1b Statistical Methods Flashcards
What is sensitivity?
The probability that the test will be positive if the disease is present (true positives).
What is specificity?
The probability that the test will be negative if the disease is absent (true negatives).
How does disease prevalence impact sensitivity and specificity of a test?
Since sensitivity is conditional on the disease being present, and specificity on the disease being absent, in theory, they are unaffected by disease prevalence.
What is a false negative rate?
The probability that the test will be negative when you are actually positive.
What is a false positive rate?
The probability that the test will be positive when you are actually negative.
How do you calculate sensitivity
Sensitivity = a/(a+c)
How do you calculate specificity
Specificity = d/(b+d)
How do you calculate the false positive rate
False Positive Rate = b/(b+d)
How do you calculate false negative rate
False Negative Rate = c/(a+c)
What is the sensitivity, specificity, false positive and false negative rate in the below example?
A sample of 410 people is taken to test if BNP can diagnose heart failure. All are tested for their BNP levels and then have an echo performed to assess if they actually do have heart failure (the standard gold test).
Number of participants = 410
Number of positive findings on BNP testing = 42
The number of positive findings on echo = 103
The number of false positives when using BNP = 68
Place the data into a 2x2 table
Sensitivity = a/(a+c) = 35/103=0.340=34%
Specificity = d/(b+d) = 300/307=0.977=98%
False Positive Rate = b/(b+d)=7/307=0.02=2%
False Negative Rate = c/(a+c)=68/103=0.66=66%
What is the positive predictive rate (aka the predictive value of a positive test)?
The probability of the patient having the disease, given a positive test result. I.e How likely a positive result is true
What is the negative predictive rate (aka the predictive value of a negative test)?
The probability of not having the disease, given a negative test result.I.e How likely a negative result is true
How do you calculate positive predictive value?
Positive predictive value=a/(a+b)
How do you calculate negative predictive value?
Negative predictive value = d/(c+d)
How does disease prevalence impact negative and positive predictive value?
If disease prevalence increases then the predictive value of a positive test would also increase, and the predictive value of a negative test will decrease.
What are the positive predictive value and negative predictive values in the below example?
Results of exercise tolerance test in patients with suspected coronary artery disease:
Number of positive tests = 930
Number of negative tests = 535
Number found to truly have coronary artery disease = 1023
Number found to truly not have coronary artery disease = 442
Number of positive cases on ETT who has CAD = 815
Number of positive cases on ETT who did not have CAD = 115
Place the numbers into a 2x2 table
Positive predictive value=a/(a+b)=815/930 =0.88
Negative predictive value = d/(c+d)=327/535 = 0.61
What is Bayes Theorem and how does it apply to medical statistics
Pre-test odds of disease * likelihood ratio = post-test odds of disease.
This is used when interpreting likelihood ratios
What is the negative likelihood ratio (LR-)
The decreased chance of having the disease once you have tested negative.
The chance of having a negative test result and having the disease VS. The chance of having a negative test result and not having the disease
What is the positive likelihood ratio (LR+)
The increased chance of having the disease once you have tested positive.
The chance of having a positive test result and having the disease VS. The chance of having a positive test result and not having the disease
How do you calculate the positive likelihood ratio (LR+)?
LR+=Sensitivity/(1-Specificity)
Aka (True positives / false positives)
How do you calculate the negative likelihood ratio (LR-)?
LR-=(1-Sensitivity/(Specificity)
Aka (False negatives / True negatives)
What is the difference between sensitivity, specificity, positive & negative likelihood ratios and positive & negative predictive values?
Sensitivity = The probability that the test will be positive if the disease is present (true positives).
Specificity = The probability that the test will be negative if the disease is absent (true negatives).
Positive likelihood ratio = The increased chance of having the disease once you have tested positive. This value is applicable to an individual patient.
Negative likelihood ratio = The decreased chance of having the disease once you have tested negative. This value is applicable to an individual patient.
Positive Predictive Rate = The probability of the patient having the disease, given a positive test result I.e How likely a positive result is true. This value is not applicable to individual patients and is dependent on prevalence.
