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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.