Questions tagged [biostatistics]
The science of statistics applied to the analysis of biological or medical data.
624
questions
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40 views
Are mixed model results valid when several missing replicates?
I want to know if it is correct to take as valid the results of a mixed model (lme) test for a triple factor experiment with several missing replicates in only one level factor situation.
My ...
0
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0answers
22 views
Negative Binomial GLM confusing effect on p value of model by changing theta
I am interested in generating a p-value for two small groups of count based data that I believe to show overdispersion. The groups are for example:
...
0
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0answers
11 views
How to correlate multiple time series data for medical data?
First of all, I apologise if the question seems stupid as my knowledge in time series is not very good.
I am working on a university project and the next step is to find the correlation between 1) and ...
3
votes
1answer
95 views
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 ...
-1
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0answers
43 views
Cost effectiveness in RStudio [closed]
I would like to perform a cost effectiveness study in which I would like to compare 3 diagnostic methods:
golden standard (diagnostic surgery): cost 3000€, sensitivity 100%, specificity 100%.
...
1
vote
0answers
29 views
How to analyse temporal variation in R---vigilance of birds
I am currently doing a project for my Bachelor degree, for which I study vigilance in birds. Obviously, I have to analyse the data statistically. However, I do not know where to begin since I do not ...
0
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1answer
13 views
How to plot a heat map by giving scaling the color for row-wise?
I have a selected data table for DEG and interested in plotting a heatmap by using a color gradient row-wise (without scaling or normalizing the data).
Giving a color key for the whole data set is ...
1
vote
2answers
20 views
How can I calculate correlations between fungi presence and forest health in two different forest sites?
I am working on an undergraduate thesis and I have extremely little knowledge on statistics so my analysis is going to have to be quite basic. In two different forest ecosystems (plantation and mature)...
0
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0answers
15 views
Analysis of very skewed RNA expression data
Recently, I've been trying to analyse sc-RNA sequencing data from the Allen brain institute (available on: https://portal.brain-map.org/atlases-and-data/rnaseq). However, since data analysis and ...
1
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1answer
22 views
Principle Component Analysis for pre-grouped variables
I have a dataset that has many overlapping factors related groups of factors, and factors that we would like to investigate if there is a relationship. 57 measured factors total, in 50 individuals (...
0
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0answers
9 views
Rescaling weights based on data-subsets of different analyses, is it statistically allowed?
I am running an analysis in R on the effect of canopy cover (OverheadCover) and the number of carcasses placed on the same location (...
0
votes
1answer
19 views
What is an appropriate transformation for the response variable “size”?
I plan to implement a hierarchical Bayesian model in an MCMC algorithm for a side project that I am working on.
I need to use Gaussian likelihood and priors for vector $\boldsymbol{\beta}$. I am ...
0
votes
1answer
25 views
Difference in differences without a control group
I am interested in learning how to do a difference in differences without a control group using SAS.
In my data, everyone has been affected by the exposure (policy change), is it even possible to do ...
1
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0answers
45 views
Odds Ratio vs. Probability? [duplicate]
I have a question about odds ratios vs. probabilities in terms of a contingency table (studying an exposure/disease). I know that once I have found an odds ratio, I can also find the probability by ...
0
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0answers
11 views
Should I use a random effects model or a sandwich estimator to adjust for inter site variability?
I am looking at the association between community (as defined by zip code of a health clinic) and hospitalization rate. I am afraid that if I used a random effects estimator for each clinic, that ...
0
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0answers
12 views
Statistical method for estimation of Penetrance
I was thinking on a problem: there is a rare disease, associated with some ultra-rare genomic variant (which means ~ 1 out of millions), and there are estimations of penetrance (how many individuals ...
0
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0answers
16 views
lunar phase influence on animal abudance in stomach content of predator species
I have a set of data presenting the abundance of prey in the stomach of one predator species. each predator was identified with an ID number and date was recorded among other info. The date was used ...
