DAISIEsims

This repository is the end product of a MSc Biology (Modelling in the Life Sciences track) mini-project of 5 ECTS (three weeks of workload). All stages of development, such as getting familiar with the code, code profiling, and coming up with a strategy fall within these three weeks.

The overarching goal of the assignment was to improve the speed and efficiency of simulations of the DAISIE model. The original model is distributed as an R package, and is thus mostly made up of R code, which is useful for such purposes, but slow. However, R allows for C++ code integration through Rcpp. The Rcpp package provides R functions as well as C++ classes, offering seamless integration of C++ and R. The goal for the three weeks, more specifically, was to make a start with C++ integration of 'slow' functions, while continuously checking whether output stays correct and consistent (through tests).

This repository is not a direct fork of DAISIE, but rather only includes code that is used by the file that was focussed on during this project; DAISIE_sim_core_cr.R. After investigation of the file, we decided to first translate all nested functions from R to C++.

At time of writing, most functions have been translated, of which most showed improved speed, especially the update_rates function. See bottom of this file for a TODO list.

Refactored functions (R --> C++)

All functions that were translated kept the original name, but _cpp was added to it.

• DAISIE_nonoceanic_spec.cpp (from DAISIE_nonoceanic_spec.R)
• DAISIE_utils.cpp (from DAISIE_utils.R):
  • DAISIE_spec_tables
• DAISIE_rates.cpp (from DAISIE_rates.R):
  • update_rates
  • island_area
  • get_immig_rate
  • get_ext_rate
  • get_clado_rate
• DAISIE_sample_event_cr.cpp (from DAISIE_nonoceanic_spec.R)
  • DAISIE_sample_event_cr
• DAISIE_sim_update_state_cr.cpp (from DAISIE_sim_update_state_cr.R)

  • DAISIE_sim_update_state_cr

    Extinction event not fully implemented yet, see TODO.

Additionally, we wrote some helper functions to facilitate smooth data transition from Rcpp Sugar objects to C++ objects and vice versa. See helper_functions.h.

TODO

• Implement remaining part of extinction event in DAISIE_sim_update_state_cr.cpp

• Translate the following functions from R to C++ using Rcpp:

  • calc_next_timeval
  • DAISIE_create_island

• Once that is done; translate the whole DAISIE_sim_core_cr.R file into C++

• As general note; implement logic when trait_pars != NULL

  As we only focussed on DAISIE_sim_core_cr.R, the trait_pars argument, when it came across, was always NULL. Hence, we did not implement cases where trait_pars was not NULL in any of the functions we rewrote.