This file documents the copyright and licensing information
for third-party code included in the deepSTRAPP package.

------------------------------------------------------------
Original package code
------------------------------------------------------------

All code and documentation files in this package,
EXCEPT those listed in the section "Third-party code" below, are:

Copyright (C) 2023–2026 Maël Doré

License: MIT

------------------------------------------------------------
Third-party code
------------------------------------------------------------

The following files and functions are derived from external sources and
are distributed under their original licenses.

File: src/treetraverse.c
  Original authors: Dan Rabosky, Mike Grundler
  Derived from: BAMMtools R package
  Source: https://cran.r-project.org/package=BAMMtools
  License: GPL (>= 2)
  This file has been copied without modifications.
  
File: inst/BAMM_template_diversification.txt
  Original authors: Daniel Rabosky, Pascal Title
  Derived from: bamm-2.5.0
  Source: http://bamm-project.org/; https://github.com/macroevolution/bamm
  License: GPL (>= 2)
  This file has been commented for deepSTRAPP.

Function: getRecursiveSequence
  Original authors: Dan Rabosky, Mike Grundler
  Source: BAMMtools R package
  License: GPL (>= 2)
  This function has been copied without modifications.

Function: makeMappedEdge
  Source file in deepSTRAPP: R/prepare_trait_data.R
  Derived from: makeMappedEdge() in phytools R package
  Original author: Liam Revell  
  License: GPL (>=3)
  Source: https://cran.r-project.org/package=phytools
  This function has been copied with minimal modifications.
  
Function: densityMap_custom
  Source file in deepSTRAPP: R/prepare_trait_data.R
  Derived from: densityMap() in phytools R package
  Original author: Liam Revell
  License: GPL (>=3)
  Source: https://cran.r-project.org/package=phytools
  This function has been modified to enhance functionalities.
  
Function: BSM_to_phytools_simmap
  Source file in deepSTRAPP: R/prepare_trait_data.R
  Derived from: BSM_to_phytools_SM() in BioGeoBEARS R package
  Original author: Nicholas J. Matzke
  License: None 
  Source: https://github.com/nmatzke/BioGeoBEARS
  This function has been modified to enhance functionalities.

Function: BSMs_to_phytools_simmaps
  Source file in deepSTRAPP: R/prepare_trait_data.R
  Derived from: BSMs_to_phytools_SMs() in BioGeoBEARS R package
  Original author: Nicholas J. Matzke
  License: None 
  Source: https://github.com/nmatzke/BioGeoBEARS
  This function has been modified to enhance functionalities.

Function: compute_STRAPP_test_for_focal_time
  Source file in deepSTRAPP: R/compute_STRAPP_test_for_focal_time.R
  Derived from: traitDependentBAMM() in BAMMtools R package
  Original authors: Dan Rabosky, Huateng Huang
  License: GPL (>= 2) 
  Source: https://cran.r-project.org/package=BAMMtools
  This function has been largely modified to enhance functionalities for deepSTRAPP.

Function: block_permute_rates_data
  Source file in deepSTRAPP: R/compute_STRAPP_test_for_focal_time.R
  Derived from: traitDependentBAMM() in BAMMtools R package
  Original authors: Dan Rabosky, Huateng Huang
  License: GPL (>= 2) 
  Source: https://cran.r-project.org/package=BAMMtools
  This function has been largely modified to enhance functionalities for deepSTRAPP.

Function: addBAMMshifts_custom
  Source file in deepSTRAPP: R/plot_BAMM_rates.R
  Derived from: addBAMMshifts in BAMMtools R package
  Original author: Mike Grundler
  License: GPL (>= 2) 
  Source: https://cran.r-project.org/package=BAMMtools
  This function has been modified to enhance functionalities.

Function: get_mean_eventData
  Source file in deepSTRAPP: R/prepare_diversification_data.R
  Derived from: getBestShiftConfiguration in BAMMtools R package
  Original author: Dan Rabosky
  License: GPL (>= 2) 
  Source: https://cran.r-project.org/package=BAMMtools
  This function has been copied without modifications.


Utility functions in C++