Questions tagged [epidemiology]

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

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8
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3answers
354 views

Why is $R_t$ (or $R_0$) and not doubling rate or time the go-to metric for measuring Covid-19 expansion?

In my head, the natural way to measure the expansion speed of an epidemic across populations of different sizes is simply fitting an exponential over recent infection numbers (with any strategy), ...
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0answers
11 views

Questions about distributed lag non-linear models (DLNM)

I am new to DLNM, I have some confused questions: My research is about the environmental impact on health, and my data records are ordered as health cases as below: I want to use DLNM to analyze the ...
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1answer
37 views

Why not always present logistic regression estimates in the response scale (probablity)?

There's a lot of discussion in epidemiology around the relative merits of odds ratios vs risk ratios. Proponents of the former cite the mathematical qualities of odds (not constrained to be between 0 ...
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1answer
16 views

from x per 100 person-years to x per 100,000 person-years?

If something is reported in per 100 person-years, like in the below table, is it possible for me to convert it into per 100,000 person-years simply by multiplying by 1,000? That is, 2.21 per 100 ...
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2answers
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Which statistical model is being used in the Pfizer study design for vaccine efficacy?

I know there's a similar question here: How to calculate 95% CI of vaccine with 90% efficacy? but it doesn't have an answer, at the moment. Also, my question is different: the other question asks how ...
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0answers
165 views

How to calculate 95% CI of vaccine with 90% efficacy?

A vaccine is reported in the news to have 90% efficacy. I'd like to know how much confidence there is in that efficacy measure. The protocol for this reports that a vaccine or placebo was administered ...
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36 views

What is the difference between categories or subgroubs for continuous variables by quartiles in logistic regression?

I am trying to analyze the effect of air pollutant on health. Firstly, I transformed the continuous pollutant concentration into category variables by its quartiles and recorded them as Q1,Q2,Q3,Q4 ...
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1answer
29 views

looking for the probability of infection (for Covid19) vs the number of days to the onset of symptoms

I have been searching for a graph of the probability of infection (for covid 19) vs the number of days to the onset of symptoms. The following graph is taken from Namilae, et al (Multiscale model for ...
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Why do some researchers use the oxymoron “prevalence rate”?

An incidence rate (whether an incidence density or an incidence proportion) measures the probability of an event (typically a new case of the relevant health condition in epidemiology) divided by time....
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Estimating True COVID-19 infection rate from Positivity Rate?

Like many, I've been watching and tinkering with COVID-19 statistics for the past 8+ months. One thought I keep coming back to is that there must be some smart Bayesian approach to blending (a) known ...
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13 views

Best way to infer number of infected from number of new cases per day

Lots of the covid-19 datasets (e.g. https://ourworldindata.org/coronavirus) only provide the new cases per day data. However to fit a model such as e.g. SIR to this ...
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1answer
65 views

Calculating risk difference and number needed to treat from hazard ratio in meta-analysis

If you have primary data, there exist several ways to calculate a risk difference (RD) or number needed to treat (NNT) from time-to-event data (see e.g. following pmid: 29955580, 31626655). However, I ...
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1answer
18 views

How to do propensity score matching for a cohort study?

Suppose I want to look at the relationship between smoking and lung cancer, and want to use propensity score matching to select a similar group of people to study. Knowing that age, and gender are ...
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1answer
41 views

Why do epidemiologists fit the number of transmission cases with negative binomial distribution?

In the recent paper on coronavirus spread in Hong Kong, the number of individuals infected by one person (relative to all transmission cases) is fit by a negative binomial distribution. Why is that? ...
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0answers
18 views

What is the relation between prevalence and positive rate?

Many of us follow closely the fluctuation of SARS-CoV-2 positive rates in different locations, but how do these rates relate to actual prevalence? Trying to work this out myself without any knowledge ...
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1answer
22 views

Can I use indirect standardization with the WHO Standard World Population?

