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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Testing when the profile of a sample has changed - degrees of freedom?
I've been messing around with the Shannon index for diversity
$
H' = -\sum_i^R {p_i \ln{p_i}}
$,
and it's associated 'evenness' measure $E = H'/H_{\text{max}}$. I'm trying to come up with a way of ...
- 131
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0
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21
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Question about design choice of Enbrel RWE study
Statisticians in 2015 analyzed real world data, hundreds of thousands of medical insurance claims involving people with rheumatoid arthritis and other inflammatory diseases, according to the Pfizer ...
- 11
6
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2
answers
396
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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 ...
- 2,665
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3
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59
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How to test whether birds spend more time in specific areas along a time-segmented track?
I have geolocation data on birds with 1 position per day (latitude + longitude) plus I have for each day, a corresponding binary time series that takes values 0 or 1.
There is periods of minimum 10 ...
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0
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2k
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Converting annual survival rate to daily mortality probability
In a peer-reviewed paper, I came across the following conversion:
Yearly survival rate -> 0.70
The authors have calculated the daily probability of death using
(1 - 0.70^(1/365.25)) = 0.000976
...
1
vote
0
answers
59
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Can you run an AIC twice in a row?
I came across this paper that seems to make a bunch of models, run an AIC, select the best models from that, then run the AIC again. Am I interpreting this correctly? And is that okay to do? Couldn't ...
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2
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1
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300
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Is Hellinger transformation suitable for repeated (in time) site-species abundance data?
I have fish survey data from four different years and several locations, where I would like to study the difference in abundance and biomass between sites and check whether time dependence influences ...
- 21
0
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1
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54
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Should I treat these variables as random? (ecology/recruitment question)
I'm working with recruitment data for caribou.
There are 13 different herds, sampled over 20+ years, once per year. Some herds are sampled consistently, some only a few times over 20 years.
I'm ...
- 11
2
votes
1
answer
2k
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Multiple testing (bonferroni?) with GLM
Hi everyone: I scored four mutually-exclusive behaviors (e.g. feeding, brooding, standing, preening) on a number of observations of birds in two different treatments, and two different nesting ...
- 101
2
votes
1
answer
866
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How to numerically solve a matrix differential equation in R? [closed]
I have interest in using the R language and environment to numerically solve a system of linear ordinary differential equations. The numerical solver, deSolve, ...
- 221
1
vote
1
answer
837
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odd insignificant results using pairwise.perm.manova
I am trying to complete pairwise comparisons of 9 forest communities. Communities were significant at p < 0.001 using adonis. However, when I use the same bray curtis matrix with the pairwise.perm....
- 31
3
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2
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151
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Getting ecological statistics right: Learning by yourself
I'm not really asking for reference on ecological statistics (such as here or here), but more on how you can be sure you're doing a new analysis you just learned correctly. I'm often stuck trying to ...
- 205
1
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1
answer
848
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How to simulate discrete data from a Poisson distribution? [closed]
I want to use R to simulate discrete data with missing values from a Poisson distribution.
I have tried this: simdata<-rpois(1000,2) but when I checked if there ...
- 21
1
vote
2
answers
346
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What model(s) are appropriate for unbounded species abundance data with 0's and environmental response variables in R?
I am conducting a research project on the vegetation composition of an abandoned mine site to determine the environmental factors that influence species abundance (cover) and composition.
Study ...
2
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0
answers
71
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Is it valid to solve an equation for multiple coefficients, then average them to obtain overall effect?
I have a regression model, the setup for which is as follows: I am using manyglm, a multivariate general linear model approach to determine the difference in several invertebrate species between two ...
- 205
2
votes
2
answers
53
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Which tests can be used for variables that are non-normal, but have homogenous variances?
I am trying to compare the effect of two treatments (planting distance) on the growth of plants (multiple species), using the variable growth rate in diameter for multiple years.
I have 4 sets of ...
- 21
1
vote
1
answer
94
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Which stats can test differences between two experiments?
I have an experiment to look at habitat preferences of beetles and the effect of competition.
In the first test, a beetle is on his own in an arena and I measured the % of time he spends in each of ...
- 151
1
vote
1
answer
70
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Which statistical analysis is most appropriate to determine differences between 3 treatments and control for monthly and yearly variation?
I have a 4-year dataset of zooplankton biomass that was sampled three times a summer (i.e. June, July, August) for all four years. There are 6 sites that were sampled in triplicate (took 3 reps): two ...
- 13
0
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0
answers
218
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Comparing species correlations between species in two habitats
I have two community data sets (samples as rows, species as columns, populated with abundance). This data comes from two habitats/sites, with differing numbers of samples at each site.
What I want ...
- 293
3
votes
1
answer
90
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Using GLMM to explain vegetation change as a function of change in soil parameters
I have a dataset that consists of vegetation datasets (species/abundancy tables) and soil parameters (tested for ten parameters per soil core). Three different rounds of these data are recorded in ...
- 213
0
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1
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79
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Multivariate techniques that discriminate community composition based on environmental variables between two a priori defined groups?
I have a methodological question that I have not been able to get an answer of. Basically, I am investigating the impacts of invasive species on soil microbial communities. I have a study design where ...
- 31
1
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1
answer
39
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Show absence of prediction for one response variable and multiple predictors
I have the following question concerning ecological statistics in a scientific study I am performing. I have measured the amount of copepods (little invertebrates) at different locations and at ...
- 111
2
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1
answer
200
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Should I use Structural Equation Models (SEM) for my Functional Diversity (FD) study? (ECOLOGY RELATED)
I'm trying to calculate various functional diversity measures (Fric, Feve and Fdiv) for bird communities by using count data which is collected annually. My ultimate aim is to compare functional ...
