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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Ways to measure deviation from a discrete uniform distribution [duplicate]

I'm looking for a way to characterize the deviation from a discrete uniform distribution. Example: 50 balls are distributed over 10 urns. In the most equal case, all urns get 5 balls. In the most ...
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How should I interpret contradictory pairwise and non-pairwise beta-diversity metrics from beta.multi and beta.model.decay functions?

I am doing a community ecology analysis and am interested in partitioning beta diversity across sites of different ages (age = time since disturbance) and determining whether beta-diversity is ...
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Comparing Gini indices and Hill numbers between groups

I'm looking for methods (and R packages) that can test for differences in Gini indices and Hill numbers between two groups. The R ...
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What is the appropriate way to statistically analyse diversity indexes?

I have been working with a soil-derived viral metagenomic data set and am looking for advice on the appropriate statistical approach to the results. I have 2 different sample areas. Within both areas ...
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How to measure if a categorical distribution is concentrated in a very few bins

I'm trying to think of a way to measure that a categorical distribution of any size is concentrated in only a few bins, so not uniform. The best way I can think of is checking entropy, but that's kind ...
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Dissimilarity only between different treatments in dataset

I am studying the impact of wildfires on vegetation species composition. I have surveyed the burnt and unburnt areas on six sites which burned at different points in time from which I now have species ...
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Metrics to compare diversity of groups on multiple characteristics

When I search for 'diversity metrics' it seems like most work has focused on ecological diversity, and I most frequently see the Simpson diversity index. This is equivalent to the economics metric, ...
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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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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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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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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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Clustering as a diversity metric?

I have this idea where I want to compute the number of clusters in subsets of the full dataset and compare this number with the total number of clusters for the full dataset as a metric for the ...
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I have diversity index values and I wish to test for statistical significance between the zones readings. How can I statistically analyse this?

I have produced a graph for each Zone, x axis = years, y axis = diversity. I would primarily like to analyse the difference in diversity between the zones, but would also be interested in analysing ...
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ecologists, if I have diversity data (Shannon's index) for years and sites how can I produce data just for the sites (explained better below)

I have 3 sites each split into the same 3 zones. With abundance data taken on 4 different years. I have produced diversity index readings for each zone at each site, for each year. If I'm not trying ...
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How can I use R to asses the biodiversity of reef zones?

I wish to analyse my dataset, and concluded with the information I have, biodiversity would be good choice. I have 3 sites each are a reef and have the same zonation (split into 3 zones). I am aiming ...
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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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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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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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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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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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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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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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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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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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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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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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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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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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How to measure whether a discrete distribution is uniform or not?

Say I have two vectors [1,2,1,2,2] and [1,2,1,1,1]. The number at each dimension is the frequency of one element. How do I measure whether these two vectors are close to the uniform distribution? I ...
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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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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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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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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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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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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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Use vegdist function before metaMDS?

I am trying to do calculate beta-diversity of bacterial community data. I have been following numerous tutorials regarding this subject and I am getting mixed advice. I am trying to calculate beta-...
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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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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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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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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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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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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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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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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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How to represent numerically the diversity of groups of datapoints with a single value?

I work for a performing arts organization, and am trying to create a numerical figure to represent the amount of genre-diversity in each of our seasons. So let's say that we have a Spring Season and a ...
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2 votes
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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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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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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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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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Herfindahl Hirschman Indices

HH indices for a particular characteristics over units of observations $i$ is defined as: $$ HH=\sum_{i=1}^{N}s_{i}^{2} $$ where $s_{i}$ denotes the share of the observation in the total of whatever ...
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