Questions tagged [epidemiology]

Epidemiology is the study of the distribution and spread of disease or illness at the population level.

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How to check confounding and mediation in large dataset?

Given a large dataset, one cannot possibly check every model. In particular, it does not seem clear to me that one can check confounding or mediation in either cases. How does one check confounding/...
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Analysis on repeated measurements with only one follow-up outcome

I would like to analyze the association between dietary intake and a specific health outcome. Now suppose I have 100 subjects, each having 10 repeated measurements of dietary intake collected from the ...
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How to prove change in a time series when the population is growing?

I have a small dataset with data on the number of heart and liver donors from deceased patients each year (from 2012 to 2021). I would like to find out if there has been a change in the number of ...
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Probability that seems to exceed 1

Suppose we have the following information based on independent events: The probability of contracting Alpha variant is .4 The Delta variant is 50% more contagious than Alpha The Omicron BA1 variant ...
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Will threshold of logistic regression change accuracy? Any relationship with the incidence of disease? [duplicate]

I am using a logistic regression model to predict breast cancer. I trained and tested the model in a population with a pretty high incidence of breast cancer(since the individuals all went to the ...
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Some help on this question about stochastic epidemic models without removals would be greatly appreciated

I get this question up until the underlined part, would someone be able to explain the rest of it to me as its had me stumped for a little while now.
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Targeted Learning in Data Science: background material

I am interested in the use of modern causal inference methods to research the association between a (non-genetic) exposure, and endogenous molecules and/or health outcomes (high-dimensional data). I ...
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Disease Control Rate for a Clinical Trial problem

Recently, I have come across a 2-armed clinical trial problem which attempts to find a "Disease Control Rate" (DCR) for patients in the treatement and placebo arms. On the Internet I found ...
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Multiple associations in Relative Risk and Odds Ratio

I am a frequent user of the package (epiR), especially in Relative Risk and Odds Ratio. Generally, I use several covariates to make the associations (RR or OR), for example: outcome (death) versus ...
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Should you include time as a continuous predictor when estimating incidence or prevalence?

Suppose one has a time series of disease counts and populations (at risk, total etc.) or, equivalently, binary events of disease status. Then suppose one wanted to present estimates of incidence or ...
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What to do if there are not enough controls per case?

I conduct a case-control study (matching by age) where I have a ratio of 1:2, i.e., 2 controls per case. However, this ratio is not sufficient for all cases. Example: If I have 30 cases with 70 years, ...
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How to interpret this formula with probability of an individual becoming infected over x days?

I am trying to understand a formula in this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5444538/#:~:text=Low%20Risk%20of%20International%20Zika,the%202016%20Olympics%20in%20Brazil). In the ...
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What is the covariance between two log relative risks?

In a randomized experiment with two groups (treatment and control), suppose the response variable, $Y$, has 3 categories (0,1,2): $y_{0_{i}}$,$y_{1i}$ and $y_{2i}$, in which $i$ denotes the $i^{th}$ ...
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Calibration of an agent based epidemic model on an HPC

I am working on HIV modeling with the EpiModel R package and we are trying to smooth our calibration process by efficiently using the Slurm clusters we have available. For reference, this is one of ...
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prevalence ratio question

I understand that prevalence ratio is ...
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Averaging time-dependent, heteroscedastic estimates of vaccine efficacy over time periods

Vaccine efficacy against Omicron has to be estimated for three months since the second dose. Efficacy data are given for shorter periods comprising three months. For example, the table, based on Fig ...
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What is the relevance of comparing the number of positive Covid cases at the same date in 2020 and 2021?

I am following the news in a country (which I will leave unnamed) where I am currently on holiday. Same as in a related question I asked last year, I find myself completely baffled and dumbfounded by ...
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HOW to determine $S$ in $SEIR$ epidemiology model

With the contact rate parameters for a $SEIR$ model as follows: $$ \begin{aligned} \beta &= 0.139\\ \gamma &= \frac{1}{10.4}\\ \sigma &= 0.1\\ R_0 &= 1.4456\\ N &= 3,787,000\\ I(0) ...
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How well do Covid-19 forecasts work?

I hope this question is in the scope of CrossValidated (I think so because it is in the end about statistical analyses and machine learning, I am not looking for individual opinions but for reviews or ...
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2 votes
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Help Requested - Bayes' Theorem posterior odds > 1 when applied to covid test

I took an antigen test yesterday and was trying to create a tool to help me interpret the results via Bayes' Theorem. I used actual sensitivity and specificity numbers from the CDC, calculated odds of ...
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How trustworthy are biomarker estimates and conclusions in this covid vaccine paper?

My question is about the Correlates of protection against symptomatic and asymptomatic SARS-CoV-2 infection paper from the developers of the ChAdOx1/Vaxzevria vaccine. The paper establishes ...
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Modeling Case Fatality Rate (CFR) outcome variable in cross-sectional study using GLM

Background I am conducting an analysis examining the association between various predictors on COVID-19 Case Fatality Rate (CFR), which is defined as the proportion of mortality among confirmed cases ...
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Time varying effect in time dependent cox model

In the case of Stanford heart transplant dataset (jasa), is it possible to check if the effect of the time dependent covariate of transplant is time varying as well ? If that's the case can we compute ...
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Time after time-dependent variable in Cox model

I am trying to create a time dependent (covariate) cox regression model for a survival analysis project I am interested in. A brief overview of my dataset: I have a cohort starting from 2011-01-01, ...
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Misclassification: differential and non-differential random and systematic

How to identify if misclassification is differential and non-differential?? Also need help distinguishing between: Differential random Differential systematic Non-differential random Non-differential ...
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Types of misclassification bias

Would someone please be able to give an explanation of when the following misclassification biases would occur? I am completely lost! Non-differential random Non-differential systematic Differential ...
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Including Intervention Group as a random effect in growth curve analysis?

