Questions tagged [biostatistics]

The science of statistics applied to the analysis of biological or medical data.

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No previous information in a clinical trial

I'm conducting a clinical trial with a treatment group and a placebo group and calculated the sample size based on a previous study. However, I would like to add two more new placebo groups with ...
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Calculate sample size for clinical trial without raw data

Usually, we calculate the sample size needed for a clinical trial based on a former clinical trial which shows there is a significant effect. What if there is no such a trial? What if there is no ...
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I have a group that contains zero data, and I want to know whether it is considered normally or not normally distributed.?

I have a group (group2) that contains zero data, and I want to know whether it is considered normal or not normally distributed. I used the SPSS software, and it showed this result. I also tried R, ...
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How to fit parametric distribution to baseline hazard in cox PH model

I develop Cox PH model with time-varying covariates to predict marginal probability of some event. The time frequency is measured in months and I have observations since 3 months to more than 160 ...
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Compare variance across time

I have an analysis question. Unfortunately my biostats collaborator is no longer involved in the project. We have a dataset of n=6 people. the study was terminated early due to covid but we are still ...
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Sex, Dose, and Repeated Measures Analysis

I am testing the hypothesis that male and female have a different timeline of withdrawal behavior, such that either males or females experience greater withdrawal symptoms from morphine across 12-24-...
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Are these data pseudoreplicated?

I have an amalgamation of independently collected datasets covering a large area of ocean where surveys to count birds have occurred sporadically over a long time. Some surveys were from boat, some ...
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What kind of analysis can I extract from bayes glm output?

I have 40 files (40 variables) that start like this from a bayes glm model output as csv files. I am a total beginner at model evaluation. ...
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2 votes
1 answer
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Estimating separate smooths for a factor with hundreds of levels using GAMs

I am fitting a smooth-factor interaction term to a longitudinal microbiome abundance data set using GAMs. ...
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MANOVA invalid type (list) for variable R studio [closed]

I have dataframe contain 600 columns and 50 row and i want to perrform MANOVA i tried the following code ...
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How can I adjust cumulative entropy of moose observations?

I have downloaded the dates of every moose (Alces alces) observation worldwide on iNaturalist. This amounts to about $2 \cdot 10^4$ observations at present. I excluded one observation that was either ...
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Combining Biological Replicates

I am doing an experiment where I track the behavior of larval zebrafish of 3 genotypes during a photomotor assay. The larvae are a result of a heterozygous cross, so following the experiment I ...
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Mathematic modelling vs. machine learning

As a biologist with some background in mathematics I am really interested in mathematical modelling of biological processes, like tumor development or therapy responses. However, looking at recent ...
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How to fit a Dirichlet mixed effect model in R?

I have a compositional data from an arena experiment in which the duration of an animal in specific zones was denoted. The time in the arena was fixed for all individuals which makes the durations ...
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1 answer
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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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1 answer
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Statistical test for PCR and bacterial culture with two different testing methods

I have previously used McNemar's test to compare PCR and bacterial culture using the same sample. I now have two different samples from the same patient taken from tonsills and quincy. So I now have 4 ...
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1 vote
1 answer
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Testing whether replicate number has an effect on outcome

I have four biological (independent) replicates in each of my experimental conditions. There is a potential issue with our equipment - it's possible that the first replicate for each condition is ...
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Questions the calculation of Z score and confidence intervals in biology

In biology, especially in some screening assays, people love to calculate a Z score between positive and negative controls. Essentially a distance calculation using the mean and sd to calculate how ...
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Correlations significant at individual level, but not at group level?

For my research I have to do correlation tests to see how different measures of animal welfare are related to each other. When i run the test using the data at individual level, it shows a weak ...
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Survival analysis on plant population data over time

I am a researcher at Kew Gardens looking to analyse survival data on populations of reintroduced Green Winged Orchids to sites in Cumbria. I want to statistically analyse the different survivals of ...
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Using multiple mean tests instead of linear model

First, I would like to apologize because I'm a beginner in statistics and I'm surely confused on some points. This is one of my first statistic work doing for university. I would like to explain a ...
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34 votes
10 answers
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The moose must flow, but how?

Background Suppose I collected a data set of the latitude and longitude of moose tracks within an irregular polygon, and also took a compass bearing of the direction that the hooves pointed in. Image ...
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1 vote
1 answer
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Multiple Comparisons Testing for Univariate Analysis of Metabolomics Data

I have an untargeted metabolomics dataset, where samples were collected over 4 timepoints (not repeated measures) from two groups of patients: A) patients treated with placebo B) patients treated ...
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Should I transform numerical variables to categorical variables in GLM?

I'm building a GLM with couple of variables and I have a problem with how to organize my data. I have both numerical and categorical data and I'm struggling as to how should I structure 3 variables. I ...
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Treatment: Mean AND variance should be optimized. What test to use/how to use (for instance t-test)?

Assume a research on the effect of applying a treatment to improve health by normalizing level of some vitamins in the bodies of some people. We measure initially the level of the vitamin of sick ...
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1 answer
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Distribution of Residuals and Response - When to use which?

I would like to analysze the relation between my continuous response 'soil moisture content [%]' and 2 categorical and 1 continuous predictors. I fit a linear mixed model and checked the distribution ...
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Which statistical test to use for 3-choice bioassay?

