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.
381 questions
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Correct binomial GLMM for temporal trends in species occurrences
I have a dataset with 80 species which were sampled in about 120 water bodies at two time periods (historical / recent). Only presence/absence of the species in each water body is considered. The data ...
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Ecological temporal statistical analysis question
I collected animal samples without replacement over three time periods from the same locality: seven years apart in the deep-sea (eg, no known seasonality). I want to know whether the mean difference ...
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Problem finding a distribution for my data (glmm)
I want to do a correlation analysis of two variables ranging from zero to one (including those values), and including other possible environmental explanatory variables.
I opted for a mixed model, ...
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Statistical test for whether two methods of measuring community composition produce the same distribution?
I'm measuring community composition (i.e., the distribution of abundance) of 30 taxa as captured in 3 samples at 1 site. For each of my samples, I've measured community composition using 2 different ...
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At what stage of the species distribution modelling to standardize variables and check for collinearity
I try to model the distribution (ecological niche) of a species using a generalized linear model (glm() in R) based on several climatic variables and then apply the ...
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cloglog vs logistic regression survival analysis
I'm not looking for an explanation of the difference between hazards and odds here, what I am curious about is determining if, as is sometimes presented, a hazard model (cloglog link) is equivalent to ...
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How to run a test between two or more groups when each data point brings a confidence interval?
I have recently started working on a dataset, but my limited experience as a recent graduate is preventing me from making progress. After performing a rarefaction (a form of bootstrapping), which was ...
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Chi-square distance for a single species' abundance
I'm looking at quantifying similarity between sites by abundance in a heatmap (and then clustering the variable site), but only for a single species (over time). I have been drawn to the chi-square ...
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How do I determine if my ecological GLMM is accurately constructed?
I am an early career ecologist/biologist and I have been working on a Generalized Linear Mixed Model in R to determine influential variables to wildlife behavior. I have been learning as I go and I ...
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What scale do I need to consider when calculating a body condition index?
I'm trying to calculate a body condition index (scaled mass index [SMI]; Peig and Green 2009) for groups of frogs and I'm having trouble understanding what scale I need to consider when calculating a ...
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Deriving Fisher's mysterious estimator for the Unseen Species Problem
From Wikipedia:
In the early 1940s Alexander Steven Corbet spent 2 years in British
Malaya trapping butterflies.He kept track of how many species he
observed, and how many members of each species ...
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Nested studydesign - Necessary to restrict permutations in betadisper?
I have the following study design: 8 locations, 5 forest types (Plots) per location (D,DB,B,FB,F). In every plot I sampled spiders and identified them. I did an NMDS with Morisita-Horn index.
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Comparing changes between two time points in ecological survey data with different survey methods
I’m working on analyzing some underwater ecological survey data, and I’m hoping to get some advice on the best statistical approach. The surveys were conducted at the same sites in 2009 and 2024, so I ...
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How to sample from all admissible populations of individuals from a given distribution?
Problem description
Below, the term "population" refers to a population of individuals in the ecological sense.
Suppose we are given a set $S \subset \mathcal{P}(T^N)$ of admissible ...
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test for significant differences in communtiy composition between habitats? required PERMANOVA sample size?
I sampled spiders in 5 different forest-stands. I originally had a sample size of 32 per forest-type, but as I had to pool the data I now just have 8 samples per forest type.
I did an ordination with ...
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Can I use ANOVA after clustering?
I am helping someone analyse data on plant species. They divided a town into equal-sized squares and collected data on the weed species growing in each square. I used cluster analysis (Ward.D2) to ...
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Permutest or TukeyHSD for group-wise comparison after significant Anova of betadisper?
I want to perform a PERMANOVA with my community-data of spider assembladges, sampled in different forest stands. Before applying PERMANOVA I wanted to find out if there is a difference in the ...
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NMDS with Morisita-Horn Index: which data-transformation makes sense?
I have a community matrix of spiders, which I captured during winter in different forest stand-types.
I now want to perform an NMDs. For that I want to use the Morisita-Horn Index from R in the ...
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Environmental filtering versus spatial resampling in species distribution modeling
I am building species distribution models using machine learning models based on GBIF data (presence-only data) and working on a very large spatial scale, encompassing all of North America. Before ...
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In MVGAM, how can I model an interaction between 1 continuous variable (Abundance), 1 discrete (time in days) and 1 factor (the Genus of eukaryotes) [closed]
I'm working in microbial ecology and I'm trying to modelize the influence of the abundance of several genuses on a single genus of interest through time in a situation of primary succession of ...
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What is the best mixed model approach for a time series of animal attack records?
I have a dataset of animal attack records for Brazilian states between the years 2007 and 2022. I have three explanatory variables, which were standardized for the analyses. To incorporate the ...
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Best solution was not repeated - no reliable result for metaMDS?
I have abundance data of spiders that I captured in different forest stands and I want to perform an NMDS. It generally works, although the stress value is relatively high. However, I get the message ...
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dubious diagnostics in species distribution modeling with mgcv gam
I am doing some marine species distribution modeling with gams and mgcv in R. The diagnostics from gam.check(), and concurvity() seem dubious. Are there issues with the specification of the model, or ...
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How to Statistically Test if a Community of Species at a Particular Site is Becoming More Like Another Type of Site
I have the following data frame (I'm using R here).
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What Statistical test to use on my project?
I am very confused about what kind of statistical test to use in RStudio on my project,
I have measured the mean salinity for 3 levels of population density (low medium and high) across 6 months (...
