Square Test (Wald) on the statistical significance of the estimated
- coefficients, with exact probabilities.
- - Odds-Ratio.
- - First Derivative of the objective function at convergence.
- - Global Chi-Square Test.
- - Likelihood Ratio Test.
- - Wald Test.
- - Estimated asymptotic covariance matrix.
- - Basal Survival Function (Kaplan-Meier) and Survival Function for a given
- set of covariates (includes density function, hazard function and the standard
- deviation for cumulative survival).
- • GRAPHICAL OUTPUT ( IN COLOR, GRAY OR BLACK AND WHITE) •
- - Basal (Kaplan-Meier) and Model survival function plots
- - Log of -Log of Survival function, for a graphical test of proportionality.
- - Residual Plots, for a graphical test of goodness of fit of data to model.
- - I.C. (95% and 99%) plots of the cumulative survival function.
- - Plot of Hazard, CumHazard and Log of Survival Function vs. Time and Log Time,
- to assess the fitting of observed data to parametric models. A future version
- of the program will include the fit of survival data to different parametric
- models.
-
- •• DESCRIPTION OF MENU COMMANDS ••
-
- • APPLE MENU
-
- • ABOUT .... Description on Survival Version and available memory
- • HELP. Shows this Help Window. If you press the Option key down while
- selecting this item a window with a description of the available Macro
- Commands is displayed instead.
-
- • FILE MENU
-
- • NEW Creates a new Text window than can be edited and saved as a Text File
- • OPEN Opens a Text file for Editing.
- • GET DATA. This command shows a dialog box with two options:
- • TEXT FILE. Data to be analyzed is in a text file (may be exported from
- another application) where each column represents a variable and each row
- an observation or case. Column fields may be delimited by tabs or commas
- • APPLICATION FILE. Data is in a custom binary file created with the SAVE
- DATA OPTION as APPLICATION FILE of the FILE MENU.
- • CLOSE. Closes the selected window. If the window is an active window and you
- have made changes, you are requested to save the changes with a dialog box.
- This is ignored if you press the Option key down while selecting the item or
- clicking the close box.
- • SAVE TEXT. Save the content of Text Windows. If the selected window is a
- Graphical one, an dialog box with an error message is displayed.
- • SAVE DATA. Like the GET DATA option, you may save the data loaded in the
- active output window as a Tab delimited Text File or a Binary Application File.
- • PAGE SETUP . Shows a dialog box with the printing options for the selected
- printer.
- • PRINT. Prints the content of the active Text Window or Plot Window. Notice
- that plots of graphical windows saved as PICT files may be edited with
- different graphical programs that accept this format (Mac DRAW, EXCEL, etc).
- You may have problems when printing the Plot window with some Image
- Writer drivers.
- • REVERT DATA. Restores the last loaded data in the activa data array. Usefull
- when data has been changed with the different macro commands. If you want
- to fix the changes issue a FIXDATA macro from the Macro Command
- Window.
- • QUIT. Closes the application. If you have modified your text windows, you are
- requested to save the changes with a dialog box.
-
- •• EDIT MENU •• Needs no further explanation if you are a Mac User.
- (for PC users converted to the FAITH and TRUTH read any Macintosh Manual)
-
- •• SURVIVAL MENU ••
-
- • MODEL. When you select this submenu command a dialog box (a big one) is shown,
- where you must select the different options of the test. If you don't have an
- active output window with loaded data, you are warned with an error message.
- -On the right side there's a box with different CONTROL PARAMETERS:
- • Status. Put here the column number of the data file where the status
- variable is located (1 = dead, 0 = censored). Defaults to the first column.
- • Time. Put here the column number of the data file where the survival times
- are located. Defaults to the second column. We recommend to use of days as
- Time Unit for further transformation in weeks, months or years.
- • Group. For stratified analysis, put the maximum number of strata followed
- by the column number where grouping variable is located (VAR box).
- Defaults to one group. See macros for additional information on how to use
- this option.
- • CutPoint. If you want to make an analysis dividing the total data into two
- groups by a given cut-point value of a variable, put this value followed by
- the column number where the variable is located (VAR box).
- • Fail Code. You usually should code the satatus of your observations as 1 for
- failed and as 0 for censored. If you have different code numbers for this
- variable, put here the number corresponding to the end of the event to be
- analyzed. Internally, the program transforms this value to 1's and the
- other values to 0,s.
- • Iterations. Maximum number of iterations for the Newton-Raphson
- algorithm. Defaults to 15. In most cases, 4 or 6 iterations are enough to
- achieve convergence. If not, suspect of multicolineality.
- • Precision. Level of precision wanted in the estimation of the coefficients
- of the Model. Defaults to 0.000001
-
- •On the left side of the dialog Box there are two boxes. The one on the left, lists
- in a scrolling window (as VAR1, VAR2, etc.) the variables in the data file that
- were loaded with the GET DATA Command. To Select the variables that should
- be included in a given model, double click with the mouse on the corresponding
- variable. The selected variable will be displayed on the box to the right. If you
- want to tell the program that the selected variable should be dealt as a TIME
- DEPENDENT covariate, press first the OPTION key on the Keyboard.The
- variable shows with an asterisk (*) on its rightmost side. You may combine in
- a model both fixed and time dependent covariates.