I have to compare mortality rates among countries for a variable where the age-specific mortality rate is not available, but the overall rate is. I want to use indirect standardization with the WHO ...
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2answers
106 views

Significance of epidemiological confounders in a generalized linear model

I am identifying risk factors for children snoring among several predictors with generalized linear model. With backward selection, age and sex do not appear to be significant so I removed them from ...
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0answers
7 views

Population Attributable Fraction adjusted for a variable

I am working in R tryign to estimate the population attributable fraction (PAF) for a binary outcome and 2 exposure variables that I had to coerce to become binary. I have used the "epi.2by2"...
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1answer
13 views

Stratum specific estimates in a model with an interaction term

Lets say I have a logistic regression model predicting the log odds of mild cognitive impairment (MCI) and my exposures of interest are age, education and carbohydrate intake. I expect that the ...
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0answers
10 views

Calculate proportion of survival and deaths from Life Table

From the life table given, how do we calculate the proportion of newborns will survive to exact age 80 years but then die before exact age 85 years? I have tried using the formula (1 - l85/l0) but not ...
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0answers
14 views

Is there an analytical formula to yield the time the Infected compartment reaches maximum

In studying the SIR model of an epidemic, there is a well known formula for the maximum value of the Infected compartment, e.g: $I_{max} = \frac{S_0}{\mathcal{R}} (log(\frac{1}{\mathcal{R}}) -1) + S_0 ...
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0answers
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How to interpret the results from Distributed linear model (DLNM package in R)?

I am using a distributed linear model (DLNM package in R) to study the effects of temperature lags on cardiovascular disease admissions. So i did as following: ...
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2answers
38 views

question concerning Covid infection data reported by the media

I tried searching stackexchange for existing posts about this, but I could not find them. Please redirect me if appropriate. My question is very simple, and perhaps partly related to the observations ...
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1answer
105 views

Computing statistical significance from experimental data

As described in my previous question, I am currently conducting an epidemiological study in a health institution where we investigate the prevalence of Corona virus infections by measuring the ...
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1answer
38 views

Inverse probability weighting for selection bias in cohort studies

I am using inverse probability weighting to calculate stabilized weights to try to account for the loss-to-follow-up in my cohort study of children from birth to 5 years. I used multiple imputation to ...
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1answer
32 views

Case control sampling strategy for longitudinal analysis

Does it sound plausible to use a case-control sampling strategy to then address a longitudinal question? For example, let's say I have a population of diabetics (N=100) and non-diabetics (N=9999). I ...
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1answer
59 views

Deaths per confirmed cases vs Deaths per population?

Recently, in a popular interview to President Trump: https://www.youtube.com/watch?v=zaaTZkqsaxY there was a discussion about the interpretation and relevance of: Number of deaths per confirmed cases ...
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0answers
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How to set break values for a cross-basis function in R's DLNM package?

I am using distributed lag non-linear model in R for a time series data. I am forming a crossbasis matrix using following script: ...
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0answers
9 views

How to choose the equally spaced values for temperature variable in R? [closed]

I am learning a distributed lag non-linear model. In that, I have to create a cross basis matrix first. For cross-basis, I need to specify the knots at equally spaced values of the temperature ...
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0answers
41 views

How to set a Richards model for epidemiology?

I have read in several papers that the Richards equation is one of the most popular choices to model epidemiologic data. I translated the equation in R's terms: ...
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0answers
16 views

Model discrete event simulation for cancer natural hostory

I am designing a programme in R to simulate two events that are 1. person get cancer or 2. die of other causes. I have data for the probability of getting cancer by age and probability of death due to ...
0
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2answers
42 views

How to calculate 14-day trends in COVID-19 infections and deaths in US States?

I'm trying to calculate 14-day trends in COVID-19 infections and deaths (as shown on the NYTimes homepage). I want to do this on a state level and have access to each state's population and daily data ...
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2answers
107 views

Understanding Medical Testing

While reading a textbook on probability I came across a question: There is a probability that a certain percentage of the population has a disease. Then a test for this disease could have a certain ...
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1answer
21 views

What is the relation between force of infection and infection rate?

