Discover oliviergimenez/phd-in-ecology-network Open Source project

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oliviergimenez

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Produce the French academic network in ecology using data from these.fr

bayesian-stats-with-R

Material for a workshop on Bayesian stats with R

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intro_spatialR

Introduction to GIS and mapping in R with the sf package

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statistics-for-ecologists-Master-courses

The material for a course on Statistics for ecologists I teach every year to Master students.

Bayesian_Workshop

Material for a Bayesian statistics workshop

reproducible-science

material for teaching reproducible science with R and RStudio

tidyverse-tips

Tidy notes I took from Dave Robinson's screencasts #TidyTuesday

banana-book

Repo for a book on Bayesian capture-recapture w/ HMMs

TeX

intro_tidyverse

Slides of my introduction to the Tidyverse

SCSS

bayesian-cr-workshop

Material for a workshop on Bayesian analysis of capture-recapture data with hidden Markov models and Nimble

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multievent_jags_R

Fit multievent capture-recapture models in R (maximum-likelihood), Nimble and JAGS (Bayesian)

oliviergimenez.github.io

My site, built with Hugo and Blogdown, and hosted on Github pages. Built and deployed with GitHub Actions from https://github.com/oliviergimenez/my_website repo.

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reproducible-science-workshop

Material for a workshop on reproducible science with R and RStudio

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learning-machine-learning

Experiments in ML with tidymodels

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IPMworkshop

Material for the 2020 workshop on Bayesian integrated population modeling (IPM) using JAGS

capture-recapture-review

material for a review on capture-recapture methods and questions

occupancy_TMB

Illustrate how to fit dynamic occupancy model in TMB. Benchmarking vs. ADMB, Unmarked and JAGS.

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intro_rmarkdown

Write reproducible and dynamic documents - Introduction to R Markdown

SCSS

popdyn-workshop

Website of workshop Quantitative Methods for Population Dynamics in R

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bayesRD

Bayesian implementation of capture-recapture models with robust design

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DLcamtrap

My personal pipeline to species identification on camera trap pix using deep learning, detection/classification with MegaDetector and RetinaNet

Python

poaching_occupancy

Inferring poaching with multispecies dynamic occupancy models and hidden Markov models

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R2ucare

R package to perform goodness-of-fit tests for capture-recapture models (and various manipulations)

computo-deeplearning-occupany-lynx

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appendix_capturerecapture_review

Analyses, R code and data for review of 2009-2019 research on capture-recapture

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2speciesoccupancy

Simulate data and fit 2-species occupancy model à la Rota et al. (2016) w/ Unmarked

bayesian-hmm-cr-workshop-valencia

Material for a workshop on Bayesian analysis of capture-recapture data with hidden Markov models and Nimble

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fitODEnimble

Fit ODEs to data with Nimble

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fitODEswithOpenBUGS

Illustrate how to fit ODEs to time-series data in OpenBUGS with R

ursus_Pyrenees_occupancy

Contains data and R code for paper on occupancy analyses of Brown bear habitat use in the Pyrenees

bias_occupancy

Calculate bias in occupancy estimate for static model

code_livre_variables_cachees

Annexes R Approche Statistiques pour les variables cachées en écologie coordonné par N. Peyrard et O. Gimenez

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bayes2speciesoccupancy

Simulate data and fit 2-species occupancy model à la Rota et al. (2016) w/ Jags and Nimble

occupancy-crash-course

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hmm-cr-nimble-isec2022-workshop

material for a workshop on Bayesian capture-recapture inference with hidden Markov models in Nimble

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estim_fitness

R and Jags codes to estimate fitness using capture-recapture data

monkseal-occupancy

Data and code for a paper on Med monk seal distribution in Greece

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indhet_in_CRmodels

Illustrate CR models with individual heterogeneity (multistate, random-effect, finite-mixture)

pyrenean-brown-bear-abundance

Code and data for the estimation of Pyrenean brown bear abundance

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SIRcovid19

Explore strategies of social distancing on epidemic w/ SIR model and R - from Gandon, Lion, Day

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predator_prey_icm

Integrated population models for interacting species

topic-isec2022

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basics_spatial_capturerecapture

Simulating and fitting SCR models for closed and open populations

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multieventRcpp

fitting multievent capture-recapture model with Rcpp

C++

GammaGompertzCR

Fit Gamma-Gompertz model to capture-recapture data using data cloning

note-information-nombre-loups

Matériel pour l'estimation du nombre de loups en France.

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social_networks_capture_recapture

Inferring animal social networks from capture-recapture data

fit-glmm-with-brms

Fit GLMM with brms

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multistate_occupancy

Code to fit a multistate occupancy model with uncertainty in Jags

sem_capturerecapture

Code for fitting structural equation capture-recapture models

marss_jags

Fit multivariate state-space autoregressive models in Jags

Rich Text Format

nimble-workshop

Material for a workshop on NIMBLE

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multistate_recaprecov

Some R/Jags code to demonstrate an issue with local max in the likelihood when fitting multistate capture-recapture models

NETDEM-workshop-survival-nimble

This repository holds the source materials used for a working group/symposium on capture-recapture models and social networks, and an introduction to capture-recapture models in nimble to estimate demographic parameters.

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tursiops_network_analysis

Bottlenose dolphin network analysis - GDEGeM project (in French)

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prezimaginecology

My first steps in deep learning: Species identification and camera traps

JavaScript

starwars_network

Social network analysis of Star Wars: The Attack of the Clones

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intro_rmarkdown_practical

Write reproducible and dynamic documents - Intro to R Markdown - Practical

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otterconnect

website of the otterconnect project

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hmm_tmb

fitting multievent/hmm capture-recapture model with TMB

C++

isec2018_tweet_analysis

Quick and dirty analyses of ISEC 2018 tweets

DLhair

Slides for short talk on DL for our team

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human-tursiops-twospeciesoccupancy

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sir_multievent

Contains functions to simulate data from and fit SIR multievent models

my_website

Source code of my website https://oliviergimenez.github.io/.

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curated-list-HMM-apps

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lasso-capturerecapture

lasso for covariates selection in capture-recapture models

PostScript

quick-intro-git-github-rstudio

Quick intro to Git and GitHub with RStudio

CSS

tidytuesday

my contributions to #TidyTuesday

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posterEuring2021

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occupancy_in_ADMB

Illustrate how to fit dynamic occupancy model in ADMB. Benchmarking with Unmarked and JAGS.

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gis_map_occupancy

Map species distribution from an occupancy model

mecastat-in-julia

Julia code to fit mechanistic-statistical models w/ Bayes and MCMC

Jupyter Notebook

textmining_isec2020

Text mining of ISEC2020 abstracts

socialseals

R codes to reproduce analyses of our paper on a IPM for elephant seals

oliviergimenez/phd-in-ecology-network

oliviergimenez

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