Hidden Markov Models

Some code in R and C++(Rcpp) written for the paper Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence

• The main code is "main-code.R".
• File "functions.cpp" provide C++ functions to support the analysis in the main R file.
• Files "drawing.R" provides plotting functions for the main R file.
• Two packages mt_1.0.tar.gz and plosM1_1.0.tar.gz are written in C++ (with Rcpp) to support fast computation in the analysis. The package mt_1.0.tar.gz runs > 100 times faster than diveMove package for extracting dives, thanks to Rcpp.