Negative Predictive Rate = The probability of not having the disease, given a negative test result. I.e How likely a negative result is true. This value is not applicable to individual patients and is dependent on prevalence.
What are the advantages of likelihood ratios?
Not affected by different populations or sample sizes
Can be used directly at the individual patient level to quantitate disease probability for an individual patient.
How do you interpret a positive likelihood ratio (LR+)?
A positive likelihood ratio of 6 means that the patient having the disease has increased by approximately six-fold given the positive test result.
An LR of 10 = A significant increase the probability of a disease
An LR of 5 = A moderate increase the probability of a disease
An LR of 2 = A small increase the probability of a disease
An LR of 1 = The test makes no difference
To translate this into an actual probability of disease use Bayes’ Theorem. Bayes’s theorem with likelihood ratios require that the probability of disease is in the form of Odds rather than a percentage.
Pre-test odds of disease * likelihood ratio = post-test odds of disease.
As well as calculating this by hand, you can also use Baye’s `Nomogram.
Using this we can see someone who originally had a 40% chance of having coronary artery disease, now has an 80% chance after the test. This is done by joining 40% on the first axis with 6 on the second axis and read off the post-test probability of 80%.
How do you interpret a negative likelihood ratio (LR+)?
The negative likelihood ratio (-LR) gives the change in the odds of having a diagnosis in patients with a negative test.
The change is in the form of a ratio, usually less than 1. For example, a -LR of 0.1 would indicate a 10-fold decrease in the odds of having a condition in a
patient with a negative test result. A –LR of 0.05 would be a 20-fold decrease in the odds of
the condition.
We can then translate this into an actual probability of disease using Bayes’ Theorem. Bayes’s theorem with likelihood ratios requires that the probability of disease is in the form of Odds rather than a percentage.
Pre-test odds of disease * likelihood ratio = post-test odds of disease.
As well as calculating this by hand, you can also use Baye’s `Nomogram.
Using a negative likelihood ratio of 0.14, we can see that someone who originally had a 17% chance of disease, now has a post-test probability of approximately 3%. This means that after a negative test the woman has a 3% chance of disease.
What is the likelihood ratio in the below example and how do you interpret it?
On clinical assessment, a 50-year-old male has a 40% chance of having coronary artery disease and so isn’t to for an exercise test. This is found to be positive. It is known that a more than 1 mm depression on exercise stress testing has a sensitivity and specificity of 65% and 89% respectively for coronary artery disease when compared to the reference standard of angiography.
Positive likelihood ratio = 0.65/(1-0.89) = 5.9
The likelihood of this patient having the disease has increased by approximately six-fold given the positive test result.
To translate this into an absolute probability of disease one must use Bayes’ Theorem.
= Pre-test odds of disease * likelihood ratio = post-test odds of disease.
This requires the odds of disease which we do not have, and so we must use Baye’s Nomogram which converts odds to percentages while doing the calculation for us.
The initial clinical assessment found that the 50-year-old man had a 40% chance of having coronary artery disease, we join 40% on the first axis with 6 on the second axis and read off the post-test probability of 80%, i.e. the patient has an 80% chance of having coronary artery disease given the positive test result.
What are the Methods for the Quantification of Uncertainty in an epidemiological study?
Standard error
Reference ranges
Confidence intervals
What are the types of standard error?
Standard error of the mean
Standard error of a proportion or a percentage
Standard error of count data
What is the standard error of the mean?
The standard error of the mean of one sample is an estimate of the standard deviation that would be obtained from the means of a large number of samples drawn from that population.
E.g. If you did 100 studies on a population, and found the standard deviation of each of their means.
Which factors impact standard error of the mean?
Population base variation - The variation between samples depends partly on the amount of variation in the population from which they are drawn. For example, a series of samples of the body temperature of healthy people would show very little variation from one to another, but the variation between samples of the systolic blood pressure would be considerable
Sample size - the more members of a population that are included in a sample the more chance that sample will have of accurately representing the population, and thus if two or more samples are drawn from a population, the larger they are the more likely they are to resemble each other
What is the Central Limit Theorem?
