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were performed using the epidemiology toolbox app, available for free for various devices including computers and handheld devices.
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7.10.1 Respiratory disease detection using gross necropsy
Table 14 provides summary counts of classification of cases based on the gold standard test columns and the gross necropsy diagnosis rows.
Table 14: Summary of classification of 215 cases of mortality by gold standard test final cause of death and the gross necropsy diagnosis outcome, using respiratory disease as the
outcome of interest
Respiratory disease Gold standard test
Final cause of death Disease +
Disease - Gross necropsy
diagnosis
Test + 90
10 100
Test - 17
98 115
107 108
215 Test assessment assumes that the gold standard test is 100 accurate. The gold standard
test has detected 107 animals with respiratory disease as the true cause of death and 108 animals where the cause of death was not respiratory disease classified as disease
negative when respiratory disease is the outcome of interest.
Gross necropsy diagnosis is then assessed based on the level of agreement between the gross necropsy diagnosis and the gold standard test.
A perfect diagnostic test would have 100 agreement with the gold standard test. A test positive + result for gross necropsy diagnosis means a gross necropsy diagnosis of
respiratory disease and a test negative – result means that respiratory disease was not
recorded as the gross necropsy diagnosis some other diagnosis was recorded. As shown in Table 14, gross necropsy diagnosis failed to detect 17 animals that died from
respiratory disease classified as disease + on the gold standard test and as disease – on
the gross necropsy diagnosis, and the gross necropsy diagnosis incorrectly assigned 10 animals to respiratory disease when the gold standard test classified these 10 animals as
having died from a cause other than respiratory disease. Both tests correctly classified the remaining 98 animals as not having respiratory disease.
Gross necropsy diagnosis therefore correctly classified most of the respiratory disease cases and incorrectly classified some disease free animals as being diseased and some
diseased animals as being disease free.
Table 15 provides estimates of the various measures that can be used to assess diagnostic test performance when assessing gross necropsy diagnosis as a method for detecting
respiratory disease as a cause of death.
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Thanh Hoa Nguyen, 2012. Epidemiology toolbox, https:itunes.apple.comusappepidemiology-
toolboxid477457802?mt=8
Page 74 of 201 Table 15: Statistical measures of diagnostic performance for gross necropsy diagnosis as a
test for detecting respiratory disease as a cause of death in cattle. Based on data in Table 14. Se= sensitivity; Sp=specificity; PPV = positive predictive value; NPV = negative predictive
value; App Prev = apparent prevalence; True Prev = true prevalence; CI = Confidence Interval.
Parameter Estimate
95 CI Lower
Upper Se
0.84 0.76
0.9
Sp 0.91
0.84 0.95
PPV 0.9
0.83 0.94
NPV 0.85
0.78 0.91
App Prev 0.47
0.4 0.53
True Prev 0.5
0.43 0.56
Sensitivity and specificity are measures of diagnostic test accuracy. Sensitivity is the probability of a test positive result Test +, given that the disease is present
Disease +. Sensitivity measures the ability of the test to correctly detect as test positive those animals that are known to have the disease of interest. Gross necropsy diagnosis has
a sensitivity of 0.84, meaning that 84 of animals that truly died from respiratory disease would be correctly classified as test positive using gross necropsy.
Specificity is the probability of a test negative result Test -, given that the disease is absent Disease -. Specificity measures the ability of the test to correctly detect as test negative
those animals that are known to be disease free. Gross necropsy diagnosis has a specificity of 0.91, meaning that 91 of animals that truly did not die from respiratory disease would be
correctly classified as test negative using gross necropsy.
One minus the Se is a measure of false negatives, meaning those animals that truly died of respiratory disease and that were classified as negative on gross necropsy n=17. These
animals are called false negatives because the gross necropsy diagnosis has classified them as test negative when in fact the gold standard test has classified those 17 animals as
dying from respiratory disease. Gross necropsy has a false negative rate of 0.16 or 16.
One minus the Sp is a measure of false positives. These animals are called false positives because the gross necropsy diagnosis has classified them as test positive when in fact the
gold standard test has classified those 10 animals as dying from causes other than respiratory disease Disease -. Gross necropsy has a false positive rate of 0.09 or 9.
While Se and Sp are useful measures of diagnostic test accuracy, they are interpreted only in the knowledge of the true disease status of each animal.
Predictive value measures provide slightly different information that is more direct use for an AAV performing a gross necropsy where the true cause of death is unknown. This is the
situation on board a ship during an export voyage. Predictive values provide a measure of the probability of a disease outcome true disease positive or negative given the results of
the diagnostic test gross necropsy. Predictive value estimates are dependent in part on the prevalence of the condition of interest in the target population. This is an important concept
to take note of particularly if it is possible that the same disease may be occurring in different
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populations at different frequencies. For example, it may be possible that respiratory disease occurrence might be different in one specific group of animals compared to another. If the
prevalence of a disease is different in different populations then applying the same diagnostic test to those different populations may produce different predictive values
because predictive value estimates are influenced by the prevalence.
For respiratory disease, gross necropsy has a positive predictive value PPV of 0.9 and a negative predictive value NPV of 0.85.
This means that if a gross necropsy is performed during a voyage and the gross necropsy diagnosis is respiratory disease, then that animal has a 90 probability of truly having
respiratory disease as the cause of death positive predictive value.
Conversely if a gross necropsy is performed and the gross necropsy diagnosis is not respiratory disease, then that animal has an 85 probability of having died from a cause
other than respiratory disease negative predictive value.
Having information on diagnostic test performance and gold standard test outcomes also provides a more detailed understanding of prevalence estimates. The prevalence of
respiratory disease as a cause of death is the probability that a mortality case died of respiratory disease.
The diagnostic test result gross necropsy classified animals as test positive or test negative and using these numbers we can generate a prevalence estimate of respiratory disease:
100215 = 47.
The term apparent prevalence is used to refer to the prevalence estimate derived from the diagnostic test gross necropsy because it is really a prevalence of a positive test result and
not the prevalence of true disease since the diagnostic test is not perfect.
If a gold standard test result is available then these results provide an estimate of the true prevalence, based on the final cause of death results.
7.10.2 Respiratory disease detection using clinical category information
