Biostatistics for the Clinician
Lesson 1: Introduction and Summary Measures of Data
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Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
Biostatistics: How Much, Why, When and What
A critical distinction between the scientific approach and other methods of inquiry lies in the emphasis placed on real world validation. Where research has shown that particular approaches are appropriate and effective for specific applications, clinicians are wise to select those approaches. Clinicians are then called upon to defend decisions on the basis of empirical research evidence. Consequently, the clinician must be an intelligent consumer of medical research outcomes, able to understand, interpret, critically evaluate and apply valid results from the latest medical research.How Much: The Six Year Old Biostatistician
Norman & Streiner (1986) tell an old story about three little French boys who happened to see a man and woman naked on a bed in a basement apartment. The four year old said, "Look, that man and woman are wrestling!". The five year old said, "You silly, they're not wrestling they're making love!" The six year old said, "Yes! And very poorly too!!" The four year old did not understand. The five year old had achieved a conceptual understanding. The six year old understood it well enough, presumably without actual experience, to be a critical evaluator. The intent of the following instruction is to make you a critical evaluator of medical research, a "six year old biostatistician". So that is the purpose of these lessons - to turn you into a six year old biostatistician.
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
Variables and Measures
Now well move into some more familiar territory. When you start to measure the impact of a treatment you have to ask yourself, "What kinds of variables am I dealing with here? What are my choices of variables?"Now, you might ask, why do I need to know about types of variables or measures? You need to know, in order to evaluate the appropriateness of the statistical techniques used, and consequently whether the conclusions derived from them are valid. In other words, you can't tell whether the results in a particular medical research study are credible unless you know what types of variables or measures have been used in obtaining the data.
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
1.1 Types of Variables
Look at Figure 1.1 below. On the left hand side you see that there are two classifications of variables. There are qualitative variables and there are quantitative variables. Now one isn't necessarily better than the other. One we're a little more used to doing stuff with. With quantiative variables for example, we can do averages and things like that, we know there are numbers, you can add them up and divide and things like that. Its a little trickier some times with qualitative variables. But in human experiments there's no way you can get around it. There are two classes those - nominal and ordinal.
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Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
Four Types of Scales
There are four types of measurement scales (nominal, ordinal, interval and ratio; see Figure). Each of the four scales, respectively, provides higher information levels about variables measured with the scale.Nominal Scales
What does nominal comes from? Name. So nominal comes from name and the important thing is there is no measure of distance between those. You're either married or not married, gender is determined, yes or no, and so there is no question of how far apart in a quantitative sense those categories are so they're just names. Nominal scales name and that is all that they do. Some examples of nominal scales are sex (male, female), race (black, hispanic, oriental, white, other), political party (democrat, republican, other), blood type (A, B, AB, O), and pregnancy status (pregnant, not pregnant; see Figure).Ordinal Scales
In the next group we have a little more sophistication than naming. What does ordinal imply? Ranking. So there in some order. Higher and lower. We don't rank gender as higher and lower. But we do rank stages of cancer for example as higher and lower. We have pain ratings that are higher and lower. So were now a t a more sophisticated level of measure. A finer tuned level of measurement. But we've now added only one element. We know that something is higher than something or lower than something or more painful than something or less painful than something. Ordinal scales both name and order. Some examples of ordinal scales are rankings (e.g., football top 20 teams, pop music top 40 songs), order of finish in a race (first, second, third, etc.), cancer stage (stage I, stage II, stage III), and hypertension categories (mild, moderate, severe; see Figure). In the next group we have a quantitative group and people divide these into interval and ratio variables. And, I wouldn't worry about the division so much.[Insert Figure 1.1 about here]
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
Interval Scales
What about interval variables? Why is that called an interval variable like temperature for example? What is the difference between 36 degrees and 37 degrees compared to the difference between 40 degrees and 41 degrees? Is the difference the same? So the intervals are the same on the scale. So now we know not only is one higher than the other but that the distances or the intervals on the scales are the same. So again it's a higher level of information that we have. Interval scales name, order and have the property that equal intervals in the numbers on the scale represent equal quantities of the variables being measured. Some examples of interval scales are fahrenheit and celsius temperature, SAT, GRE and MAT scores, and IQ scores. The zero on an interval scale is arbitrary. On the celsius scale, 0 is the freezing point of water. On the fahrenheit scale, 0 is 32 degrees below the freezing point of water (see Figure).[Insert Figure 1.1 about here]
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
Ratio Scales
Ratio scales have all the properties of interval scales plus a meaningful, absolute zero. That is, zero represents the total absence of the variable being measured. Some examples of ratio scales are length measures in the english or metric systems, time measures in seconds, minutes, hours, etc., blood pressure measured in millmeters of mercury, age, and our common measures of mass, weight, and volume (see Figure).[Insert Figure 1.1 about here]
They are called ratio scales because ratios are meaningful with this type of scale. It makes sense to say 100 feet is twice as long as 50 feet because length measured in feet is a ratio scale. Likewise it makes sense to say a Kelvin temperature of 100 is twice as hot as a Kelvin temperture of 50 because it represents twice as much thermal energy (unlike fahrenheit temperatures of 100 and 50).
