Introduction to Health Informatics

Transcription

1 Introduction to Health Informatics Introduction to Hospital Episode Statistics (HES) Session 3 - Looking at several diagnoses for each age - Merging data files Date: 21/08/07 16:37:09 Written by: Robin Beaumont robin@organplayers.co.uk Status: Draft 1 Contents 1. Comparing different diagnoses for each age - Merging data files Specifying the data set required Creating a data file containing all episodes for each age Creating a data file containing all episodes for each age for each diagnosis Merging data files together Review Analysing the age specific frequency of diagnoses Creating a calculated variable Investigating the proportions of episodes for a particular diagnosis Viewing several diagnoses at once Optional exercises: /08/ :40:06 C:\HIcourseweb new\hes\backup1\hes\spss1\3of4\ses3.doc page 1

2 1. Comparing different diagnoses for each age - Merging data files In the previous session we investigated the incidence of diagnoses for particular ages. In this session we will take the investigation of diagnoses one stage further and consider the relative proportion of episodes for several diagnoses simultaneously for each age. The final exercise in this session will provide you with the skills to produce charts similar to the one below.3 Proportion of episodes for age localised primary osteoarthritis intracranial injury nos no open intracranial wound Age at start of admission The above chart clearly shows the relationship between osteoarthritis and one type of head injury for each age. What conclusions can you draw from the above chart? Such information can be used to help guide the clinician to a possible diagnosis. Additionally by taking into account other factors a decision support system can be developed. To produce the above chart from the Tando1 data file we will need manipulate the data. This involves producing several SPSS data files ('*.sav' files) and then merging them together to produce the necessary data file. 21/08/ :40:06 C:\HIcourseweb new\hes\backup1\hes\spss1\3of4\ses3.doc page 2

3 1.1 Specifying the data set required Analysing HES data session three By looking at the data file menu option graphs -> line and Multiple lines for individual cases option it would appear that we eventually need a set of scores in four columns as shown below: Age Diagnosis Number of Total number episodes for of episodes for age age for = b diagnosis = a Proportion of all episodes for age = b/a We will begin by creating the first and third columns in the above diagram, that is obtain the total number of episodes for each age. 1.2 Creating a data file containing all episodes for each age We will begin by producing a file which contains the total number of episodes for each age. We will save this file on floppy disk and call it 'totfage.sav' being short in my mind for 'totals for ages'. We do this by what SPSS calls, aggregating the original data file (Tando1.sav). The exercise below explains how to do this. Aim to create a data file which has the total number of episodes for each age. 1 Make sure you have the 'Tando1.sav' dataset open 2 Make sure you have the data window selected (to move to the correct window choose the menu option 'Window' and select the appropriate window). 3 Select the menu option Data -> Aggregate to aggregate the file. You should now be presented with the dialogue box shown below 4 Move the 'startage' variable into the 'Break Variables' box. This instructs SPSS to create a new case (record) in the new datafile for each unique age 5 Make sure the 'Save number of cases in break group...etc.' is chosen 6 Type on the box 'totage' This is my shorthand for 'total no. of records for each age' 7 Make sure the 'Create new data file.' option is chosen 8 Click on the 'File' BUTTON. This will bring up the dialogue box shown below: 9 Change the 'Save in' option to A: as shown opposite 10 In the 'File name' box type in 'totfage'. Don't type the quotes 11 Click the 'save' button to return you to the previous, Aggregate data, dialogue box 12 Click the OK button on the 'aggregate data' dialogue box. You now need to inspect to results of your work, that is open the new data file you have just created. 21/08/ :40:06 C:\HIcourseweb new\hes\backup1\hes\spss1\3of4\ses3.doc page 3

