Fitting scale-dependent landscape effect with greta
A large number of ecological processes depend not only on the local conditions but also on the surrounding landscape. Think of birds being measured at a numb...
Blog
Below you may find all posts I wrote, some were previously hosted at a wordpress blog so the layout of the code snippet might be weird. I will try to work down the posts and fix this.
Feel free to leave comments, also I am always happy to hear about posts ideas.
Recurrent themes in my work: covariance
Some themes keeps popping up in different projects or aspects of my work and I would like to reflect a bit on them in a series of posts.
Meeting With Yves Rosseel
Following some mail exchange with Yves Rosseel about the simulation work I have been doing on SEMs, finding out that we both live in the same city we organiz...
Simulating SEMs: part 2 extensions
Back in May I published a first post which simulated simple Structural Equation Models (SEMs) to check the capacity of piecewieseSEM to deal with noise. At t...
Categorical random effects with lme4
The aim of this post is to see how to fit mixed effect models with varying effects when the explanatory variable that varies is a categorical variables. For ...
Mind the gap: when the news article run ahead of the science
This is a quick post on a blatant example on how careful and prudent interpretation in scientific articles are over-simplified in news article.
Interpreting three-way interactions in R
A reader asked in a comment to my post on interpreting two-way interactions if I could also explain interaction between two categorical variables and one con...
Introduction to point pattern analysis for ecologists
Point pattern analysis is a set of techniques to analyze spatial point data. In ecology this type of analysis may arise in several context but make specific ...
Cause, mechanism and prediction in ecology
This is a theme that bugged me for the past few months, through reading (Peters’ critique for ecology, Shipley’s path analysis book), meetings and discussion...
Adding group-level predictors in GLMM using lme4
Sometime I happen to be wrong, this is one of these instance. The issue: a colleague measured individual plant growth and measured light irradiation received...
On the price of (my) higher education
With my higher education studies behind me, I wanted to reflect a bit on the different amount of tuition fees that I experienced moving around European unive...
Adding standard errors for interaction terms
This is something that bugged me for some time, how do we add up standard errors? This is relevant when you fit a model with interaction terms and you are in...
Simulating SEMs for piecewiseSEM: part 1 the basics
Structural Equation Models are being used more and more frequently by ecologists due to the appeal of linking variables together in complex web of interactio...
How not to control for multiple testing
While reading the method section of a recent article by Solivares et al, I came upon the following paragraph:
About my PhD defense in Germany
I recently held my defense and will most certainly make a couple of posts in the ”near” future on important aspects of the PhD that might helped current or f...
Interpreting random effects in linear mixed-effect models
Recently I had more and more trouble to find topics for stats-orientated posts, fortunately a recent question from a reader gave me the idea for this one.
Making a case for hierarchical generalized models
Science is also about convincing others, be it your supervisors or your collaborators, that what you intend to do is relevant to get the answers sought. This...
Tendances des élections présidentielles francaises des 50 dernières années
[An english version for this article is available here]
Patterns across 50 years of French presidential election
[Une version francaise de cette article est disponible ici]
Prediction in ecology -implementing a priority.
In this post I would like to comment a bit on the recent forum paper by Houlahan et al on the importance of prediction to demonstrate ecological understandin...
Review of the Fun from 2016
One year as passed, now is the time to look back at my activity for 2016, explore some stats and take some blogging resolutions for 2017. This post was inspi...
Spatial Dynamic in a Host-Parasitoid system
In this post I will explore the spatial dynamic that arise from a simple deterministic host-parasitoid model with migration in a homogeneous environment. If ...
Crossed and Nested hierarchical models with STAN and R
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 modell...
Hierarchical models with RStan (Part 1)
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 ...
150 years of ecology: lessons for the future
Last week I was at the annual meeting of the german, austrian and swiss ecologists (GfÖ) which took place in Marburg (DE). The title of the conference referr...
Shiny and Leaflet for Visualization Awards
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...
Simulating local community dynamics under ecological drift
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-asse...
Exploring the diversity of Life using Rvest and the Catalog of Life
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 fo...
Exploring Spatial Patterns and Coexistance
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...
Discussion on Biodiversity trends in the Anthropocene
So today at our group meeting I made a talk inspired by the McGill et al (2015) paper.