- If you are not happy about the variables you selected, you may clear the
- variables box by selecting with the mouse the CLEAR button. If you don't select
- any variable a Kaplan-Meier product limit estimator will be computed.This
- estimator is used for the program as the arbitrary basal function to assess
- the effect of the covariates included in a given model upon death rates.
- • Other options in the dialog box control the survival Time Units, the Output of
- different numerical functions, Graphical Plots, Labeling of the selected
- variables, Labeling of Groups, and Graph Title. If you wand a printout in black
- and white check the Use Line Patterns option. (The groups are identified
- by lines with different shade patterns in the survival plots).
- Notice that if you select the time unit to be in weeks, months or years, it is
- supposed that survival times in your database are recorded in days for
- subsequent transformation. Otherwise you should use your original time unit
- with the CUSTOM box selected in the TIME UNITS pop-up menu.
- • You may also enter the value of the coefficients for estimation of the
- survival function, provided they have been previously estimated, by checking
- the USER COEFFICIENTS radio button.
- • Select the USER COVARIATE PATTERN to estimate the survival function for
- a given covariate set. A dialog box is diplayed for this purpose. If you select
- any variable as categorical the 'Enter Covariate Pattern' dialog box is
- displayed after the transformation process into new indicator or deviation
- variables has been completed.
- • if the CONTROL key is pressed while selecting a covariate in the variable
- window o the DEFINE MODEL dialog box a (c) sign appears in the rightmost
- side of the variable in the model window.
- This ENABLES the internal transformation of categorical variables into k-1
- INDICATOR or DEVIATION variables, where k is the max number of
- categories of the selected variable. If you want to use the DEVIATION coding
- scheme, uncheck the USE INDICATOR VARIABLES box.
- • You may obtain the same results with the TRANSFORM option of the MODEL
- menu but you have to manually include the different variables in the model.
- In the output window the coefficients are labeled as VAR1-1, VAR1-2, etc.
- or as NAME-1, NAME-2, NAME-3 .. etc if you previously checked the LABEL
- VARIABLES option.
-
- **** VERY IMPORTANT ****************************************
-
- All the variables selected as categorical (Control Key Down) must be done in
- ASCENDING ORDER.
- If you try to select,for example, variable 6 if you previously selected a variable
- whose column number es equal or less than variable 6 the program beeps, the model
- window will be CLEARED and You'll have to start the variables selection again. This
- rule is also applied when in a model you combine categorical with non-categorical
- variables.
- Non-categorical variables alone may be selected in any order
-
- ******************************************************
-
- • ESTIMATE. This option starts the computation of MLE's and Survival Functions.
- If you have not previously selected the MODEL option you're warned with
- an error message.
-
- • CLEAR OUTPUT WINDOW. Clears the Text in the output window. You should
- use this option after saving the results of a Test. Avoid to fill the output window
- with Text because it slows down the performance of the program. This is
- specially critical with System 6.xx versions.
-
- • OUTPUT FORMAT. Shows a dialog box where you can edit the length and the
- number of digits after the decimal point for both numerical output and Data listing.
-
- • OUTPUT OPTIONS. This is a hierarchical menu with three different options. If
- you press the Option key down while selecting the two last items a header with
- the name of the columns or groups are also saved.
-
- • SAVE MODEL. Saves the Kaplan-Meier estimate and the coefficients of the
- Model that will be used with the SURVIVAL CHART option. If you press the
- Option Key down, the survival function adjusted for the effect of the
- covariates included in the Model will be saved instead and will be used
- by the SURVIVAL CHART option as the base-line function until you define and
- save another Model.
- • SAVE BASAL FUNCTIONS. Saves the different baseline (Kaplan-Meier) survival
- functions
- • SAVE MODEL FUNCTIONS. Saves the survival functions after adjusting for the
- effect of the covariates included in the model.
- • MACRO MESSAGE . This itme toggles on (checked) and off (unchecked) the
- message that some macros display on the active Outpu Window after the
- requested action has been successfully performed (otherwise you'll get an
- error message). These Macros are SORTBY, FIXDATA, REVERT, SELECTIF,
- OMITIF, COUNTIF and SAVETEST. The default is on
- • OUTPUT IN SPANISH. This itme toggles on (checked) and off (unchecked)
- the output in Spanish for the numerical results of the Test and all graphical
- Plots. Menus, Macro commands, Dialog boxs and warning messages are not
- changed.
-
- • TRANSFORM.This option internally transforms categorical variables into either
- Indicator variables or variables coded according to the Deviation Contrast scheme.
- If you want another category (defaults to the first value) as reference, change its
- value in the dialog box before double-clicking on the variable to be transformed.
-
- • LIST DATA. List the variables from the active data file in the output window.
-
- • SURVIVAL CHART. This option graphically estimates the probability of survival
- for a patient based on: 1) a previously saved model; 2) an user-defined baseline
- survival function and 3) an user entered covariate pattern.
