Random pieces of code

This code is provided as is without warranty of any kind. If you find a bug or anything, feel free to get in touch or fill an issue on GitHub.

You may find other pieces of code in papers.

Last update: July 2024.

Introduction to Git and GitHub with RStudio [ slides] [ material]
Writing dynamic and reproducible documents with R Markdown [ slides] [ material] [ practical] [ interactive dashboard] [ website]
Manipulate and visualise data in the tidyverse [ slides] [ material] [ tips]
Focus on GIS and spatial data with sf package [ slides] [ material]

Quantifying bias in mortality estimates when ignoring imperfect detection – R, Shiny
Capture-recapture models as HMMs – R, Jags
Spatial capture-recapture models for closed and open populations – R, Nimble
Jolly-Seber capture-recapture models – R, Jags
Multievent capture-recapture models – R, Jags, Nimble
Multievent capture-recapture models with Rcpp – R, Rcpp
Multievent SIR models and capture-recapture data – R, TMB
Local minima and multistate capture-recapture models; see also there for mixture of recaptures and recoveries – R, Jags, ADMB, Stan, unmarked
Animal social networks and capture-recapture data – R, Jags
Individual fitness in the wild and capture-recapture data – R, Jags, E-SURGE
Gompertz capture-recapture model with a Gamma frailty – R, Jags
Many correlated covariates in capture-recapture models – R, RMark
Structural equation capture-recapture models – R, Jags
Abundance estimation using capture-recapture models – R, RMark
Band-recovery models with time random effects in a frequentist framework – R
Bayesian implementation of capture-recapture models with robust design – R, Jags
Predator-prey integrated community models – R, Jags

Dynamic analysis of brown bear habitat use in the Pyrenees – R, unmarked
Dynamic occupancy models in TMB and ADMB – R, TMB, ADMB
Multistate occupancy model with uncertainty – R, Jags
HMM formulation of a multispecies dynamic occupancy models – R
Simulation and fit of a 2-species occupancy model à la Rota et al. (2016) here with unmarked and there with Jags and Nimble
Bias in occupancy estimate for a static occupancy model, with an interactive dashboard – R and unmarked

Animated map of wolf presence in France – R
Distribution map from an occupancy model, with Eurasian or Balkan lynx – R, unmarked
Introduction to GIS and mapping in R using the sf package with slides – R

Dynamic models based on ODEs here and there – Nimble
Explore strategies of social distancing on epidemic w/ SIR model – R
Zombie apocalypse and a Bayesian approach for fitting an epidemiological model to data – R, OpenBUGS
Julia code to fit mechanistic-statistical models w/ Bayes and MCMC, check out outputs here – Julia

Piégeage photo et pipeline pour l’identification d’espèces via deep learning – Python, R

Content analysis of French articles in newspapers about wolf – R
Bibliometric and textual analyses of the last decade of research in capture-recapture – R
Quick and dirty analyses of ISEC 2018 tweets – R
Text mining of the ISEC 2020 abstracts – R

Introduction to the tidyverse – R
Some notes I have taken on David Robinson’s screencasts, with R tidyverse tips and tricks – R
Analyses of wolf depredation in France – R
Visualizing trends in French deaths – R

Decoding the hidden message in Perseverance parachute with R – R
Visualising the Metropolis algorithm on a simple 1D example – R
Export, clean up and tabulate questions and answers from a Slack work space with several channels into HTML tables – R and json
Illustration of the delta-method – R
Creating a hex sticker for the R2ucare package – R
Simulate data with Jags – R, Jags
First steps in Python – Python
Bayesian Multivariate Autoregressive State-Space models - MARSS – R, Jags