Questions tagged [biostatistics]

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

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14 views

Should Cohen's Kappa or simple percentage agreement be used in molecular assay validation with contrived samples?

I recently got some peer-review edits back on a manuscript validating a binary molecular detection assay protocol (accepted, subject to peer reviewers approval). One of the results was from an inter-...
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Accounting for unequal sample sizes - offset() code and which data to use

I have a set of data that contain two separate species placed in 4 habitat types. One of the species has 10 less organisms than the other for a particular habitat and I was hoping to account for the ...
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Combining the discovery and replication data sets to calculate final statistics?

I have a question about calculation and reporting of statistics combining data from replication studies. Our techniques don't involve ML, but ML techniques have me thinking about this. Often in ML ...
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Statistical test for pair-wise comparisons of 36 different counts

I have 36 different population types that vary in combinations of three parameters (s, g, d). g and g has 3 discreet variations (0.2, 0.8, 0.95 and 10, 100, 500 respectively) and d has 4 (1.0, 0, 0.1, ...
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Data Analysis help or suggestions? Water quality biostatistics high school research project, Lake Erie

I am looking for any advice or suggestions. So, I am a high school student, and I am taking AP Research. This is a class where we spend a year working on a research project, that is intended to be ...
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Is there a way to increase the number of predictor in a logistic regression when sample size is small?

One of the dependent variables in my dataset is a binomial variable indicating whether an invasive species has been eradicated (with $n_{1}$ = 23) or not (with $n_{0}$ = 75) after the use of a certain ...
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1answer
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Problem with a seemingly simple 2-way ANOVA

I want to test for the effects of two factors ('Habitat' and 'Population') on a continuous variable ('Trait'). I'm using R to call this seemingly simple 2-way ANOVA: ...
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Generating Error Data

I am currently doing a project on finding the HMM parameters for a channel which takes a DNA sequence as an input and aims to output the same sequence. However, the channel has insertion, deletion, ...
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Randomised or generalised block design?

sorry to ask a basic question, but I have not been super familiar with those types of experimental design yet and took over an already established experiment. Imagine those two set-ups: Three ...
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mouse experiment with different doses of the same drug

Assuming I am running an experiment in mice with a drug treatment at different doses I have been originally thinking that a Dunnett's Test is the right analysis to perform: compare each group against ...
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Correlation of X and Y, Log and transformation

I have two types of values that I need to look for association. It's basically genomic data for which we want to estimate scores (X) based on how much we have defined it (Y) W is a count and X is the ...
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What should i use lme or glm? (Biostatistics, diversity)

I am trying to work on the data of my master thesis. I have to create some model, but I am stuck due to my lack of knowledge in statistics (I am working on it). My data are 58 sample points each has ...
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Using a variable both as fixed and random effect? [duplicate]

We want to know whether leaf length depends on the amount of nutrients in the soil or by the family it originates from. We collected 10 seeds of the parent plant (i.e. the “family”) of which 5 are ...
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Benjamini-Hochberg FDR Correction using partially observed p-values

I am working on something called eQTL analysis. My result is extremely huge, there are about 28 million rows (with its corresponding p values) per dataset, and I have 10 dataset. I tried to do some ...
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Why do the standardized residuals of a general linear mixed model using transformed data show a negative slope? [duplicate]

My data is no. of individuals of a certain age-class in a group, and it is right skewed. When I did a general linear mixed model with the number of individuals in a group as a dependent variable and a ...
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Relating Temp / Size / Time to Mortality Rates from Catch and Release Fishing

I am conducting a fish catch and release mortality study and have hit a wall with the statistics portion of my report and could use a nudge in the right direction. I am trying to relate a few ...
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Multiple lines on graph/line going in multiple strange directions [migrated]

Hi I am trying to plot number of trips against number of sightings in the graph below ]1 This graph was produced with the following code; ...
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1answer
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When are ROC curves to compare imaging tests valid? (Focus on the example below)

I would like to ask what criticism could be raised in the following case example: In this paper they test a way of detecting narrowing of the cervical canal on radiographs using a ratio of ...
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using IQR as a scale for a continuous independent variable

I'm Trying to understand how associations between continuous exposures and health outcomes are typically reported. When reading studies that report on the relationship between air pollution or ...
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Options when model complexity and separation causes non-convergence in logistic regression

I have created an example data set here My data represent the presence/absence of a particular animal species (data$outcome) and measurements of trees. I would like ...
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annualised complication rate

I audited my clinical practice of ventriculo-peritoneal shunts. These can block any time after they have been inserted (you can assume they block randomly). I have audited my practice of 2 years and 7 ...
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1answer
20 views

How to calculate sample population with species of known probability

I have a sample of n=200,000 from 300 species. 8 species cover 80% of the samples. How can I calculate the right sample size such that each species has at least 1000 samples?
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Is this logistf approach the right way to deal with complete separation in my logistic regression?

I am performing lots of association tests between genotypes and binary diseases. The genotypes can be very rare, and my tests often have extreme case control imbalance (e.g. 500 controls for every ...
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How can I get the variances between groups from a PCA? Using R

I'm performing a selection test following Ackermann & Cheverud (2002) to find out whether the differences among my study groups are due to selection or drift. I don't know how to get the "...
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What test can I use use to compare variables over time for accidental records of a species?