- The program loads first the basal survival function and the values of the
- coefficients of the previously saved model. An error message is displayed if no
- model data has been saved or the model data is at a different Volume or Folder.
- When you select this option the first time the overlay plot option box appears
- dimmed. After you click the New Chart button another dialog box is displayed
- requesting the user to enter the covariates values for the current survival chart.
- The final plot shows the Baseline survival function and the survival function
- adjusted for the previously entered covariate values. If you select again the
- Survival Chart item from the Model menu, this time the Overlay Plot option is
- activated. Notice that you may identify the survival function to be ploted by
- checking the Label Plot box.
- If you press the Option key down while slecting this option the plots are displayed
- with dashed lines to identify the groups insted of colors.
- I've added the Overlay Plot option so you can show in a single plot the baseline
- survival function against different levels of the covariates, for comparative
- and illustrative purposes.
-
- •TEST OF HYPOTHESIS. Performs a Wald Test for a subset of variables in the
- model. Helps to assess the statistical significance of a group o variables while
- keeping constant the effect of the remaining variables, e.g. when you recode a
- categorical variable in k-1 Indicator variables and want to assess the joint effect
- of the different categories.
-
- •• GRAPH MENU ••
-
- • WHITE/BLACK BACKGROUND. Changes the background color of the Plot
- window to white or black.
- • SAVE GRAPH PLOT. Saves the active Plot Window in standard PICT II
- format.
- • SEPARATE PLOTS.This option shows the base line survival survival
- function and the model survival function in a different plot window.
- • LOGLOG PLOT. Plot of Log(-Log) of Survival Function. Currently used to
- Test the proportionalty assumption
- • RESIDUALS PLOT. Plot of Cumulative Hazard function of Residuals against
- residuals itself. Useful to assess the goodness of fit of data to model.
- • INTERVALS PLOT [95% and 99%]. Plot of 95% and 99% confidence
- interval limits for the Kaplan-Meier estimate.
- • LOG AND LIN FUNCTIONS PLOT. Helps to graphically assess the fit of
- your data to parametric models.
-
- •• MACRO MENU ••
-
- • EDIT MACRO
- Opens a dialog box to select the macro file you want to edit. If you press the
- Cancel button an empty Macro Window is shown. Use the SAVE TEXT command of
- the FILE MENU to save changes. You're also requested to save changes when you
- close the window.
-
- • INSERT MACRO
- Inserts a New Macro file at the end of the MACRO MENU. If a macro file
- has different macro definitions every macro is listed as a different item of the
- MACRO MENU. To execute a macro just select the item with the mouse from
- the MACRO MENU.
- To use macros with the Time Dependent Option you should INSERT a macro file
- with a single macro definition before running the Test; otherwise an error
- message is shown. (see example the 'Survival Macros' file)
-
- • DELETE MACRO
- Deletes a previously inserted macro file from the MACRO MENU.
-
- • RUN MACRO
- Executes the macro defined in the active Macro Window or the first macro listed
- in the MACRO MENU.
-
- •• WINDOW MENU ••
-
- •MACRO COMMAND shows a dialog box with a text edit field, where you can
- enter any of the Custom Commands listed in the Macro Commands Help Window.
- Use a semmicolon as delimiter if you use different commands in a single string.
- The max length of the string is 255 characters. The program adds internally a
- dummy macro definition so yo don't need to open a Macro window to execute the
- command.
- When you issue a Macro Command all macros Inserted in the Macro Window are
- cleared.
-
- •Every time you open a Data Window or a Text Window, its name is appended to
- the window menu from where you can select it. Useful to easily access a given
- window when you have multiple windows in your desktop.
-
- --------------------------------------------------------------------------
-
- SURVIVAL IS PUBLIC DOMAIN AND ITS ONLY PURPOSE IS TO DIVULGE
- THIS EXCELENT STATISTICAL TOOL AND MAKE IT EASY TO BOTH
- CLINICAL AND NON CLINICAL INVESTIGATORS WHO WANT TO APPLY
- THIS METHOD ON THEIR INVESTIGATION WORK.
- PLEASE FEEL FREE TO GIVE A COPY OF THE PROGRAM TO ANY PERSON
- CONCERNED WITH SURVIVAL ANALYSIS.
-
-
- •If you use Survival and want to make and acknowledgment, please use the
- following reference:
-
- Urrutia Avisrror, M. Estadistica multivariante en la Investigacion Urologica (III):
- Analisis de Supervivencia (Editorial). (1989). Act. Urol.Esp, 323-327.
-
- ••••• PLEASE REPORT ANY BUG, PROBLEM OR COMMENT TO ••••
-
- 1) MANUEL URRUTIA AVISRROR, M.D. P.h. D.
- Hospital Universitario de Salamanca
- Department of Urology
- Paseo San Vicente s/n
- 37007 SALAMANCA - ESPAÑA
-
- 2) MANUEL URRUTIA AVISRROR, M.D. P.h. D.
- Calle Perdices 53
- Urbanización Valdelagua
- 37191 SALAMANCA-ESPAÑA
-
- 3) email Internet:urrutia@gugu.usal.es
-
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-