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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,55 +1,53 @@ | ||
| { | ||
| "title": "secsse: Several Examined and Concealed States-Dependent Speciation and Extinction", | ||
| "license": "GPL-3.0", | ||
| "upload_type": "software", | ||
| "description": "<p>SecSSE is an R package designed for multistate data sets under a concealed state and speciation (hisse) framework. In this sense, it is parallel to the 'MuSSE' functionality implemented in diversitree, but it accounts for finding possible spurious relationships between traits and diversification rates ('false positives', Rabosky & Goldberg 2015) by testing against a 'hidden trait' (Beaulieu et al. 2013), which is responsible for more variation in diversification rates than the trait being investigated. <\/p>", | ||
| "keywords": [ | ||
| "Evolving traits", | ||
| "macroevolution", | ||
| "phylogenetic tools", | ||
| "speciation rates", | ||
| "model", | ||
| "maximum-likelihood", | ||
| "parameter estimation" | ||
| ], | ||
| "access_right": "open", | ||
| "language": "eng", | ||
| "contributors": [ | ||
| { | ||
| "name": "Janzen, Thijs", | ||
| "affiliation": "University of Groningen", | ||
| "orcid": "0000-0002-4162-1140", | ||
| "type": "ProjectMember" | ||
| }, | ||
| { | ||
| "name": "Hildenbrandt, Hanno", | ||
| "affiliation": "University of Groningen", | ||
| "orcid": "0000-0002-6784-1037", | ||
| "type": "ProjectMember" | ||
| }, | ||
| { | ||
| "name": "Santos Neves, Pedro", | ||
| "affiliation": "University of Groningen", | ||
| "orcid": "0000-0003-2561-4677", | ||
| "type": "ProjectMember" | ||
| } | ||
| ], | ||
| "creators": [ | ||
| { | ||
| "name": "Herrera Alsina, Leonel", | ||
| "affiliation": "University of Aberdeen", | ||
| "orcid": "0000-0003-0474-3592", | ||
| }, | ||
| { | ||
| "name": "van Els, Paul", | ||
| "affiliation": "Sovon Dutch Centre for Field Ornithology", | ||
| "orcid": "0000-0002-9499-8873", | ||
| }, | ||
| { | ||
| "name": "Etienne, Rampal S.", | ||
| "affiliation": "University of Groningen", | ||
| "orcid": "0000-0003-2142-7612", | ||
| }, | ||
| ], | ||
| "notes": "Compiled code (*.cpp and *.h files) is licensed under the BSL-1.0. See file COPYRIGHTS and LICENSE.note for mode details", | ||
| } | ||
| "title": "secsse: Several Examined and Concealed States-Dependent Speciation and Extinction", | ||
| "license": "GPL-3.0", | ||
| "upload_type": "software", | ||
| "description": "<p>SecSSE is an R package designed for multistate data sets under a concealed state and speciation (hisse) framework. In this sense, it is parallel to the 'MuSSE' functionality implemented in diversitree, but it accounts for finding possible spurious relationships between traits and diversification rates ('false positives', Rabosky & Goldberg 2015) by testing against a 'hidden trait' (Beaulieu et al. 2013), which is responsible for more variation in diversification rates than the trait being investigated. <\/p>", | ||
| "keywords": [ | ||
| "Evolving traits", | ||
| "macroevolution", | ||
| "phylogenetic tools", | ||
| "speciation rates", | ||
| "model", | ||
| "maximum-likelihood", | ||
| "parameter estimation" | ||
| ], | ||
| "access_right": "open", | ||
| "language": "eng", | ||
| "contributors": [{ | ||
| "name": "Janzen, Thijs", | ||
| "affiliation": "University of Groningen", | ||
| "orcid": "0000-0002-4162-1140", | ||
| "type": "ProjectMember" | ||
| }, | ||
| { | ||
| "name": "Hildenbrandt, Hanno", | ||
| "affiliation": "University of Groningen", | ||
| "orcid": "0000-0002-6784-1037", | ||
| "type": "ProjectMember" | ||
| }, | ||
| { | ||
| "name": "Santos Neves, Pedro", | ||
| "affiliation": "University of Groningen", | ||