I have a bioassay containing 3 different treatments. A single individual is allowed to choose between the 3 choices and their choice is recorded. This test is perform 30 times, each with a different ...
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1 answer
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How to compare before and after evolutions of a binary variable between two groups of treatment

Here is what look like my data ...
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1 vote
1 answer
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Welch's t test vs Mann-Whitney for very unequal groups

I have two vastly unequal groups (n1=18 and n2=400), and want to test mean differences between the groups for some 700 parameters (more specifically, RNA expression levels for 700 genes). While I ...
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5 votes
1 answer
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Motivating use of Bayesian splines in excess mortality estimation

I'm reading this paper estimating excess deaths induced by the pandemic. That is, roughly, it constructs a model to estimate how many deaths (from all causes) would have occurred if the pandemic had ...
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1 vote
1 answer
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How to form the hypothesis and which statistical test to use when we have before-after data of two individual groups?

So basically I have medical data where the data is collected from two different treatment groups and various variables are measured for individuals in the two groups. Data was measured before, during, ...
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3 votes
1 answer
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Comparing percentages from different sample sizes

We have questions about how to run statistical tests for comparing percentages derived from very different sample sizes. Specifically, we would like to compare the % of wildtype vs knockout cells that ...
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Anosim vs Permanova: What are their suitability when computing differences between groups?

I am back with more questions, this time about multivariate analysis. As before I am new to this all so apologies in advance if the question is not well formulated. The problem We are trying to ...
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SEM in Lavaan in favor of comparison

I am struggling with properly applying the lavaan package in R to estimate the latent variables and their relationships with the observed variables in my data ...
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Longitudinal analysis with different baseline value for the groups

We have four mice groups and each mouse had to find a platform in a pool in this experiment. On D14 (the first day) they did this task for the first time and the latency to the platform (time to find ...
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Account for different amount of observations per participants without using a regression approach?

I am trying to figure out the statistics of a study where I have 60 participants with varying amounts of observations per participant. I am measuring facial muscle activity after a button press over a ...
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1 vote
1 answer
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How to deal with bias caused by data collected with different methods on a GLM?

I have two datasets from different years (2020 and 2021) that I needed to merge because my sample was too small. I'm investigating which morphological features (sex, age, weight, fat reserves and ...
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3 votes
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Is inference about interior bear population from observation boundary an un"bear"able estimation problem?

The following map shows a density-coloured grid of observations of American black bear reported on iNaturalist. In the top half of the province you can see a loose boundary of observations around an ...
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4 votes
1 answer
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Should I use a two-tailed t-test to generate p-values?

I have a data set similar to the one below. The real data set has 89 values in each column. I'm looking at the expression of RNA between two different treatments (treatment $X$ and treatment $Y$). <...
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2 votes
1 answer
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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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Confidence interval for difference of means

Doing exercise on Bioequivalence Study, taking data from here. Model defined as $\log Y_{i,j,k} = \mu + s_{i,k} + \pi_j + \tau_{[i=j]} + \lambda_{[j=2]\cdot(1+[i=1])} + \varepsilon_{i,j,k}$, where $\...
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Should I use GLMM or GAM in my analysis?

I am analyzing data on polar bears and trying to figure out if different variables influence their movement. My data has a mix of categorical (e.g. bear ID number) and numerical variables (e.g. bear ...
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1 answer
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Validity of external cross validation using data generated by the fit model?

Context: A paper I'm reading uses PDEs to characterise the effects of cancer treatments on the tumour microenvironment. The exact wording used in the paper is: The predictive power of the [...
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1 vote
1 answer
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What do the % variances mean on a Bray curtis dissimilarity plot?

I'm new to microbiome data analysis but what do the percentages on the Axis mean? This plot is comparing two groups (SPF n=8 and ABX n= 4 mice). I can't figure out what these mean. I thought the axis ...
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Interpreting output of models with categorical variables in R

I have a data set that contains coral reef data- count of fish (C_TOTAL), the habitat complexity measurement rugosity (RUGOSITY), and the area of the reef that the data was collected at (ZONE- 5 ...
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1 vote
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How to correct for unequal sample size per group in neg. binomial regression

My data contains information on the time, location, and present conditions of a fish catch. The problem we often have in the field is that not all locations can be consistently visited every time. ...
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1 vote
1 answer
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Inflated or not inflated: true zero dilemma in GLMM

I have the models with overdispersion and almost 40% of the data set are true zeros with biological meaning. I'd like to study the temperature (temp) and time ...
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1 vote
1 answer
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one-sample t-test on zero variance sample

I have to compare many gene-expression values between a group of 3 patients and a control patient. I choose to apply the one sample t-test (ttest_1samp from python <...
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Statistical Analysis on R with Count/Observation Data, multiple explanatory variables [duplicate]

I am running an analysis using R to determine if boat activity impacted shark residence times. I have observation data that includes number of observations within ONE observation event (e.g. number of ...
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Multiple mice (subjects) grouped by genotype (condition) with multiple measurements per mouse

I am trying to analyze fertility data for a cohort of mice with several different genotypes and I am stumped. 3 mice have genotype A, 3 have genotype B, and so on. Each mouse has several litters over ...
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