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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48 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 ...
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1answer
1k views

GLMM or LME? Repeated measures help?

I am having trouble using the correct test and r code for my experiment. Essentially I measured insect emergence daily from artificial streams with 3 treatments.: ...
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1answer
54 views

Test if number of fish differ by location

I have a dataset which consists of location ID's (1 to 29 different locations) and each location has a couple of repeated measures (max n = 780, min n = 50). Each measurement consists of a number of ...
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396 views

Confidence intervals on a predicted regression line cross

I have carried out a model on some long-term data I have looking at bird arrival dates in relation to different weather conditions and have run into some problems when plotting the results. I have ...
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1answer
2k views

Time-series analysis of categorical data

I am attempting to look at nest attendance patterns in birds. I have a dataset looking at 5 nests, every 5 minutes I assessed whether the male=1, female=2, both birds=3 or no birds=4 were at each nest....
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1answer
81 views

Final test for statistical significance of bird aggression scores

Introduction I'm doing a small pilot research in bird aggression in a colonising frontier regarding their breeding ground. Background The study was conducted over multiple years, presenting the ...
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1answer
6k views

Principal component analysis with group data

In my experiment I have used 30 different accessions of a species. One group is challenged drought and the other group is control. I have collected data on 6 different parameters. I want to know which ...
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1answer
65 views

Comparing two groups: a risk of pseudoreplication

I am growing coral on two different structures. I want to compare whether one structure (a table) grows coral more quickly than the other one (a tree). Both structures hold 60 pieces of coral, so a ...
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2answers
1k views

mixed effects and lme4: Do I need nesting?

I am analyzing data from a field experiment, and I am interested in the effects of fauna and altitude (fixed). Altitude has two levels, and at each site I have 5 blocks for the three levels of fauna (...
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29 views

Generalized Linear (Mixed) Modelling for different scales

I am struggling conceptually with how I can best model my dataset. My data is the abundance of spiders collected from 20 permanent traps in a forested area. These traps have been repeatedly re-...
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82 views

Need help to understand the equation of stable population

I was reading this paper on non-stable and stable population momentum. There the authors have shown the formula for stable population $Q$ as: $$Q=\dfrac{\int_0^\beta n(x)v(x)dx}{bA_r},$$ $v(x)$ is ...
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1answer
28 views

What's the best statistical method for comparing perceived versus measured ecological functioning?

I'm comparing survey results of respondents' perceptions of creek environmental health to environmental health as measured by scientists with the city. What's the best way to analyze the difference?
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1answer
33 views

Causation in an agroecosystem?

I'm working in an agroecosystem with one specific crop and am interested in understanding how certain treatments influence given ecosystem characteristics (such as soil organic carbon). Variables that ...
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1answer
3k views

Why is a correlation coefficient threshold of r = 0.6 among predictors commonly used in ecology?

In my field of study (wildlife ecology), a correlation coefficient of r = 0.6 is a commonly-used threshold for identifying collinearity among pairs of predictor variables. In other words, predictors ...
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3k views

What is PERMANOVA and when to use it instead of multivariate ANOVA?

I have some data on spatial and temporal variation of macrobenthic species. I tried to test the difference between seasons and sites, and noticed that PERMANOVA is recommended in the literature. (But ...
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1answer
96 views

Outputting indicative variables within a specific factor

I have a dataset on bugs that has been processed to incorporate a series of traits (e.g. size; feeding habitats) through displaying proportional values of different properties (e.g. small, medium, ...
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1answer
1k 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, ...
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105 views

Occupancy vs mark-recapture?

What are the differences between occupancy models and mark-recapture in ecology? As I understand it, we use occupancy models when we aren't sure if detectability is a given (not sure of presence/ ...
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1answer
256 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 ...
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1answer
155 views

What's the most adequate test/tests for this study?

I'm a PhD student (Biodiversity and Animal Ecology). I am preparing a scientific article to submit and I need help in statistical analysis of my data. In this message I will try to provide as much as ...
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28 views

Estimating proportion of region cropped by proportions in random samples

I have a series of quadrats placed randomly across aerial photography of a region. In each quadrat I have estimated the proportion of the quadrat under cropping and my goal is to estimate the ...
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187 views

Multinomial response with repeated measures

I'm studying how sex influences habitat use. I'm looking for suggestions on how to analyze a repeated measure design with a multinomial response variable. I should note that the number of repeated ...
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1answer
129 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 ...
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82 views

Detrended correspondence analysis

I have relative abundance data of monkey species in 4 different types of habitat. I would like to use detrended correspondence analysis. Is this a correct way to display my data? If so, how should I ...
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1answer
709 views

Do I have to normalise the data for PERMANOVA?

Why do I have to normalise my dataset to do a PERMANOVA? What is the difference between Euclidean distance and Bray-Curtis similarity? Which is the most suitable for CPUE (abundance) data?
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1answer
972 views

Best books for a population-ecology and biology statistics [closed]

I know that there is question that's similar to this (Books on statistical ecology?). I've got recommendations from that, but want to ask you for an advise following this list of books: 1. Applied ...
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475 views

Representing experimental data by unconstrained ordination: PCA, PCoA, or NMDS?