4 1 Choose the menu option file -> open 2 Move to the A: drive 3 Select the 'totfage' data file you have just created. If you are prompted to change any results choose 'No'. You should now be presented with a data window similar to the one opposite. For each start age ('startage' variable) the total number of records in the original file is given in the 'totage' variable. Comparing this data file structure with that which is eventually required we see that we have the first and third columns now. 1.3 Creating a data file containing all episodes for each age for each diagnosis We will now create a data file which contains the total number of episodes for each age for each diagnosis. The resulting file, we will call 'totagedn.sav' being short in my mind for 'totals for each age for each diagnosis'. Aim to create a data file which has the total number of episodes for each age for each diagnosis. 1 Open the Tando1 data file (Menu option file -> open) 2 Select the menu option Data -> Aggregate to aggregate the file 3 Move the 'startage' variable into the 'Break Variables' box. This instructs SPSS to create a new case (record) in the new datafile for each unique age 4 Move the 'diag_1' variable into the 'Break Variables' box. This instructs SPSS to create a new case (record) in the new datafile for each unique diagnosis as well 5 Make sure the 'Save number of cases in break group...etc.' is chosen 6 Type on the box 'totagedi' This is my shorthand for 'total no. of records for each age and diagnosis' 7 Make sure the 'Create new data file.' option is chosen 8 Click on the 'File' BUTTON Change the 'Save in' open to A: As you want the file to be on your floppy disk In the 'File name' box type in 'totfdiagn'. Don't type the quotes Click the 'save' button to return you to the previous, Aggregate data, dialogue box Click the OK button. You should now have the data sheet window clearly in view with no dialogue boxes obscuring it. 21/08/ :40:06 C:\HIcourseweb new\hes\backup1\hes\spss1\3of4\ses3.doc page 4

5 As before when you created an aggregated data file you now need to inspect to results of your work. This is described in the exercise below: 1 Open the 'totfdiagn' data file you have just created (menu option file -> open ). If you are prompted to change any results first choose 'No'. You should then be presented with a data window which shows for each start age ('startage' variable) and each diagnosis the total number of records in the original file in the 'totagedi' variable. 1.4 Merging data files together We now have three data files: Tando1 The original data file totfage A data file containing the number of episodes for each age totfdiagn A data file containing the number of episodes for each diagnosis for each age We will now merge the totfage and totfdiagn data files to get one step closer to the data we require. We do this by what SPSS calls merging the variables from each of the files. 1 Make sure the 'totfdiagn' data file is open if it is not open it now. 2 Choose the menu option Data -> Merge files -> add variables. (Note: don't choose the add cases option). You will then be presented with the dialogue box shown below. 3 Choose the 'totfage' data file be clicking on it to make it highlighted. The name should now appear in the 'file name' box as shown above. 4 Click on the open button. You will now be presented with the 'Add variables' dialogue box shown below. 5 Select the 'startage' variable in the excluded variables box. It will become highlighted. 6 Click on the box beside 'Match cases on key variables in sorted files'. A tick sign should appear in it. 7 Click on the second option 'External file is keyed table'. The bubble should then be blackened (i.e. selected). 8 Move the 'startage' variable into the 'Key variables' box by clicking on the button with the arrow sign on it beside the box. The dialogue box should now look like the one opposite. 9 Click on the OK button 21/08/ :40:06 C:\HIcourseweb new\hes\backup1\hes\spss1\3of4\ses3.doc page 5

6 10 The following dialogue box will appear. Because of the way we created the two files we know they are sorted on the relevant field. Therefore click the OK button. 11 You will also be asked if you want to save the current data file. As you have not changed anything in it since opening it click on the 'No' button. Depending on how SPSS is working you may need to click on these dialogue boxes twice. Eventually you will be presented with the following data: We now have four of the five variables specified in section 1.1 above. After getting this far saving the data is the first priority. Save the data file onto you floppy disc as 'diagage.sav', which to me means diagnosis for each age. 1.5 Review At this point we will review what we have done so far in the form of a diagram: Totals for each age TOTFAGE.SAV Aggregate original file TANDO1.SAV Combined files DIAGAGE.SAV Totals for each diagnosis for each age TOTFDIAGN.SAV Although we have only merged two files you can merge large numbers of files together. For example you may have demographic details of subjects in one data set and a separate data set for each trial they may have been included in. 21/08/ :40:06 C:\HIcourseweb new\hes\backup1\hes\spss1\3of4\ses3.doc page 6

