Merge branch 'release/speedups_using_ctmc_caching_and_parallele_computations' into develop
Introduction text
Initial description of how to specify J
Finished section on building HMMs
CTMC construction described
Merge branch 'feature/documentation' into develop
Only clean up the cache when we have doubled its size.
simulation results
Merge remote branch 'origin/develop' into feature/simulation_study
added simulation results
Plottet results from larger data.
Merge branch 'feature/simulation_study' into develop
Simulation plotting
updated simulations
Plotting new results
Different parameterisation of likelihood optimiser
Added optimiser option
Looking at choice of optimiser...
Added unit tests for break_points and statespace_generator.
Ignore R history files