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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30 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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35 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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24 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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30 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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1answer
67 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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25 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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28 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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22 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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63 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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11 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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19 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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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
128 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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56 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
36 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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33 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
114 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
97 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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30 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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58 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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18 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
23 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
41 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
52 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
109 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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53 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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98 views

Pseudoreplication and overdispersion in logistic regression

I'm running a logistic regression to evaluate the effect of geography (longitude) on fruit herbivory of a plant species. Essentially, I want to know how herbivory varies over space. The actual dataset ...
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1answer
37 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
62 views

Correlation Matrix or Covariance Matrix in PCA [duplicate]

I have 4 metrics, three of them measured on the scale 0 to 1, and one measured on the scale 0 to 6. When I stored my data, I converted the fourth one by dividing it by 10, so that I can get values ...
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29 views

Modelling resource selection in savanna ungulates

I am amidst an analysis of an 8 year data set that was collected from wildlife surveys over an 8 year period for my MSc thesis. 2 surveys were conducted each season for the three discernible seasons ...
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0answers
14 views

Estimating proportion

In the context of an ecological study, I am trying to estimate the proportion of a certain mode of transmission on total incident cases of a disease (i.e. "x % of the incident cases transmitted by Z"),...
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1answer
27 views

Using a species distribution model as an environmental variable in another distribution model

I'm interested in examining which of a suite of environmental variables is most important to predicting the distribution of a given species A, given a set of presence/absence points. I would like to ...
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1answer
32 views

How to address large sampling units but small sample sizes?

I've got data from eight one-hectare tropical forest plots, with all trees greater than a certain size measured and identified within them. These plots are different forest ages with two replicates ...
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2answers
49 views

Model specification in nlme: Random effects

My design has a total of 20 sites. 5 sites belong to each of four land covers: A, B, C and D. In each site, I have 5 sampling locations, 2 metres from each other. From each sampling location, I ...
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2answers
84 views

Statistical test to find association between two variables

I'm dealing with ecological data. Broadly speaking, i've counted the plant abundance (discrete variable) in a number of points (small blocks,one number for each ...
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189 views

Input data for Canonical Correspondence Analysis (CCA)

I'm going to conduct Canonical Correspondence Analysis (CCA). In the tutorial I've found at: CCA environmental data are discrete ...
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0answers
66 views

Exploratory data analysis before pefrorming Canonical Correspondence Analysis (CCA)

I want to perform CCA, but I read that, remember that observations (for example, species abundances) have to present unimodal distributions along gradients (for example, environmental variables). ...
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59 views

Detrended Correspondence Analysis or Non-metric multidimensional scaling

For an ecology project I am analysing how and if the species composition of a habitat type (heathland for example) changes through time. This was done by measuring fixed plots within a habitat type ...
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2answers
547 views

Dealing with Overdispersed Negative Binomial using glmmTMB

I'm new to the world of statistical modeling, but I was wondering if anyone had any input on how to handle overdispersed negative binomial data? I'm working on modeling bat activity as a response ...
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29 views

Testing for extinction using the binomial distribution

I'm using quadrat sampling to determine whether a species of plant is present in a given area - my end goal is to work out how many quadrats need to be checked without finding anything before I can ...
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0answers
33 views

How to analyze a contingency table with time series?

I have a contingency table with frequency of food items (rows) measured across 10 years (columns). I wonder what kind of analysis I should use to model the variation in food frequencies with time (...
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2answers
165 views

Don't understand why glmm random effect variance is zero. Have reviewed similar questions still dont get it

I study a colonially-nesting bird species. I am trying to perform an AICc evaluation of GLMMs for a nest site selection study. I collected data at nest sites and paired random sites. I want to ...
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2answers
72 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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9 views

Question about design choice of Enbrel RWE study

Statisticians in 2015 analyzed real world data, hundreds of thousands of medical insurance claims involving people with rheumatoid arthritis and other inflammatory diseases, according to the Pfizer ...
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2answers
133 views

Camera trapping and the Poisson distribution

I am currently working with data from camera-trapping, where individuals from multiple species have been taken pictures of when they pass in front of one of the cameras (which are placed on a large ...
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3answers
50 views

How to test whether birds spend more time in specific areas along a time-segmented track?

I have geolocation data on birds with 1 position per day (latitude + longitude) plus I have for each day, a corresponding binary time series that takes values 0 or 1. There is periods of minimum 10 ...
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245 views

Converting annual survival rate to daily mortality probability

In a peer-reviewed paper, I came across the following conversion: Yearly survival rate -> 0.70 The authors have calculated the daily probability of death using (1 - 0.70^(1/365.25)) = 0.000976 ...

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