Questions tagged [compositional-data]
Refers to variables representing fractions of a total, i.e. all lying in $[0,1]$ interval and necessarily summing to one. Analysis of such data is often called compositional data analysis.
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Any reasons I shouldn't calculate the difference between CLR transformed variables to analyze my data in a time-independent way?
First time posting, so apologies for any missing info and the like.
I have some microbiome data collected from two different treatment groups over two timepoints. I want to look at the compositional ...
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How to handle zeros before carrying out CLR transformation to deal with compositionality before Spearman correlation?
My data is very zero inflated - even when carrying out previous filtering, such as getting rid of data that has very low counts and have values in more than 60% of samples.
However, the 0 values still ...
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Can I transform the difference between two isometric log-ratio balances to interpret is as the ratio between two geometric means?
Suppose I have several compositions of 4 parts $A_i, B_i, C_i,$ and $D_i$ with $i = 1, \ldots , n$ taken from two locations ($X$ and $Y$), which are coordinates in the simplex $S^4$. I apply the ...
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How to model the additive components of a random variable whose value is known
I would like to model the variables $Y_1, Y_2, …, Y_n$, which satisfy the constraint $Y_1 + Y_2 + … + Y_n = Y$; where $Y$ (or at least an accurate estimate $\hat{Y}$ thereof) is readily available. ...
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Statistical analysis of compositional data - what test to use?
For one of my studies, I am playing with what seems to be a compositional data.
In short, I have some signal that I decompose in 4 frequency bands (B1 to B4) in a way that I get the relative ...
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How to use partial correlation on compositional (counts) data? (e.g., as described in Erb et al. 2020)
I've read through this paper: https://www.sciencedirect.com/science/article/pii/S2590197420300082
Which introduced me to the concept of partial correlation. I typically use Proportionality when ...
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Are there any compositional data models applicable to panel data?
I have a dataset spread across N departments and T years. I am interested in how voting shares change as a reaction to some regressor X. The dependent variable Y is vote shares: every department casts ...
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Constant sum suvey data!
I have conducted a survey where respondents had to allocate 100 points over 3 choices. There were 8 questions like this in total, where the choices were the same but the attributes on the choices were ...
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Am I correct that removing the intercept allow you to analyse compositional data?
I've heard that one solution to analyzing compositional data (in my case five predictors that are proportions summing to 1) is to simply remove the intercept.
This seems like a much simpler solution ...
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Regression with proportion values in the independent variables
I want to perform a regression where my independent variables all sum to 1. The independent variables are proportions of money invested in different categories.
What I have done:
When checking the ...
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How to test differences (over time and between treatments) of a specific species in DNA metabarcoding sequencing data?
I have DNA metabarcoding sequencing data in the following format:
plot
Time_point
reads_species_A
Reads_species_B
reads_species_C
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T1
0
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T1
48
455
0
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T1
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T3
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564
2
T3
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Dirichlet for panel data: correlated random effects?
I was wondering whether I can apply a Dirichlet regression model to panel data (using either dirifit in Stata or DirichReg in R)?...
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Understanding why CLR transformed compositional data should not be used with correlation analysis
A colleague of mine asked me why use proportionality when they could instead use CLR transformation followed by Pearson/spearman/biweight midcorrelation.
I vaguely remember reading why correlation ...
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Can I use logistic regression when all of the regressors sum to 1?
Let's say I want to perform a logistic regression (binomial) as :
X ~ P1 + P2 + P3 + P4 + P5
where X is binary variable (0 or 1) and P1, P2, P3, P4, P5 are ...
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Proper approach for modeling multi-class probabilities (proportions/compositional data)
I have a dataset in which the target values are counts of objects within each class, example (Xs are input features, Ys are values to be predicted):
...
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How to fit Multinomial-Dirichlet regression for correlated compositional count data in R?
I have compositional data where $K$ compositions (the abundance of $K$ cell populations) are measured on $n$ samples at baseline and repeated at 1 or more follow-up times. The $n$ samples are divided ...
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Trying to find the appropriate statistical method(s) to answer a marketing question — analyzing composition of groups
I’ve got roughly 90k rows of data, where each one represents a customer at my company. One of the columns tells me the channel that brought that customer to my company.
I’m looking at the channel mix ...
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Metric or Method to examine the correlation of a ratio
Let $X$, $Y$, $W$, and $Z$ be random variables where $X$ and $Y$ are different metrics of the same data point and $W$ and $Z$ are also different metrics of the same baseline datapoint. The assumption ...
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Linking features via correlations
I am comparing two tables with different size of features (rows), but the same number of samples (columns). I know that a significant part of the features are the same in the two tables, but they are ...
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Compositional Data in R
I'm writing a work on the Aitchison geometry for compositional data and I have seen an Image I want to reproduce in R.
I work with the "compositions" library and I want to understand how to ...
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centered log ratio transformation of overlapping compositions
I have a total of $N$ units that are assigned to $D$ classes based on certain combinations of characteristics. If each unit is assigned to only one class, then the problem reduces to the usual ...
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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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How does removal of symmetry (e.g. via constraints) in a Bayesian optimization search space affect search efficiency?
There are many examples of search space symmetry in real-world optimization problems in the physical sciences. To motivate this, here are some that come to mind:
When optimizing a formulation such as ...
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Compare paired before and after composition proportions
I have some data on the composition of purchases by households, before and after an intervention. This composition is known at the number of items or amount spent level within 7 categories, and can be ...
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What is the best imputation method for missing values in compositional data?
