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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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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1
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What is the "horseshoe effect" and/or the "arch effect" in PCA / correspondence analysis?
There are many techniques in ecological statistics for exploratory data analysis of multidimensional data. These are called 'ordination' techniques. Many are the same or closely related to common ...
18
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4
answers
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Interpreting random effect variance in glmer
I'm revising a paper on pollination, where the data are binomially distributed (fruit matures or does not). So I used glmer with one random effect (individual plant)...
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2
answers
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Analysed non-linear data with GAM regression, but reviewer has suggested fitting exponential or logarithmic curves instead. Which to use?
I am trying to publish my Masters thesis which looked at elephant impacts on vegetation, with a focus on the effect of artificial waterholes. I have made my initial submission and am now performing ...
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3
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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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Question about logistic regression
I want to run a binary logistic regression to model the presence or absence of conflict (dependent variable) from a set of independent variables over a 10 year period (1997-2006), with each year ...
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12
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3
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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:
$$
\textrm{Height}=...
11
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3
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Variance of a distribution of multi-level categorical data
I am currently analyzing large data sets with various characteristics (such as city). I wanted to find a measure which would essentially say how much or how little of a variance there was across the ...
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What criteria to use for separating variables into explanatory variables and responses for ordination methods in ecology?
I have different variables that interact within a population. Basically I have been doing an inventory of millipedes and measuring some other values of the terrain, like:
The species and the amount ...
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11
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2
answers
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Deriving Fisher's mysterious estimator for the Unseen Species Problem
From Wikipedia:
In the early 1940s Alexander Steven Corbet spent 2 years in British
Malaya trapping butterflies.He kept track of how many species he
observed, and how many members of each species ...
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10
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1
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Interpreting output of dredge
I ran a GLM for the first time in R and am not sure how to interpret the result.
This is the input:
...
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10
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2
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What is the distribution of the error around logistic growth data?
In ecology, we often use the logistic growth equation:
$$ N_t = \frac{ K N_0 e^{rt} }{K + N_0 e^{rt-1}} $$
or
$$ N_t = \frac{ K N_0}{N_0 + (K -N_0)e^{-rt}} $$
where $K$ is the carrying capacity (...
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3
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Can I test for correlation between variables before standardize them?
What I want to do is to construct GLMM's to evaluate resource selection, and I have a set of variables (some representing distances and others representing % of land cover).
Can I test for ...
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9
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3
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Books on statistical ecology?
I know this question was asked before: Reference book for ecological studies but it is not what I am looking for.
What I am looking for is if anyone could recommend a good book (or a canonical ...
9
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1
answer
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How to construct quadrats for point processes that differ greatly in frequency?
I want to perform quadrat count analysis on several point processes (or one marked point process), to then apply some dimensionality reduction techniques.
The marks are not identically distributed, i....
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8
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1
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Hellinger transformation with relative data
It is my understanding that the Hellinger transformation is basically the square root of relative abundance data (if rows are samples). However, my row sums do not represent the total community (I am ...
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8
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1
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Which link function could be used for a glm where the response is per cent (0 - 100%)?
I am thinking about building a model (glm) where the response variable (y) is the cover (in per cent) of a plant species in a defined area, dependant of environmental variables.
However, I don't think ...
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8
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Specifying hierarchical GAM for ecological count data---annual bird migration counts
I'm working with a data set of annual bird migration counts, and I'd like to fit phenological models to determine how timing of migration has changed over the last few decades. Weather permitting, ...
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8
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1
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Does using box-cox transformation on individual data sets prevent these data from being comparable?
I have been using the box-cox transformation to normalise data for input to an Ecological Niche Factor Analysis software, as recommended by the software creators.
However, it has occurred to me that ...
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7
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2
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Don't understand why glmm random effect variance is zero. Have reviewed similar questions still dont get it
I study a colonially-nesting bird species. I am trying to perform an AICc evaluation of GLMMs for a nest site selection study. I collected data at nest sites and paired random sites. I want to ...
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7
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1
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Are the posteriors "different"? How does one discuss the result?
First, I realize this may be a basic question. However, when I search the web for references on this issue, I run into the problem of wondering if the description I'm reading is applicable to the ...
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7
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1
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Principal component analysis with group data
In my experiment I have used 30 different accessions of a species. One group is challenged drought and the other group is control. I have collected data on 6 different parameters. I want to know which ...
7
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2
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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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1
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Species Richness, Dominance and Diversity Differences
I have collected 70 organisms from 4 different sites; two sites of treatment 1 and two sites of treatment 2. I also have a continuous explanatory variable (average temperature) which is different ...