| "orcid": "0000-0003-2561-4677", | ||
| "type": "ProjectMember" | ||
| } | ||
| ], | ||
| "creators": [{ | ||
| "name": "Herrera Alsina, Leonel", | ||
| "affiliation": "University of Aberdeen", | ||
| "orcid": "0000-0003-0474-3592" | ||
| }, | ||
| { | ||
| "name": "van Els, Paul", | ||
| "affiliation": "Sovon Dutch Centre for Field Ornithology", | ||
| "orcid": "0000-0002-9499-8873" | ||
| }, | ||
| { | ||
| "name": "Etienne, Rampal S.", | ||
| "affiliation": "University of Groningen", | ||
| "orcid": "0000-0003-2142-7612" | ||
| } | ||
| ], | ||
| "notes": "Compiled code (*.cpp and *.h files) is licensed under the BSL-1.0. See file COPYRIGHTS and LICENSE.note for mode details" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,92 +1,131 @@ | ||
| # secsse 3.0.0 | ||
| # secsse 3.0.1 | ||
|
|
||
| Version 3.0.0 extends the C++ code base used for the standard likelihood to the "cla_" | ||
| likelihood, harnessing the same computation improvement. | ||
| Version 3.0.1 patches some inaccuracies in simulation functions, and | ||
| deprecates expand_q_matrix, as this was making some incorrect | ||
| assumptions. | ||
|
|
||
| ## Breaking changes | ||
| * Function name changes: | ||
| * `create_lambda_matrices()` is now called `create_lambda_list()` | ||
| * `create_transition_matrix()` is now called `create_q_matrix()` | ||
| * `create_mus()` is now called `create_mu_vector()` | ||
| * `create_default_q_list()` is now called `create_default_shift_matrix()` | ||
| * `create_default_lambda_list ()` is now called `create_default_lambda_transition_matrix()` | ||
| * `create_default_q_list()` is now called `create_default_shift_matrix()` | ||
| * Package data files renamed: | ||
| * `phylo_Vign` is now called `phylo_vignette` | ||
| * `traitinfo` is now called `traits` | ||
| * `phy` is now called `example_phy_GeoSSE` | ||
| * `plot_state_exact()` argument `steps` renamed to `num_steps` and argument | ||
| `focal_tree` renamed to `phy` for consistency with other functions. | ||
|
|
||
| - The function expand_q_matrix is now deprecated, please use | ||
| q_doubletrans | ||
|
|
||
| ## Minor changes | ||
|
|
||
| - Added conditioning of simulation of complete trees on complete tree | ||
| size | ||
| - Fixed some issues with setting `pool_init_states` | ||
| - Added option to return a histogram of simulated tree sizes, across | ||
| all successful and failed trees. | ||
|
|
||
| # 3.0.0 | ||
|
|
||
| Version 3.0.0 extends the C++ code base used for the standard likelihood | ||
| to the "cla\_" likelihood, harnessing the same computation improvement. | ||
|
|
||
| ## Breaking changes | ||
|
|
||
| - Function name changes: | ||
| - `create_lambda_matrices()` is now called `create_lambda_list()` | ||
| - `create_transition_matrix()` is now called `create_q_matrix()` | ||
| - `create_mus()` is now called `create_mu_vector()` | ||
| - `create_default_q_list()` is now called | ||
| `create_default_shift_matrix()` | ||
| - `create_default_lambda_list ()` is now called | ||
| `create_default_lambda_transition_matrix()` | ||
| - `create_default_q_list()` is now called | ||
| `create_default_shift_matrix()` | ||
| - Package data files renamed: | ||
| - `phylo_Vign` is now called `phylo_vignette` | ||
| - `traitinfo` is now called `traits` | ||
| - `phy` is now called `example_phy_GeoSSE` | ||
| - `plot_state_exact()` argument `steps` renamed to `num_steps` and | ||
| argument `focal_tree` renamed to `phy` for consistency with other | ||
| functions. | ||
|
|
||
| ## Major changes | ||
|
|
||
| * Vastly improve the computational speed of "cla_" likelihood calculation. | ||
| * Optimization of parallelization resulting in better scaling with more threads | ||
| and faster run time for standard secsse and cla_secsse likelihood calculations. | ||