I have a dataset composed by presence of different bacterial families in function at different pesticide treatment. I need to find a good representation of my data but I don't know which method (...
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1answer
1k views

Controlling for age and sex in a multiple regression with a backward model selection

So, I have this dataset with a hormonal measure as independent variable and behavioral measures as dependent variables. I am using a linear regression as my model and after a backward selection, ended ...
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1answer
9k views

What is the “horseshoe effect” and/or the “arch effect” in PCA / correspondence analysis?

There are many techniques in ecological statistics for exploratory data analysis of multidimensional data. These are called 'ordination' techniques. Many are the same or closely related to common ...
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1answer
1k views

ANOVA table for 4-factor split-plot

Hopefully I can explain this clearly. Reference diagram below if needed. I'm planning a large field experiment that I think will have to be a split plot design. There are six sites (outlined in red)...
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4answers
17k views

Interpreting random effect variance in glmer

I'm revising a paper on pollination, where the data are binomially distributed (fruit matures or does not). So I used glmer with one random effect (individual plant)...
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1answer
167 views

Intraspecific variation in MCMCglmm

I want to use MCMCglmm to account for phylogenetic autocorrelation on my GLMM. However I have more than one trait measurement for certain species. Is there a way ...
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1answer
9k views

Hellinger transformation with relative data

It is my understanding that the Hellinger transformation is basically the square root of relative abundance data (if rows are samples). However, my row sums do not represent the total community (I am ...
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1answer
253 views

Can I perform PCA on species count differences instead of species counts themselves?

I'm busy with the analysis of bird community change through time on a couple of sites and want to relate it to environmental covariates. I use the R-package vegan ...
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4answers
10k views

Statistical test to perform on species diversity / Simpson's diversity index

I have a set of data from each of the two sites I am measuring for plant species diversity. I plan on using the Simpson's diversity index (SDI), which combines species richness (number of different ...
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43 views

Describing Differences between Two Inferred Populations

I am interested in the size of an animal in two populations, and found reliable estimates of the population provided by NOAA. The data was in the form of estimated total population within discrete ...
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1answer
1k views

Calculating Diversity using normalized species counts

I am trying to calculate the change in diversity of species encountered throughout time. My dataset is comprised to detections of tagged fish for 48 consecutive weeks. My thought was to bin the ...
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364 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 ...
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1answer
908 views

Validity of stepwise regression in DistLM

I have a set of nutrient fluxes data and I would like to know which environmental drivers explains the fluxes. I used DistLM and the marginal test showed that none ...
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1answer
1k views

Should ordinal variables be normalized for PCA?

I need to analyze my (ecological) data with PCA, but the data don't seem to meet the assumption of normality very well. The problem is, that out of my 9 variables only two are continuous and the ...
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0answers
7k views

interpreting PERMANOVA (adonis function) output?

I am trying to look at expression of some genes and relate the dist matrix (Sm) to a number of different factors that I collected on the individuals (e.g., litter size, licking behavior, group housing ...
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208 views

Use of compana and adehabitatHS

I am analysing habitat use vs. availability by a bird species and have been using 'Manly selection ratios' (3rd order selection) to graph the preferences of 9 different habitats. I also wanted to ...
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54 views

Reduction of species variables in vegetative analysis

Edited following helpful feedback. I have vegetation species data for a number of grassland habitat sites, and am preparing to begin Exploratory Data Analysis. Data was collected in 100 quadrats over ...
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64 views

Quantifying tree height diversity or heterogeneity

I am analyzing data collected in the field for a habitat selection study of a large mammal. I have ~1300 plots that were sampled. I am trying to find a good way to quantify the diversity of tree ...
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1answer
2k 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 ...
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0answers
506 views

Can Hedges' d be used to compare unlike effects?

I've got a question related to the use of Hedges' d in a meta-analysis of insect fitness information. Here is a link (pdf) to the paper I'm working with. In the appendices, the fitness information ...
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1answer
103 views

Basic question about getting esimated probabilities in R

I've got what I think is a fairly basic problem. I'm not sure if it is a conceptual question or software question, but I'm fairly new to using R and these kinds of stats, so it could be either or both....
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1answer
133 views

“Explaining” a time series - conceptual explanation needed

Imagine I have a time series for an animal population and a time series for a climatic variable during the same time period and at the same location. Unfortunately the data are observational (i.e., no ...
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0answers
71 views

Spatially explicit model to test effects of multiple variables

What is the appropriate model to test the effects of location, species, and size on tree growth? So I have both categorical and continuous variables I want in the model. The following graphic just ...
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836 views

Suitable method for modelling (underdispersed?) count data with lots of zeros and long tail

I have a small data set of counts of bees. I tried a simple Poisson model without random effects but it was very overdispersed (3.95). When I fit a GLMM with random effects (using glmer in lme4) it ...