PUBH7611 Epidemiology in Practice

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PUBH7611 Epidemiology in Practice
Assessment 3: Analysis & Interpretation of Epidemiologic Data

Due: Friday 25 October 2024 (2pm), via Turnitin

Weighting: 40%

Context:

This assessment is based on the learning objectives and concepts in Weeks 4-12 (including readings, lecture material and relevant workshop exercises) as well as previous knowledge from PUBH7600 Introduction to Epidemiology.

There are a total of 100 marks and this assessment will contribute 40% towards the total assessment for this subject.

Your assessment should be submitted in the form of a publishable journal article (based on the instructions for the write-up, specified in the instructions for Assessment 3). Assessments should be submitted as a Word document via Turnitin on Blackboard. Be as concise as possible in your answers (without compromising on required detail) and note that there are specified spacelimitations for each component.

Late assessments will not be accepted without prior approval. If an extension is required, you must apply online via my.UQ (see the SPH policy on late submissions and extensions).

Please note that this is an individual exercise and should be done independently of others. The University of Queensland takes academic misconduct (including collusion and plagiarism) very seriously. Please refer to UQ’s student policy regarding student integrity and misconduct (https://ppl.app.uq.edu.au/content/3.60.04-student-integrity-and-misconduct) for further information. Before submitting this assessment, you need to ensure that you have completed the online Academic Integrity Tutorial, which can be accessed via SI-net. By submitting your assessment via Turnitin you declare that you are aware of the consequences of plagiarism and the principles associated with preventing plagiarism. The University of Queensland has approved the use of plagiarism detection software and the School uses this as part of their check for academic misconduct.2

TASK DESCRIPTION:

You have been asked to perform an analysis using the dataset Assignment3.dta to examine the following causal research questions:

1) Is alcohol consumption (exposure) causally associated with depression (outcome)?

2) Is there an interaction between alcohol consumption and sex on the risk of depression?

3) Is there an interaction between alcohol consumption and general health status on the risk of depression?

4) Graphically display the interactions above.

The dataset used to answer these questions is a random sample of 4,888 adults (20 to 80 years old) taken from the National Health and Nutrition Examination Survey (NHANES) from the United States of America. For the purposes of this assessment, data from only one time-point has been provided.

Table 1 contains a list of the variables in the Stata dataset that will be used for your analyses.

Table 1: Description of variables contained in Assignment3 dataset

Variable
Description
Coding Key
id
Unique personal identifier for study participants
-
age
Age in years at the time of survey completion
*continuous variable*
sex
Sex of the participant
0=Male
1=Female
education
Highest level of education completed
0=High school
1=College or above
marital
Marital status
1=Married
2=Not married
health
General health status
1=Excellent
2=Very good
3=Good
4=Fair
5=Poor
height_cm
Height (cm)
*continuous variable*
9999=missing
weight_kg
Weight (kg)
*continuous variable*
9999=missing
smoking_any
Have you ever smoked at least 100 cigarettes in life
1=Yes
2=No
smoking_current
If you have ever smoked, do you still currently smoke cigarettes?
1=Yes
2=No
alcohol_day
On days that you drink alcohol, self-reported average number of standard alcoholic drinks consumed

*continuous variable*

999 = missing

depression_score
Patient Health
Questionnaire (PHQ-9)
*continuous variable*
Refer to Appendix A

ADDITIONAL INSTRUCTIONS:

Variable categorisations:


  1. The outcome (depression) should be categorised as a binary variable. Categorise scores of ≤9 as the reference category of minimal to mild depression. Scores of ≥10 equate to the presence of moderate to severe depression.
  2. Alcohol consumption (the exposure) should be categorised as a binary variable. Please categorise 4 drinks or less on a single occasion as the reference category (low risk drinking) and 5 or more alcoholic drinks on a single occasion as your exposed category (risky drinking). Be careful of missing values.
  3. General health status (health) should be categorised as a binary variable. Categorise ‘very good’, ‘excellent’ and ‘good’ as the reference category and ‘fair’ to ‘poor’ and as your exposed category.
  4. Body mass index (BMI) should be categorised as a binary variable. Someone is classified as being obese if their body mass index (BMI) is ≥30kg/m2 . Anyone with a BMI <30 kg/m2 should be included in the reference category. BMI is calculated by dividing someone’s weight (in kilograms) by someone’s height squared (in metres) i.e., BMI = weight(kg)/(height(m)2 ). Be careful of missing values.
  5. Smoking status should be classified as a categorical variable with 3 categories – never smoker (reference category), ex/past smoker, and current smoker. To create this new variable, you will need to use information from both of the smoking variables (smoking_any and smoking_current) in your dataset.
  6. The variables age (continuous), sex (male=reference category), and education (no=reference category) and marital (married=reference category) and can be left as they are already defined in the dataset for all analyses. Some characteristics will only be used to describe the participants.