[Insert Figure 1.1 about here]
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
1.2 Qualitative vs. Quantitative Variables
Nominal and ordinal scales are called qualitative measures. Interval and ratio scales are called quantitative measures (see Figure).[Insert Figure 1.1 about here]
With the ratio variables the only difference that we have is there is a true zero so that you can actually talk about ratios. That is a person's lung capacity can be twice somebody else's lung capacity. In order to do that you have to have a true zero to develop ratios like that. But really for all statistical purposes it makes no difference. The important thing is If you measures like these interval measures you should keep them at the finest level of measure you have. Don't put say temperature measures into categories like the temperature was less than this or greater than that or in another group less than this and greater than that and so on. Don't cluster or group those and make them into ordinal variables. If you dothen you're throwing away information. So if you have information at the interval level record it at the interval level. If its at the ordinal level record it at that level. And of course if you're at the nominal level you're stuck with recording it at that level. So never cluster your variables together when you begin your experiments in a way that you lose information.
Now, when statistical analyses are applied,
the statistics must take into account the nature of the underlying
measurment scale, because there are fundamental differences in the
types of information imparted by the different scales (see Figure).
Consequently, nominal and ordinal scales must be analyzed using what are
called non-parametric or distribution free statistics. On the other hand,
interval and ratio scales are analyzed using parametric statistics.
Parametric statistics typically require that the interval or ratio variables
have distributions shaped like bell (normal) curves, a reasonable assumption
for many of the variables frequently encountered in medical practice.
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
(Show kinds of variables transparency)
Dependent variables and independent variables.
Basically what your trying to do generally is say that we're looking at an outcome like gastric
ulcers and you determine other variables that may or may not affect that out come so the
independent variables are the ones you manipulate, the treatments that you manipulate, and the
dependent ones are the measures that are the outcomes of that.
[Insert Figure 1.1 about here]
[Insert Figure C.R.A.P Detector about here] There are a couple little C.R.A.P. detectors you can use here you can look at. CRAP detectors to find circular reasoning and other kinds of stuff.
1.3 C.R.A.P. Detector #1.1
Dependent variables should be sensible. Ideally, they should be clinically important, but also related to the independent variable.1.4 C.R.A.P. Detector #1.2
In general, the amount of information increases as one goes from nominal to ratio. Classifying good ratio measures into large categories is akin to throwing away data.Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
2: Central Tendency:
Why Important?
Why do you need to know about measures of central tendency? You need to be able to understand summaries of large amounts of data that use simple measures to best represent the location of the data as a whole. Collectively, such measures or values are referred to as measures of central tendency. Measures of central tendency are ubiquitous in the medical research literature. The most frequently used measures of central tendency are the mean, median and mode.(Show Central Tendency transparency) We do try to display information in some graphical form. And, this is a display of physicians salaries in 1999 after all the health plans have come forward and... No this was old data actually. But, the point of this slide is to show you that there are various ways to represent a distribution of data. The mode is the most frequent, the median has equal numbers above and below it and the mean is the average value. And, if the distribution is a nice symmetric distribution, all three of those collapse into one.
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
2.1 Mean
The most frequently used measure of central tendency is the mean. The mean, or more formally, the arithmetic mean, is simply the average of the group. That is, the mean is obtained by summing all the numbers for the subjects in the group and dividing by the number of subjects in the group. The mean is useful only for quantitative variables (see Figure).[Insert Figure 2.3 about here]
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
2.2 Median
The median is the middle score. That is, the median is the score for which half the subjects have lower scores and half have higher scores. Another way to say this is that the median is the score at the fiftieth percentile in the distribution of scores (see Figure).[Insert Figure 2.3 about here]
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
2.3 Mode
The mode is the most frequent score. Another way to say this is that the mode is the score that occurs most often (see Figure)..[Insert Figure 2.3 about here]
2.4 Summary Principle
In a symmetric distribution with one mode like the normal distribution the mean, median and mode all have the same value. But, in a non-symmetric distribution their values will be different. In general, as the distribution becomes more lopsided the mean and the median move away from the mode. With extremely skewed distributions the mean will be somewhat misleading as a measure of central tendency, because it is heavily influenced by extreme scores. So for example, if we take a distribution of doctor's incomes, some doctors make huge sums of money, and the median or the mode is more representative of doctor's incomes as a whole than the mean, because the very high incomes of some doctors inflates the average, making it less representative of doctors as a whole (see Figure 2.3).[Insert Figure 2.3 about here]
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
3: Variability
Why Important?
