# 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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### Constrained ordination (CAP) pairwise ANOVA

Is there any way to perform pairwise ANOVA test from Constrained ordination for multiple factors in a variable? e.g. I am trying to figure out whether microbial communities among five plant genotypes ...
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### What kind of training in statistics should an undergraduate in ecology be subjected to? [closed]

How many 1 semester courses on statistics do you feel would be a bare minimum for a biologist? What are the topics that you think should be fundamental to be covered when providing a 1 semester module?...
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### Does the distance matrix have to be symmetric for a cluster analysis using Ward's method?

Does a distance matrix used in a cluster analysis need to be symmetrical? My past experience with cluster analysis usually involved a lower triangular distance matrix but a recent method I came across ...
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### What is the correct bayesian formulation for the zero-truncated Poisson lognormal model?

In ecology we use compound distributions to describe species-abundance data. One example is the Poisson Lognormal (PLN) distribution which is a Poisson distribution with rate parameter $\lambda$ that ...
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### Specifying a correct model using glmmTMB while experiencing unusually large coefficients and z-statistics

I have a data set of an beetle community where I want to analyse species richness (for example). The experimental design is as follows: 4 blocks 19 plots 2 different treatments 3 samples of the ...
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### The moose must flow, but how?

Background Suppose I collected a data set of the latitude and longitude of moose tracks within an irregular polygon, and also took a compass bearing of the direction that the hooves pointed in. Image ...
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1 vote
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### How to compare trend of two different datasets?

I have two different datasets (ID 1 and 2) which show the number of animals per hectare for each year. I need to know if the trend for the first periode is different then the trend for the second ...
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1 vote
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### What do the % variances mean on a Bray curtis dissimilarity plot?

I'm new to microbiome data analysis but what do the percentages on the Axis mean? This plot is comparing two groups (SPF n=8 and ABX n= 4 mice). I can't figure out what these mean. I thought the axis ...
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### How should I interpret contradictory pairwise and non-pairwise beta-diversity metrics from beta.multi and beta.model.decay functions?

I am doing a community ecology analysis and am interested in partitioning beta diversity across sites of different ages (age = time since disturbance) and determining whether beta-diversity is ...
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### How can I quantify temporal variation into a single value without losing magnitude?

For my ecological research on the impacts of intensity of space-use on vegetation structure I need to quantify temporal variation in the intensity of space-use across years (resulting in a single ...
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### PCoA plots in R on presence/absence community data: rows filled with zeros give an error

I am currently making PCoA plots on Presence/Absence community data. My rows are populated with samples and my column headings are different taxa that were detected. However, since the experiment is a ...
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### GAM - setting K-values before or after testing the different models

I'm working with GAM and I'm testing different models with and without certain variables, and I need to set k-values for the different smoothers. Do I need to use the exact same k-values prior to ...
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### Comparing Gini indices and Hill numbers between groups

I'm looking for methods (and R packages) that can test for differences in Gini indices and Hill numbers between two groups. The R ...
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### What is the appropriate way to statistically analyse diversity indexes?

I have been working with a soil-derived viral metagenomic data set and am looking for advice on the appropriate statistical approach to the results. I have 2 different sample areas. Within both areas ...
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### How to best make site-comparisons of pollutant concentrations with few observations of pooled tissue samples (average of many individuals)?

I have data on mercury in fish from three different lakes. What I want is to fit a model to investigate differences between mercury content between the lakes. However, mercury in the fish were not ...
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### Comparing capture efficiencies of sampling gear?

I have capture data for a fisheries population assessment. Two different crews were used that did surveys separately, each with variations in specifications of the gear that they used (same gear type/...
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### Valid to only use random slope for linear term when the variance of quadratic slope term is near-zero?

I am performing some habitat analyses across a large area and am incorporating random slopes in my models for landscape predictors and a random intercept for individual animal. According to this post ...
25 views

### Compositional data: is it possible to make products of components/features in a composition?

I've never asked about Stack OverFlow, even though it's been so useful to me on many occasions! I'm sorry if this topic has already been discussed previously, perhaps I wasn't able to find the good ...
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### When does a group specific dispersion parameter for the negative binomial distribution make sense?

If you have overdispersed observed abundance of multiple species including zero inflation the negative binomial distribution seems to be a reasonable choice. But if some species occur much more ...
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### Analyzing variance around groups of population parameters- making statistical vs practical inferences

I am trying to compare variances of parameter estimates between groups that signify different levels of sampling effort put forth to obtain said estimate. Below is an image of a plot showing the ...
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### Showng distinct clusters/groups in microbial community data and accounting for different number of replicates?

I have 16S data to look at the microbial communities of two types of hot springs; I've been working with this in R. Some of the data is from 2017-2019, but the bulk of the data is from last year. ...
1 vote
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### How to determine the significant association between pathogen and plant species?

What's the best way to determine if a particular host plant species (host_plant column) was infected in significantly higher number by a certain pathogen genus (pahothogen_genus column)? I have ...
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### Constrained Clustering via Distance-Based Multivariate Regression Trees in R?

I was wondering if distance-based multivariate regression trees (or distance-based multivariate random forests) are implemented any R package? De'ath (2002) describes multivariate regression trees ...
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### Weights in a resource selection function with logistic regression

My understanding from Fithian and Hastie 2013 is that to do a resource selection function with logistic regression, you need to weight the available points much more heavily than the used points. I am ...
1 vote
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### Dissimilarity only between different treatments in dataset

I am studying the impact of wildfires on vegetation species composition. I have surveyed the burnt and unburnt areas on six sites which burned at different points in time from which I now have species ...
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### How to combine response data of different types for modelling fruit crop size?