If we draw a series of samples and calculate the mean of the observations in each, this series of means generally conform to a Normal distribution, and they often do so even if the observations from which they were obtained do not.
How do you calculate the standard error of the mean?
SEM=SD/√n
Standard error of the mean = Standard deviation of means/Square root of sample size
What is the standard error of the mean in the below example?
A general practitioner has been investigating whether the diastolic blood pressure of men aged 20-44 differs between printer workers and farm workers. For this purpose she has obtained a random sample of 72 printers and 48 farmers and calculated the mean and standard deviations, as shown.
To calculate the standard errors of the two mean blood pressures the standard deviation of each sample is divided by the square root of the number of observations in the sample.
SEM=SD/√n
Printers: SEM=4.5/√72=0.53 mmHg
Farmers: SEM=4.2/√48=0.61 mmHg
How do you interpret the standard error of the mean?
Standard error tells you how much your statistic differs from the true value of population, i.e. how precise your estimate is.
For example, imagine we have sample of respondents and their income. We can compute the mean income of our sample, but we aren’t sure about how good this estimate is. So we compute standard error of the mean, which roughly tells us how much our estimate varies around the true mean of the population. The lower the standard error, the more we can be sure that our estimate of mean income is close to what the income for entire population is.
What is the standard error of a proportion or a percentage?
Just as you can calculate a standard error associated with a mean, you can also calculate a standard error associated with a percentage or a proportion.
Here the size of the sample will affect the size of the standard error but the amount of variation is determined by the value of the percentage or proportion in the population itself, and so we do not need an estimate of the standard deviation.
How do you calculate the standard error of a percentage or proportion?
SE % =√(p*q)/n)
p = one percentage
q = (100-p) = the other percentage
n = number in the sample
Note that the above formula uses percentages. If you are given proportions, you can either convert these to percentages (multiply by 100), or use the modified formula below:
What is the standard error of the percentage in the below example?
A senior surgical registrar in a large hospital is investigating acute appendicitis in people aged 65 and over. As a preliminary study he examines the hospital case notes over the previous 10 years and finds that of 120 patients in this age group with a diagnosis confirmed at operation 73 (60.8%) were women and 47(39.2%) were men.
SE % =√(p*q)/n)
SE% = √(39.2*60.8)/120) = 4.5
What is the Standard error of count data?
Standard error can also be calculated for count data, where you are given a number of events over set period of time.
For example the number of cardiac arrests in an A&E department every year, or the number referral rate from primary care to a specialist service per 1,000 patients per year.
How do you calculate the standard error of count data?
Standard Error of Count Data = √λ
Where λ = The count
For example, a GP in a busy practice sees 36 patients in a given day. The standard error is therefore √36 = 6.
What is the standard error of count data in the below example?
A GP sees 36 patients in a given day.
Standard Error of Count Data = √λ = √36 = 6.
What is Pooling standard errors of two groups and why might it be done?
One way of comparing two groups is to look at the difference (in means, proportions or counts) and construct a 95% confidence interval for the difference.
As part of this process, we are required to calculate a pooled standard error of the two groups. The formulae required are similar to those used normally to calculate the standard error of the mean/proportion/percentage/count, however, each calculation within the square root is done twice, once for each group, before the square root is applied. This can be seen by comparing the formulae below:
How do you calculate a pooled standard error of the mean?
How do you calculate a pooled standard error of the proportion/percentage?
How do you calculate a pooled standard error of the count?
What are confidence intervals?
A range of values that’s likely to include a population value with a certain degree of confidence. It is often expressed as a % whereby a population mean lies between an upper and lower interval.
How are confidence intervals formed?
Confidence intervals come from combining the concepts of standard deviation, the central limit theorem and the standard error of the mean.
95% of data following a normal distribution falls within 1.96 standard deviations of the mean.