There are different models to define the SIRD/SEIRD models of infection, for instance in one manual: dS/dt = S - (α/N)SI where S...
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0answers
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Panel data analysis

I am working with longitudinal data. Participants attended annual study visits. Both the predictor and outcome were measured multiple times and are continuous and normally distributed. Additionally, ...
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0answers
28 views

How is the reproductive number R being calculated?

The reproductive number $R(t)$ quantifies the expected number of secondary infections caused by an infected individual at time $t$. Thus, an R number below 1 will be likely to stop a disease like ...
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0answers
24 views

How to “convert” deterministic model to stochastic?

Hello dear forum members, I am seeking your feedback on the question that I have limited knowledge about (i.e., stochastic modeling). Say, I am working with a variant of a standard epidemiological ...
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0answers
30 views

Am I interpreting predicted Poisson regression correctly?

I have a dataset with time to outcome (t3) and the outcome (mmop_num) plotted by Poisson regression using the predict() function in R. (1) Am I correctly interpreting the y-axis as the likelihood of ...
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0answers
14 views

How to relate R0 to force of infection in epidemiology?

modelling of infection is based on the differential equation d/dt S(t+1) = S(t) - λS(t) where S is the number of susceptible and ...
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1answer
85 views

Fixing convergence in SIR model using modified fit-model to fit COVID-19 data

I'm trying to model the data for covid-19 using SIR model in R. I followed the answer of the question, and the blog. I'm using the suggested code, However, the data does not converging. Any suggestion ...
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1answer
682 views

COVID in Germany, LOO-CV for time series

The paper in Science [1] infers change points in COVID spread in Germany. The authors fit the number of daily cases assuming one (red), two (orange), and three (green) change points. Every change ...
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6answers
7k views

A chart of daily cases of COVID-19 in a Russian region looks suspiciously level to me - is this so from the statistics viewpoint?

Below is a daily chart of newly-detected COVID infections in Krasnodar Krai, a region of Russia, from April 29 to May 19. The population of the region is 5.5 million people. I read about it and ...
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0answers
15 views

How to estimate epidemiologic parameters directly from epidemic data?

Is it possible to estimate the parameters needed for an epidemic modelling directly from life tables with numbers of incidence or do these need to be calculated experimentally? IN other words: the ...
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0answers
10 views

How to compare the similarity of two time-series “loosely” in order to “ignore” temporal shift and scale difference?

I am new to time-series but here is the challenging problem I need to solve. I've created an agent-based model that can model infectious disease transmission and outcomes (such as tracking the number ...
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1answer
32 views

Can someone explain as simply as possible why you use OR in retrospective studies while using RR in prospective studies?

I've really tried to understand why you can't use RR in retrospective studies but for some reason I can't understand it. Has anyone been able to convey this simply to their students?
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1answer
89 views

Poisson regression for modeling standardized mortality ratio (SMR)

I have a data set with individuals with a certain diagnosis who are observed from the time of their diagnosis until death or the end date of the study. I want to calculate SMR for the whole group, and ...
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0answers
61 views

Parameter Estimation for the SIRD model via Kalman Filter (Part II)

0 Introduction This is my fourth attempt to tune a good prediction SIRD model for the COVID-19 outbreak here in Italy. The model in question is the following: $$\tag{29}\begin{cases} S_{t}&=S_{t-1}...
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0answers
11 views

For retrospective analysis, inclusion and exclusion criteria can be used in it?

I have read some articles, and some scholars believe that the inclusion criteria and exclusion criteria are specific terms for prospective research. If they are used in retrospective analysis, it is ...
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0answers
7 views

What MV analysis to use when examining relationship positive ID (dependent variable) and varied number of instances of the independent variable (B)

What is the best epidemiological multivariate analysis to use when examining relationship between dependent (A) variable and independent variable (B) (tests), when each patient had a different number ...
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1answer
307 views

Understanding the relationship between R0, doubling time, and the epidemic curve

New to infectious disease epidemiology here and am just trying to understand some basics. I've read basic texts on SIR esque compartmental models. However, I'm struggling to understand how to align ...

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