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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13
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4answers
18k views

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)...
2
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1answer
177 views

Intraspecific variation in MCMCglmm

I want to use MCMCglmm to account for phylogenetic autocorrelation on my GLMM. However I have more than one trait measurement for certain species. Is there a way ...
5
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1answer
9k views

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 ...
1
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1answer
264 views

Can I perform PCA on species count differences instead of species counts themselves?

I'm busy with the analysis of bird community change through time on a couple of sites and want to relate it to environmental covariates. I use the R-package vegan ...
4
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4answers
10k views

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 ...
2
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0answers
43 views

Describing Differences between Two Inferred Populations

I am interested in the size of an animal in two populations, and found reliable estimates of the population provided by NOAA. The data was in the form of estimated total population within discrete ...
3
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1answer
1k views

Calculating Diversity using normalized species counts

I am trying to calculate the change in diversity of species encountered throughout time. My dataset is comprised to detections of tagged fish for 48 consecutive weeks. My thought was to bin the ...
0
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0answers
383 views

How to account for repeated measurements and unequal sample sizes in RDA

I have a question going in the same direction as this one: Restricted Permutations However, I have a dataset of multiple Locations from which I have samples of sometimes 5 sometimes only 3 years. Not ...
1
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1answer
925 views

Validity of stepwise regression in DistLM

I have a set of nutrient fluxes data and I would like to know which environmental drivers explains the fluxes. I used DistLM and the marginal test showed that none ...
3
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1answer
1k views

Should ordinal variables be normalized for PCA?

I need to analyze my (ecological) data with PCA, but the data don't seem to meet the assumption of normality very well. The problem is, that out of my 9 variables only two are continuous and the ...
1
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0answers
8k views

interpreting PERMANOVA (adonis function) output?

I am trying to look at expression of some genes and relate the dist matrix (Sm) to a number of different factors that I collected on the individuals (e.g., litter size, licking behavior, group housing ...
1
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0answers
215 views

Use of compana and adehabitatHS

I am analysing habitat use vs. availability by a bird species and have been using 'Manly selection ratios' (3rd order selection) to graph the preferences of 9 different habitats. I also wanted to ...
0
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0answers
55 views

Reduction of species variables in vegetative analysis

Edited following helpful feedback. I have vegetation species data for a number of grassland habitat sites, and am preparing to begin Exploratory Data Analysis. Data was collected in 100 quadrats over ...
2
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0answers
65 views

Quantifying tree height diversity or heterogeneity

I am analyzing data collected in the field for a habitat selection study of a large mammal. I have ~1300 plots that were sampled. I am trying to find a good way to quantify the diversity of tree ...
9
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1answer
2k views

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 ...
1
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0answers
542 views

Can Hedges' d be used to compare unlike effects?

I've got a question related to the use of Hedges' d in a meta-analysis of insect fitness information. Here is a link (pdf) to the paper I'm working with. In the appendices, the fitness information ...
1
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1answer
103 views

Basic question about getting esimated probabilities in R

I've got what I think is a fairly basic problem. I'm not sure if it is a conceptual question or software question, but I'm fairly new to using R and these kinds of stats, so it could be either or both....
1
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1answer
134 views

“Explaining” a time series - conceptual explanation needed

Imagine I have a time series for an animal population and a time series for a climatic variable during the same time period and at the same location. Unfortunately the data are observational (i.e., no ...
2
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0answers
71 views

Spatially explicit model to test effects of multiple variables

What is the appropriate model to test the effects of location, species, and size on tree growth? So I have both categorical and continuous variables I want in the model. The following graphic just ...
3
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0answers
847 views

Suitable method for modelling (underdispersed?) count data with lots of zeros and long tail

I have a small data set of counts of bees. I tried a simple Poisson model without random effects but it was very overdispersed (3.95). When I fit a GLMM with random effects (using glmer in lme4) it ...
6
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2answers
655 views

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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0answers
704 views

Herbivore density and group density modelling: Poisson GLM that overfits the data, or higher ranked negative binomial model that underfits the data?

I am an ecologist that has counted 11 different species of herbivores in about 110 blocks of two habitat types over 18 months, and I am interested in predicting the density across the study area from ...
9
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3answers
4k views

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 ...
7
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2answers
899 views

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} + \...
0
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1answer
769 views

How to fit (linear regression) a ratio of all independent variables?

I am trying to find the best fit between an species dataset and prevailing climatic conditions, in order to be able to predict the environmental conditions from the species dataset (paleoclimate ...
4
votes
1answer
130 views

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 ...
0
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1answer
56 views

Estimating the number of birds in a specific area

I want to count the birds in an area. What's the proper statistical method for it? What are the good references for this topic?
3
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0answers
628 views

How to compare species communities between two years? [closed]

I would like to compare the data of a community of species between two years. I used to compare communities based on different levels of a factor (for example, a treatment). The case of a treatment is ...
2
votes
1answer
550 views

What does “return rate” mean in population ecology models?

What does "return rate" (tasa de retorno in spanish) mean in population ecology models? In context of capture-mark-recapture models. I have found many articles on ...
4
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0answers
118 views

Regressing on many outcomes in a spatial model [closed]

I'm measuring many microbe populations in a 'river model' ecosystem by sampling at two points. I want to test the hypothesis that key species upstream are the best predictors for any given population ...
5
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0answers
124 views

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 ...
5
votes
2answers
3k views

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 ...
4
votes
4answers
535 views

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 ...
5
votes
1answer
866 views

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 ...
4
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1answer
2k views

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 ...
8
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1answer
441 views

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 ...
2
votes
1answer
785 views

Is it possible to use common principal components for assessing covariance matrix similarity in R?

Is it possible to use common principal components for assessing covariance matrix similarity in R? This approach was championed by Flurry, 1988 but this paper is what I have in mind. References Flury ...
5
votes
1answer
88 views

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 ...
4
votes
0answers
441 views

Comparing two non-linear biological models: differences in y vs. differences in slope

I'm an ecology PhD student, but unfortunately not a very mathematically sophisticated one. I am interested in ways to compare two non-linear models. I was really impressed with this answer, which ...
10
votes
2answers
465 views

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 (...
14
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2answers
3k views

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 ...
2
votes
1answer
888 views

Type of input data (proportions or log-ratios) for compositional analysis

I am comparing tree species use vs. availability within bird territories. I am using the R compana() function which uses Aebischer et al. (1993) method (package ...
7
votes
1answer
4k views

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 ...
9
votes
1answer
369 views

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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