How many 🐺🐶 hybrids are there?! @NSantostasi shows how to estimate prevalence w/ #HMM imperfect detection in her @Ecol_Evol #Euring17 paper https://t.co/KwiHB2ZBpX #openaccess 🤝 work w/ @SapienzaRoma @ISPRA_Press @wolfappcenter @umontpellier @CNRS_OccitaniE @INEE_CNRS 🇮🇹🇫🇷 pic.
🤩🐺 New paper by unstoppable @LouvrierJulie "Accounting for #misidentification and #heterogeneity in #occupancy studies using #HMMs" https://t.co/UqJfbkFjbW #teamboulet #openaccess @EcoHMM #carnivorepapersbywomen @ONCFS_officiel @umontpellier @IsiteMUSE @CNRSenLR @INEE_CNRS pic.twitter.com/YGgPNjzRUE
— Olivier Gimenez 🥐 (@oaggimenez) 19 septembre18
Following my recent attempt to [fit a HMM model to capture-recapture data with TMB](https://oliviergimenez.github.io/post/multievent_in_tmb/) and the rather estonishing outcome (the code was > 300 time faster than the equivalent R code!), I was curious to add TMB to the [list of options I tried to fit dynamic occupancy models](https://oliviergimenez.github.io/post/occupancy_in_admb/). Well, the least I can say is that TMB is fast, damn fast!
Following my attempts to fit a HMM model to [capture-recapture data with Rcpp](http://localhost:1313/post/multievent_in_rcpp/) and to [occupancy data with ADMB](http://localhost:1313/post/occupancy_in_admb/), a few colleagues suggested TMB as a potential alternative for several reasons (fast, allows for parallel computations, works with R, accomodates spatial stuff, easy implementation of random effects, and probably other reasons that I don't know).
Following my previous post on [using ADMB to fit hidden Markov models](https://oliviergimenez.github.io/post/occupancy_in_admb/), I took some time to learn how to use Rcpp ([Eddelbuettel & Francois 2011](https://www.jstatsoft.org/article/view/v040i08); [Eddelbuettel 2013](http://www.springer.com/us/book/9781461468677)), a package that gives friendly access to the power of C++ and increase the speed of your R programs. Kudos to Dirk Eddelbuettel, Romain Francois and their colleagues, Rcpp is awesome!
Laura Cowen from the Department of Math and Stat at University of Victoria (Canada) will be on a sabbatical with us for 3 months. We will be working on the applications of hidden Markov models to capture-recapture data.