7 1.6 Analysing the age specific frequency of diagnoses Analysing HES data session three We will begin by looking at the relative frequency of one of the most common diseases (see section 3 of the previous handout): 7151 Localised primary osteoarthritis We do this by setting up a filter for diag_1 = "7151-" 1 Choose the menu option Data -> select cases This brings up the 'Select cases' dialogue box 2 Click on the 'If condition is satisfied' option 3 Click on the 'If...' button to bring up the 'Select cases: if' dialogue box show below 4 Type into the box at the top right: diag_1 = "7151-" 5 Click the continue button 6 Click the OK button on the 'Select cases' dialogue box. We will now check our results by drawing a chart, this is the following exercise. 1 Choose the menu option Charts -> line 2 Select the Muliple option 3 select the 'Values of individual cases' option 4 Click the 'define' button to bring up the next dialogue box 5 Move the 'Totage' variable into the 'Lines Represent' box 6 Move the 'Totagedi' variable into the 'Lines Represent' box 7 Select the 'Categories Labels - variable' by clicking on the option 8 Move the 'Startage' variable into the 'Variable' box You should end up with a result similar to that shown below. 9 Click the OK button to obtain the graph Value TOTAGE TOTAGEDI shown below. STARTAGE 21/08/ :40:06 C:\HIcourseweb new\hes\backup1\hes\spss1\3of4\ses3.doc page 7

8 Unfortunately the x axis in the above chart is unhelpful, the x axis being unevenly spaced, to obtain a chart with a more sensible x axis we can use the scatter plot option: 1 Choose the menu option Graphs -> Scatter 2 Choose the 'overlay' option 3 Select the totage variable (it becomes highlighted) 4 Select the startage variable (both variables are now highlighted) 5 Click on the button with the arrow to move them both into the 'Y - X pair' box 6 Select the totagedi variable (it becomes highlighted) 7 Select the select the startage variable (both variables are now highlighted) 8 Click on the button with the arrow to move them into the 'Y - X pair' box The dialogue box should now look like the one opposite. 9 Click on the OK button to produce the chart shown below You can now go into the chart and edit it to produce the desired effect: TOTAGEDI STARTAGE TOTAGE 0 STARTAGE TOTAGEDI 0 TOTAGE While the above chart is useful to see the number of episodes for a particular diagnosis and how this roughly relates to the total for each age It would be nice to see the exact proportional value. To be able to do this we need to create a new variable described below. 21/08/ :40:06 C:\HIcourseweb new\hes\backup1\hes\spss1\3of4\ses3.doc page 8

9 1.7 Creating a calculated variable Analysing HES data session three What we need to do now is add the missing variable to the data file representing the proportion of episodes for a particular diagnosis for a particular age. The data file will then be identical to that specified in section 1.1 above. 1 Make sure you have the diagage data file open. If not open it now. 2 Choose the menu option Transform -> compute The dialogue box is shown below. 3 Type in the 'Target Variable' box 'proption'. This stands for proportion in my mind. Don't type the quotes. 4 Type the following into the 'Numeric Expression' box: totagedi / totage These informs SPSS to compute a new variable from the 'totagedi' and 'totage' variables called 'proption'. The new variable takes the value of the 'totagedi' variable for each case divided by the corresponding 'totage' value. 5 Click on the OK button After a few seconds the new variable appears in the data editor window. We now have a data file containing the data in the correct format as specified in section 1.1 With this new variable we can obtain exact values for the proportions of episodes a particular diagnosis accounts for, for any age. This is demonstrated in the next section. Explain the meaning of the new 'proption' variable. 1.8 Investigating the proportions of episodes for a particular diagnosis We will do this by creating several charts. 1 Choose the menu option Charts -> line 2 The 'simple' option should be chosen be default 3 select the 'Values of individual cases' option 4 Click the 'Define' button to bring up the next dialogue box 5 Move the 'Poption' variable into the 'Line Represents' box 6 Select the 'Categories Labels - variable' by clicking on the option 4 Move the 'Startage' variable into the 'Variable' box 5 Click the OK button to produce the chart shown on the next page 21/08/ :40:06 C:\HIcourseweb new\hes\backup1\hes\spss1\3of4\ses3.doc page 9

