All Questions
Tagged with ecology multivariate-analysis
36 questions
3
votes
1
answer
32
views
Statistical test for whether two methods of measuring community composition produce the same distribution?
I'm measuring community composition (i.e., the distribution of abundance) of 30 taxa as captured in 3 samples at 1 site. For each of my samples, I've measured community composition using 2 different ...
- 31
1
vote
1
answer
60
views
Nested studydesign - Necessary to restrict permutations in betadisper?
I have the following study design: 8 locations, 5 forest types (Plots) per location (D,DB,B,FB,F). In every plot I sampled spiders and identified them. I did an NMDS with Morisita-Horn index.
...
- 69
2
votes
1
answer
46
views
Permutest or TukeyHSD for group-wise comparison after significant Anova of betadisper?
I want to perform a PERMANOVA with my community-data of spider assembladges, sampled in different forest stands. Before applying PERMANOVA I wanted to find out if there is a difference in the ...
- 69
0
votes
0
answers
89
views
How to Statistically Test if a Community of Species at a Particular Site is Becoming More Like Another Type of Site
I have the following data frame (I'm using R here).
...
- 297
1
vote
1
answer
247
views
Transforming count data for NMDS?
I am looking at species count data. Due to large counts of certain species, I initially fourth root transformed the data. I am using Bray-Curtis distance measurement.
However when using vegan::metaMDS,...
- 63
0
votes
0
answers
9
views
Should data be transformed for NMDS? [duplicate]
I am looking at species count data. Due to large counts of certain species, I initially fourth root transformed the data. However when using vegan::metaMDS-Bray Curtis distance, the stress value for ...
- 63
0
votes
1
answer
22
views
How to apply RLQ ordination to communities with different species?
I am analyzing the relationship between bird traits and environmental variation using the RLQ ordination corrected for spatial autocorrelation and phylogeny, i.e., the method in Pavoine et al. 2011
...
- 1
0
votes
0
answers
18
views
multivariate analysis for seasonal patterns among rivers
I sampled three different rivers over one year during the four seasons. In addition, in the autumn and winter seasons I sampled both during an event of high (drought period) and low water (flood ...
1
vote
0
answers
57
views
Controlling for strongly collinear variables in a multivariate model
I am looking for some advice for a research project I am working on. My project involves analysis of fish abundance data from rivers around NSW Australia, with an aim of assessing the impacts of dams ...
- 11
1
vote
0
answers
47
views
Is it reasonable to apply different offsets to different species in community analysis?
I am using the manyglm function from the mvabund package. I have a site X species/family dataset of counts. One organism in the community is vastly more abundant ...
- 11
1
vote
1
answer
1k
views
Very low values of explained variance for the first Axes from PCoA
I am comparing different sites based on their floristic composition in R. Therefore, I have created a huge community datamatrix (presence/absence data) from 53 sites including over 1000 species. To ...
- 11
1
vote
0
answers
83
views
PERMANOVA: removing dominant species to avoid dispersion effect
Dear StackExchange community,
I have an ecological dataset that contains several species from different sample sites. One species is extremly abundant that contributes 80 - 90 % to the entire ...
- 33
1
vote
0
answers
278
views
NMDS with species-sites matrix and iterations
How could I conduct an NMDS-ordination for a species-sites matrix with multiple iterations? I know how to conduct a NMDS with a "normal" species-sites matrix, but I couldn't find any ...
- 11
1
vote
0
answers
271
views
Accounting for spatial structure in constrained ordination analysis (vegan)
I am looking to use ordination to test whether certain environmental measures influence the microbial community in soil samples. I am a bit confused about the correct way to define the model and ...
- 1,118
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
2
votes
0
answers
950
views
How does adonis2 (Permanova) handle continuous variables? [duplicate]
I'm working with a matrix of community count data. We collected both continuous and categorical environmental information.I would like to use adonis2 (R package vegan) to apply permutational analysis ...
- 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
0
votes
0
answers
964
views
Confusing F and p values in Two-way Permanova output
I am using 'adonis' from the vegan package in R to perform a permanova on butterfly species composition in tropical forest. I have two independent variables: Habitat (Undisturbed, Logged, Burnt) and ...
- 43
2
votes
1
answer
3k
views
How to analyse community composition in relation to environmental variables with nMDS?
