## Lecture: Symptom Screening for Covid-19
## Assigned Reading- Comparison of symptom screening and home tests Read►
- Non respiratory symptoms of COVID-19 Read►
- Symptom clusters for COVID-19 Read►
- Pairwise comparison of order of variables Wiki► Slides►
## AssignmentFor this assignment you can use any statistical software.
- Describe the order of occurrence of the variables
- Assume that age, and gender occur at birth. Assume that vaccination information occurs before onset of symptoms. Assume home tests occurs after onset of symptoms. Assume that laboratory PCR test occurs after home test.
- Establish the order with which symptoms occur
- Count for each pair of symptoms, the number of times one symptom occurs before another. Use column AK in the database to identify if one symptom has occurred before another.
- Use the pairwise count of one symptom occurring before another to establish a sequence of occurrence of symptoms.
- Create a Causal Network for clusters of symptoms of COVID-19
- Create the structure of the network:
- Using LASSO, regress the PCR test results on all variables and pairwise or triple cluster of variables that precede it.
- Using LASSO, regress each variable that is a direct predictor of PCR test results on all preceding variables. In these regressions, statistically significant variables are parents in the Markov blanket of the regression response variable.
- Draw the network using Netica.
- Estimate the parameters of the network
- Using the LASSO regression, calculate the predicted value for all combinations of the parents in the Markov blanket of the regression's response variables. Enter this information into Netica Tables.
- Create the structure of the network:
- What is the probability of COVID for a patient less than 30, female, with runny nose, muscle aches, and with unknown fever status. What is the same probability if we knew that the patient does not have COVID.
- What are the parents in the Markov blanket of fever?
The following resources may be helpful: - Data Data►
- First, LASSO regress the disease variable on all symptoms, age and gender. This regression will identify variables in the Markov blanket of the disease.
- Second, identify parents and children in the Markov Blanket of the disease variable. Symptoms, by definition, occur after the disease and demographic variables occur prior to the disease. Using Netica software, draw an arrow from the disease variable to symptoms that were statistically significant in the LASSO regression. Similarly, draw an arrow from demographic variables to the disease, if the demographic variable was a significant predictor in the LASSO regression.
- Third, use each symptom that is statistically significant in first
step as a response variable for a new LASSO regression. The
independent variables in these regressions are the disease variable,
other symptoms, and gender. Using Netica, draw an
arrow from the variables that are statistically significant to the
symptom used as response variable. Repeat for other symptoms as
response variable. Here is a sample of the results of these
regressions. Note that findings above 0.15 or below -0.15 are
listed, the choice of 0.15 is arbitrary focus on large magnitude
associations. The relationships from age and gender to the symptoms
are not listed as all were not significant. Relationships that can
create a cycle are crossed out.
Aches Chest Pain Chills Red Eye Cough Diarrhea Fatigue Fever Head- ache Nausea Runny Nose Short Breath Vomit Wheeze Aches 0.24 0.17 0.37 0.22 Chest Pain ~~0.17~~Chills ~~0.18~~0.41 ~~0.16~~Red Eye ~~0.40~~Cough 0.27 ~~0.17~~Diarrhea Fatigue ~~0.36~~~~0.18~~0.18 Fever ~~0.21~~Headache ~~0.21~~0.21 0.18 0.16 Nausea ~~0.54~~Runny Nose -0.16 0.21 ~~0.15~~Short Breath 0.28 ~~0.36~~Vomit 0.15 0.69 Wheeze 0.21 0.38
- Fourth, enable Netica software to learn the parameters of the model.
- Fifth, report the probability of COVID-19 in a patient with fever, cough and runny nose and unknown other symptoms. Set these three nodes to symptom being present and read the network probability for COVID-19.
Resources for question 2: - Data Download►
- Rapid analysis of symptoms of new diseases: COVID-19 PubMed►
- Data (no missing values) Download►
- Ghaida Alsadah's Teach One YouTube►
Resources for Question 3 ## MoreFor additional information (not part of the required reading), please see the following links: - No-lab diagnosis of COVID-19 Read►
This page is part of the course on Comparative Effectiveness by Farrokh Alemi, Ph.D. Home► Email► |
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||