Plotting regression curves with confidence intervals for LM, GLM and GLMM in R
[Updated 22nd January 2017, corrected mistakes for getting the fixed effect estimates of factor variables that need to be averaged out]
Ecology at the Interface in Rome
Last week I was at the European Ecological Federation conference in Rome, I presented the results of one experiment that we ran last year (THE one big experi...
Two little annoying stats detail
UPDATED: Thanks to Ben and Florian comments I’ve updated the first part of the post
Count data: To Log or Not To Log
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...
Confidence Intervals for prediction in GLMMs
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 ...
Exploration of Functional Diversity indices using Shiny
Biological diversity (or biodiversity) is a complex concept with many different aspects in it, like species richness, evenness or functional redundancy. My f...
A function to help graphical model checks of lm and ANOVA
As always a more colourful version of this post is available on rpubs.
Generating ANOVA-like table from GLMM using parametric bootstrap
[UPDATE: I modified a bit the code of the function, now you do not need to pass as character the random effect terms]
Evenness effect on ecosystem functioning
Most biodiversity ecosystem function (BEF) experiment focus on one aspect of diversity: species richness, and had to it some functional composition flavour. ...
Using and interpreting different contrasts in linear models in R
When building a regression model with categorical variables with more than two levels (ie “Cold”, “Freezing”, “Warm”) R is doing internally some transformati...
What roles should ecologist have in the society?
This post is a reflection on the roles that ecologist should have in the society, it was sparked by some discussion I had at the BES/SFE meeting in december....
Summary and thoughts of the BES/SFE meeting
This week was the British Ecological Society/ Société Francaise d’Écologie meeting in Lille, and as I am sitting on the train on the way home I’d like to giv...
Talk at the meeting of the entomological society of Thuringia
So this week-end I talked about why and how we do biodiversity-experiment research and showed some results from our long-term (12 years) field site. What was...
Biodiversity and Ecosystem Function research: Part 1 setting the scene
In this post I try to define the framework in which my PhD is into, I will define some key terms that we use a lot and present briefly the field experiment I...
Lecture on Biodiversity Ecosystem function
I gave today a lecture to master student in ecology about this field of research I am working on which is biodiversity and ecosystem function. You may find t...
Happy birthday biologyforfun
This blog is now two years old, I started it in November 2012 as I was finishing my third semester of my master degree, the idea at that time was to use this...
DataFrame manipulation in R from basics to dplyr
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 usu...
First scientific conference; Inspiration, Meetings and Walking
I was attending this week my first scientific conference and I will give here some thoughts and impression I kept from it. The conference was located in Hild...
Ploting SEMs in R using semPlot
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 plot...
Using bootMer to do model comparison in R
Setting the right random effect part in mixed effect models can be tricky in many applied situation. I will not talk here about choosing whether a grouping v...
Regular expression and associated functions in R
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...
Pourquoi je vais aller voter le 25 mai
Entre le 22 et le 25 mai prochain les européens éliront leurs représentants au parlement européen, cette élection est souvent marqué par un désintérêt, un ma...
Importing 100 years of climate change into R
This is a flashback post, I was working on species distribution shifts over the last 40 years last summer and recently Rémi Genevest contacted me asking me h...
Fonctions récursives (avec R)
Les fonctions récursives sont des fonctions qui s’appellent elle mêmes lors de leurs exécution voir: https://fr.wikipedia.org/wiki/Fonction_r%C3%A9cursive.
Checking (G)LM model assumptions in R
(Generalized) Linear models make some strong assumptions concerning the data structure:
Interpreting interaction coefficient in R (Part1 lm) UPDATED
(going through this post again three years after I posted it. Made some, hopefully useful, changes)
Now on r-bloggers
All the R related post of this blog can know be found into the aggregated r-bloggers website! Check it out it is great: http://www.r-bloggers.com/
Generalized Linear Mixed Models in Ecology and in R
I had a nice workshop two weeks ago in Tübingen (south-germany) concerning Generalized Linear Mixed Models (GLMM) in R. The course was given by two ecologist...
Computing R square for Generalized Linear Mixed Models in R
R square is a widely used measure of model fitness, in General Linear Models (GLM) it can be interpreted as the percent of variance in the response variable ...
Adding color to R plot: a function
A friend of mine told me that she was spending her day colouring R plot because she never understood how to put color in them. This triggered a nerdy reactio...
Science vs Obscurantisme
Les nouvelles françaises font écho en ce moment d’un débat assez malsain sur la non-existante théorie du genre. Une frange nauséabonde de la population franç...