Analyses:

  1. Adjust all relevant analyses for the following covariates: age (continuous), sex and marital status.
  2. Create a graph for each interaction of interest between alcohol consumption and (i) sex and (ii) general health status. You can choose to graph variables as the original continuous variable or as the newly categorised variable. You are not required to graph adjusted results. Note that a simple graph is often best.
  3. You are not required to consider the missing data within variables (e.g., the models will just drop those with missing data). Simply make sure missingness is coded appropriately and take note of the total number of participants in the final models that you run for the paper.

Write-up:

In the write-up of your assessment, please provide the following:

Results:

  1. A table describing the demographics of the participants (based on variables included in your dataset) [5 marks]
  2. A table of results for research question 1 [8 marks]
  3. A table of results for research question 2 [9 marks]
  4. A table of results for research question 3 [9 marks]
  5. Graphs [6 marks]
  6. A results section written up to describe your findings for research questions 1-3 (including a brief description of the demographics of the participants). Note: results from your graphs should also be included within the text. (maximum 1.5 pages, not including tables or graphs) [18 marks]

Discussion:

7. A discussion section that includes:
  • A brief overall summary of your main findings (1 paragraph) [4 marks]
  • A comparison of your findings to other studies in the literature (maximum 3 paragraphs) [10 marks]
  • A discussion of the limitations of your analyses (including the data you have/don’t have available) relating to your ability to make valid (accurate) causal inferences about the relationship between alcohol consumption and depression. Note: you do not need to discuss the study design here but instead should focus on the limitations of the analyses themselvesin their ability to provide true causal estimates of the association between the exposure and the outcome. (maximum 2 paragraphs) [10 marks]

Supplementary Material (Appendix):

8. An annotated version of your Stata syntax (a copy of your .do file including notes, pasted into your Word document as supplementary material) which could be used by a colleague to rerun your analyses (including any data manipulation of variables) and generate all results obtained from your study. [5 marks]

Other considerations for marking:

Communication [8 marks]

Marks will be awarded based on the structure of your assessment and writing. Headings and subheadings should be used. The flow of ideas should be logical (rather than jumping from one idea to another and back again, for example). Minimal grammatical, spelling or punctuation errors and appropriate use of English language and scientific writing style.

References [8 marks]

Provide a reference list of all articles/sources cited in your assessment; use Harvard or Vancouver style.

APPENDIX A
Patient Health Questionnaire (PHQ-9)

Kroenke K, Spitzer RL, William JB. The PHQ-9: validity of a brief depression severity measure. J Gen Intern Med 2001; 16: 1606-13. 

PHQ-9 has a range of 0 to 27 calculated from responses to the following questions:

Over the last 2 weeks, how often have you been bothered by any of the following problems?


Not at all
Several days
More than half the days
Nearly every day
1. Little interest or pleasure in doing things
0
1
2
3
2. Feeling down, depressed, or hopeless
0
1
2
3
3. Trouble falling or staying asleep, or sleeping too much
0
1
2
3
4.Feeling tired or having little energy
0 1 2 3
5. Poor appetite or overeating
0 1 2 3
6. Feeling bad about yourself – or that you are a failure or have let yourself or your family down
0 1 2 3
7. Trouble concentrating on things, such as reading the newspaper or watching television
0 1 2 3
8. Moving or speaking so slowly that other people could have noticed. Or the opposite – being so fidgety or restless that you have been moving around a lot more than usual
0 1 2 3
9. Thoughts that you would be better off dead, or of hurting yourself
0 1 2 3

Add columns:
TOTAL:


Interpretation of total score
1-4
5-9
10-14
15-19
20-27
Minimal depression
Mild depression
Moderate depression
Moderately severe depression
Severe depression

PUBH7611 Assessment 3 – Analysis & Interpretation Summary Marking Matrix

Criteria
Description
Marks
Relation to published work


Results Tables
Demographics table
Table of results for research question 1
Table of results for research question 2
Table of results for research question 3
Graphs (2)
5
8
9
9
6
Results Write-up
Findings for research questions 1-4
18
Discussion
Summary of main findings
Comparison of findings to other studies in the literature
Discussion of the limitations of analyses
4
10
10
Stata
Annotated version of Stata syntax
5
Communication
Structure, style, format, error-free
8
References
Appropriately acknowledged with consistent and accurate referencing (in-text and reference list)
8
Total

100

























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