10 .3 Value PROPTION From the graph opposite we can clearly see the peak around the 70 year age where episodes for Localised Primary Osteoarthritis account for nearly a third of all admissions. Optional exercise: Repeat the above exercise using the 'scatter' graph option to produce an appropriately spaced x axis. STARTAGE 1.9 Viewing several diagnoses at once. This can be done several ways. The way described below has been chosen to demonstrate the use of the 'If' option in SPSS. This allows you to place a set of values for a particular diagnosis in a separate variable. We will compare the proportion of episodes for Ostearthritis (7151) against those for Intracranial injury (8540) for each age. Draw very roughly what you would expect to see on the chart. 1 Remove any filter you have on the data file by choosing the menu option Choose the menu option Data -> Select cases Click on the 'Select all cases' option then Click the OK button. 2 Select the menu option Transform -> Compute Variable 3 Type the new variable name 'd8540' in the 'Target Variable' box This new variable is going to contain only values for those episodes which have a diagnosis of Type or, select and move, the 'proption' variable into the 'Numeric Expression' box 5 Click on the 'if' button lower down in the dialogue box. This will allow you to specify that only those episodes which have a diagnosis of 8540 will be copied into the new variable. 6 The 'Compute Variable: if Cases' dialogue box now appears, as shown below 7 Select the 'Include if cases satisfy condition' option. 8 Type the following into the text box: diag_1 = "8540-" 9 Click the 'continue' button. 10 Click the 'OK' button in the 'compute variable' dialogue box. You should now have a new variable in the data file called 'd8540' which only comtaing values when the diag_1 is /08/ :40:06 C:\HIcourseweb new\hes\backup1\hes\spss1\3of4\ses3.doc page 10

11 Repeat the above steps to produce another variable which contains only values for diagnosis 7151 by substituting the value 7151 for 8540 in each of the above steps. You should now have a data file with two extra variables each providing details for a particular diagnosis. We will now produce a graph of the combined results. 1 Choose the menu option Graphs-> Line 2 Select Multiple 3 Select 'values for individual cases' 4 Click the 'Define' button You will now be presented with the following dialogue box. 5 Move the two new variables into the 'Lines Represent' box, as shown above 6 Select the 'Category labels' option 7 Move the 'startage ' variable into the 'Variable' box. 8 Click the OK button 9 You will now be presented with the following graph..3.2 Value D7151 D8540 STARTAGE 21/08/ :40:06 C:\HIcourseweb new\hes\backup1\hes\spss1\3of4\ses3.doc page 11

12 Unfortunately the points have not been jointed up for you. To do this you need to edit the chart and unselect the 'Break line at missing' which is a menu item in the 'Format' menu (Note: this may be different for version 6 of SPSS). The final result should look like something like the chart below..3.2 Value D7151 D8540 STARTAGE Because we used the Line type graph the X axis is rather misleading for example the sharp rise where the chart indicates 88 is actually the set of values for the under one year olds (the 7001 etc. Age values, see the previous handout for details). It would have been more appropriate to use the scatter chart, with the age filter, with the overlay option described earlier in this handout. This is left as a final exercise for you to do. Clearly you can add as many diagnoses as you want to the charts to provide interesting comparisons. 21/08/ :40:06 C:\HIcourseweb new\hes\backup1\hes\spss1\3of4\ses3.doc page 12

13 1.10 Optional exercises: Analysing HES data session three 1 Produce a scatter chart with the overlay option of the above data. Hint 1: You need to apply the filter to exclude those startage values above 7000 first. Hint 2. When in the 'Overlay Scatterplot' dialogue box you need to click on the 'Options' button to set the 'Missing values' option to 'Exclude cases variable by variable'. Otherwise you will end up with a blank chart. The final result, with some additional editing is given opposite Select several diagnoses, from the list provided in the session two handout, Section 3, and repeat the exercise. 3 Re-run the aggregate commands to find out the proportion of deaths for each diagnosis regardless of age. 4 Re-run the aggregate commands to find out the proportion of deaths for each diagnosis for each age localised primary osteoarthritis 8540 intracranial injury nos no open intracranial wound 21/08/ :40:06 C:\HIcourseweb new\hes\backup1\hes\spss1\3of4\ses3.doc page 13

14 1.11 Appendix A similar result to some of the charts produced during this session could have been created directly from the original Tando1 data file DIAG_1 Count STARTAGE The chart abve was produced by: 1 Setting a filter to: (diag_1 = "8540-" or diag_1 = "7151-") and startage < Selecting the menu option Graphs -> line and the 'multiple' and 'Summaries for groups of cases' option. 3 Clicking on the defin button produces the dialogue box below. Set up the options as indicated. Note that the '% of cases' option is chossen. Finally click the OK button. End of handout. 21/08/ :40:06 C:\HIcourseweb new\hes\backup1\hes\spss1\3of4\ses3.doc page 14