Questions tagged [diversity]

measures of diversity (or uniformity or inequality) such as: biodiversity in ecology, income inequality in economic. Examples are entropy and simpson's indices.

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Diversity index and categorical variables,-

Is it possible to calculate a diversity index (Simpson's or eventually Shannon's index) from ordinal data? As in, we surveyed 50 transects and recorded several species' "abundance" in 4 ...
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28 views

How do I decide if it's ok to pool data?

I have biodiversity data (fish species, and their individual length, through electrofishing) from 8 different stretches of the same river, for 7 different seasons. We would like to see if it's ok to ...
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170 views

What's the most adequate test/tests for this study?

I'm a PhD student (Biodiversity and Animal Ecology). I am preparing a scientific article to submit and I need help in statistical analysis of my data. In this message I will try to provide as much as ...
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1answer
890 views

What is the most appropriate transformation method for performing analyses on species composition data?

I would like to compare differences in fish diets between sampling sites using a Bray-Curtis dissimilarity matrix and non-metric multidimensional scaling techniques. My raw data consists of counts of ...
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16answers
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What is the role of the logarithm in Shannon's entropy?

Shannon's entropy is the negative of the sum of the probabilities of each outcome multiplied by the logarithm of probabilities for each outcome. What purpose does the logarithm serve in this equation? ...
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12 views

Calculating Diversity of a continuous variable

Hi I'm trying to calculate diversity for a continuous variable. In the research, we have a network of people (they all know each other other but may not be friends) who all have different social media ...
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27 views

How to include standard deviations in diversity calculations?

I have community abundance data where each species has a mean and a standard deviation (determined by replicate samples). I am comparing the diversity of two communities. The various diversity metrics ...
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2answers
160 views

How to include the observed values, not just their probabilities, in information entropy?

Shannon entropy measures the unpredictability in a random variable's outcome as the weighted average of the probabilities of that variable's outcomes or observed values. However, it discards the ...
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1answer
211 views

What route is best for comparing diversity between 2 different sites

I am considering fungi presence and diversity in two different forest sites and looking for correlation between fungi presence/diversity and forest health. I am very new to stats, basically know ...
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34 views

Significance test for the difference in Simpson's Diversity Index values?

I've taken several samples of categorical data and calculated the spread of each using Simpson's Diversity Index. I would now like to perform a significance test to see if these spreads are similar or ...
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1answer
50 views

Comparing species communities between sites with different numbers of replicates

I'm working with ecological community data collected from different sites and want to make comparisons between the sites using descriptors like richness, Shannon Weiner's diversity, and Simpson's ...
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20 views

Is the Bray-Curtis dissimilarity/similarity independent of richness/diversity?

I was told about potential issues with the Bray-Curtis dissimilarity/similarity measure. Specifically, I have been asked if Bray-Curtis is independent of richness/diversity. I am unsure how to answer ...
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1answer
32 views

Build tree to calculate beta diversity

I am trying to calculate beta diversity using the UniFrac distance on my data, each sample having OTUs values. To calculate it, I saw it required building a tree with percentages that represented the ...
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1answer
41 views

Is there a minimum number for the calculation of the Herfindahl index?

Is there a minimum number of observations in order to assess concentration or not?
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1answer
68 views

Clustering on n features while maximizing the heterogeneity on m remaining features

We have a random vector $X\sim p(X)$, and a set of realizations of the random vector $S=\{X_i\}_{i=1}^N$. The random vector has $n$ continuous and $m$ categorical features. I want to cluster $S$ so ...
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42 views

Continuous (not categorical) measures of diversity?

