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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,67 +1,66 @@ | ||
| Package: DAISIErobustness | ||
| Title: Test the Robustness of DAISIE to Geodynamics and Traits | ||
| Version: 2.6.0.9000 | ||
| Date: 2023-01-27 | ||
| Authors@R: c( | ||
| person(given = "Joshua W.", | ||
| family = "Lambert", | ||
| role = c("aut", "cre"), | ||
| email = "[email protected]", | ||
| comment = c(ORCID = "0000-0001-5218-3046")), | ||
| person(given = "Pedro", | ||
| family = "Santos Neves", | ||
| role = c("aut"), | ||
| email = "[email protected]", | ||
| comment = c(ORCID = "0000-0003-2561-4677")), | ||
| person(given = "Shu", | ||
| family = "Xie", | ||
| role = c("aut"), | ||
| email = "[email protected]", | ||
| comment = c(ORCID = "0000-0001-9594-946X")), | ||
| person(given = "Richèl J.C.", | ||
| family = "Bilderbeek", | ||
| email = "[email protected]", | ||
| role = c("ctb"), | ||
| comment = c(ORCID = "0000-0003-1107-7049")), | ||
| person(given = "Rampal S.", | ||
| family = "Etienne", | ||
| email = "[email protected]", | ||
| role = c("ctb"), | ||
| comment = c(ORCID = "0000-0003-2142-7612")), | ||
| person(given = "Luis", | ||
| family = "Valente", | ||
| email = "[email protected]", | ||
| role = c("ctb"), | ||
| comment = c(ORCID = "0000-0003-4247-8785"))) | ||
| Description: Conducts a robustness test of the island biogeography DAISIE model | ||
| to the effects of geodynamics or trait dependency. Tests processes such as | ||
| island ontogeny, sea-level change and land-bridge dynamics. | ||
| Contains acessory code for easy use with the University of Groningen | ||
| Peregrine HPCC. | ||
| License: GPL-3 | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| Depends: R (>= 3.5.0) | ||
| Suggests: | ||
| testthat (>= 2.1.0), | ||
| lintr, | ||
| knitr, | ||
| rmarkdown, | ||
| dplyr, | ||
| ggtext, | ||
| glue, | ||
| patchwork | ||
| Imports: | ||
| sessioninfo, | ||
| DAISIE (>= 4.3.0), | ||
| nLTT, | ||
| testit, | ||
| ggplot2, | ||
| cowplot | ||
| Remotes: | ||
| rsetienne/[email protected], | ||
| thijsjanzen/nltt | ||
| URL: https://github.com/Neves-P/DAISIErobustness | ||
| BugReports: https://github.com/Neves-P/DAISIErobustness/issues | ||
| RoxygenNote: 7.2.3 | ||
| VignetteBuilder: knitr | ||
| Package: DAISIErobustness | ||
| Title: Test the Robustness of DAISIE to Geodynamics and Traits | ||
| Version: 2.6.0.9000 | ||
| Date: 2023-01-27 | ||
| Authors@R: c( | ||
| person(given = "Joshua W.", | ||
| family = "Lambert", | ||
| role = c("aut", "cre"), | ||
| email = "[email protected]", | ||
| comment = c(ORCID = "0000-0001-5218-3046")), | ||
| person(given = "Pedro", | ||
| family = "Santos Neves", | ||
| role = c("aut"), | ||
| email = "[email protected]", | ||
| comment = c(ORCID = "0000-0003-2561-4677")), | ||
| person(given = "Shu", | ||
| family = "Xie", | ||
| role = c("aut"), | ||
| email = "[email protected]", | ||
| comment = c(ORCID = "0000-0001-9594-946X")), | ||
| person(given = "Richèl J.C.", | ||
| family = "Bilderbeek", | ||
| email = "[email protected]", | ||
| role = c("ctb"), | ||
| comment = c(ORCID = "0000-0003-1107-7049")), | ||
| person(given = "Rampal S.", | ||
| family = "Etienne", | ||
| email = "[email protected]", | ||
| role = c("ctb"), | ||
| comment = c(ORCID = "0000-0003-2142-7612")), | ||
| person(given = "Luis", | ||
| family = "Valente", | ||
| email = "[email protected]", | ||
| role = c("ctb"), | ||
| comment = c(ORCID = "0000-0003-4247-8785"))) | ||
| Description: Conducts a robustness test of the island biogeography DAISIE model | ||
| to the effects of geodynamics or trait dependency. Tests processes such as | ||
