Questions tagged [epidemiology]

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

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References regarding epidemic modeling [closed]

Please, could you provide any references (books, journals or articles) regarding: Mathematical epidemic modeling. Frecuentist epidemic modeling. Bayesian epidemic modeling. A comparison between them (...
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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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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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COVID in Germany, LOO-CV for time series

The recent paper in Science [1, 2] 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 ...
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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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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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Why for some countries in the John Hopkins data the COVID-19 cumulative cases diminish over time? [closed]

I am kind of confused about the global time series data available at John Hopkins repository. If I understand correctly, the data there is meant to be cumulative cases over time so I was expecting a ...
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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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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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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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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-...
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Risk ratio for multiple outcomes model

I was wondering if there is a way to calculate risk ratios for multiple outcomes in R using a modeling approach that allows me to adjust for confounders. Using a binary outcome approach, I have: <...
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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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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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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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Death adjusted recovery rate

Let the recovery rate from an infection be $\gamma$ per day ie. the length of infected period is 1/$\gamma$ days Let the death rate of a person be $\beta$ per day ie. the lifetime of a person is 1/$\...
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What's the correct regression model for a contagious disease like COVID-19?

I'm examining how COVID-19 has struck different states asymmetrically, with some in the early stages of growth and others in which the number of daily cases is now coming down. Here's what the ...
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Using different nodes in a networked Compartmental Model (SIR) for different regimes?

I'm trying to model COVID-19 in New York, and in particular to model the death rate in light of the pre- and post-NY-On-Pause regimes. So I essentially have two SIR models running in parallel: one ...
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If number of infected people grow exponentially, is R0(basic reproduction number) the coefficient in exponential function?

I am trying to learn basic reproduction number and have a very basic question. In a given time window, If number of infected people grows exponentially, for example $N_{d+1}=1.15N_{d}$ Can we say ...
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Nearcasting disease spread: Why assume +1 immunized person per unit time?

I wouldn't normally consider the Stats SE to be the best place for this question, but neither the Medical Sciences SE nor the Biology SE seems to focus on macroscopic modelling, while this SE seems to ...
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1answer
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Parameter Estimation for the SIRD model via Kalman Filter (Part I)

0 Introduction This is my third attempt in tuning a good prediction SIRD model for the COVID-19 outbreak. The model in question is the following: $$\tag{12}\begin{cases} S_{t}&=S_{t-1}-\alpha\...
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What are the consequences of using year of birth, rather than age, as a covariate in logistic regression?

Would this affect the estimates of other effects in the model? Would it affect the estimated impact of age/YOB? I have a cohort but since they are all recruited at different times, I don't know which ...
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Use of probabilistic sensitivity analysis in determining incidence over time

I'm plotting incidence (y, per 10,000 population) over time (x, years) using results from a simulation model. And seeing when the incidence reaches below a certain incidence target (1/10,000). It was ...
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How do the units of the SIR model cancel out?

I was having trouble trying to understand the parameters of the simplest SIR model. If beta is the effective contact rate and s is the percentage of people who are susceptible, then how do the units ...
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How to define the “R” in SIR model - removed or recovered?

I have been trying to learn more about the SIR model since hearing about it due to recent events. In the process, I have heard various contradictory things. So I am ...
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Emergency Use Auth (EUA) for SARS-CoV-2 Tests

Problem: After the EUA for SARS-CoV-2 tests, we have a diagnostic test that passes both of the following criteria: All first five true-negative samples each produce a negative test result. All ...
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How to calculate the doubling rate for infections?

I'm playing with the JHU nCOV data and looking to calculate the doubling rate in my region (Western Australia) - I can get it down to an integer value via a kind of brute force (halve the current case ...
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SIR model parameter estimation in R

searched on google about the sir model in r and I came up with the following code. ...
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How many tests should we do to estimate the percentage of people who contracted COVID-19 in Lombardy?

Lombardy, a region of Italy, registered many severe cases of COVID-19 in the last few months. Unfortunately the available data don't allow us to estimate the percentage ...
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How is the gamma distribution used in the model developed by the Imperial College COVID-19 Response Team?

The Imperial College COVID-19 Response Team report mentions, "Individual infectiousness is assumed to be variable, described by a gamma distribution with mean 1 and shape parameter 0.25." With that ...
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Detailed description/scripts of mathematical models for Coronavirus

Pretty much the title, I am looking for some more in-depth explanation of the models used in the papers from Imperial College and The Lancet. In the second one, they are using something called a ...
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Calculating amount of infected in the background population?