- 351
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2
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868
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is it possible to use a vector object a dependent variable in GLM?
I would like to write certain model in R.
I would like to o use a vector object as a dependent variable in my general linear model. The model is supposed to explain how some environmental factors, ...
6
votes
1
answer
1k
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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 ...
- 63
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2
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14k
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What's the difference between an ecological study and a cross-sectional study?
What's the difference between an ecological study and a cross-sectional study? And could you provide an example?
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0
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2k
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Canonical Correspondence Analysis: how to interpret results
I am using Canonical Correspondence Analysis (CCA) to analyze phytolith abundances (similar to pollen) over environmental gradients. As I am new to CCA, I read some background info. The following ...
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2
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2
answers
354
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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 ...
2
votes
1
answer
325
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Method named 'BEST' in multivariate analysis - what is it?
I've read a few ecological papers where a 'BEST' procedure is used to assess effect of environmental parameters on biological community composition, after multivariate analysis like MDS. For instance ...
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3
votes
1
answer
703
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GAM: Plotting gam models of different treatments?
I want to figure out the best way to plot gams, but I am getting confused about the best way to do this for my data. Please note that I am not a statistician, so 'stats/coding for dummies' answers are ...
- 191
3
votes
1
answer
283
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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 ...
2
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1
answer
84
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What are some simple ways i can analyse changes in relative abundance
I am looking (to begin with) some simple ways to analyse changes in relative abundance of species numbers over time. All we have is a inventory list of the number of species for each four seasons, ...
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3
votes
2
answers
376
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Growth rate patterns through time: ARMA an appropriate approach?
The Data
Total Biomass and Annual Growth Rates for 37 permanent sample (i.e., repeated sample) forest plots that have been ...
- 2,345
0
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0
answers
170
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Can I use a correlation between between Gender Inequality Index and Crude divorce rate obtained from different countries?
If I have to find a link between Gender equality and Divorce rates, can I then use a correlation between between Gender Inequality Index and Crude divorce rate obtained from different countries? If ...
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3
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2
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314
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Which correlation test should I use? ANOVA? PCA? Other?
I have the following problem and some help would be wonderful.
I have 50 origins for tree seeds. Each origin has several recorded climate variables like average temperature, precipitaion, wind etc.
...
- 33
0
votes
1
answer
85
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Effect size calculation
I am conducting a meta-analysis on the diet of predators. This diet is expressed as the proportion of aquatic vs terrestrial prey. I have a value (% of aquatic prey) for each species for each site of ...
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1
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1
answer
139
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How to handle non-detects in duplicate samples
I took two separate water samples (one sample per bottle) in twenty one river locations (n=42). For the purpose of this question I am calling the two bottles duplicates.
I am trying to show how ...
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0
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87
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Which statistical test should I use to compare land use type and species abundance?
I have abundance data for a species of bird and data on land use type in the areas where the bird data was collected. I want to test whether land use type affects bird abundance but I don't know what ...
- 21
3
votes
1
answer
71
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Analysis of a dataset including dichotomial, ordinal and % data
I'm working on a dataset which is giving me trouble. I have 200 samples (Sample 1, Sample 2...). An example dataset (limited to 15 samples) is here. My dataset is structured with the following ...
- 61
0
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0
answers
107
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how do I calculate overyielding in ecological temporal stability
I am investigating diversity-stability relationships and
I am trying to test for the portfolio effect and insurance effect with my data.
I understand that overyielding indicates the portfolio effect ...
- 151
2
votes
0
answers
114
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Spatial clustering analysis on binomial data collected on a grid
I am new to spatial statistics and need help figuring out how to assess if there is spatial clustering in my dataset using R.
I am assessing if acorn consumption is different inside timber harvest ...
- 21
3
votes
1
answer
160
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Does the Mann-Whitney U-test need to be adjusted in twin studies?
I have data from 44 twin pairs (88 patients total) and they are split into group_A (n=50) and group_B (n=38). For each of the ...
- 1,482
5
votes
1
answer
229
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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 ...
- 311
3
votes
1
answer
53
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Proportion of cells with certain number of mutation in dividing population
I managed to reduce a problem in my research to the following: Suppose that we have a population of cells which starts with a single cell that has zero mutations, and at each time step each cell ...
- 325
1
vote
2
answers
59
views
How to choose the statistic metrics to describe the patterns of trees near the tree line?
I have tree inventory data: about 700 points of trees with known locations (X;Y;Z) and measured heights and diameters of stems at the breast height (DBH). The trees are located along the elevation ...
1
vote
0
answers
165
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Family in GLM - how to choose the right one? [duplicate]
When modeling data sampled in the field, I often come across the problem of determining the Family of the dependend variable for GLM (or GLMM). An example: in an ecological study, I have ~ 60 patches. ...
- 447
1
vote
1
answer
184
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It is correct to use units other than individuals or samples on X axis of rarefaction curves?
The rarefaction curve is a very useful statistical tool for biodiversity analysis. It represents the number of species on Y axis, adjsted by individuals, samples (Gotelli & Graves,1996; Gotelli &...
- 49
2
votes
1
answer
181
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What in cross validation from co-correspondence analysis indicates sufficient axes numbers?
The coca function at cocorresp package disponible for R provides a predictive way to relate two biological composition datasets. I need help to understand one step from examples on documentation ...
- 49
2
votes
0
answers
87
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Comparing biological diversity before and after
I've got counts of two species in two treatments at two timepoints. I've got six replicates of each treatment.
I'd like to know how to compare treatment diversity.
As it is, I've calculated the ...
- 161
1
vote
0
answers
350
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Comparing Composition of Samples
I have data on the composition of two different types of animal droppings. There are 15 observations of Animal 1 and 40 observations of Animal 2. I have the makeup of each dropping broken up into ...
- 2,692