0
votes
1answer
42 views
Binomial & numerical variables as dependent and independent + random variable
I am new to statistics and trying to figure out how to analyze my data correctly. I completed a biological study with the following variables:
(I have converted my binary variables to 1 and 0)
-Type ...
0
votes
1answer
56 views
GLMM with presence/absence dataset
I want to know if a treatment effectively reduces the abundance of a particular species in some location. For that, I trapped the animals and identified each individual captured, releasing the animals ...
1
vote
0answers
24 views
Linear regression to model the association between microbiome composition and a health outcome? [closed]
I have stool samples assess at time 1 (T1) and a continuous health outcome measure assessed at time 2 (T2). Is regression the best method to assess the association between these two variables? Note ...
2
votes
1answer
26 views
How to select best feature set?
I am currently using feature selection approaches like filter, wrapper, embedded etc.
All these methods give different set of features and I rank them based on their frequency of occurrence in other ...
1
vote
1answer
32 views
mutual information for testing set enrichment?
I've created a process that associates members of two sets, specifically codes from the International Classification of Diseases (ICD) hierarchy and the semantically richer Monarch Disease Ontology (...
0
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0answers
38 views
Interpreting results of resemblance-based permutation methods: PERMANOVA and PERMDISP?
I am working with an invertebrate data set (i.e., counts of individuals per invertebrate order, captured by pitfall trap) and am exploring trends in community composition in relation to environmental ...
1
vote
1answer
24 views
Poisson regression for # of acute toxicities as outcome variable?
I have a data set of N=200 comprised of patients who either received Treatment A (N=50) or Treatment B (N=150). I have treatment toxicity outcomes (binary yes or no) across 4 domains: hematologic, ...
1
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0answers
19 views
Interaction effect and collinearity: important or not? Influence of precipitation on foraging behavior?
I am facing a pretty straightforward case. I wish to test whether precipitation, represented as interaction effect between two numerical variables (number of strong showers x highest rainfall recorded ...
1
vote
2answers
54 views
Problem with non-normal residuals (lmer function)
I work with animal personality and I am trying to analyze individual differences in response to certain stimuli.
Taking this particular dataset as an example, I am analyzing how much distance ...
1
vote
1answer
33 views
Plot of probability of 1-year survival event vs. variable value? Would be derived from a Cox model
I am hoping to plot the probability of a patient surviving to 1 year without progression (status==0) vs. the value of a continuous variable (...
0
votes
1answer
25 views
How to calculate the sample size for a categorical independent variable with a dichotomous dependent variable
Suppose that in a large population group you have 5 different ethnic groups, and you wish to calculate the prevalence of a disease in each ethnicity(percentage of people in each ethnic group having ...
2
votes
1answer
178 views
How can I know if two distributions have the same mean and standard deviation?
I have some cells which fluorescence and I can detect their fluorescence. So for each cell I get a number N that says how much light it emitted.
I also have two ...
0
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0answers
18 views
Combining datasets when working with PCA
I'm largely a statistics novice, and I've gotten into a discussion with my lab mate about the application of PCA.
Previously I've applied PCA only to a uniform dataset (results from cells all ...
1
vote
1answer
57 views
How to perform multiple tests of contingency tables with more power: Fisher's / Barnard's test vs Logistic regression
I have a sample of answers to Yes / No questions:
\begin{array} {c | c c c c}
\hline
\text{Case} & X_1 & X_2 & X_3 & X_4 \\
\hline
1 & 1 & 1 & 1 & 1 \\
2 & 0 & ...
2
votes
1answer
59 views
How to compare nonlinear regression vs piecewise linear regression?
We have time series of plant growth (length vs time) and we can reasonably model these with two approaches:
With a nonlinear model length(time)=length0*exp(r*time) where length0 is lenght at initial ...
0
votes
1answer
27 views
Would “correcting” for patient characteristic in a cohort study always strengthen the study?
If we are doing a cohort study and investigating whether a variable has an effect on an outcome (say tumor size on nausea), and we run a regression (or chi2) with nausea as a dependent variable and ...