I'm wondering if there's a method to calculate/predict the amount of infected in the population, knowing the R0, amounts of currently tested positive, amount of deaths, sensitivity of tests, ...
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How to correctly analyze fatality rate and daily deaths of Chinese and Italian COVID-19 outbreak?

This is a strange case of difference in fatality rate between Chinese and Italian covid-19 outbreak. In my knowledge, fatality rate is a ratio between deaths from a certain disease compared to the ...
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How could one (tentatively) estimate the actual number of COVID-19 infections in an area, using hard data like age-adjusted death rate?

A big problem with the current COVID-19 epidemic is the difficulty of getting tested (due to mild symptoms and lack of testing kits). This makes it impossible for patients with little or no symptoms ...
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Poisson Regression to estimate mortality

I am trying to estimate the rate of death for patients with epilepsy over a period of 13 years. I have the number of people known epileptics who died and all causes of death. This is the way I have ...
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1answer
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How can I update a disease prediction model with new treatment group data while maintaining the original causal relationships?

Context: I have a prediction model which predicts the probability of getting a disease. This prediction model has been created based on data of patients who did not get any form of treatment. I use ...
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Comparing Surveillance Positive Cases' Demographics

I am examining surveillance data of two diseases. I have frequencies of demographics such as age, sex, race/ethnicity and would like to compare the rates of these demographics between the two diseases....
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How do you calculate a paired risk ratio and its confidence interval?

I have some data showing the number of times individuals make GP appointments at the week and at the weekend, over a period of about 5 years. The data also show the number of times each individual ...
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Convenience sample equivalent of “prevalence”

EDIT: To clarify, my original (sleep-deprived) post: We used the term 'prevalence' to describe the proportion of patients with a certain characteric in a cross-sectional convenience sample. A ...
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Bayesian estimation of case fatality rate?

Let's say we're tracking a global epidemic, such as COVID-19, and we want to estimate the case fatality rate (CFR). The formula for CFR is just ...
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COVID-19: Do epidemiologists use censoring methods to calculate case fatality rates with undercount?

In case of the coronavirus COVID-19 (or 2019-nCoV), it seems that there are a lot of mild cases which do not require medical intervention, see here: For every person who is sick enough to come to ...
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Stochastic epidemic models with branching process

I am looking for an academic survey article that uses branching process in stochastic epidemic models. There are journal articles in epidemic and bio statistics that deal with specific transmittable ...
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Finding best conditional logistic regression model with unbalanced strata

I am interested in fitting the best possible model for the case of conditional logistic regression where the strata are unbalanced. Although I have not seen it specified, but I understand that there ...
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Coronavirus growth rate and its possibly spurious resemblance to vapor pressure model

I collected the latest data on the coronavirus from Johns Hopkins University as shown and fitted different curves to this data to model the relationship between the number of confirmed patients $P$ ...
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How to best characterize uncertainty for an incidence rate? [duplicate]

Here is the scenario I am trying to model. I have a population of people who are susceptible to developing a disease. I observe each person for a different amount of time, summing to a total of 3000 ...
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retrospective cohort study design - temporal cutoffs

I'm conducting a study examining the association between exposure to particular prescriptions and the odds of subsequently getting a disease (binary outcome). In my design, I have patients who get the ...
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What is the name of this design/model? (Age-period-duration, Lexis cells)

We have an observational study of the relationship between diabetes and cancer. In order to handle multiple time scales, we use Lexis cells as observational units, i.e. a row in our data set as ...
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Fitting SIR model with 2019-nCoV data doesn't conververge

I am trying to calculate the basic reproduction number $R_0$ of the new 2019-nCoV virus by fitting a SIR model to the current data. My code is based on https://arxiv.org/pdf/1605.01931.pdf, p. 11ff: <...
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The appropriate match ratio between case and controls: the obsession with 1:5 [duplicate]

My intention with this question is to collect relevant references or literature for a recurrent methodological approach commonly applied in health research. The main question is: what is the ...
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Inverse probability of treatment weights and linear mixed effects models

I am encountering a problem when using inverse probability of treatment weights with linear mixed-effects models for a difference-in-differences analysis. I have longitudinal data on participants. I ...

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