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Transforming count data for NMDS?
I am looking at species count data. Due to large counts of certain species, I initially fourth root transformed the data. I am using Bray-Curtis distance measurement.
However when using vegan::metaMDS,...
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Is there a way to perform a Hierarchical Partitioning with NMDS in R?
I performed non-metric multidimensional scaling (NMDS) on my ecological data and I was satisfied with my results, but I was told that I should use hierarchical partitioning in my analysis to check for ...
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Should data be transformed for NMDS? [duplicate]
I am looking at species count data. Due to large counts of certain species, I initially fourth root transformed the data. However when using vegan::metaMDS-Bray Curtis distance, the stress value for ...
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Dealing with Underdispersion in Poisson Regression (GLM) with count data as a response variable
Related to glm() in R, I am working with count data (number of mammal species on islands) and following statistical theory, I have fitted a ...
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How to apply RLQ ordination to communities with different species?
I am analyzing the relationship between bird traits and environmental variation using the RLQ ordination corrected for spatial autocorrelation and phylogeny, i.e., the method in Pavoine et al. 2011
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What is a good p-value adjustment for a permutational analysis like pairwise PERMANOVA?
I am comparing plant community responses to experimental treatments using the pairwise.permanova function in R.
However, there are no clear answers regarding which ...
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glmmTMB for non-regression ecological count data?
Study design: I am analyzing ecological count data for fish in a pre-existing database with observations of fish species abundances(zero_filled). Each species were recorded at a site twice a month of ...
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Is there a best approach for statistical power for field experiment?
I'm setting up a field experiment and want to make a solid plan for the analysis, since that's whereI get stressed in the process. I will deploy 26 pairs of traps. 13 pairs will be in urban forest, ...
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Lotka-Volterra ordinary differential equation model to describe oscillations in a single observed entity
Background
The Lotka-Volterra model is the starting point for any model of ecological dynamics. It can be described as a set of two ordinary differential equations (ODEs) with varying complexity. ...
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How can one measure spatial clustering of continuous (non-count) data?
I am currently teaching an ecology class how to use the variance to mean ratio (VMR) as a method for looking at the spatial clustering of individual organisms across a landscape. This method takes the ...
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How to compare two species community matrices that were measured differently
I have two species community matrices, where each row is a site and each column is a species. The rows and columns are the same for each matrix (i.e., row 1 = site 1, column 1 = species A for both ...
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SIMPER results interpretation
I am doing a SIMPER analysis(R::vegan) where I want to determine which species are contributing the most to differences between thermo groups-warm and cold.
(I am count data that is separated by years....
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Data is not normal, want to test for interaction too Any non-parametric test? [duplicate]
I have a sample size of $310$ individuals that comprises samples collected along the elevation gradient and at different times. I want to see how the variables differ along the elevation, and with ...
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multivariate analysis for seasonal patterns among rivers
I sampled three different rivers over one year during the four seasons. In addition, in the autumn and winter seasons I sampled both during an event of high (drought period) and low water (flood ...
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Glmer with count data, repeat measurements and how to interpret output
I'm very new to mixed models (this is my first attempt) and have about 2 months experience in R so please forgive my ignorance. I am seeking guidance on my current project analysing the relationship ...
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Which dissimilarity index to use with categorical ecological data
I am currently working on data representing the abundance of microorganisms in a categorical way, like 0 = no organisms; 1 = 1-5 organisms; 2 = 6-10 and so on (5 being the highest number). And i am ...
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Unsure of statistics needed while working with replicates
I apologize if the question is considered too broad, but I'm hoping to get at least a basic starting point as I'm somewhat stuck with how to approach this.
I am working with community ecological data-...
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Interpreting Logistic Regression with categorical variable
Please help! I am using binary logistic regression to model the probability of nesting in 5 different habitat types, with 1 = nest presence and 0 = random point. I have 5 different habitat types and ...
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How to test the importance of environmental variables to a crocodile when selecting a nest site (geographic location)
I don't have a background in stats so please bear with me. I'm developing a study on where saltwater crocodiles nest. I want to see how variables such as slope of the bank, sun exposure, vegetation ...
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Why don't vegan::vegdist and vegan::metaMDS produce equivalent results?
This question has been discussed before but the proposed solution (https://stats.stackexchange.com/a/459820/170801) is no longer reproducible for some reason. As a refresher - it has been suggested ...
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Chi-squared test with more than two variables, or should I run a different test?
I am looking at whether certain animals or categories of animals are more likely to use human-made trails than natural trails. We used camera traps and recorded for every case which animal it was, ...
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Performing Chi-Square test (or similar) across a spatial grid
I have a dataframe in R where each row is an sf-formatted geospatial grid. For each grid, I have the number of venomous snakes and the number of non-venomous snakes seen in that area. I also have data ...
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PCA with soil cover of plant species
8 plots (quadrants 3 x 3 meters), 4 invaded with an alien plant, 4 without the alien plant.
I have measured the soil cover (as %) of the species found in these 8 plots.
If I make a PCA with log (n+1)...
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Whether to include a random effect that is potentially collinear with a fixed effect
I am trying to model bird migratory departure dates using linear or mixed effects models (although open to other model suggestions). I am interested in knowing whether latitude, sex, wing length (a ...
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Applications of total least squares and related pitfalls (in biology/ecology)
I recently discovered TLS for a bio-statistical (ecological) problem I am working on. However, I was not able to find a lot of (ecological) literature that uses TLS in their analysis. From other ...
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