If a series of samples are drawn and the mean of each calculated, these means will follow a normal distribution and thus 95% of the means would be expected to fall within the range of 1.96 standard errors above and 1.96 below the mean of these means.
We can use this to ascertain that if we have a mean from a sample, we can be 95% sure that the true population mean will fall between 1.96 standard deviations either side of this mean. This range is called the 9% confidence interval.
Other commonly used limits are the 90% and 99% confidence interval, in which case the 1.96 may be replaced by 1.65 (for 90%) or 2.58 (for 99%).
How do you calculate a 95% confidence interval for a mean?
95% CI = Estimate ± (1.96 x Standard error)
Estimate =Mean, Proportion, Percentage or Count
SE = The relevant standard error of the estimate used e.g. SE of mean or SE of a proportion.
How can you use confidence intervals to compare two pieces of data and see if there is a likely difference?
Two options:
1) Calculate the confidence intervals for both sets of data, if the intervals do not cross you can say with 95% certainty that there is a significant difference between the two sets.
2) Calculate a confidence interval for the difference between the two estimates. If these do not include the null value (likely 0), then you can be 95% certain that there is a difference between the two data sets.
How do you calculate a confidence interval for the difference between two estimates and how is it interpreted?
95% CI for difference = (Estimate 1 - Estimate 2) +/- 1.96 (Pooled standard error).
Step 1) Calculate the pooled standard error,
Calculate whether or not there is a significant difference in the findings below using the confidence interval for the difference method.
The prevalence of teenage pregnancies in a city was 49 per 1000 in 2005 and 25 per 1000 in 2015.
1) Calculate the pooled standard error
Pooled SE= √(λ1+λ2) =√(49+25)=8.6
2) Calculate the 95% confidence interval
95% CI = (λ1−λ2) +/- 1.96(SE) = (49 – 25) ± (1.96 x 8.6)
= (7.1, 40.9)
3) Interpret
As the null value (0 in this case) is not included in the confidence interval range, then we can say that there is a statistically significant difference between the two results.
Calculate whether or not there is a significant difference in the findings below by calculating two separate confidence intervals for the data.
The prevalence of teenage pregnancies in a city was 49 per 1000 in 2005 and 25 per 1000 in 2015.
1) Calculate the pooled standard error
SE of count = √λ (Where λ = The count)
SE #1 = √49 = 7
SE #2 = √25 = 5
2) Calculate the confidence intervals
95% CI = Estimate ± (1.96 x Standard error)
95% CI #1 = 49 ± (1.96 x 7) = (35.3, 62.7)
95% CI #2 = 25 ± (1.96 x 5) = (15.2, 34.8)
3) Interpret
As the two confidence intervals do not cross at any point, we can say with 95% certainty that the two data sets are statistically significant.
What is the difference between a reference range and a confidence interval?
There is precisely the same relationship between a reference range and a confidence interval as between the standard deviation and the standard error. The reference range refers to individuals and the confidence intervals to estimates.
A confidence interval gives a range for which the true mean is likely to sit (with 95% confidence), and is used to estimate the true mean.
A reference range gives a range in which 95% of the values of a sample will likely lie and thus is used to distinguish when a result is abnormal. THis is used on an individual result in a sample to detect if they are abnormal.
Not, neither reference ranges nor CI have to always be 95%. For example, the WHO reference range for birth weight is 80%.
In appropriate circumstances the interval may estimate the reference interval for a particular laboratory test which is then used for diagnostic purposes.
What is the normal distribution?
Normal distribution describes continuous data which have a symmetric distribution, with a characteristic ‘bell’ shape.
Most Healthcare data is normally distributed and in a sample whose histogram has the approximate Normal shape, that population is presumed to have exactly, or as near as makes no practical difference, to have a Normal shape.
The Normal distribution is completely described by two parameters μ and σ, where μ represents the population mean, or centre of the distribution, and σ the population standard deviation. It is symmetrically distributed around the mean.
Only in normally distributed data sets do 95% of the values lie within 1.96 standard deviations of the mean.
What is the binomial distribution?
