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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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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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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Model specification in nlme: Random effects
My design has a total of 20 sites. 5 sites belong to each of four land covers: A, B, C and D. In each site, I have 5 sampling locations, 2 metres from each other. From each sampling location, I ...
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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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How to properly perform constrained ordination (RDA) when the sums of the rows of the constraining matrix are equal to the same value?
When performing an RDA where the constraining matrix displays equal sums of rows, the last column in the matrix is always considered aliased and therefore dropped. I am asking why this happens and how ...
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Book about ordination in ecology
I am looking for a book that would cover a lot of different ordinations techniques (indirect gradient analysis e.g. PCA, CA, DCA, MDS, nMDS but also direct gradient analysis e.g. CCA, CCorA, RDA) with ...
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How do I find the number of unique permutations for a PERMANOVA with an unbalanced design?
From the PRIMER manual (p. 28 about Monte Carlo permutations; http://updates.primer-e.com/primer7/manuals/PERMANOVA+_manual.pdf), the number of unique permutations for a PERMANOVA with $a$ groups and $...
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Several single-species GLMMs -> A multi-species GLMM (random effects syntax?)
I'm looking to describe annual relative abundance for several species over several years by analyzing point count data. I'm using a Poisson GLMM in glmmTMB for each ...
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At what stage of the species distribution modelling to standardize variables and check for collinearity
I try to model the distribution (ecological niche) of a species using a generalized linear model (glm() in R) based on several climatic variables and then apply the ...
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OLS difference between individual level and aggregate level estimates
I am new here, so please accept my apologies if this does not belong here.
My question essentially concerns what appears to me a special case of the ecological fallacy. Consider a simple model that ...
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Standard error of estimated sum or product mean
Updated question: Given two sample means ($\bar X, \bar Y$) and sample standard deviations ($S_X, S_Y$) with different sample sizes ($n_X, n_Y$), I want to calculate the standard errors ($SE_\theta, ...
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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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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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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 ...
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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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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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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 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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What distribution to use for response variable which is a ratio of counts (that are not independent) where it can be >1?
I have two sets of counts, bat passes and feeding buzzes. A feeding buzz is not independent of a bat pass. In a single bat pass, there can be multiple feeding buzzes. My response variable is buzz ...
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Problem with Clamping mask in Biomod2
I'm trying to project an alien species distribution with Biomod2, algorithm GBM, random pseudo-absences in equal number to presences, background restricted to the zoogeographic realms in which the ...
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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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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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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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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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1
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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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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 ...
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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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493
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Working with Discrete-Time Survival Analysis with Random Factors in R
I'm working with some data on artificial (fake) bird nests, looking into their 'survival' from animal attacks. I visited the nests once every two days, for 2 weeks (so my time points are 2,4,8,10,12,...
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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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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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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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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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2
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1
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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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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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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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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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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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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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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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GLMM - how unbalanced is unbalanced, how under-dispersed is under-dispersed?
I have a large data set, with vegetation data sampled at plots that are Sand or Clay soil type at 20 sites. I plan to fit a GLMM to the data, with 'soil type' as both a fixed effect and as a random ...
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2
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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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Poisson Binomial Distribution - confidence intervals for sum of unequal probabilities estimated with uncertainty
I believe my question is related to, but distinct from this one:
Poisson Binomial Distribution - confidence intervals
I am working to estimate species richness by summing the results of 12 individual ...
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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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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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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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