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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3
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1answer
85 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
19 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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0answers
17 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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0answers
22 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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0answers
12 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
17 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/...
3
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1answer
40 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
44 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
55 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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0answers
30 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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0answers
18 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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0answers
73 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 ...
2
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1answer
27 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
45 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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1answer
30 views

Measuring variation explained in community matrix using both geographic distance and and environmental variables

So I have this dataset where I have species community data from a variety of sites. I’m trying to explain what are the factors that drive the variation in these data. For each site, I have a ...
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0answers
28 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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1answer
25 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
30 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
43 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
79 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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0answers
97 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
59 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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0answers
33 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
262 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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0answers
28 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 (...
5
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2answers
145 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 ...
2
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2answers
70 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 ...
6
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2answers
123 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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0answers
39 views

Can you run an AIC twice in a row?

I came across this paper that seems to make a bunch of models, run an AIC, select the best models from that, then run the AIC again. Am I interpreting this correctly? And is that okay to do? Couldn't ...
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1answer
71 views

Is Hellinger transformation suitable for repeated (in time) site-species abundance data?

I have fish survey data from four different years and several locations, where I would like to study the difference in abundance and biomass between sites and check whether time dependence influences ...
0
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1answer
44 views

Should I treat these variables as random? (ecology/recruitment question)

I'm working with recruitment data for caribou. There are 13 different herds, sampled over 20+ years, once per year. Some herds are sampled consistently, some only a few times over 20 years. I'm ...
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1answer
166 views

Multiple testing (bonferroni?) with GLM

Hi everyone: I scored four mutually-exclusive behaviors (e.g. feeding, brooding, standing, preening) on a number of observations of birds in two different treatments, and two different nesting ...
0
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1answer
125 views

odd insignificant results using pairwise.perm.manova

I am trying to complete pairwise comparisons of 9 forest communities. Communities were significant at p < 0.001 using adonis. However, when I use the same bray curtis matrix with the pairwise.perm....
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2answers
60 views

Getting ecological statistics right: Learning by yourself

I'm not really asking for reference on ecological statistics (such as here or here), but more on how you can be sure you're doing a new analysis you just learned correctly. I'm often stuck trying to ...
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1answer
143 views

How to simulate discrete data from a Poisson distribution? [closed]

I want to use R to simulate discrete data with missing values from a Poisson distribution. I have tried this: simdata<-rpois(1000,2) but when I checked if there ...
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2answers
53 views

What model(s) are appropriate for unbounded species abundance data with 0's and environmental response variables in R?

I am conducting a research project on the vegetation composition of an abandoned mine site to determine the environmental factors that influence species abundance (cover) and composition. Study ...
2
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0answers
41 views

Is it valid to solve an equation for multiple coefficients, then average them to obtain overall effect?

I have a regression model, the setup for which is as follows: I am using manyglm, a multivariate general linear model approach to determine the difference in several invertebrate species between two ...
2
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2answers
36 views

Which tests can be used for variables that are non-normal, but have homogenous variances?

I am trying to compare the effect of two treatments (planting distance) on the growth of plants (multiple species), using the variable growth rate in diameter for multiple years. I have 4 sets of ...
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1answer
36 views

Which stats can test differences between two experiments?

I have an experiment to look at habitat preferences of beetles and the effect of competition. In the first test, a beetle is on his own in an arena and I measured the % of time he spends in each of ...
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1answer
48 views

Which statistical analysis is most appropriate to determine differences between 3 treatments and control for monthly and yearly variation?

I have a 4-year dataset of zooplankton biomass that was sampled three times a summer (i.e. June, July, August) for all four years. There are 6 sites that were sampled in triplicate (took 3 reps): two ...
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0answers
62 views

Comparing species correlations between species in two habitats

I have two community data sets (samples as rows, species as columns, populated with abundance). This data comes from two habitats/sites, with differing numbers of samples at each site. What I want ...
3
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1answer
47 views

Using GLMM to explain vegetation change as a function of change in soil parameters

I have a dataset that consists of vegetation datasets (species/abundancy tables) and soil parameters (tested for ten parameters per soil core). Three different rounds of these data are recorded in ...
0
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1answer
36 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 ...
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1answer
32 views

Show absence of prediction for one response variable and multiple predictors

I have the following question concerning ecological statistics in a scientific study I am performing. I have measured the amount of copepods (little invertebrates) at different locations and at ...
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1answer
66 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 ...
0
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1answer
94 views

is it possible to use a vector object a dependent variable in GLM?

I would like to write certain model in R. I would like to o use a vector object as a dependent variable in my general linear model. The model is supposed to explain how some environmental factors, ...
5
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1answer
280 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 ...
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0answers
206 views

Canonical Correspondence Analysis: how to interpret results

I am using Canonical Correspondence Analysis (CCA) to analyze phytolith abundances (similar to pollen) over environmental gradients. As I am new to CCA, I read some background info. The following ...