All Questions
33 questions
0
votes
0
answers
91
views
How to run a test between two or more groups when each data point brings a confidence interval?
I have recently started working on a dataset, but my limited experience as a recent graduate is preventing me from making progress. After performing a rarefaction (a form of bootstrapping), which was ...
11
votes
2
answers
255
views
Deriving Fisher's mysterious estimator for the Unseen Species Problem
From Wikipedia:
In the early 1940s Alexander Steven Corbet spent 2 years in British
Malaya trapping butterflies.He kept track of how many species he
observed, and how many members of each species ...
- 318
1
vote
1
answer
37
views
Unsure of statistics needed while working with replicates
I apologize if the question is considered too broad, but I'm hoping to get at least a basic starting point as I'm somewhat stuck with how to approach this.
I am working with community ecological data-...
- 63
0
votes
1
answer
73
views
Why don't vegan::vegdist and vegan::metaMDS produce equivalent results?
This question has been discussed before but the proposed solution (https://stats.stackexchange.com/a/459820/170801) is no longer reproducible for some reason. As a refresher - it has been suggested ...
14
votes
3
answers
1k
views
Quantifying diversity of bird species
I’m wondering if anyone could recommend a diversity index to look at the differences in breeding bird territories between two sites. These are my data - the numbers represent the number of breeding ...
- 14.6k
0
votes
1
answer
98
views
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 ...
1
vote
0
answers
248
views
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 ...
- 11
1
vote
1
answer
236
views
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, ...
- 1,312
2
votes
0
answers
324
views
Diversity index and ordinal 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 ...
- 21
0
votes
0
answers
514
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 ...
- 232
2
votes
1
answer
142
views
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 ...
- 85
3
votes
1
answer
755
views
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 ...
- 85
2
votes
1
answer
946
views
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 ...
- 85
1
vote
1
answer
836
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 ...
- 13
4
votes
1
answer
223
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 ...
- 41
1
vote
0
answers
525
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 ...
- 351
0
votes
0
answers
779
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 ...
- 121
1
vote
1
answer
221
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 ...
- 25
1
vote
1
answer
140
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 & ...
- 11
3
votes
2
answers
2k
views
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-...
- 143
2
votes
1
answer
407
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 ...
- 157
2
votes
2
answers
83
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 ...
- 131
2
votes
1
answer
200
views
Should I use Structural Equation Models (SEM) for my Functional Diversity (FD) study? (ECOLOGY RELATED)
I'm trying to calculate various functional diversity measures (Fric, Feve and Fdiv) for bird communities by using count data which is collected annually. My ultimate aim is to compare functional ...
- 351
0
votes
0
answers
107
views
how do I calculate overyielding in ecological temporal stability
I am investigating diversity-stability relationships and
I am trying to test for the portfolio effect and insurance effect with my data.
I understand that overyielding indicates the portfolio effect ...
- 151
2
votes
0
answers
87
views
Comparing biological diversity before and after
I've got counts of two species in two treatments at two timepoints. I've got six replicates of each treatment.
I'd like to know how to compare treatment diversity.
As it is, I've calculated the ...
- 161
1
vote
1
answer
424
views
Statistical test for comparing species diversity based on frequency at two points
I am trying to quantify similarity between these two locations taking into account species frequency:
Chicago
Blue Jay: 0.79
American Crow: 0.25
Blackpoll ...
- 281
11
votes
3
answers
10k
views
Variance of a distribution of multi-level categorical data
I am currently analyzing large data sets with various characteristics (such as city). I wanted to find a measure which would essentially say how much or how little of a variance there was across the ...
- 213
2
votes
1
answer
184
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 ...
- 21
1
vote
1
answer
188
views
Vectors for biodiversity indices in RDA plot
I'm doing partial distance based (db-)RDA analysis of nematode community data.
I have got the triplots already. They contain vectors of environmental data.
Is it possible to overlay a second set of ...
- 309
4
votes
4
answers
18k
views
Statistical test to perform on species diversity / Simpson's diversity index
I have a set of data from each of the two sites I am measuring for plant species diversity. I plan on using the Simpson's diversity index (SDI), which combines species richness (number of different ...
- 41
3
votes
1
answer
2k
views
Calculating Diversity using normalized species counts
I am trying to calculate the change in diversity of species encountered throughout time. My dataset is comprised to detections of tagged fish for 48 consecutive weeks. My thought was to bin the ...
- 103
2
votes
0
answers
84
views
Quantifying tree height diversity or heterogeneity
I am analyzing data collected in the field for a habitat selection study of a large mammal. I have ~1300 plots that were sampled. I am trying to find a good way to quantify the diversity of tree ...
- 417
7
votes
1
answer
5k
views
Species Richness, Dominance and Diversity Differences
I have collected 70 organisms from 4 different sites; two sites of treatment 1 and two sites of treatment 2. I also have a continuous explanatory variable (average temperature) which is different ...
- 1,267