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2
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Population model to model year to year dynamics
My task is to assess how various environmental variables affect annual population fluctuations. For this, I would use a model like:
$$
\mbox{log} ( \mu_{i,j+1} ) = \mbox{log} ( \mu_{i,j} ) + R_{j} + \...
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6
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1
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Check for significant difference between numbers of sightings per cardinal direction
I have data in a form like this:
quantity direction
10 n
5 e
6 ne
12 n
20 nw
5 s
8 n
1 sw
3 se
2 ne
6 nw
8 n
2 se
3 e
4 w
9 nw
The information behind these ...
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6
votes
2
answers
4k
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Initialize ARIMA simulations with different time-series
I have a fairly long time-series of annual abundances ($N_t$) of a wildlife species (73 years of abundances). To forecast the population’s trajectory, I have used ARIMA modeling. Examination of the ...
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6
votes
2
answers
394
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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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6
votes
2
answers
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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 ...
6
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1
answer
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Difference between NA and None in biological dataset
I have collected environmental data on animals, and am seeking help on how to deal with certain variables where a non-numeric value is informative, but also problematic. I have three variables that ...
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6
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2
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How to use a mathematical model for data analysis in R
I am looking to use a mathematical model developed by Firbank & Watkinson (1985) J. App. Ecol. 22:503-517 for the analysis of competition between plants grown in mixture.
The model is as follows:
...
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6
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1
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Custom power analysis in R
Distance sampling is a common technique used to estimate the abundance of wildlife species (such as deer or turkey). This technique employees line-transect based sampling where perpendicular distance ...
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5
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1
answer
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Why is a correlation coefficient threshold of r = 0.6 among predictors commonly used in ecology?
In my field of study (wildlife ecology), a correlation coefficient of r = 0.6 is a commonly-used threshold for identifying collinearity among pairs of predictor variables. In other words, predictors ...
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5
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2
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GLMM- relationship between AICc weight and random effects?
I am developing GLMM's in order to assess habitat selection (using GLMMs' coeficients to construct Resource selection functions).
I have (telemetry) data from 5 study areas, and each area has a ...
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5
votes
1
answer
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Estimating species distribution and rate of expansion using only positive data
Short version: is there any statistical method that can be used to develop estimates of abundance, spatial distribution, and/or rate of spread of a species when my dataset only includes presence data ...
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5
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2
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Ecological count data and offset terms
When using GAMs to model ecological count data (e.g., fish counts) using Poisson or negative-binomial distributions, the response variable is raw counts and the offset (e.g., log-transformed fishing ...
5
votes
2
answers
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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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5
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1
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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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5
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0
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Help with designing the analysis of a radio telemetry study
I was wondering if there are any spatial ecologists out there who can provide some insight on the trouble I'm having with my Masters research.
I am looking at the association a bat species to high ...
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4
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4
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Books about model selection in ecology
I am an ecology student and have to deal with 10 or 20 field variables, including species frequencies. I need to screen out what variables are most important in the occurrence of a bird species. What ...
4
votes
3
answers
934
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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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4
votes
1
answer
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Best practice MLR vs GLM(M)
I am modelling timeseries of organism traits (7 different traits in total) using GLM(M)s in R. The data was collected at very irregular intervals and from 6 different locations. For every location 5-...
4
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1
answer
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Post hoc for Fisher's exact test with a 2x6 contingency table
I am looking to see if and how tree height differs between areas of undisturbed and historically logged forests. Height was estimated in meters but categorically (1-6, 6-11, 11-16, 16-21, 21-26, 26-31)...
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4
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2
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Dealing with Overdispersed Negative Binomial using glmmTMB
I'm new to the world of statistical modeling, but I was wondering if anyone had any input on how to handle over dispersed negative binomial data? I'm working on modeling bat activity as a response ...
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4
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1
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Ecological mixed data cluster analysis: Transformations required? Use K-means or hierarchical methods?
I am trying to identify habitat types from 85 plots. I intend to do a cluster analysis to identify habitat types, and hope to fit additional plots into the identified clusters.
(For context, I took ...
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4
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4
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Statistical test to perform on species diversity / Simpson's diversity index
I have a set of data from each of the two sites I am measuring for plant species diversity. I plan on using the Simpson's diversity index (SDI), which combines species richness (number of different ...
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4
votes
2
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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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4
votes
1
answer
164
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Example of danger of ecological correlation of rates?
Lots of textbooks and websites warn about drawing conclusions from "ecological correlations" which are defined as correlations between rates or averages. All the places I've looked at have used the ...
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4
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1
answer
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Unbalanced mixed-effect model for repeated measures
I have a large set of point count data from 15 different sites that I wish to compare using R studio. Each site was surveyed multiple times each month from 2006-2015, except for some sites which were ...
user104122
4
votes
1
answer
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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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