Articles by grumble10

Patterns across 50 years of French presidential election

January 5, 2017 | grumble10

[Une version francaise de cette article est disponible ici] This year (2017) we will have our presidential election between April and May in France. A while ago I discovered the open data website of the French government publishing public data with free access and promoting utilization by anyone. So in this ... [Read more...]

Crossed and Nested hierarchical models with STAN and R

December 8, 2016 | grumble10

Below I will expand on previous posts on bayesian regression modelling using STAN (see previous instalments here, here, and here). Topic of the day is modelling crossed and nested design in hierarchical models using STAN in R. Crossed design appear when we have more than one grouping variable and when ...

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Hierarchical models with RStan (Part 1)

November 10, 2016 | grumble10

Real-world data sometime show complex structure that call for the use of special models. When data are organized in more than one level, hierarchical models are the most relevant tool for data analysis. One classic example is when you record student performance from different schools, you might decide to record ...

$\mu_{ij} = \beta_{0j} + \beta_{1j} * Temperature_{ij} + \beta_{2j} * Nitrogen_{ij}$

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Shiny and Leaflet for Visualization Awards

September 4, 2016 | grumble10

Next week will be the meeting of the German (and Swiss and Austrians) ecologists in Marburg and the organizing team launched a visualization contest based on spatial data of the stores present in the city. Nadja Simons and I decided to enter the contest, our idea was to link the ... [Read more...]

Simulating local community dynamics under ecological drift

August 14, 2016 | grumble10

In 2001 the book by Stephen Hubbell on the neutral theory of biodiversity was a major shift from classical community ecology. Before this book the niche-assembly framework was dominating the study of community dynamics. Very briefly under this framework local species composition is the result of the resource available at a ...

[Read more...]

Exploring the diversity of Life using Rvest and the Catalog of Life

July 18, 2016 | grumble10

I am writing the general introduction for my thesis and wanted to have a nice illustration of the diversity of Arthropods compared to other phyla (my work focus on Arthropods so this is a nice motivation). As the literature I have had access so far use pie charts to graphically ...

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Exploring Spatial Patterns and Coexistance

June 11, 2016 | grumble10

Today is a rainy day and I had to drop my plans for going out hiking, instead I continued reading “Self-Organization in Complex Ecosystems” from Richard Solé and Jordi Bascompte. As I will be busy in the coming weeks with spatial models at the iDiv summer school I was closely ...

$N_{1,t+1} = \phi_{N_{1}}(N_{1,t},N_{2,t}) = N_{1,t} * exp[r_{N_{1}} * (1 - N_{1} - \alpha_{12} * N_{2})]$

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Plotting regression curves with confidence intervals for LM, GLM and GLMM in R

October 8, 2015 | grumble10

Once models have been fitted and checked and re-checked comes the time to interpret them. The easiest way to do so is to plot the response variable versus the explanatory variables (I call them predictors) adding to this plot the fitted regression curve together (if you are feeling fancy) with ...

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Two little annoying stats detail

August 31, 2015 | grumble10

A very brief post at the end of the field season on two little “details” that are annoying me in paper/analysis that I see being done (sometimes) around me. The first one concern mixed effect models where the models built in the contain a grouping factor (say month or ...

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Count data: To Log or Not To Log

July 22, 2015 | grumble10

Count data are widely collected in ecology, for example when one count the number of birds or the number of flowers. These data follow naturally a Poisson or negative binomial distribution and are therefore sometime tricky to fit with standard LMs. A traditional approach has been to log-transform such data ...

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Confidence Intervals for prediction in GLMMs

June 17, 2015 | grumble10

With LM and GLM the predict function can return the standard error for the predicted values on either the observed data or on new data. This is then used to draw confidence or prediction intervals around the fitted regression lines. The confidence intervals (CI) focus on the regression lines and ...

[Read more...]

