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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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How to test when the profile of a sample has changed?

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 $J = H'/H_{\text{max}}$. I'm trying to come up with a way of ...
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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
47 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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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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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 ...
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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
39 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 ...
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1answer
49 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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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
61 views

Analysing count data for biology

I have twenty observations of three dependent variables and of sixteen independent variables. The dependent variables are: 1) number of species, 2) number of individuals, and 3) index of Shannon. The ...
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1answer
51 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
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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 ...
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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 ...
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2answers
34 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
44 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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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 ...
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1answer
39 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 ...
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1answer
29 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
31 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
38 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 ...
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1answer
38 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, ...
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1answer
123 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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55 views

R, vegan: Is it possible to get effect direction from adonis results?

I used the vegan package and the adonis function to test the impact of a variable on communities. As far as I understand, the output tells me that there is an effect, but it does not tell me if there ...
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130 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 ...
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1answer
78 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 ...
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1answer
43 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 ...
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1answer
151 views

GAM: Plotting gam models of different treatments?

I want to figure out the best way to plot gams, but I am getting confused about the best way to do this for my data. Please note that I am not a statistician, so 'stats/coding for dummies' answers are ...
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1answer
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What are some simple ways i can analyse changes in relative abundance

I am looking (to begin with) some simple ways to analyse changes in relative abundance of species numbers over time. All we have is a inventory list of the number of species for each four seasons, ...
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2answers
176 views

Growth rate patterns through time: ARMA an appropriate approach?

The Data Total Biomass and Annual Growth Rates for 37 permanent sample (i.e., repeated sample) forest plots that have been ...
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2answers
65 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. ...
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1answer
48 views

Effect size calculation

I am conducting a meta-analysis on the diet of predators. This diet is expressed as the proportion of aquatic vs terrestrial prey. I have a value (% of aquatic prey) for each species for each site of ...
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1answer
42 views

How to handle non-detects in duplicate samples

I took two separate water samples (one sample per bottle) in twenty one river locations (n=42). For the purpose of this question I am calling the two bottles duplicates. I am trying to show how ...
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Which statistical test should I use to compare land use type and species abundance?

I have abundance data for a species of bird and data on land use type in the areas where the bird data was collected. I want to test whether land use type affects bird abundance but I don't know what ...
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1answer
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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 ...
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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 ...
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Spatial clustering analysis on binomial data collected on a grid

I am new to spatial statistics and need help figuring out how to assess if there is spatial clustering in my dataset using R. I am assessing if acorn consumption is different inside timber harvest ...
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1answer
67 views

Modelling % cover that do not add up to 100% : GLM distribution families

I have an experimental set-up that consists in studying the impact of diversity of plant mixtures on the development of invasive species. On each plot, we recorded the % cover of each species which ...
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2answers
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How to choose the statistic metrics to describe the patterns of trees near the tree line?

I have tree inventory data: about 700 points of trees with known locations (X;Y;Z) and measured heights and diameters of stems at the breast height (DBH). The trees are located along the elevation ...
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Family in GLM - how to choose the right one? [duplicate]

When modeling data sampled in the field, I often come across the problem of determining the Family of the dependend variable for GLM (or GLMM). An example: in an ecological study, I have ~ 60 patches. ...
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1answer
85 views

It is correct to use units other than individuals or samples on X axis of rarefaction curves?

The rarefaction curve is a very useful statistical tool for biodiversity analysis. It represents the number of species on Y axis, adjsted by individuals, samples (Gotelli & Graves,1996; Gotelli &...
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1answer
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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 ...
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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 ...
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0answers
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Comparing Composition of Samples

I have data on the composition of two different types of animal droppings. There are 15 observations of Animal 1 and 40 observations of Animal 2. I have the makeup of each dropping broken up into ...
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1answer
446 views

Random and fixed effects for observational/ecological studies

I was wondering if anyone had any insight to offer on the question of deciding which variables are random effects and which are fixed effects for ecological studies that are based on observations in ...
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1answer
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ecology community sample comparisons

I have 2 batches of tree species and abundance data collected for a city. The difference between them is the sampling strategy - one was random unstratified, and the other was stratified and clustered....
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183 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 ...
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0answers
155 views

How to calculate growth rates up and down from a local maxima?

Problem: I am currently doing my Msc-thesis on rodent population dynamics. One of my aims is look at symmetry in oscillation topography. For this I want to calculate the growth rates up and down from ...
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1answer
47 views

What distribution to use for response variable which is a ratio of counts (that are not independent) where it can be >1?

I have two sets of counts, bat passes and feeding buzzes. A feeding buzz is not independent of a bat pass. In a single bat pass, there can be multiple feeding buzzes. My response variable is buzz ...
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1answer
63 views

Repeated measures field experiment: statistical design

In a study on a bird, breeding territories were mapped in 1990 and controlled in 2017. Each territory is one sample with the dependent variable territory abandoned (possible values: "yes" and "no"). I ...