Instructions

GraphROC for Windows - User Instructions

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New tools for clinical test evaluation

GraphROC for Windows is a program for estimating clinical characteristics of quantitative laboratory tests. Special attention has been paid to rapid and accurate management of frequency distributions to facilitate calculations on large data sets obtained from clinical laboratory databases.

The program includes the following features:

Microsoft Windows commands and user interface
rapid import of source data as a simple text(ASCII)file containing all original observations
display of the distribution with a possibility to rapidly calculate any percentile and the corresponding confidence limits
estimation of non-parametric reference limits, median or any percentile in the distribution with the corresponding confidence limits
possibility to choose statistically optimized bin width for illustrative presentation of frequency histograms
display of two distributions for comparison of health- and illness-related data
automatic updating of clinical sensitivity and specificity values with mouse movement
display of clinical sensitivity and specificity with the corresponding confidence intervals, positive and negative likelihood ratios, predictive values and efficiency at any level of test result
rapid updating of predictive values and efficiency to any entered prior probability of disease
optional presentation of sensitivity, specificity and/or efficiency curves for the complete range of possible cutoff limits
Receiver operating characteristics (ROC-) curve features include
- display of one or several curves
- calculation of areas under curve by non-parametric method including estimation of respective standard errors for the area
- statistical comparison of areas under two ROC curves either by the paired or unpaired method
- statistical comparison of points on two ROC curves either by the paired or unpaired method
- optional possibility to estimate partial areas under ROC curves
quick and simple data import and export between GraphROC and other software
easy export of graphs for editing and e.g. for making slides or figures for publication

The following features of the program have, to our knowledge, not been included in previously available laboratory test evaluation software:

possibility to automatically optimize the bin width for display of frequency histograms and producing non-parametric ROC curves (Kairisto, 1995)
possibility to estimate also partial areas under the ROC curve (see Zweig & Campbell, 1993)
estimation of non-parametric reference change limits and corresponding confidence limits
optional indirect estimation of "health" related limits from patient data, where majority of the values can be considered to be representative of health-related values
optional indirect estimation of "health" related change intervals from unselected or partially selected serial patient data, where majority of the values can be considered to be representative of health-related values (Kairisto, Virtanen, Uusipaikka et al. 1993)

Full advantage of all features in GraphROC for Windows will be achieved if the program is used together with other programs running under Microsoft Windows. Data import and export, graph export, and switching from one program to another allow convenient use of GraphROC together with other Windows applications.

GRAPHROC LICENCE AGREEMENT

GraphROC for Windows software product is furnished subject to the terms and conditions of this licence agreement. Starting the downloading or installation procedure for the software will constitute acceptance of the licence terms. GraphROC is available for a trial period of one month free of charge. If the software licence is not purchased after this trial period, the program and any possible copies of it should be deleted/destroyed. You may not disassemble, decompile or reverse engineer GraphROC in any way. GraphROC software is available both for individual and institutional use. The individual version may be run only in one computer at a time, while the institutional version may be run in up to ten computers within the same institution simultaneously. You may make copies of GraphROC for archival and back-up purposes only.

LIMITATION OF WARRANTY

The software and documentation is provided "as is" without warranty of any kind. The developers of this software as well as anyone else who has been involved in the creation, production, or delivery of this software disclaim all warranties relating to this software, whether expressed or implied, including but not limited to any implied warranties of merchantability and fitness for a particular purpose, and all such warranties are expressly and specifically disclaimed.

EXCLUSIVE REMEDY

Your exclusive remedy arising from or in connections with the software and/or documentation shall be, at the software producer�s option, the replacement of the software diskette and/or the instructions booklet.

LIMITATIONS OF LIABILITY

In no event shall the developers of this software, or anyone else who has been involved in the creation, production, or delivery of this software, be liable for any direct, indirect, consequential or incidental damages, arising out of the use or inability to use this software.

COPYRIGHT NOTICE

The individual version of GraphROC is intended for single user only. Installation of it to multiple computers or making it accessible through local network violates the copyright of the software developers. The institutional version of GraphROC may be installed to a maximum of 10 computers within a specified institution and used by a maximum of 10 simultaneous users. Copying the program for use outside the specified institution violates the copyrights of the software developers.
Program updates in 1996 will be sent free of any additional charge to all registered GraphROC users.

Program installation

If you have downloaded GraphROC through Internet…
Starting the downloading and the installation procedure will constitute acceptance of the licence terms. To start the installation please create a directory/folder named DISK1 into the root directory of your hard disk. Copy the downloaded graphroc.zip file into this directory. Before starting the installation it is necessary to unzip the zipcompressed file. This can be done, for example, by PKUNZIP or by any other unzipping program. After completing the unzipping, start the installation as follows:
Windows 3.x: Start Microsoft Windows, open the FILE MANAGER, choose File Run and select the directory /disk1, write setup and press enter.
Windows 95: Choose Start and Run, use the browse option to select the folder /disk1 where the unzipped installation files are located and select the file setup.exe there, press OK by your mouse pointer.
GraphROC for Windows will be automatically installed to your hard disk in a subdirectory named GRAPHROC. The required disk space is about 800 kB. When the setup asks for your registration number just press enter, the evaluation version of GraphROC will become installed. The evaluation version functions exactly as the fully registered version except that it has a "time out" feature, which will disable its function after about six weeks of installation. To assure uninterrupted use of GraphROC, please place your order for the registered version in good time, i.e., as soon as you have evaluated the software.