Exploration of Functional Diversity indices using Shiny

April 27, 2015 | grumble10

Biological diversity (or biodiversity) is a complex concept with many different aspects in it, like species richness, evenness or functional redundancy. My field of research focus on understanding the effect of changing plant diversity on higher trophic levels communities but also ecosystem function. Even if the founding papers of this ... [Read more...]

A function to help graphical model checks of lm and ANOVA

March 25, 2015 | grumble10

As always a more colourful version of this post is available on rpubs. Even if LM are very simple models at the basis of many more complex ones, LM still have some assumptions that if not met would render any interpretation from the models plainly wrong. In my field of ...

[Read more...]

Generating ANOVA-like table from GLMM using parametric bootstrap

February 26, 2015 | grumble10

This article may also be found on RPubs: http://rpubs.com/hughes/63269 In the list of worst to best way to test for effect in GLMM the list on http://glmm.wikidot.com/faq state that parametric bootstrapping is among the best options. PBmodcomp in the pbkrtest package implement such ... [Read more...]

Using and interpreting different contrasts in linear models in R

January 13, 2015 | grumble10

When building a regression model with categorical variables with more than two levels (ie “Cold”, “Freezing”, “Warm”) R is doing internally some transformation to be able to compute regression coefficient. What R is doing is that it is turning your categorical variables into a set of contrasts, this number of ...

[Read more...]

Interpreting regression coefficient in R

November 23, 2014 | grumble10

Linear models are a very simple statistical techniques and is often (if not always) a useful start for more complex analysis. It is however not so straightforward to understand what the regression coefficient means even in the most simple case when there are no interactions in the model. If we ...

[Read more...]

DataFrame manipulation in R from basics to dplyr

October 11, 2014 | grumble10

In my surroundings at work I see quite a few people managing their data in spreadsheet software like Excel or Calc, these software will do the work but I usually tend to do as little data manipulation in them as possible and to turn as soon as possible my spreadsheets ...

[Read more...]

Ploting SEMs in R using semPlot

August 10, 2014 | grumble10

This is a short post presenting the great package semPlot developed by Sacha Epskamp (check out his nice website: http://sachaepskamp.com/) to make nice plots from your SEMs. SEMs are a modelling tool that allow the researcher to investiguate complex relationships between the variables, you may find here many ... [Read more...]

Using bootMer to do model comparison in R

July 13, 2014 | grumble10

Setting the right random effect part in mixed effect models can be tricky in many applied situation. I will not talk here about choosing wether a grouping variable (sites, individuals …) should be included as a fixed term or as a random term, please see Gelman and Hill (2006) and Zuur et ... [Read more...]

Regular expression and associated functions in R

June 1, 2014 | grumble10

When working with strings regular expressions are an extremely powerful tool to look for specific patterns in the strings. In informatics a string is several characters put together, this can be words, sentences, or DNA code. Regular expression were developed for the language of Perl (http://www.perl.org/) and ... [Read more...]

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Articles by grumble10

Patterns across 50 years of French presidential election

Crossed and Nested hierarchical models with STAN and R

Hierarchical models with RStan (Part 1)

Shiny and Leaflet for Visualization Awards

Simulating local community dynamics under ecological drift

Exploring the diversity of Life using Rvest and the Catalog of Life

Exploring Spatial Patterns and Coexistance

Plotting regression curves with confidence intervals for LM, GLM and GLMM in R

Two little annoying stats detail

Count data: To Log or Not To Log

Confidence Intervals for prediction in GLMMs

Exploration of Functional Diversity indices using Shiny

A function to help graphical model checks of lm and ANOVA

Generating ANOVA-like table from GLMM using parametric bootstrap

Using and interpreting different contrasts in linear models in R

Interpreting regression coefficient in R

DataFrame manipulation in R from basics to dplyr

Ploting SEMs in R using semPlot

Using bootMer to do model comparison in R

Regular expression and associated functions in R

Articles by grumble10

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