I have a big data set (over 1000 observations) with abundances of over 60 species at 15 different sites over two years. Each site was divided into 30 sampling points and these were each sampled four ...
- 33
0
votes
1
answer
79
views
Multivariate techniques that discriminate community composition based on environmental variables between two a priori defined groups?
I have a methodological question that I have not been able to get an answer of. Basically, I am investigating the impacts of invasive species on soil microbial communities. I have a study design where ...
- 31
6
votes
1
answer
1k
views
Difference between NA and None in biological dataset
I have collected environmental data on animals, and am seeking help on how to deal with certain variables where a non-numeric value is informative, but also problematic. I have three variables that ...
- 63
2
votes
2
answers
354
views
Book about ordination in ecology
I am looking for a book that would cover a lot of different ordinations techniques (indirect gradient analysis e.g. PCA, CA, DCA, MDS, nMDS but also direct gradient analysis e.g. CCA, CCorA, RDA) with ...
2
votes
1
answer
325
views
Method named 'BEST' in multivariate analysis - what is it?
I've read a few ecological papers where a 'BEST' procedure is used to assess effect of environmental parameters on biological community composition, after multivariate analysis like MDS. For instance ...
- 459
3
votes
2
answers
314
views
Which correlation test should I use? ANOVA? PCA? Other?
I have the following problem and some help would be wonderful.
I have 50 origins for tree seeds. Each origin has several recorded climate variables like average temperature, precipitaion, wind etc.
...
- 33
3
votes
1
answer
71
views
Analysis of a dataset including dichotomial, ordinal and % data
I'm working on a dataset which is giving me trouble. I have 200 samples (Sample 1, Sample 2...). An example dataset (limited to 15 samples) is here. My dataset is structured with the following ...
- 61
2
votes
1
answer
181
views
What in cross validation from co-correspondence analysis indicates sufficient axes numbers?
The coca function at cocorresp package disponible for R provides a predictive way to relate two biological composition datasets. I need help to understand one step from examples on documentation ...
- 49
1
vote
0
answers
335
views
Residuals of symmetric Procrustes analyses are not symmetric
I am trying to replicate the analysis I saw in a paper. One of the step is to describe the relationships between two data tables. I use the procrustes() function ...
- 195
1
vote
0
answers
58
views
Predictions based on constrained ordination
This question is aimed at the use of CCA (or similar) in ecology.
What we know for constrained ordination: axes summarizing compositional variation are constrained to be weighted combinations of the ...
- 11
2
votes
1
answer
926
views
Replicates in Canonical Correspondence Analysis or PERMANOVA
My problem is the statistical analysis of community data with gradients of environmental data.
I have a table of species occurrences (from metabarcoding) per sample site and measurements of ...
- 23
1
vote
0
answers
59
views
How to incorporate intraspecific variation in discrete characters in comparative analysis?
I'd like to run a multivariate analysis (Pavoine et al. 2011) that aims to disentagle the effect of environmental gradients on traits, considering its autocorrelation with phylogeny and space. It uses ...
- 502
7
votes
2
answers
2k
views
Ecological modelling: multivariate abundance time-series data
I am working with a dataset that consists of abundance counts of 6 microbial taxa in a lake measured weekly for 20 weeks. I also have environmental data (temperature, nutrient concentrations, ...
- 181
3
votes
1
answer
533
views
Multivariate data with repeated measures - restricted permutations
I have a data frame of multivariate abundances (species) that have been measured from sites under two different treatments. These same sites have been repeatedly measured over multiple years.
I am ...
- 31
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
0
votes
0
answers
682
views
How to account for repeated measurements and unequal sample sizes in RDA
I have a question going in the same direction as this one:
Restricted Permutations
However, I have a dataset of multiple Locations from which I have samples of sometimes 5 sometimes only 3 years. Not ...
- 175
11
votes
1
answer
3k
views
What criteria to use for separating variables into explanatory variables and responses for ordination methods in ecology?
I have different variables that interact within a population. Basically I have been doing an inventory of millipedes and measuring some other values of the terrain, like:
The species and the amount ...
- 213
9
votes
1
answer
389
views
How to construct quadrats for point processes that differ greatly in frequency?
I want to perform quadrat count analysis on several point processes (or one marked point process), to then apply some dimensionality reduction techniques.
The marks are not identically distributed, i....
- 505