Why do you need to know about measures of variability? You also need to be able to understand summaries of large amounts of data that use simple measures to best represent the variability in the data. Measures of variability also occur very frequently in the medical research literature. If all data values are the same, then, of course, there is zero variability. If all the values lie very close to each other there is little variability. If the numbers are spread out all over the place there is more variability. Again there are many measures of variability. Some of the most frequently used measures of variability are the standard deviation, interquartile range and the range.Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
3.1 Standard Deviation
(Show standard deviation formula transparency) We can measure the spread of information or data by looking at the standard deviation and its just the mean value which we extract from the information. We sum the individual values subtracted from the mean, square it, divide it by the number of values and take the square root. The reason for that is pretty clear. The reaon that we subtract and square is pretty clear. Whether the value is above the mean or below the mean it comes out the same when we square it. So positive and negative makes no difference here. When you divide by the number of values to get an average we square root this whole thing here because we square it up here, to get back to the original measures. So by squaring to get rid of the negative and postive values we get squared measures and we square root it to get back to the original kinds of measures like feet cubic inches or whatever else it might be. The standard deviation can be thought of as the average distance that values are from the mean of the distribution (see Figure).. This means that you must be able to compute a meaningful mean to be able to compute a standard deviation. Consequently, computation of the standard deviation requires interval or ratio variables. In a distribution having a bell (normal) curve, approximately 68% of the values lie within 1 standard deviation of the mean. On the other hand, approximately 2.1% of the values lie in each tail of the distribution beyond 2 standard deviations from the mean (see Figure)..[Insert Figure 2.5 Normal Distribution about here]
[Insert Figure SD Formula Figure about here]
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
3.2 Interquartile Range
Remember the median was the point in the distribution where 50% of the sample were below and 50% are above. Quartiles can be defined at the 25th percentile, the 50th percentile, the 75th percentile and the 100th percentile. The interquartile range, then, from the 25th percentile to the 75th percentile, includes 50% of the values in the sample. The interquartile range is the distance between the 25th percentile and the 75th percentile. The interquartile range is a measure of variability that can be appropriately applied with ordinal variables and therefore may be used especially in conjunction with non-parametric statistics (see Figure)..[Insert Figure for Interquartile Range & Range about here]
(Show EDA transparency) Another way to display data thats been proposed by exploratory data analsys is to rank the data from low to high then measure the median and then the quartile values that is the values between which one half of the data resides. The rest of the data is out in the wings here. And here you find the interquartile range which is the range from the lower to the upper quartile. And, the range is the extreme values (max -min)Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
3.3 Range
The range is simply the difference between the highest and lowest value in the sample (see Figure)..[Insert Figure for Interquartile Range & Range about here]
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
4: Exploratory Data Analysis (EDA)
Why Important?
Why do you need to know about exploratory data analysis (EDA)? The purpose of EDA is to provide a simple way to obtain a big picture look at the data and a quick way to check data for mistakes to prevent contamination of subsequent analyses. Exploratory data analysis can be thought of as a preliminary to a more in depth analysis of the data (see Figure)..A primary tool in exploratory data analysis is the box plot (see figure). What does a box plot tell you? You can, for example, determine the central tendency, the variability, the quartiles, and the skewness for your data. You can quickly visually compare data from multiple groups. A small rectangular box is drawn with a line representing the median, while the top and bottom of the box represent the 75th and 25th percentiles, respectively. If the median is not in the middle of the box the distribution is skewed. If the median is closer to the bottom, the distribution is positively skewed. If the median is closer to the top, the distribution is negatively skewed. Extreme values and outliers are often represented with asterisks and circles (see Figure)..
