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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Need some advice in selection of GAM model - choosing family, etc

I am not a statistician (clearly) and am trying to wrangle environmental data. My data looks like (note data is on time scale - 1 = Day 1, 650 = Day 30: I am developing a GAM model which predicts the ...
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Can I test for differences in frequency data?

So I am investigating if an animal is being sighted more frequently in recent years. I have data that includes group size of this data - ie. year Group Size 2018 4 2018 26 2019 10 2019 46 2020 9 ...
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Appropriate statistic for comparing Population Matrix Model predicted values to observed values

I have 2 different hindcast population matrix models (left and right) that predict annual nest numbers (median black line, 50 and 95 CI blue ribbons). These models are completely independent of any ...
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How to choose number of sites and number sub-sites within each site in planning stage of a study? (ecology)

I have a situation in which I am going to perform a study on live blue mussels. The research question is how the prevalence of mussels affects the prevalence of other animals living on the sea floor. ...
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DHARMa diagnostics: what to do with sig. KS test and quantile deviations

I am fitting a GLMM to powerline collision data for a bird species- using distance to seasonal water, habitat and the presence/absence of line markers as predictors. Incident is a binary response (50 ...
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Binomial GLM for attracting large mammal from presence/absence data

This is my first post here so I apologise if it is formatted incorrectly or missing key info. I need a little bit of help/direction with interpreting R results for a project. Basic premise of project ...
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Several single-species GLMMs -> A multi-species GLMM (random effects syntax?)

I'm looking to describe annual relative abundance for several species over several years by analyzing point count data. I'm using a Poisson GLMM in glmmTMB for each ...
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What test to use after a PCA?

Need some help answering a prac exam question "An ecologist is interested in the morphological adaptations of goannas to their microhabitat. She wishes to determine if goanna shape differs for ...
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How to deal with stress over 0.2 in NMDS in large dataset [closed]

I am analysing a large dataset (2000 rows by 250 columns) of the presence of species in several locations over the last 20 years. I have conducted a NMDS in order to identify differences between the ...
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Post hoc on mixed model ANOVA with one fixed variable on random independent variable in r

https://www.youtube.com/watch?v=FuiUvwflkVQ In essence, I want to do the exact equivalent to what this video does, but in R rather than SPSS. So far I've used the following code, where DV is my ...
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How do you count the number of parameters in a mixed model? [duplicate]

I'm trying to build my first linear mixed model. I ran some experiments in which I looked at whether the biomass of 40 ecosystems depended upon two conditions (x1 and x2) and their interaction (x1*x2)....
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How to quantify temporal overlap of species abundance?

I want to compare the extent of overlap of species abundances in the following two secanrios. In the first scenario, species barely overlap so the index or overlap value should be zero. in the second ...
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How to interpret the niche overlap index (sensu Piyanka, Gotelli) 1-tail and 2-tail 95% CI?

I am trying to make sure I understand how to interpret Piyanga's niche overlap index and it's simulations in EcoSimR In short, if index is 0 (no overlap) and 1(complete overlap). I calculated temporal ...
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Could I fit a third-order response surface given this experimental design?

My supervisors and I are planning to run an ecological experiment in the very near future. They have proposed an experimental design and I would like to get some feedback on it. In particular, I am ...
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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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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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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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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 ...
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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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Similarity and distance measures from Presence-Absence data

I am doing some ecological analysis with presence-absence count data. I am interested in similarity and distance measures that have the form using the standard notion of: $$ \begin{array}{c|cc|c} &...
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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. ...
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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 ...
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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 ...
2 votes
1 answer
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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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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. <...
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Diversity index and ordinal 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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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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