Questions tagged [ecology]

Ecology is the study of how organisms interact with their environment & each other. Ecology uses some specialized statistical techniques (eg ordination methods). Use this tag to indicate applications of statistics that are unique to ecology or that require a recognition of the ecological context.

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Analysis of One Binary Variable and Continuous Variables - Ecological Data

I have a dataset that I am trying to analyse, it consists of: A binary variable which indicates a tree species (0 = deciduous 1 = evergreen) with 100 measurements each. N which is leaf nitrogen ...
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25 views

What distribution to use for left-skewed data in generalized linear mixed models (for use with structural equation modelling)?

I'm trying to run a GLMM with a response variable that is left-skewed. Eventually this model will form part of a piecewise structural equation model (using piecewiseSEM). I have data from 480 plots, ...
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99 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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18 views

finding the most reliable covariate for replicates

I am working with garden bird data from the British Trust of Ornithology (BTO), and the way I have organised the data is in a long-format, where I have combined the habitat metric with the bird values ...
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40 views

Best practice MLR vs GLM(M)

I am modelling timeseries of organism traits (7 different traits in total) using GLM(M)s in R. The data was collected at very irregular intervals and from 6 different locations. For every location 5-...
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34 views

Ecological modelling of abundance in time and space

I'm working with ebird data which looks like this: ...
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1answer
23 views

Linear regression on clustering result

I've got a data about mammal body weight responses to increasing air temperature. I want to know whether there are some mammals that respond to the increasing air temperatures differently. Hence, I ...
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12 views

ANCOVA with count Data (GLM, Quasipoisson) and multiple Covariates (R)

at the moment I am working on my Bachelor Thesis and I got a problem in Data Analysis with ANCOVA in R. Unfortunally the experimental Design leads to a small number of samples. I got 12 Days and 3 ...
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1answer
28 views

Error : Linear mixed model in r; Can't compute random effect variances

In order to analyse which factors have greater weight in the proportion of incidence (number of infected inidivuals against total individuals), the interaction of all factors (habitat, site and ...
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17 views

How to best represent missing count data?

I have BTO data within the region of Norfolk over the last 10 years. For the counts, there are no values for the majority of the data, this may be because someone forgot to mention how many birds they ...
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26 views

Help interpreting a nested PERMANOVA model required

My study looks into the effects of fishing on the ecological community. There are n=4 sites in a marine reserve and the adjacent fished area. The ecological community was sporadically sampled every 1-...
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Specifying model in mvabund - is GLMM an option?

I'm looking to use some of the packages in mvabund to do a fourth corner analysis and was wondering if I can use glmm within this package. Everything's been laid ...
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32 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 ...
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12 views

What method should i use to analyze the effects of rainfall and temperature on birds?

Which method should I use to analyze the effect of temperature and rainfall on birds? I need to analyze the effects of rainfall and temperature on Frugivorous birds in a wildlife reserve. We don't ...
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50 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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26 views

SECR AIC compatibility

I'm a student in ecology and I'm currently doing an internship to validate the first year of my master degree in France. I have to calculate roe deer density for the Mavrovo National Park in Macedonia ...
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50 views

How does adonis2 (Permanova) handle continuous variables?

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 ...
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9 views

Area and time adjusted counts

In 2019 I went to a site and counted 4 species of birds. The size of the site was 130 hectares and I spent a total of 54 hours counting the birds. The peak counts of the 4 bird species are presented ...
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23 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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Which type of analysis of the change from baseline is better: GLS + Dunnett on post values or GLS + ANOVA on changes?

Dears, I'm preparing for a project in ecology. We will analyse change from baseline as a reaction to some chemical substance. Let's assume the data will be collected like this: ...
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1answer
48 views

Working with Discrete-Time Survival Analysis with Random Factors in R

I'm working with some data on artificial (fake) bird nests, looking into their 'survival' from animal attacks. I visited the nests once every two days, for 2 weeks (so my time points are 2,4,8,10,12,...
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41 views

Corrections for logistic regression (multiple comparisons?)

I'll cut to the chase. Here's what I'm doing: looking at the influence of water temperature and salinity on the presence of water-borne parasites for a certain estuarine bird population birds are ...
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33 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 ...
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35 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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103 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 ...
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26 views

Standardize species richness by elevation

I am studying the effect of forest structure on recruitment. One of the variables is species richness defined as the number of species. The aim is to quantify the effect of species richness on ...
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38 views

Doubts about the use of Cross-Validation in GLMM

I've recently ask in statckoverflow about some doubts with logistic regression fitted with a GLMM and an user recommend me asking in this forum. So, here it goes. I work with a wild population of a ...
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37 views

extending BACI analysis to lme, glm

I am analyzing data from a BACI (before-after, control-impact) design. BACI analyses typically look for changes in the mean response before(B) and after(A) at control(C) and impact(I) sites, but I ...
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113 views