| - Vastly improve the computational speed of "cla\_" likelihood | ||
| calculation. | ||
| - Optimization of parallelization resulting in better scaling with | ||
| more threads and faster run time for standard secsse and cla_secsse | ||
| likelihood calculations. | ||
|
|
||
| ## Minor changes | ||
| * Added a `NEWS.md` file to track changes to the package. | ||
| * Documentation reworked into `default_params_doc()`. | ||
| * Several documentation formatting improvements and linking. Documentation now | ||
| follows and allows for roxygen2 markdown. | ||
| * A new vignette: | ||
| * _Using secsse with complete phylogenies (with extinction)_ `vignette("complete_tree", package = "secsse")` | ||
| * A new [pkgdown website](https://rsetienne.github.io/secsse/index.html)! | ||
| * It contains all the documentation and vignettes of the package, along with | ||
| additional interesting information like the _Secsse versions_ article with | ||
| details on performance and the development history of secsse. | ||
| * Revise, combine and simplify the _Using SecSSE ML search_ and _Setting up a | ||
| secsse analysis_ into the _Starting secsse_ vignette | ||
| `vignette("starting_secsse", package = "secsse")`. | ||
| * `secsse_sim()` argument `conditioning` now defaults to `"obs_states"` from | ||
| `"none"`. | ||
| * No longer Import package 'stringr' and Suggest package 'testit'. | ||
| * New organisation of code in .R, .cpp and .h files. (Developer side). | ||
| * Start archiving in Zenodo, with new .zenodo.json metadata file. | ||
|
|
||
| - Added a `NEWS.md` file to track changes to the package. | ||
| - Documentation reworked into `default_params_doc()`. | ||
| - Several documentation formatting improvements and linking. | ||
| Documentation now follows and allows for roxygen2 markdown. | ||
| - A new vignette: | ||
| - *Using secsse with complete phylogenies (with extinction)* | ||
| `vignette("complete_tree", package = "secsse")` | ||
| - A new [pkgdown | ||
| website](https://rsetienne.github.io/secsse/index.html)! | ||
| - It contains all the documentation and vignettes of the package, | ||
| along with additional interesting information like the *Secsse | ||
| versions* article with details on performance and the | ||
| development history of secsse. | ||
| - Revise, combine and simplify the *Using SecSSE ML search* and | ||
| *Setting up a secsse analysis* into the *Starting secsse* vignette | ||
| `vignette("starting_secsse", package = "secsse")`. | ||
| - `secsse_sim()` argument `conditioning` now defaults to | ||
| `"obs_states"` from `"none"`. | ||
| - No longer Import package 'stringr' and Suggest package 'testit'. | ||
| - New organisation of code in .R, .cpp and .h files. (Developer side). | ||
| - Start archiving in Zenodo, with new .zenodo.json metadata file. | ||
|
|
||
| ## Bug fixes | ||
| * `secsse_sim()` fix bug causing error when simulating trees with extinct | ||
| species. | ||
|
|
||
| - `secsse_sim()` fix bug causing error when simulating trees with | ||
| extinct species. | ||
|
|
||
| # 2.6.0 | ||
|
|
||
| ## Major changes | ||
| * C++ code base for the standard likelihood, making smarter use of | ||
| parallelization, this marks another 10-fold increase in speed. | ||
|
|
||
| - C++ code base for the standard likelihood, making smarter use of | ||
| parallelization, this marks another 10-fold increase in speed. | ||
|
|
||
| ## Minor changes | ||
| * Add a number of helper functions: `fill_in()`, `create_default_q_list()`, | ||
| `create_default_transition_list()`, `create_mus()` | ||
| * Implemented necessary changes to comply with CRAN clang16 build and solve | ||
| issue with the boost odeint library uninitialized variable | ||
