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 define the lag range for prediction in a DLNM? [closed]
I use the dlnm package in r (distributed non-linear model) for a time-series analysis on the health effect of temperature. I specified in the crossbasis function (cb) 10 lags. Now, I want to plot the ...
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How can mortality rate of a cohort population be converted to a +/- number of months or years from average life expectancy?
How can mortality rate of a cohort population (eg: 65/1000 annually for those who smoke 1 pack per day) be converted to a plus or minus number of months or years from average life expectancy, as seen ...
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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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12 views
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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1answer
48 views
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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1answer
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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 ...
2
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1answer
48 views
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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23 views
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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14 views
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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1answer
36 views
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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How to determine “per” population size for incidence rate
I am reading notes for a given assignment and incidence rate is defined as
$$
\frac{new cases}{observed population} x 10^n
$$
The only thing that is confusing me is that what to use for ...
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1answer
38 views
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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2answers
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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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28 views
How to estimate prevalence with a zero incidence (rare disease)? [duplicate]
I had to solve the following problem.
Newborn screening has been implemented for a very rare pathology.
For 6 months, and out of 50,000 births observed, no sick case was observed.
What is the ...
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2answers
24 views
Is it ok to use volunteers for prospective cohort studies
Prospective cohorts are ones where the exposure is known but not the disease outcome.
Volunteer bias is where volunteers tend to be healthier.
I've been told because of this volunteer bias, we should ...
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1answer
26 views
Estimate recovered/infectious for SIR model
I like to fit a SIR model to COVID-19 data of UK. If i understood it correctly i need the numbers of I (infected) people (and not the reported case daily case data) which i would calculate as followed:...
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27 views
How do I incorporate clustering in a matched case-control analysis?
I am trying to analyze a 3:1 matched case control study (matched on age and date of medical encounter) but realized that there may be household clusters represented among cases and controls. Cases ...
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15 views
Calculating significance on incidence rates
This is my first time attempting a project like this so my question might be quite wordy.
I am analysing the trends in incidence of disease X on the population over 30 years. I have grouped the 30 ...
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685 views
A new strain of covid-19 is 70% more infectious/transmissible. What does that mean and how has it been estimated/measured? [closed]
70% in the media
https://www.dailymail.co.uk/news/article-9070683
Prime Minister Boris Johnson told a Downing Street briefing that early analysis showed the new strain could increase the reproductive ...
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3answers
582 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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22 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
54 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
27 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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2answers
624 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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1answer
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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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34 views
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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0answers
48 views
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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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 ...
2
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1answer
99 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
25 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
72 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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1answer
28 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 ...
3
votes
2answers
115 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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14 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
21 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
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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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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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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
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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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vote
1answer
108 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
108 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
52 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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votes
1answer
61 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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41 views
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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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
62 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 ...
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vote
2answers
72 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 ...
3
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2answers
120 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 ...
