# 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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### 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 ...
2answers
3k views

### Question about logistic regression

I want to run a binary logistic regression to model the presence or absence of conflict (dependent variable) from a set of independent variables over a 10 year period (1997-2006), with each year ...
4answers
18k 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)...
2answers
461 views

### What is the distribution of the error around logistic growth data?

In ecology, we often use the logistic growth equation: $$N_t = \frac{ K N_0 e^{rt} }{K + N_0 e^{rt-1}}$$ or $$N_t = \frac{ K N_0}{N_0 + (K -N_0)e^{-rt}}$$ where $K$ is the carrying capacity (...
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 ...
3answers
4k views

### Books on statistical ecology?

I know this question was asked before: Reference book for ecological studies but it is not what I am looking for. What I am looking for is if anyone could recommend a good book (or a canonical ...
1answer
10k views

### Interpreting output of dredge

I ran a GLM for the first time in R and am not sure how to interpret the result. This is the input: ...
1answer
369 views

### How to construct quadrats for point processes that differ greatly in frequency?

I want to perform quadrat count analysis on several point processes (or one marked point process), to then apply some dimensionality reduction techniques. The marks are not identically distributed, i....
3answers
6k views

### Variance of a distribution of multi-level categorical data

I am currently analyzing large data sets with various characteristics (such as city). I wanted to find a measure which would essentially say how much or how little of a variance there was across the ...
1answer
436 views

### Does using box-cox transformation on individual data sets prevent these data from being comparable?

I have been using the box-cox transformation to normalise data for input to an Ecological Niche Factor Analysis software, as recommended by the software creators. However, it has occurred to me that ...
3answers
515 views

### Can I test for correlation between variables before standardize them?

What I want to do is to construct GLMM's to evaluate resource selection, and I have a set of variables (some representing distances and others representing % of land cover). Can I test for ...
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 ...
1answer
4k views

### Species Richness, Dominance and Diversity Differences

I have collected 70 organisms from 4 different sites; two sites of treatment 1 and two sites of treatment 2. I also have a continuous explanatory variable (average temperature) which is different ...
2answers
894 views

### Population model to model year to year dynamics

My task is to assess how various environmental variables affect annual population fluctuations. For this, I would use a model like:  \mbox{log} ( \mu_{i,j+1} ) = \mbox{log} ( \mu_{i,j} ) + R_{j} + \...
1answer
285 views

### Check for significant difference between numbers of sightings per cardinal direction

I have data in a form like this: quantity direction 10 n 5 e 6 ne 12 n 20 nw 5 s 8 n 1 sw 3 se 2 ne 6 nw 8 n 2 se 3 e 4 w 9 nw The information behind these ...
2answers
140 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 ...
2answers
645 views

### How to use a mathematical model for data analysis in R

I am looking to use a mathematical model developed by Firbank & Watkinson (1985) J. App. Ecol. 22:503-517 for the analysis of competition between plants grown in mixture. The model is as follows: ...
2answers
3k views

### Initialize ARIMA simulations with different time-series

I have a fairly long time-series of annual abundances ($N_t$) of a wildlife species (73 years of abundances). To forecast the populationās trajectory, I have used ARIMA modeling. Examination of the ...
2answers
182 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 ...
1answer
88 views

### Estimating species distribution and rate of expansion using only positive data

Short version: is there any statistical method that can be used to develop estimates of abundance, spatial distribution, and/or rate of spread of a species when my dataset only includes presence data ...
1answer
417 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 ...
1answer
135 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, ...
1answer
865 views

### Custom power analysis in R

Distance sampling is a common technique used to estimate the abundance of wildlife species (such as deer or turkey). This technique employees line-transect based sampling where perpendicular distance ...
0answers
124 views

### Help with designing the analysis of a radio telemetry study

I was wondering if there are any spatial ecologists out there who can provide some insight on the trouble I'm having with my Masters research. I am looking at the association a bat species to high ...
4answers
529 views

### Books about model selection in ecology

I am an ecology student and have to deal with 10 or 20 field variables, including species frequencies. I need to screen out what variables are most important in the occurrence of a bird species. What ...
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 ...
1answer
2k views

### Ecological mixed data cluster analysis: Transformations required? Use K-means or hierarchical methods?

I am trying to identify habitat types from 85 plots. I intend to do a cluster analysis to identify habitat types, and hope to fit additional plots into the identified clusters. (For context, I took ...
2answers
2k views

### GLMM- relationship between AICc weight and random effects?

I am developing GLMM's in order to assess habitat selection (using GLMMs' coeficients to construct Resource selection functions). I have (telemetry) data from 5 study areas, and each area has a ...
1answer
109 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)...
1answer
128 views

### Are the posteriors “different”? How does one discuss the result?

First, I realize this may be a basic question. However, when I search the web for references on this issue, I run into the problem of wondering if the description I'm reading is applicable to the ...
1answer
125 views

### Example of danger of ecological correlation of rates?

Lots of textbooks and websites warn about drawing conclusions from "ecological correlations" which are defined as correlations between rates or averages. All the places I've looked at have used the ...
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 ...
1answer
234 views

### Multivariate Analysis of Ecological Data: Procrustes analyses or GLM?

I have a dataset containing 6 variables (vegetation cover in percent) and the number of species found in 30 areas. I would like to test if the different vegetation covers explain species richness. ...
1answer
66 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 ...
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, ...
1answer
73 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 ...
0answers
118 views

### Regressing on many outcomes in a spatial model [closed]

I'm measuring many microbe populations in a 'river model' ecosystem by sampling at two points. I want to test the hypothesis that key species upstream are the best predictors for any given population ...
0answers
441 views

### Comparing two non-linear biological models: differences in y vs. differences in slope

I'm an ecology PhD student, but unfortunately not a very mathematically sophisticated one. I am interested in ways to compare two non-linear models. I was really impressed with this answer, which ...
1answer
36 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-...
1answer
95 views

### Does the Mann-Whitney U-test need to be adjusted in twin studies?

I have data from 44 twin pairs (88 patients total) and they are split into group_A (n=50) and group_B (n=38). For each of the ...
2answers
224 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 ...
1answer
49 views

### 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 ...
1answer
140 views

### Circular statistics for discrete, irregular sector data

A colleague wants to examine the directionality of amphibian dispersal to and from a pond. He set up a drift fence around the pond and had buckets at different positions to capture the amphibians. He ...
1answer
65 views

### Can I reduce the AICc penalty for multiple variables, when some variables should be grouped?

I have a data set of mean trait values for each of 18 populations, and want to test whether several ecological variables are related to variation in traits. I'm using the corrected Akaike information ...
1answer
2k views

### When to use distance biplot vs. correlation biplot in PCA

I wonder what could be good examples of using scaling 1 and 2 for a principal component analysis biplot. By examples, I mean ecological examples or applied examples of the PCA scaling so that one can ...
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 ...
2answers
341 views

### What is the difference between a logistic curve and something that overshoots?

In population dynamics, the growth of a population can have exponential growth, or a logistic curve growth up to its carrying capacity, or it can overshoot the carrying capacity and fluctuate before ...
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....
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 ...
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 ...