| (see https://github.com/boostorg/odeint/issues/59 and more details at | ||
| https://github.com/rsetienne/DAISIE/pull/158) | ||
| * Updated Copyright license to the Boost Software License, Version 1.0 for | ||
| included C++ code (R code remains GPL>=3). | ||
|
|
||
| - Add a number of helper functions: `fill_in()`, | ||
| `create_default_q_list()`, `create_default_transition_list()`, | ||
| `create_mus()` | ||
| - Implemented necessary changes to comply with CRAN clang16 build and | ||
| solve issue with the boost odeint library uninitialized variable | ||
| (see <https://github.com/boostorg/odeint/issues/59> and more details | ||
| at <https://github.com/rsetienne/DAISIE/pull/158>) | ||
| - Updated Copyright license to the Boost Software License, Version 1.0 | ||
| for included C++ code (R code remains GPL\>=3). | ||
|
|
||
| ## Bug fixes | ||
| * Fix memory leaks | ||
|
|
||
| - Fix memory leaks | ||
|
|
||
| # 2.5.0 | ||
| Version 2.5.0 appeared in 2021 on GitHub and was published in May 2023 on CRAN. | ||
| Version 2.5.0 marks the first version using C++ to perform the integration, | ||
| and it used tbb (from the RcppParallel package) to perform multithreading. This | ||
| marks a ten fold increase in speed over previous versions. | ||
| Secondly, 2.5.0 introduces the function `secsse_sim()` to simulate a | ||
| diversification process using the (cla) secsse framework. | ||
| Lastly, in version 2.5.0 functions were added to allow visualisation of | ||
| inferred rates of speciation across the tree (e.g. `plot_state_exact()` and | ||
| `secsse_loglik_eval()`). | ||
|
|
||
| Version 2.5.0 appeared in 2021 on GitHub and was published in May 2023 | ||
| on CRAN. Version 2.5.0 marks the first version using C++ to perform the | ||
| integration, and it used tbb (from the RcppParallel package) to perform | ||
| multithreading. This marks a ten fold increase in speed over previous | ||
| versions. Secondly, 2.5.0 introduces the function `secsse_sim()` to | ||
| simulate a diversification process using the (cla) secsse framework. | ||
| Lastly, in version 2.5.0 functions were added to allow visualisation of | ||
| inferred rates of speciation across the tree (e.g. `plot_state_exact()` | ||
| and `secsse_loglik_eval()`). | ||
|
|
||
| # 2.0.0 | ||
| Version 2.0.0 appeared in June of 2019 on CRAN and extended the package with the | ||
| cla framework, e.g. including state shifts during speciation / asymmetric | ||
| inheritance during speciation. | ||
|
|
||
| Version 2.0.0 appeared in June of 2019 on CRAN and extended the package | ||
| with the cla framework, e.g. including state shifts during speciation / | ||
| asymmetric inheritance during speciation. | ||
|
|
||
| # 1.0.0 | ||
| The first version of secsse appeared in January of 2019 on CRAN. It used the | ||
| package deSolve to solve all integrations, and could switch between either using | ||
| a fully R based evaluation, or use FORTRAN to speed up calculations. | ||
| Furthermore, using the foreach package, within-R parallelization was | ||
| implemented. However, parallelization only situationally improved computation | ||
| times, and generally, computation was relatively slow. | ||
|
|
||
| The first version of secsse appeared in January of 2019 on CRAN. It used | ||
| the package deSolve to solve all integrations, and could switch between | ||
| either using a fully R based evaluation, or use FORTRAN to speed up | ||
| calculations. Furthermore, using the foreach package, within-R | ||
| parallelization was implemented. However, parallelization only | ||
| situationally improved computation times, and generally, computation was | ||
| relatively slow. |
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