If you install GraphROC from the installation disk…
Starting the installation procedure for the software will constitute acceptance of the licence terms. Put the installation diskette in the diskette drive A: (or B: etc.) of your computer.
Windows 3.x: Start Microsoft Windows, open the FILE MANAGER, choose File Run and write A:\setup and press enter.
Windows 95: Choose Start and Run, use the browse option to select the disk drive and the file setup.exe there, press OK by your mouse pointer.
GraphROC for Windows will be automatically installed to your hard disk in a subdirectory named GRAPHROC. The required disk space is about 800 kB. Please have your registration number ready, when starting the installation. If you do not enter the registration number during installation, the evaluation version of GraphROC with "time out" feature will become installed.

Starting the program

Quick reference:
Double click by mouse the GraphROC icon in the GraphROC program group.

The starting of GraphROC is similar to that of any Windows program. The installation procedure creates a GraphROC icon and a GraphROC program group. These can also be separately created and reorganized by standard Windows procedures. Without using any icon, the program can be started from the Windows Program Manager by selecting File Run (in Windows 95 Start and Run command) and writing the path and the name of the program file, for example C:\GRAPHROC\REFER.EXE. Note, however, that on the installation disk the files are compressed and they can not be run before installing them.

Data import

Quick reference:
Alternative 1: To import data of all original observations, select File Open and name the textfile containing the data
Alternative 2: To import data already grouped as a reference distribution, copy the data first to Windows clipboard in some other Windows program, in GraphROC select File New and Data Paste.

Alternative 1: Importing source data as original observations

Data is imported by the File Open command. Importable data files are simple ASCII(text)files containing numerical observations in columns, one numerical observation on each row of the column. For one distribution procedures, the source data file should contain one column, and for two distributions procedures, the source data file should contain two columns of observations. Health related data should be in the first column and illness related data in the second one.

When using two column source data files, please note, that the two columns should be separated from each other by the tab symbol. For example Microsoft Excel^TM inserts a tab sign between the two columns automatically when saving the file in tab delimited text-format. Such text files can be imported into GraphROC without difficulty. However, some worksheet programs, like Lotus 1-2-3^TM, insert only empty spaces between the two columns in textfiles and consequently GraphROC can not recognize the two columns as separate which will result in incorrect data input. If tab delimited files can not be created it is advisable to import the source data as one column files and make the necessary file combinations for two distribution analysis within GraphROC.

Please check that the default for decimal separator sign (either point or comma) is the same in your source data file and in your Windows settings. If needed, you can change the decimal separator in the Windows Control Panel under International and Number format. Note that the decimal separator should not be the same sign as the thousands separator. Mismatch between the decimal separators defined in the Control Panel and used in the source data will lead to incorrect data input.

The source data file should not contain any empty rows between observations. The default file name extension is .SM1 (one column) or .ROC (two columns). Except for the source data, the file may not contain any other data or text. When creating the source file for example by a worksheet program, be sure that all the worksheet cells, except those containing the data, are empty. Failure to follow these instructions may lead to incorrect data input. In case of difficulty, you can check the contents of the source data file by any text editor program. The size of the imported data set is limited only by the size of the random access memory of the computer. In practice tens of thousands of observations can be imported without difficulty. If the imported data has a very high numerical precision (i.e. more than five or six significant digits), the program function will be considerably slowed. In such cases it may be advisable to round the observations to fewer significant digits before importing the data into GraphROC. Note that the values in the data window are always shown with two decimals and that this default can not be changed in the Windows Control Panel. In case the original bin width in your source data is less than 0.01, the only practical way to treat the data in GraphROC is to multiply each value by a suitable multiple of 10 in order to shift the decimal separator so that there will not be more than the maximum of two decimals.

The imported data will be visible as a numerical frequency distribution in the left sided data window and as a graph in the right sided window. The sizes of the windows can be adjusted by the mouse. Also the widths of the columns in the data window can be adjusted by the mouse by dragging the column borders in the title row.

Alternative 2: Importing source data as frequency distributions

Data, which is already grouped into a frequency distribution, can also be imported from other Microsoft Windows applications via the Windows clipboard. In this case, the data must consist of two columns. The first column includes the bins (upper class limits of frequency distribution) and the second column the corresponding class frequencies. Note that the data must be in two columns and that there may not be any empty cells.

The data can be transferred to clipboard, e.g. from Excel or any worksheet program, by selecting cells in two adjacent columns and giving the Edit Copy command. To import the data into GraphROC, give first File New command and select One distribution or Two distributions and give the Edit Paste command. When pasting data for two distributions analysis, please note, that the data must be pasted for one distribution at a time so that health related and sickness related data are imported separately. The left sided first two columns should contain the frequency distribution of health related data and the next two columns the frequency distribution of illness related data. To paste data into correct positions select the top left corner cell of the correct columns in the data table by clicking there the left mouse button. This should be done before giving the Edit Paste command.

These Edit Copy data and Edit Paste commands also offer a convenient possibility to transfer data within GraphROC from one distribution analysis to two distribution analysis. In one distribution analysis, select first the data for the frequency distribution (the two first columns in the left-hand data table). This can be done by putting the cursor by mouse over the top title cell of the first column and then moving by the mouse to the title cell of the second column while keeping the left mouse button down. This procedure will change the background colour in these two columns showing that this data has now been selected. After this, give the Edit Copy data command, open the two distributions analysis by the File New command, select the appropriate column in the data table as instructed above, and give the Edit Paste command. Data for the second distribution can be imported by repeating this procedure. Do not put the cursor over the graph before both distributions have been imported. Putting the cursor to the graph window-area before both distributions are available will cause an error and a termination of the program.

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