Which measures of diversity are used where? When I search for diversity indicators I find the Simpson and Shannon index, but these are both for categorical data. If I have data with some structure (e....
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29 views

Measuring entropy/concentration in multivariate datasets

I am interested in measuring how concentrated or widely dispersed a certain binary property is among a population, which is defined by a number of categorical variables. For instance, let's say I have ...
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0answers
12 views

Statistical Test for Trends in Samples from a Possibly Changing Distribution

I have some data of quantitative measurements of the language in books from the years 1800 to 2000. For each year I have between 0 and 50 samples, mostly about 10 samples per year. If I bin the data ...
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1answer
30 views

Remove points, but preserve diversity

Given a finite set of points in $\mathbb{R}^n$, all at finite distances from each other I would like to remove a certain proportion of points, in such a way as to penalise clustering. For example for $...
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5answers
342 views

How to measure the "well-roundedness" of SE contributors?

Stack Exchange, as we all know it, is a collection of Q&A sites with diversified topics. Assuming that each site is independent from each other, given the stats a user has, how to compute his "...
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1answer
172 views

Measuring how well data is evenly dispersed

I am trying to measure how well scores from members of a group are dispersed over possible values. Think of it as a measure of diversity function. Thus, ...
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0answers
36 views

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
67 views

Distance matrix time series analysis? (Ecology/diversity)

I am trying to analyze a time series of ecological data. Each time point in the series is a matrix of animals-by-foods (that they were observed to eat). For each of these time points, I compute the ...
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5answers
12k views

Observational vs quasi-experimental design?

I am having some difficulty understanding the difference between and identifying an observational vs quasi-experimental design. From my understanding, an observational study is one in which the ...
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33 views

How to choose which models to include in an ensemble

I have a variety of binary classification models (SVM, Logistic regression, LSTM, CNN, naive bayes etc.) which i want to ensemble to create a more robust model. What theories are useful here? What ...
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0answers
212 views

How should I deal with spatial autocorrelation in beta GLMM (glmmTMB)? (Bird diversity)

I am trying to compare certain a taxonomic diversity index (for bird communities) calculated for squares in a map grid system (a total of 34 squares) for two different years: 1998 and 2018. My ...
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0answers
58 views

A reference request for a population statistic---experienced population density?

We all know that countries (for example) have population densities, but suppose we want to know what is the actual experienced population density (that is, if, say, in Sweden 95% of the population ...
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216 views

Which test should I use to compare the effect of a parasite infection on gut microbiome across time serie data point

I am interested in the effect of an intestinal parasite infection on the rat gut bacterial community. I have two groups of rats ("infected" and "non-infected") each consists of 6 ...
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189 views

PCoA/MDS on sqrt transformed Bray-Curtis dissmilarity using cmdscale

I would like to use PCoA to visualize beta diversity of a large community. I chose Bray-Curtis as distance measure to calculate the dissimilarity matrix and would like to apply a square root ...
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78 views

Test homogeneity of multivariate dispersion with regard to the Modified Raup-Crick Metric

Please find a citation for the modified Raup-Crick Metric below Modified Raup-Crick Metric (Chase et al. 2011 As an extremely brief review, this metric generates a dissimilarity matrix containing ...
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1answer
587 views

Can you use bray-curtis distances to evaluate standardized abundances in an NMDS?

So I'm trying to run an NMDS (using the vegan package in R) for a species X site matrix. Unfortunately the abundances of species are not inherently equal (If you can use that word) meaning that not ...
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1answer
49 views

What are the ways to normalize the vegetation data when the plot sizes of samples are different?

I have collected data on mangrove tree species density and composition from two habitat categories (sample groups) by using belt transects of various lengths between 100 x 10 M to 500 x 10 m. (3 & ...
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4answers
485 views

How is the Herfindahl-Hirschman index different from entropy?

The Herfindahl–Hirschman Index (HHI) is a concentration measure defined as $$H = \sum_i p_i^2,$$ where $p_i$ is the market share of firm $i$. It's maximized when one firm has a monopoly and minimized ...
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1answer
756 views

In VEGAN ADONIS, what does "method='bray' do when I pass in a distance matrix I already have (UNIFRAC)?