Installing rJava in R>=3.0
This is just a blog post for me to remember this hack that bother for some time, if it can help other people this is even better.
Bringing together R and LaTex
So as some of you may have noticed I am particularly enthusiast about R. For some time now I have also being using LaTex for my reports and presentation. Th...
Simulating dice throws in R
I am currently following a course on probability theory in coursera (https://www.coursera.org/course/probas) and I’ve seen some graphs concerning the outcome...
Libertés individuelles et internet
A short update: here is the link to the english version of the manifest: https://www.change.org/petitions/a-stand-for-democracy-in-the-digital-age-3
First Lecture ever
So .. just a quick post to share with you my first lecture ever. It was for a master course that my working group is running on Experimental design and stati...
Will the next generation ecologists be parasites?
A recent article by Lidenmeyer and Likens talking about the new development of open-access data in ecology (the fact that dataset are published through a pee...
Manipulation of the legend in ggplot2 (R)
You are one click away from a post on the various way one can change the legend title in ggplot2, combine several aesthetic, remove the legend in ggplot2. ht...
Non-linear regression in R
Here is the link to the article:
Why should we care about Biodiversity?
With the european economy being stuck under gloomy economic conditions after the banking cisis of 2008, government have been dramatically slowing their roadp...
Generalized Linear Modelling in R (part 1)
In classical linear modelling we are assuming that the response variable (Y) is normally distributed, however for certain type of data like count data or pre...
Advanced settings in ggplot2 (R)
Here is a post with some information to control the layout of your graph produced by the ggplot library:
Using the rasterVis package for raster plotting (in R)
Here is a post discussing the possibilities of the rasterVis package:
Impact Factors in Science: time to leave them behind
In science nowadays the quality of a researcher is assessed through its publication in journals with a high impact factors. The impact factors was created by...
Drawing lines in raster cells (in R), with application to species distribution mapping
I guess we all had this demand from one of our tutor saying: “look at this nice output a previous intern did, well I’d like you to do the same”. In my case t...
Ploting raster stacks (in R)
Here is the link to a new R-related post on some really nice functionalities of the raster::plot function: http://rpubs.com/Lionel/5476
Making maps in R using ggplot,
Here is a new post, one click away, on how to make maps using the functions implemented by ggplot: http://rpubs.com/Lionel/5242
A little change in the blog,
From now on every R related post will be posted there: http://rpubs.com/Lionel Since it is very nice and easy for me to upload R code and graphics using Rmar...
Taking control of the legend in raster (in R)
The basic default options of the raster package depict well continous data but when plotting caterogical data on maps like land use or species presence/absen...
Using Spatial Data in R;
Nowadays more and more spatial data analysis are performed in Biology due to the ever expanding information freely available on the internet, as for example ...
The day I stoped using for loops (in R);
For loops are great, they allow you to go elements by elements through a list, data frame… and to perform operations on these subsets of data. This is very u...
Bringing the powers of SQL to R;
One of the biggest flaw of R is the fact that the data you load and use into it are stored in the memory (on the RAM) and not on the disk. Hence as you are w...
IPBES is on its way
Since last year a new UN body has been created aiming at increasing the awareness of decision makers about the current biodiversity crisis. This new body is ...
Making Graphs using ggplot2 in R:
The base package in R allow nice graphs to be drawn but more advanced packages allow better control and still nicer graphs to be created. Two packages are ma...
Correlation and Linear Regression in R
Before going into complex model building, looking at data relation is a sensible step to understand how your different variable interact together. Correlatio...
Assigning Names to object within a Loop in R
I just came across a great solution today to one of my recurring problems in R. When I run a for loop for example I create/modify some object and then I some...
Threat to biodiversity (about butterfly, polar bears and Brad Pitt);
Everyone care about the environment and enjoy a sunny day walk through the woods (apart for certain categories of people like hardcore gamers), yet these nic...
Manipulating data frame in R
Here you will learn about transforming, merging, ordering a data frame, changing the column order, removing a variable, subsetting and indexing
The United Nations and the safeguarding of the environment (Basic)
Even if few peoples are aware of it there are many UN conventions (an agreement between states) working to find solutions to the current environmental issues.
The 6 functions that save your life (in R)
In this article I will introduce to you the functions that make your life in R so much easier. For example purposes I will use the “mtcars” data frame.
Perl Basics
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R at your fingertips
R is an open source statistical software, which mean that it is free and that you can access all the codes that you are using.