Data which can take only a binary (0 or 1) response, such as treatment failure or treatment success, follow the binomial distribution provided the underlying population response rate does not change.
It describes the probability of getting r events out of n trials.
What is the Poisson distribution?
The Poisson distribution is used to describe discrete quantitative data such as counts in which the population size n is large, the probability of an individual event is small, but the expected number of events, n, is moderate (five or more). Typical examples are the number of deaths in a town from a particular disease per day, or the number of admissions to a particular hospital.
Poisson distribution describes the distribution of binary data from an infinite sample. Thus it gives the probability of getting r events in a population.
What is the t-distribution?
Student’s t-distribution is a continuous probability distribution with a similar shape to the Normal distribution but with wider tails.
t-distributions are used to describe samples which have been drawn from a population, and the exact shape of the distribution varies with the sample size. The smaller the sample size, the more spread out the tails, and the larger the sample size, the closer the t-distribution is to the Normal distribution.
Whilst in general the Normal distribution is used as an approximation when estimating means of samples from a Normally-distribution population, when the same size is small (say n<30), the t-distribution should be used in preference.
What is the Chi-squared distribution?
The chi-squared distribution is continuous probability distribution whose shape is defined by the number of degrees of freedom. It is a right-skew distribution, but as the number of degrees of freedom increases it approximates the Normal distribution (Figure 4). The chi-squared distribution is important for its use in chi-squared tests.
These are often used to test deviations between observed and expected frequencies, or to determine the independence between categorical variables. When conducting a chi-squared test, the probability values derived from chi-squared distributions can be looked up in a statistical table.
What is a null hypothesis?
The hypothesis that there is no difference between groups.
What is a type 1 error?
When you reject the null hypothesis when it is in fact true. The level at which a result is declared significant is known as the type I error rate, often denoted by α.
What is meant by rejecting the null hypothesis?
Rejecting the null hypothesis means that you have gathered suitable evidence to be confident that the null hypothesis is incorrect i.e. you have more than 95% confidence that there is a difference between the two groups.
Not rejecting the null hypothesis is not the same as proving the null hypothesis right, it just means you cannot reject it.
How do you reduce the risk of a type 1 error?
Increase the range of your confidence intervals by more standard deviations e.g. a 99% confidence interval instead of a 95% confidence interval.
Make sure P-values are covered somewhere.
What is a studies alternative hypothesis?
When performing a study, you develop a hypothesis. The alternative hypothesis is the hypothesis you would be looking to prove if the null hypothesis were correct.
E.g. Hypothesis may be that regular aspirin reduces the rate of heart attacks whereas the alternative hypothesis would be that regular aspirin has no effect on the rate of heart attacks .
What is a type 2 error?
A type 2 error is when you do not reject the null hypothesis when in fact there is a difference between the groups.
The type II error rate is often denoted as β
What is study power?
The power of a study is defined as 1-β and is the probability of rejecting the null hypothesis when it is false.
How do you reduce the risk of type 2 errors?
Increase the study size.
How do you calculate the required sample size for a study?
Usually, the significance level is predefined (5% or 1%).
Select the power you want the study to have, usually 80% or 90% (i.e. type II error of 10-20%)
For continuous data, obtain the standard deviation of the outcome measure.
For binary data, obtain the incidence of the outcome in the control group (for a trial) or in the non-exposed group (for a case-control study or cohort study).
Choose an effect size. This is the size of the effect that would be ‘clinically’ meaningful.
For example, in a clinical trial, the sort of effect that would make it worthwhile changing treatments. In a cohort study, the size of risk that implies a public hazard.
Use sample size tables or a computer program to deduce the required sample size.
Often some negotiation is required to balance the power, effect size and an achievable sample size.
One should always adjust the required sample size upwards to allow for dropouts.
How can you limit multiple testing?
- Specify clearly in the protocol which are the primary outcomes (few in number) and which are the secondary outcomes.
- Specify at which time interim analyses are being carried out, and allow for multiple testing.
- Carefully review all published and unpublished studies before starting a trial.