I'm a little newbie at statistics, so I'm sorry if my question is too dumb.
I'm working with compositional datasets with several chemical elements (continuous data; arranged in columns), but also some ...
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Compositional data: is it possible to make products of components/features in a composition?
I've never asked about Stack OverFlow, even though it's been so useful to me on many occasions! I'm sorry if this topic has already been discussed previously, perhaps I wasn't able to find the good ...
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Continuous independent variables that sum up to 100%
As I am studying the capital structure of firms, the total of proportions owned by different ownership types (free float, institutional ownership ... etc.) will be 100% of the company shares. In my ...
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Is it OK to transform non-normal proportional data
I have a dataset for 'time spent' (hours) carrying out 'behaviours' (walking, lying, standing, grazing), during day or night 'periods' of cattle. Time spent is my dependent variable, with behaviours ...
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Compositional data using R and difference between groups?
could you please help me in my research.
I have a problem that can summarize: Is there a difference between stores in terms of the share of sales percentage in the 4th quarter.
...
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How to model choice among three quantities, subject to a constraint
I have a response variable that is the amount in monetary units (m.u.) that a person can choose to donate among three alternatives, subject to a constraint that the total amount should be equal to 100 ...
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Log-ratio transformations, Aitchison Geometry, why logs?
I'm recently diving into the field of compositional data analysis and I'm still wondering why the log transformations that Aitchison proposes work.
What I understand is that, having a $D$- part ...
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Replacement of true zeros in compositional data
How does one go about replacing true zeros in compositional data sets? There is a lot of information on handling rounded zeros, such as multiplicative replacement (MultRepl in R), but not on true ...
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Compositional data analysis
I have one independent categorical variable "Period" (day or night) and 4 dependent continuous variables "Behaviours" (walking, lying, standing, grazing) which are compositional in ...
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GLM using proportions/percentage response variables
I have a dataset for time (hours decimal format) spent carrying out different behaviours of cattle in a day. I'm trying to run a general linear mixed model with two independent variables (lactation ...
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I'm looking for a statistical test more robust than the sign test for my experimental analysis
I made an exploratory experiment that consists of a pair of readings. I used Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS) to read elements on several mineral surfaces, getting ...
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Should I use Linear Regression in this case?
I'm doing a personal project on regression and I hope I can get some advice from you on several problems. The dataset I'm having is about cuisine, shape is 180x9, and the 2 continuous variables are &...
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Using compositional data analysis to represent chemical compounds
I've recently got some insights about compositional data analysis, wondering whether it could be suitable for the framework I'm currently in.
Recently, I've been very interested in trying to find some ...
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Compositional Data with Time Series
I have time series data corresponding to different entities. My goal is to train a model on the set of entities I have, and then provided a new entity to predict the whole time series for it.
For ...
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Non-logarithmic approaches to compositional data
Background
Compositional data ($x_i>0, \sum_i x_i=c$) are usually analyzed using some kind of log-transformation (alr/clr/ilr), to take into account naturally the fact that, in presence of the sum ...
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MCMC sampler on simplex: choosing a proposal distribution
I'm fitting a model using Bayesian MCMC. The model parameters include a parameter vector $\beta$ which is assumed to reside on a simplex $$S^d=\left\{ \beta=(\beta_1,\beta_2,\cdots,\beta_d);\space \...
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Can I use compositional data in a GLM?
I have landing data (kg) of five species where I try to identify which factors may be contributing most strongly to the high catch. Before, I had 4 predictor variables (Depth, Chlorophyll, Temperature ...
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How to calculate percent similarity between two sets of compositional data
I have data that is in the form:
...
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Bayesian compositional regression using ilr
I'm trying to fit a compositional data regression from a Bayesian perspective and using ilr coordinates. Once the ilr is computed for the response variable, a multivariate Gaussian regression has to ...
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How to model proportional data of >2 categories on continuous predictor variables
I am trying to model data in which I have 2 continuous predictors and a proportional response, but it isn't a single proportional value, but rather 5 different categories, whose proportions all sum up ...
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transformation or GLM approaches for compositional explanatory variables and a fractional outcome
I have a model where the outcome $y \in (0,1)$ is a share variable.
The four explanatory variables $x_1,x_2,x_3,x_4$ are compositional, so they sum to one. They are also all in $(0,1)$.
My goal is to ...
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Which algorithm suits for classification of multivariate time series data?
I have multivariate time series data, where the goal is to predict a binary label, which is changing in time. For illustration: there are 20 individuals, for each of them I measure 50 values (...
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Is difference in relative data (compositional data) is still a a compositional data?
The table below shows an example of relative data collected in two different time steps:
Y is an independent variable that is not part of the composition.
The goal is to study the regression between ...
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Compositional Data Analysis: What is the connection between Soft-max Regression / Logistic Regression and Linear Regression in the Simplex Space?
As someone just learning Compositional Data Analysis, my understanding is the following:
The sample space for Compositional Data Analysis is the Simplex Space. Useful transformations like ALR/ILR/CLR ...
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What is the probability that a parameter is greater than other parameters given we know the posterior distribution
Suppose that we have have some form of compositional data $x_i, i\in[1, n]$ which we propose comes from a Dirichlet distribution such that
$$ x_i \sim \mbox{Dir}(\lambda \alpha),$$ where $x_i=(x_1^{(i)...
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constant sum question results analysis - please help
I ran a study with a constant sum question: participants had to divide 100 units (I called the units USD) between 5 possibilities. In other words, they had to bet on five possibilities: 1 object out ...
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