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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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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Strange Looking NMDS Plot
I have a NMDS plot from a fish abundance matrix.
I was wondering why it has come out looking so strange. I am using it because of my data but I am not sure why. Here is a sample of what my matrix ...
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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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Testing the hypothesis that $\sum_i^N p_i^2 =(N-1)/2N$ given $\sum_i^N p_i=1$
In ecology there is a simple index for measuring diversity known as the Simpson index. In it simplest formula, it takes a series of proportions, representing the relative abundance (number of ...
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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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How to create a mixed model with count data and random effects in R for complex ecological data?
I have a question about performing a mixed effects model with random effects in R. I want to test whether there are differences in symbiont genus between coral genera from 4 different types of reef ...
Chiara
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How to estimate population size, recapture rate and survival probability with spatial CJS model
I would like to ask for some help. I am new to data analyses in R and I need some help with my current analyses. I need to make a spatial CJS model with normal dispersal to estimate population size, ...
Kris42
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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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What is the N on a product mean?
I want to sum the means of various measures within a treatment group, and found previous posts helpfully describing how to calculate the Standard error of estimated sum or product mean. My question is,...
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Controlling for strongly collinear variables in a multivariate model
I am looking for some advice for a research project I am working on. My project involves analysis of fish abundance data from rivers around NSW Australia, with an aim of assessing the impacts of dams ...
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How to do Multiple Comparisons of Fitted mle2 Model Coefficients
Is there a way to do a multiple comparison test (similar to tukey HSD test) of coefficient estimates from a mle2 model in R?
Here is my specific application:
I have a large dataset containing ...
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How do I present averages from different sample sizes across years?
I have 20 years' worth of observations that either say YES or NO to the question of whether breeding was observed. I want to present the averages of the YES observations across the years, ...
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Combining multiple observations across quadrats to estimate relative frequency: how do I account for "unobserved" species?
I am trying to figure out if/how I can understand if animals are choosing particular plant species for foraging or just using them based on their availability. To do this, I need to characterize the ...
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What are suitable statistical approaches to examine temporal variation of species abundance/ community composition across multiple sites?
I'm looking for appropriate types of analysis for a data set that contains counts of different crab species across 4 sites with 3 replicates per site (12 in total) over a time period of 1.5 years - 5 ...
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Using statistics to find significant relations between fishmigration movements and acidity in water
I am studying relations between migration movements of different types of fish and acidity (pH) of water. I am stuck on which statistical test i should use to find those significant correlations and/...
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Heavily unbalanced sampling design - Structure of GLMM (ecology)
I am currently working on a dataset (count data) from a rather heavily unbalanced sampling design.
In particular, I would like to be able to predict the abundance of the studied species according to ...
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What is the appropriate statistical test for count data with uneven groups and uneven sampling effort?
I have a problem I've been going over and over for weeks and I'm not sure what statistical test to use for my analysis. I'm planning to execute the analysis in R, so any demonstration of the relevant ...
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Ideas for binomial generalized linear mixed model with both phylogeny and random intercepts?
I've been struggling to find a description of an approach to a situation like mine or any R packages that seem capable of handling my needs. I have a large dataset (~80,000 rows) where my dependent ...
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Confused! Two tailed t-test in r with equal variance
I am a complete novice in this but just trying to have a go. I have a dataset which has the number of birds in my garden each day for one month in June 2020 and June 2021. I would like to see if there ...
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how to test for differential abundance on a subset of samples?
My dataset comprise several samples spanning two treatments $(m1, m2)$ and three timepoints $(n_1, n_2, n_3)$. For each sample DNA and RNA were collected. All together, I have control X treatment, ...
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Index or measure of Host Specificity
I have a dataset that includes occurrence data for different genera of parasitoids as well as their host species. Each data point is one rearing of a parasitoid from a particular host. Some ...
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What do the weights in the specaccum function actually do?
I am trying to create a species accumulation curve that accounts for different areas of each sample. For example, samples were obtained from different sized quadrats. I think the weights argument in ...
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How do I extract the extrapolation prediction when setting the gamma argument in the specaccum function?
I am trying to use the specaccum function from the R vegan package to develop species accumulation curves.
However, I am trying ...
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Looking for advice on what statistical test to run
New master student here and not familiar with statistics, but trying! I have collected data from an experiment but I’m struggling to figure out what type of statistical test I need to run to answer 2 ...
user379508
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Quantifying diversity of bird species
I’m wondering if anyone could recommend a diversity index to look at the differences in breeding bird territories between two sites. These are my data - the numbers represent the number of breeding ...
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Can I ignore high multicollinearity in a proportional binomial GLM from a fully factorial experimental design dataset?
I am running proportional binomial GLMs with 2 factors (Test Salinity and Region) but I am running into an issue with high multicollinearity. The reason for this is because this is a lab experiment ...
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How do you use numPerms to get the total number of unique permutations for a PERMANOVA?
I am trying to calculate the number of unique permutations for a PERMANOVA using the R adonis2 function but I am getting stuck on defining my permutation scheme.
As ...
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Which type of regression can be used to calculate the relationship between zero-inflated percentages and a continuous variable?
I used spearman correlations to test associations between relative abundances (percentages of each microbe present in each sample) of certain microbes and continuous variables. Many people have zero ...
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What statistical test would be appropriate for my study?
I am looking at the difference in flow rate on composition of coarse matter.
I have set flow rate into two categories. Above and below 3700 L/s.
I have raw data that consists (grams of matter for ...
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Singularity in Poisson GLMM - when is it better to switch to GLM?
I am analysing count data (count of observations per day of certain mammal species) at 12 different sites. My dataset consists of ~120 days of observations at each of the different sites. For each ...
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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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Chi-squared on goose counts
I counted geese in two different areas - east and west. Geese were either dark-bellied or light-bellied. I want to know if the proportions of geese differ in the two different areas. So I did the chi-...
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Understanding the unit used to measure the estimate of population density of bears
I do not have a strong stats background, so I apologize in advance if this is a silly question.
I'm currently reading about population density for wildlife. I've read a paper that reports the ...
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nls() singular gradient matrix at initial parameter estimates error
I am trying to run a nls() to interpolate height growth of a tree given a series of samples, where each sample has a value of age, and height. I am using the Richards (1959) method:
$$
\textrm{Height}=...
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Statistical test to assess significant difference in landcover selection
I have GPS collar data that I have used to extract values to points through ArcGIS Pro on MODIS landcover data. From this, I have a record of the number of times the animal has been in each landcover ...
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Statistical test for count data in three different environments
I'm an undergrad student working on a small research project while studying abroad and I was looking for a statistical test that I could use to compare species richness between three forest types.
I ...
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Methods for meta-analyzing ecological community dissimilarity matrices
What would be an appropriate method for meta-analyzing a set of five ecological dissimilarity matrices to generate an overall 'pooled' effect size? I have five ecological monitoring datasets that each ...
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Accounting for 0 observations in presence/absence community data, PCoA/PCA: is this idea credible?
I have a solution in mind for this problem, but I'm not sure if it is defensible (which is why I'm asking you all!). I have a data frame where each row represents an individual site, each column ...
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Is short vector length in PCA problematic? Why are my points so far from my vectors?
I am using PCA to examine the relationships between environmental factors of a couple of different types (physical properties, concentrations, relative abundance of genes). I have log-transformed the ...
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My data is right skewed and I don't have independent observations, which statistical model should I use in R?
I have biomass data collected at 3 different distances from 42 different ant mounds (at the edge of the mound, 1m and 4m away). In total there's 42 ant mounds, from 11 plots at 5 different elevations (...
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