I am using growth curve analysis to model the impact of a randomized intervention on a patient sample over 5 time points. The treatment as usual condition is a health education session and the ...
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Calculation of 95% Confidence Interval for an Incidence Rate Difference

Suppose that I have two pre-computed Incidence Rates with 95% CI, calculated from the same sample. Let's say IR1: 10.0% [8.0-12.0%] IR2: 21.0% [15.0-27.0%]. If I want to calculate an IR difference, ...
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Interpretation of the E-value for non-epidemiologists

A recent method for sensitivity analysis is the E-value (VanderWeele and Ping, 2017). Yet, I'm still struggling with the interpretation of such a value. Coming from outside of epidemiology, where risk ...
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Calculating patient-years from average follow-up

I need to estimate patient-years for some studies, in which this data is not reported. However, I do have total population and mean follow-up. Would it be suitable to estimate the number of patient-...
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Retrospective cohort study and case control study

What study would best suit looking at the association between low birthweight and later academic performance? Note - 1000 low birth weight children and 3000 normal birthweight children were included ...
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Error models for COVID-19 prevalence data

1) Some background I'm currently learning about compartmental ODE modeling for epidemiology (inspired by the current pandemic!) and I've been exploring parameter estimation of SIR-like models using ...
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Why can't we reliably compare states?

I came across this catchy visualization on reddit showing the percentage of adults reporting binge or heavy drinking in the US: https://www.reddit.com/r/dataisbeautiful/comments/nve04b/...
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Understanding a simple post-hoc power analysis of effect size

I am trying to understand a relatively straightforward paragraph found in "Gun Shows and Gun Violence: Fatally Flawed Study Yields Misleading Results" by Wintermute et al that appeared in ...
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How to implement this two-stage regression model (nutrition research)

The textbook Modern Epidemiology 3rd edition (pages 435-437) introduces a very interesting hierarchical model for studying the effect of food consumption on disease. The typical model for studying the ...
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Multimodal SIR model

I am trying to model covid 19 infected number of cases, given current data in my region, the number of infected people is a graph with 3 peaks, is it possible for an SIR model to incorporate this? I ...
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How can we distinguish the effects of a lockdown from those of a vaccine?

My question is related to Covid-19 specifically, but it can be generalized to any infectious disease. I am asking this since I am reading a lot of information on several Social Media regarding one ...
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2 votes
1 answer
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"Have you ever …" as a question for measuring cumulative incidence

In Gordis Epidemiology, it is stated that the interview question Have you ever had asthma? can be used to measure cumulative incidence. Cumulative incidence was ...
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SIR: parameter estimation and optimization here (R)

From here https://ourworldindata.org/coronavirus/country/israel I have extracted the Covid Data for Israel, with some manipulations, I have obtained the plot of the daily new infections in Israel If I ...
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To match or not to match when 2 exposures are inextricably confounded with other variables?

I want to study the effect of two Groups of patients ($X_1$) on $y$ (a test performance score), in a GLM framework. Age ($X_2$) and Education ($X_3$) are potential confounders on $y$. However its not ...
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How to calculate proportion of the population

I am trying to calculate population attributable fraction. The formula that i am using is $$ \frac{P_e(RR-1)}{P_e(RR-1) + 1} $$ I am using this website as guide: https://sphweb.bumc.bu.edu/otlt/mph-...
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Estimating future graph size given partial graph size

(This question compares a branching-fiction novel to a disease, bear with me.) This is for fun, my friends and I are writing a branching-fiction novel: A black node is a concluding chapter ("The ...
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Why are most epidemic models continuous-time?

Most classical epidemic models such as SIR and variants are formulated as differential equations. However, to me discrete-time models feel more natural to measure the evolution of a disease on a day-...
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6 votes
1 answer
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How and why do epidemiology and econometrics models handle multi-collinearity differently?

Linear multiple-regression models are often built differently according to discipline. In epidemiology, a linear multiple-regression may be fit to test associations using hypotheses about model ...
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2 votes
1 answer
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How is the vaccine effect calculated?

I'm trying to understand this study about the vaccine effect for the COVID. In the results the authors state: We found that VEs increased over time until a peak at day 28-34 days post-vaccination for ...
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Ignoring random effects when few data points are correlated

Suppose we have covariates $X_{ij}$ and responses $Y_{ij}$ where there is correlation in the response with the same $i$. This amounts to the data being correctly modelled by a mixed effects models, ...
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Do health departments inform hospitals/clinics of disease trends?

For example, during a common cold epidemic, do doctors get reported beforehand that there is a trend going on so that they can use this information to suspect diagnosis? Does every health care unit ...
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How to estimate the change of rate of COVID-19 infections when accounting for vaccine effectiveness and increased transmissibility of mutated strains?

The world has reasonably accurate numbers of the transmissibility of the strains of COVID-19 that have ravaged humankind. Now, two changes are afoot: Some wealthy regions have access to limited ...
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Fitting SIR model for COVID-19 Data UK

I want to fit a COVID-19 SIR model for UK to evaluate the lockdown measures (here: the first lockdown). My code is based on https://kingaa.github.io/clim-dis/parest/parest.html#overdispersion-a-...
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Why do we measure incidence, if we can measure the prevalence of a disease for two successive years instead?

Why do we measure incidence, if we can measure the prevalence of a disease for two successive years and then subtract the latter year's figure from the former years number and find out the incidence? ...
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