Some context first: For a section of my research project I am investigating how environment (soil, climate) influence the number of fruit (crop size) produced by individual trees of the same species ...
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### What's the right statistical analysis for temperature effects on turtle hibernation over time?

I have an assignment in which I am supposed to create a theoretical study design within a biological field. Currently, I have data from a group of seven turtles. For the assignment, I thought it would ...
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### Standard deviation vs. standard error for error bars in observation studies?

I need some help understanding why error bars/confidence intervals (C.I.), i.e. plus/minus 1.96*standard error, are important in observation type studies. I understand them as: "If an experiment ...
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### How to interpret the result of this box plot?

I'm relatively new to statistics and am working on my first independent research. I produced this box plot to display whether plant height had an effect on egg oviposition. I'm having a little trouble ...
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### How would you interpret this scatter plot?

The number of eggs oviposited based on plant height shows that there is a significant correlation. However, I am finding it difficult to understand whether it is the lower plant height that allows ...
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### Metrics to compare diversity of groups on multiple characteristics

When I search for 'diversity metrics' it seems like most work has focused on ecological diversity, and I most frequently see the Simpson diversity index. This is equivalent to the economics metric, ...
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### Time-series/autocorrelated data in Redundancy Analysis (RDA)

My problem is about the RDA analysis of time-series audio data with environmental data. I have time-series data (Y) - one data frame with audio data (represented by acoustic indices) which is for 20 ...
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### Should I use random effect or spatial correlation structure?

I'm working on a vegetation analysis, where I am comparing different remote sensing indices' ability to predict field measured vegetation characteristics. Sample size is 56. The study design: Two ...
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### Show statements for error residual and Taylors Law

I have some data from a lake. "Counts" is the response variable and is a number for the organism in the lake. I also have a variable "stations" that indicate every parts of the ...
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### RStudio Binomial Test providing strange results

I am running a series of binomial tests for different trials. I ran 319 trials, and no matter the number of successes, my p-value is still < 2.2e-16. This includes when my trial had 0 successes. <...
1 vote
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### Diversity index and categorical variables,-

Is it possible to calculate a diversity index (Simpson's or eventually Shannon's index) from ordinal data? As in, we surveyed 50 transects and recorded several species' "abundance" in 4 ...
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### Disparity between observation depth and the depth a candidate predictor was modelled at: use in interaction term or set as weight?

I have been fitting GLMs and GAMs in a marine (benthic) species distribution modelling context. Various candidate predictors I have been using were sourced by intersecting the occurrence points with ...
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### Is n-dimensional hypervolume different from n-dimensional state space?

Is there any difference between Hypervolumes (e.g. Blonder et al., 2014; Barros et al., 2016) and state spaces (sensu von Bertalanffy, 1972; e.g. Tett et al., 2013)? If so, what is it? It seems that ...
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### Differences between nested ANOVA and two-way ANOVA, without a repeated measures structure and a small number of levels per factor

My question is rather simple, and it's not so much about R, but about how to analyse a very simple dataset. I have 6 sites, and 2 ecosystem type (3 sites per ecosystem). From each site I have 3 ...
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### GLMs: Calculating a response variable from a predictor variable?

I am wondering if it is statistically acceptable to include a predictor variable in a GLM that was used to calculate the response variable. For example: I am looking at fisheries data. I have a ...
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### How do I model occupancy for species with high occupancy values?

I'm trying to produce separate single-species occupancy models for 59 beetle families. Some of the families have very high occupancy across all sites (125/127) which gives me large parameter estimates ...
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### Analysed non-linear data with GAM regression, but reviewer has suggested fitting exponential or logarithmic curves instead. Which to use?

I am trying to publish my Masters thesis which looked at elephant impacts on vegetation, with a focus on the effect of artificial waterholes. I have made my initial submission and am now performing ...
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### How to include standard deviations in diversity calculations?

I have community abundance data where each species has a mean and a standard deviation (determined by replicate samples). I am comparing the diversity of two communities. The various diversity metrics ...
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### How to use the chi squared test (a biological investigation)

Imagine four habitats - A, B, C and D - set up in a choice chamber and two species of the same family, X and Y, 20 individuals of each. In a series of experiments, we put these species into the choice ...
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### Very low values of explained variance for the first Axes from PCoA

I am comparing different sites based on their floristic composition in R. Therefore, I have created a huge community datamatrix (presence/absence data) from 53 sites including over 1000 species. To ...
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### Understanding offsets for continuous variables

I'm currently trying to write a linear model with data from some behavioural experiments with termites. I started to read Ben Bolker's "Ecological Models and Data in R", which has been a ...
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### How to correct pattern in residuals when using a negative binomial distribution? Is it due to overdispersion?

I have a large dataset with the count data and I computed the following full model (covariates are all scaled) : ...
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### How to correct spatial autocorrelation with glmmTMB when there are several observations on sites?

I have a large dataset of several species' activity parameters during nights and I want to account for spatial autocorrelation (tests and graphs show that my models suffer from it). However, I cannot ...
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### I have diversity index values and I wish to test for statistical significance between the zones readings. How can I statistically analyse this?

I have produced a graph for each Zone, x axis = years, y axis = diversity. I would primarily like to analyse the difference in diversity between the zones, but would also be interested in analysing ...
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