Nimble and HMM

Playing around w/ awesome @R_nimble to fit multievent #HMM capture-recapture models to data - Code and data here Comments welcome ๐Ÿค— — Olivier Gimenez ๐Ÿ–– (@oaggimenez) December 2019

New paper!

New paper by #SarahBenhaiem & @LMarescot ๐Ÿคฉ๐Ÿ‘ "Robustness of Eco-Epidemiological Capture-Recapture Parameter Estimates to Variation in Infection State Uncertainty" #HMM #multievent #TMB #WomenInSTEM #carnivorepapersbywomen #heynas #serengeti — Olivier Gimenez ๐Ÿ‰ (@oaggimenez) 28 aoรปt 2018

Fitting HMM/multievent capture-recapture models with TMB

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).

Fitting multievent capture-recapture models with Rcpp

Following my previous post on [using ADMB to fit hidden Markov models](, I took some time to learn how to use Rcpp ([Eddelbuettel & Francois 2011](; [Eddelbuettel 2013](, 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!