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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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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 ...
Samuel beauregard-tousignant's user avatar
2 votes
1 answer
42 views

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 ...
Mauricio's user avatar
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1 answer
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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 ...
Jenny s.'s user avatar
2 votes
0 answers
100 views

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 ...
Thanasis's user avatar
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0 answers
68 views

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). ...
David Moore's user avatar
1 vote
0 answers
40 views

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 (...
Willa's user avatar
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1 answer
59 views

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,...
user390865's user avatar
0 votes
1 answer
21 views

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 ...
Michael 's user avatar
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7 views

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 ...
user390865's user avatar
2 votes
0 answers
60 views

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 ...
ykk's user avatar
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1 answer
15 views

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 ...
michela's user avatar
1 vote
0 answers
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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 ...
Reesamu's user avatar
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0 answers
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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 ...
user390865's user avatar
0 votes
0 answers
13 views

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, ...
E10's user avatar
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0 answers
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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. ...
Luka Seamus Wright's user avatar
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17 views

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 ...
Michael L's user avatar
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1 vote
2 answers
89 views

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 ...
aeiche01's user avatar
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0 answers
349 views

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....
user390865's user avatar
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0 answers
39 views

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 ...
scholar101's user avatar
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0 answers
17 views

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 ...
Rudy Benetti's user avatar
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0 answers
33 views

Species differential abundance across time series samples

Apologies if it is a stupid question or has been asked before or I have phrased it the wrong way, but I have been looking for an answer for days and I could not find anything - so any help will be ...
Panos Sapou's user avatar
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0 answers
26 views

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 ...
JMenezes's user avatar
  • 539
2 votes
1 answer
133 views

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 ...
RFD1998's user avatar
  • 23
1 vote
2 answers
83 views

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 ...
Fabi B's user avatar
  • 11
1 vote
1 answer
35 views

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-...
user390865's user avatar
1 vote
1 answer
80 views

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 ...
Jimmy's user avatar
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1 vote
0 answers
35 views

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 ...
CharlieD's user avatar
0 votes
0 answers
37 views

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 ...
user avatar
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0 answers
20 views

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, ...
user avatar
0 votes
1 answer
60 views

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 ...
befriendabacter's user avatar
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0 answers
59 views

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, ...
Manon Obdeijn's user avatar
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0 answers
45 views

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 ...
Bradley Allf's user avatar
1 vote
0 answers
32 views

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)...
dandelion's user avatar
2 votes
1 answer
99 views

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 ...
purplebubbles93's user avatar
2 votes
1 answer
166 views

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 ...
Dunen's user avatar
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0 votes
0 answers
71 views

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,...
Amanda D's user avatar
1 vote
0 answers
54 views

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 ...
Lukian Adams's user avatar
1 vote
0 answers
31 views

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 ...
PlantModeler's user avatar
3 votes
1 answer
490 views

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, ...
SamR's user avatar
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1 vote
0 answers
40 views

Is it reasonable to apply different offsets to different species in community analysis?

I am using the manyglm function from the mvabund package. I have a site X species/family dataset of counts. One organism in the community is vastly more abundant ...
user370084's user avatar
2 votes
1 answer
45 views

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 ...
Susanne Bähr's user avatar
3 votes
0 answers
56 views

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 ...
Lea_M's user avatar
  • 103
0 votes
1 answer
65 views

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 ...
Brad Carlson's user avatar
3 votes
1 answer
52 views

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 ...
NoviceNeedsHelp's user avatar
0 votes
1 answer
159 views

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 ...
planktonQ's user avatar
0 votes
1 answer
139 views

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 ...
planktonQ's user avatar
14 votes
3 answers
988 views

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 ...
luciano's user avatar
  • 14.5k
0 votes
0 answers
56 views

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 ...
Darby's user avatar
  • 1
2 votes
1 answer
138 views

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 ...
planktonQ's user avatar
0 votes
0 answers
38 views

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 ...
Desiree Chase's user avatar

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