[Insert Box and Whisker plot about here]
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
4.1 Hinges
The top and bottom edges of the box plot are referred to as hinges or Tukey's hinges (see Figure)..[Insert Box and Whisker plot about here]
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
4.2 Ranges
? (see Figure).[Insert Ranges Figure about here]
[Insert Box and Whisker plot about here]
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
4.3 Outliers
Outliers and extreme values are often represented with circles and asterisks, respectively. Outliers are values that lie from 1.5 to 3 box lengths (the box length represents the interquartile range) outside the hinges. Extreme values lie more than 3 box lengths outside the hinges. In a box and whisker plot the actual values of the scores will typically lie adjacent to the outlier and extreme value symbols to facilitate examination and interpretation of the data (see Figure)..[Insert Box and Whisker plot about here]
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
4.4 Box & Whisker plots
Box and whisker plots represent more completely the range of values in the data by extending vertical lines to the largest and smallest values that are not outliers, extending short horizontal segments from these lines to make more apparent the values beyond which outliers begin (see Figure).[Insert Box and Whisker plot about here]
(Show infant mortality transparency) I have an example here which is a plot of infant mortality in Houston Texas in 1978 and this show two congressional districts 15 & 18. And what you see here is the median (about 20 deaths per thousand live births). And here you see some census tracks (number of live births in the census tracks) (on the left) and these are the number of live births (on the right) in those census tracks and this is the ratio of those infant mortalities. So there were a hundred deaths per thousand live births in census track 126 (apparently 176 live births). Here in Houston Texas we have infant mortality rates that approach those in Bangladesh and other undeveloped countries. And this kind of diagram shows you those extremes very dramatically.Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
5. Standard Scores
Why Important?
Why do you need understand standard scores or z-scores? Again, they appear frequently in the medical literature. A natural question to ask about a given value from a sample is, "How many standard deviations is it from the mean?". The z-score answers the question. The question is important because it addresses not only the value itself, but also the relative position of the value. For example, if the value is 3 standard deviations above the mean you know it's three times the average distance above the mean and represents one of the higher scores in the distribution. On the other hand, if the value is one standard deviation below the mean then you know it is on the low end of the midrange of the values from the sample. But, there is much more that is important about z-scores.Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
5.1 z-Scores
For every value from a sample, a corresonding z-score can be computed. The z-score is simple the signed distance the sample value is from the mean. There is a simple formula for computing z-scores (see Figure):[Show z-score formula transparency here]
And lastly we want to talk about how we take a whole bunch of data...If I have a mean value of originally you know we talked about the mean value of how long people are going to live and we had to somehow be able to take that value and compare to other values from other experments. How do we collapse all that stuff? Well we have a way of normalizing or collapsing it and generally what you do is you get something like this mean value and subtract from each one of the values and divide it by its standard deviation and that then parametizes this distribution so this distribution has a mean of 0 all the time and a standard deviation of 1 an so you can build tables for it. So no matter what your data looks like, no matter what the mean value is, you can reduce it to a table if you reformulate your data like this. So we can take all kinds of experiments then and build tables for them because we can normalize it or reduce it by doing things like forming a z value.Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
5.2 General z-Score Properties
Because every sample value has a correponding z-score it is possible then to graph the distribution of z-scores for every sample. The z-score distributions share a number of common properties that it is valuable to know. The mean of the z-scores is always 0. The standard deviation of the z-scores is always 1. The graph of the z-score distribution always has the same shape as the original distribution of sample values. The sum of the squared z-scores is always equal to the number of z-score values. Furthermore, z-scores above 0 represent sample values above the mean, while z-scores below 0 represent sample values below the mean (see Figure).[Insert z-score graph about here]
5.3 Gaussian z-Score Properties
If the sample values have a Gaussian (normal) distribution then the z-scores will also have a Gaussian distribution. The distribution of z-scores having a Gaussian distribution has a special name because of its fundamental importance in statistics. It is called the standard normal distribution. All Gaussian or normal distributions can be transformed using the z-score formula to the standard normal distribution. Statisticians know a great deal about the standard normal distribution. Consequently, they also know a great deal about the entire family of normal distributions. All of the previous properties of z-score distributions hold for the standard normal distribution. But, in addition, probability values for all sample values are known and tabled. So, for example, it is known that approximately 68% of values lie within one standard deviation of the mean. Approximately 95% of values lie with 2 standard deviations of the mean. Approximately 2.1% of values lie below 2 standard deviations below the mean. Approximately 2.1% of values lie above 2 standard deviations above the mean (see Figure).[Insert standard normal z-score graph about here]
Lesson 1: Summary Measures of Data
Biostatistics for the Clinician
6. Distributions
Why Important?
Why do you need to know about distributions? Again the primary answer is that various kinds of distributions occur repeatedly in the medical research literature. Any time a set of values is obtained from a sample, each value may be plotted against the number or proportion of times it occurs in a graph having the values on the horizontal axis and the counts or proportions on the vertical axis. Such a graph is one way in which a frequency distribution may be displayed, since a frequency distribution is simply a table, chart or graph which pairs each different value with the number or proportion of times it occurs.It turns out that some distributions are particularly important because they naturally occur frequently in clinical situations. Some of the most important distributions are Gaussian, Binomial and Poisson distributions.