0
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0answers
28 views
p-value in restricted cubic splines regression
How to calculate the p for overall and p for nonlinearity for a RCS model in STATA?
Like what they did in this picture.
4
votes
1answer
50 views
Mixed-effects modelling of mortality rates
I have a dataset with annual observations (1990-2016) on neonatal mortality rates (dependent variable) for countries 1, 2, 3, 4, 5, and 6. The independent variables are indicators 1, 2, 3, 4, and 5. ...
0
votes
1answer
39 views
What ANOVA test to use?
I'm doing a study on whether 2 groups of physicians: radiologists and oncologists differ in the volume of their contours. Each group has 3 participating physicians and all physicians contour a ...
0
votes
2answers
98 views
Is there a method to look for significant difference between two linear regression lines
I have two data sets, Fladen A and Fladen B. These are two locations in the North Sea. For each dataset, I have both Age and Height data for a marine mollusk. I have plotted and produced a linear ...
2
votes
0answers
40 views
Survival Analysis and multiple observations
I am currently conducting a survival analysis for the first time and I am finding the conceptual aspects of the analysis a bit tricky. I have a hospitalization dataset that spans over a 20 year period ...
1
vote
2answers
25 views
What exactly is critical value in statistics? I confuse it with p-value and always get it wrong [duplicate]
I learnt that a p-value lower than the alpha value of 0.05 leads us to reject the null hypothesis and vice versa. It seems to be the opposite for critical values. What then, is this critical value - ...
0
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0answers
19 views
How to sample pairs in order to create a significant result
I develop a similarity function for genes in general. I would like to find the correlation of the similarity values of the developed function to a ground truth. For the ground truth, I use a model ...
0
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0answers
11 views
How can I predict the total number of cell with Poisson process
I detected cells in circulation with our own system, the cell is very rare compared to other blood cells, I acquired the temporal information of each cell and calculated intervals between 2 cells. The ...
1
vote
1answer
51 views
Generation of pseudo-absences with R Biomod2
I have started working in species distribution and I'm not at ease on the subject yet. I'm using biomod2 package in R, with several rasters to apply to species with ...
0
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0answers
13 views
What is Importance Value?
I am reading this paper that talks about Principle Components analysis and Importance Values(IV) here
Is this Importance Value a statistical concept? I could not find any information about it in ...
1
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0answers
49 views
Differences between cumulative link models (ordinal) and multinom (nnet) for fitting multinomial data
I'm trying to understand cumulative link models and how they differ from multinom models in R. Here's a simple example of a multinom model and plot output using the nnet package:
...
0
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0answers
22 views
How to determine degrees of freedom for regression when not all observations are independent?
I'm trying to determine the degrees of freedom for my dataset. (Purpose: to determine the confidence interval for the slope of the regression line.)
The problem is, the explanations of degrees of ...
2
votes
1answer
159 views
Splitting of bimodal distribution, use in regression models
I have a bimodal length-frequency distribution for the females of a species with a one-year life span. This pattern is not observed in the males.
I suspect that the bimodality is due to different ...
1
vote
0answers
31 views
What is the probability of regex pattern occurrence in a string of length n?
I have a string of length n, composed of 20 characters of equal probability. What is chance of occurrence of a regular expression pattern, like 'WP[^WFHY]{5}W' by chance? In case you are not familiar ...
0
votes
1answer
52 views
Response is count and the first explanatory is binary second is continuous. Which GLM should I use?
So I've got a response variable with count data e.g. number of species found and two explanatory. The first is a treatment I did or did not applied -> Yes or No, so binary. My second explanatory would ...
0
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0answers
10 views
log values in coxph model?
I have a data frame of gene expression values (sequencing).
When I do CPM-normalization without doing log2, I get much "better" (lower) p-values compared to when I do log2-CPM. What is the ...
0
votes
1answer
34 views
Attirbutable risk from competing risks
There are a number of ways to estimate attributable risk fractions from Cox regression and logistic regression. Does anyone know how to estimate attributable risk from a competing risks regression ...