Suppose I have a distance matrix created by applying the weighted unifrac measure. For instance, using a phyloseq object: ...
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1answer
57 views

Understanding the assumptions of a Poisson regression model? Modeling plant diversity

I have data on plant diversity in response to a fully crossed treatments of fertilizer and light in grassland systems: ...
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1answer
98 views

Zero Denominator in Yule's Q-statistics?

In Concept Drift Adaptation by Exploiting Historical Knowledge they use Yule's Q-statistics to compute diversity between a collection of predictions. I think the context is not really important. I ...
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1answer
265 views

Help with creating a formula for "diversity coefficient"

I am creating a small webapp and a part of it is generating a number (I like to call it diversity coefficient) that would represent how "diverse" someone's listening habits are. The problem is I am ...
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15 views

Creating a fair coefficient for prize competition

I am trying to boost sales in our sales divisions by creating a small competition between them. However, the elaboration is quite tricky in order to guarantee a fair competition. There are 20 sales ...
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1answer
646 views

What is statistical diversity and how is it measured? (dataset with properties of materials)

I'm curious how one would define and measure statistical diversity for a research project of mine. My motivation is to understand the statistical space of materials. Each material has a set of ...
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83 views

Is there a way calculate a gradient of dissimilarity across multiple sites using presence/absence data?

I’ve been trying to come up with a metric for species (dis)similarity for fish in a series based on presence or absence data that gives a value of 1 or 0 for each lake. From my research, it seems like ...
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1answer
120 views

Rao-Stirling diversity index

I need help to calculate the Rao-Stirling diversity index. I tried it several times but cannot achieve equal results to R packages yet (e.g. diverse). I used the Rao-Stirling diversity index as ...
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0answers
141 views

Post hoc analysis survival data and maximum lifespan survival correction

Before presenting my problem I apologize that I create the same topic on the forum stackoverflow, but I think the best place for my question was here. I'm a PhD student and I'm working on survival ...
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26 views

What can I use to compute a similarity (or diversity) index for a sample with "multidimensional" attributes?

Current problem: We have a batch of $n$ items for which we capture their details with $m$ attributes. It could look something like this: The goal is to compute an "index" that says how "similar" this ...
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1answer
39 views

Analysing count data for biodiversity

So I'm confused about how to analyze some data for a biodiversity survey I'm undertaking. Incidences of birds are recorded at 25 stations on four sites (so 100 points in total). My response variable ...
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1answer
119 views

Shannon Index normalization with S distinct species per site

Given S different species and M sites . Where in every site species are unique (not repeated within the site,that is there are no 2 individuals from the same species in the same site , but can be ...
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1answer
559 views

Calculation of the Shannon Index plotwise or over the entire population

Imagine I inventarized a forest with 28 plots. Do I calculate the Shannon-Index for each plot and take the average, or should I calculate the Shannon-Index over the whole population? I use R and the ...
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1answer
571 views

R: Statistically testing NMDS community differences

Situation I am comparing species communities at 6 different sites. Communities at each site were measured repeatedly over 5 years. I used NMDS plots, based on bray-curtis distance matrices using ...
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2answers
74 views

Testing when the profile of a sample has changed - degrees of freedom?

I've been messing around with the Shannon index for diversity $ H' = -\sum_i^R {p_i \ln{p_i}} $, and it's associated 'evenness' measure $E = H'/H_{\text{max}}$. I'm trying to come up with a way of ...
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1answer
1k views

Standard error for Shannon's index in R

I am interested in examining how the species diversity of bird communities change following timber harvest and have used Vegan in R to run my analyses. Below is a sample of my count data. Plot names ...
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194 views

Confusion about Pareto Principle and Pareto distribution

The Pareto principle, applied to wealth for example, says that around 20% of the population holds 80% of the wealth. Accordingly, it is said that a person's wealth follows a Pareto distribution. I'm ...