I have records (presence) for an invasive species, from opportunistic data for 10 years, less than 10 records for each year. I have calculated distances form watercourses, % of land use in buffers and ...
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1answer
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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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Estimated survival functions for interaction terms in Aalen Model, Cox Ph Model, and Kaplan Meier

I have this question: For each of the four interaction groups     (1)  no smoking, no alcohol,     (2)  smoking, no alcohol,     (3)  no smoking, alcohol,     (4)  smoking, alcohol – produce plots of ...
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1answer
41 views

Why are we interested in proportion?

In (bio)statistics, sometimes I see that the proportion is of interest. I am looking for justification, why we do that. For example, in this article, "key secondary end points were the proportion ...
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1answer
34 views

Response distribution for GLM when variable is real number between 0 and 1

I am trying to fit a mixed model with a fixed and a random component in Matlab. My response variable is a real number that can only be between 0 and 1. The data is left-skewed, meaning that many ...
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1answer
83 views

Using Chi-squared test when perfect separation in logistic model?

My dataset is similar to this; it describes the presence/absence of a parasite in six species of animal from two locations. Each row in the dataset represents a different individual animal. I would ...
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1answer
31 views

Would it be appropriate with a Chi-2 test in this case?

First of all, thank you for such a warm welcome to this forum. I am doing a study to see what diagnoses are the most common in a specific group (1) compared to another group (2). I want to show that ...
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How can I quantify the difference in the correlation between two variables in two data sets?

I am working on a regression equation trying to predict the weight of various species based on body measurements. I am doing this by log transforming both weight and body measurements and regressing ...
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Plot aggregated species on RDA (redundancy analysis)

I have a microbial dataset that has different hierarchical levels of phylogeny (e.g. 3 phyla --> 10 genus --> 50 species). I want to do a RDA (redundancy analysis) using the lowest hierarchical ...
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1answer
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Can you use ANOVA to compare two models that are not nested?

Is it possible to use ANOVA to compare to non-nested models that have the same response variable? If not, what is the best way to compare non-nested models that have the same response variable?
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1answer
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ANOVA or multiple t tests?

My experiment involves adding different compounds to the same cell line and then comparing it to the control to see if there's any difference. I am under the impression that ANOVA is used when the ...
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1answer
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Avoid trial field test using previous data: use of chi-squared test to show that carcass removal do not change significantly over time

I am implicated on the analysis of mortality rates of bats and birds in wind farms. For this purpose, I need to go to the field and count the number of carcasses found around the turbines. However, ...
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1answer
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Which test should I use for non-normal dataset with lots of zero values

I'm trying to do a before and after analysis. The dataset consists of bat passes in 2011 before a wind farm was built and again in 2012 after the wind farm was built. The data is paired and consists ...
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What statistical analysis do I use for two independent groups over time?

I am running a hypothetical experiment with a control and treatment group, taking samples from each group every day for 50 days. The control group and the treatment group are independent. What type of ...
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1answer
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Bayesian fitting of a nonlinear model [closed]

Some years ago I developed a nonlinear model and java fitting engine that performs well enough to be useful, but is definitely a hack. I would like to modernize and publish an open-source tool (...
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how to interpret the contribution of a variable, when univariate vs multivariate analysis result differs (survival analysis) [duplicate]

Not well versed in statistics so I do not know if my question is limited to survival analysis or has a general solution to similar types of questions. I saw a clinical trial study demonstrating that ...
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How to compare community diversity of longitudinal and independent samples?

We are wanting to compare the diversity of biofouling species on longitudinal and independent samples. The first set of samples is repeated measures data, as we measured percent cover of species on ...
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1answer
113 views

Confidence interval true/false questions

A sprinkler system is being installed in a large office complex. Based on a series of test runs, a 99% confidence interval for the population mean $\mu$, the average activation time of the sprinkler ...
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1answer
27 views

Analysis for a design with variation among and within trees

I'm planning an experiment that involves sampling insects from four trees along each of five streets (each street being an experimental site). My focal tree species has distinct male and female ...
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Comparison of variances with multiple factors using fligner kileen test

Hope my question fits in here and I have described everything well enough. Somehow I cant quite get my head around it. I have a data set with pesticide residue data in flowers, which had been obtained ...
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How to include phylogeny in GLMM? (not community ecology)

I have a dataset derived from a multi-species experiment that I carried out. I have 30 different plant species from several families and 3 geographical groups. I applied 6 different treatments to 5 ...
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Can I use `Y ~ X + X:Z` when `Z` does not follow a linear relationship with `Y`?

General case I want to model the relationship between Y and X, but I am also interested in knowing if this relationship changes ...
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1answer
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Am I to calculate the 95% confidence interval in this question?

MI5 has finally decided that 007 doesn't have to be a man but they still need to be British and shorter than 175.3 cm. The average height of all British citizens is 160 cm and the standard deviation ...
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1answer
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Is it valid to use rank data with a general linear model?

I have electrophysiological data in the form of skin resistance in fish. I wish to explore if there is any variation in resistance based on the location on the body where the skin is taken from. In ...
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What is a reasonable method for two sample test on cut-off measurements?

This is a question regarding biostatistics. I am digging into some statistical analysis with SingleCellSignalR, which is a tool to predict cellular interaction with single-cell RNA-seq data. I was ...
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Do I need to balance my data when I am using a logistic regression model for statistical inference and not prediction?

I am looking into how various features affect an outcome using a logistic regression model. I do not care about prediction right now. My dataset is imbalanced where class 0 accounts for 88% of the ...

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