Post hoc for Fisher's exact test with a 2x6 contingency table

I am looking to see if and how tree height differs between areas of undisturbed and historically logged forests. Height was estimated in meters but categorically (1-6, 6-11, 11-16, 16-21, 21-26, 26-31)...
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19 views

Dealing with highly skewed residuals in GLMM

I am trying to see if there is a relation between the proportion of target vs non target species in some communities and their phylogenetic structure. I cannot show you the real data but it looks ...
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12 views

Statistically deciding time intervals for independent events

I am working with camera trapping data and am trying to decide on a time interval to classify independent events. I have many images of wild dogs that were captured on 60 camera traps that are ...
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20 views

What type of PCA to run with only two environmental variables and 1 factor?

I study soil insects, and sample monthly for insects. Each month, I sample at 8 different sites. Each site is divided roughly into 4 meter square quadrants. From each quadrant, I pick out a random sub-...
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17 views

How to analyze data for spatial aggregation and niche overlap with no specific GPS points over time?

I study soil insects, and sample monthly for insects. Each month, I sample at 8 different sites. Each site is divided roughly into 4 meter square quadrants (shown in figure). From each quadrant, I ...
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2answers
217 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-...
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84 views

Ecological count data and offset terms

Problem: When using GAMs to model ecological count data (e.g. fish counts) using Poisson or negative-binomial distributions, the response variable is raw counts and the offset (e.g. log-transformed ...
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1answer
39 views

What is the general process of choosing, confirming, and supporting the distribution used in a generalized linear model?

I am trying to better understand the process of choosing and validating a distribution for a generalized linear model (glm). I understand that for the most part, you can narrow it down to a few ...
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59 views

Unmarked OccuMulti function

I have a question about the occuMulti function in the package “unmarked”. I have fitted the following model for a two-species interaction between puma and peccary: ...
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1answer
136 views

Specifying hierarchical GAM for ecological count data---annual bird migration counts

I'm working with a data set of annual bird migration counts, and I'd like to fit phenological models to determine how timing of migration has changed over the last few decades. Weather permitting, ...
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1answer
101 views

GLM on non-integer data

I'm looking for a recommendation on what GLM I could do with non-integer data. Brief background of what I am doing: I'm wanting to combine calculated herbivory rates with abundance data, to compare ...
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2answers
26 views

How can I calculate correlations between fungi presence and forest health in two different forest sites?

I am working on an undergraduate thesis and I have extremely little knowledge on statistics so my analysis is going to have to be quite basic. In two different forest ecosystems (plantation and mature)...
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35 views

Hierarchical clustering: distance/linkage combination that allows starting in the middle of the dendrogram

I want to use hierarchical clustering to classify some ecological data (species abundances on different places), so I would like to use a Manhattan type distance that doesn't account for double ...
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116 views

Warning messages in occupancy modelling (unmarked)

I have an issue with occupancy modelling and I have some warning messages that I don’t understand. I hope you can explain to me what they mean and how I can resolve them. I am building single-species, ...
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22 views

How to control for group membership in multivariate community analysis (CCA) when group is confounded with explanatory variables of interest?

I am studying differences in microbiome composition across 11 different populations and attempting to identify correlations between microbiome community beta diversity and population-level covariates. ...
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1answer
26 views

Presence/absence data

I'm working on a study where I am testing whether individual species that I observed or didn't observe (presence/absence of observing species A on each survey) during drought and non-drought (presence/...
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1answer
42 views

GLM with random factors for observational design

I would love your help: I have 50 houses where I have counted the number of Mosquito's eggs once a week for 4 months. I have 5 fixed factors (temperature, NDVI, precipitations, etc) and I want to add ...
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1answer
62 views

problems with transforming proportion data in GLMM model

I'm comparing the effects of a single treatment on multiple response variables from a BACI study. Most of my data are normally distributed, but I also have some proportion data (binomial) and count ...
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1answer
130 views

GLMM with presence/absence dataset

I want to know if a treatment effectively reduces the abundance of a particular species in some location. For that, I trapped the animals and identified each individual captured, releasing the animals ...
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69 views

Poisson Binomial Distribution - confidence intervals for sum of unequal probabilities estimated with uncertainty

I believe my question is related to, but distinct from this one: Poisson Binomial Distribution - confidence intervals I am working to estimate species richness by summing the results of 12 individual ...
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22 views

What is cross validation doing in my spatial ecology model, and how necessary is it to run?

I'm currently using the R latticeDensity package to estimate home ranges of animals. Within the documentation, The minimum uvc (Unbiased CrossValidation ...
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1answer
50 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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