| island ontogeny, sea-level change and land-bridge dynamics. | ||
| Contains acessory code for easy use with the University of Groningen | ||
| Peregrine HPCC. | ||
| License: GPL-3 | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| Depends: R (>= 3.5.0) | ||
| Suggests: | ||
| testthat (>= 2.1.0), | ||
| lintr, | ||
| knitr, | ||
| rmarkdown, | ||
| dplyr, | ||
| ggtext, | ||
| glue, | ||
| patchwork | ||
| Imports: | ||
| sessioninfo, | ||
| DAISIE (>= 4.3.0), | ||
| nLTT, | ||
| testit, | ||
| ggplot2, | ||
| cowplot | ||
| Remotes: | ||
| thijsjanzen/nltt | ||
| URL: https://github.com/Neves-P/DAISIErobustness | ||
| BugReports: https://github.com/Neves-P/DAISIErobustness/issues | ||
| RoxygenNote: 7.3.1 | ||
| VignetteBuilder: knitr |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,131 +1,132 @@ | ||
| # DAISIErobustness (development version) | ||
|
|
||
| * Remove unused argument `replicates` from `calc_error()`. #68, thanks @Yangshen0325 | ||
|
|
||
| # DAISIErobustness 2.6.0 | ||
|
|
||
| * Depend on DAISIE v4.3.0. | ||
| * New traits parameter space considering different carrying capacity among | ||
| states, as well as the case without asymmetric transitions. The parameter sets | ||
| are recorded in two files called `trait_CES_2K.csv` and `trait_no_trans.csv`. | ||
| * Update data analysis files for trait-dependent simulations. | ||
|
|
||
| # DAISIErobustness 2.5.0 | ||
|
|
||
| * Suggest `'patchwork'` to assist in figure layout. Used in conjunction with | ||
| previous package `'cowplot'` for generating publication ready figures. | ||
| * Update layout of faceted plots to comply with journal requirements. | ||
|
|
||
| # DAISIErobustness 2.4.0 | ||
|
|
||
| * Update and tweak visuals of figures for publication as requested by journal. | ||
| * Minor style and linting. | ||
|
|
||
| # DAISIErobustness 2.3.0 | ||
|
|
||
| * Depend on DAISIE v4.1.1. | ||
| * Restructured parameter spaces using scripts in `/data-raw/`. | ||
| * Changes to summary metrics. | ||
| * Added new diagnostic functions that use generated log files. | ||
|
|
||
| # DAISIErobustness 2.2.1 | ||
|
|
||
| * Change plot legend to read "colonisation multiplier" rather than "immigration multiplier". | ||
|
|
||
| # DAISIErobustness 2.2.0 | ||
|
|
||
| * Completely rework all plotting functions for Santos Neves, Lambert, Valente, and Etienne 2021. Scripts associated with the paper can be found in the `scripts/folder/` and the necessary functions are found in the sub directory `scripts/folder/functions`. | ||
| * Add functions for reading log files and checking checking correlations between error and run time. Functions are `calc_ed95_param_set()`, `read_runtime_log()`, `read_param_space_log()`, `read_param_set_log()`, `get_runtime_params()`, `calc_runtime_ed95_cor()`, and `plot_cor()`. | ||
| * Rename `calc_stat_diff()` to `calc_ed_95_for_plot()`. This is the function upon which | ||
| the plotting functions for publications rely. Add tests for this function. | ||
| * `load_param_space()` no longer uses the function `read_csv2()` from the `readr` package in favour of base R `read.csv2()`. This change was prompted by the release of `readr` v2.0.0, which parses column types in a different way, resulting in the incorrect reading of `K` from the parameter spaces. Either character vectors or `NA`s were returned due to a combination of ',' as decimal and `Inf` in the data set. The change to `read.csv()` is functionally the same. | ||
| * Improve `run_robustness()` documentation. | ||
|
|
||
|
|
||
| # DAISIErobustness 2.1.1 | ||
|
|
||
| * Depend on DAISIE v4.0.2 to make use of all of it's corrections. See [here](https://github.com/rsetienne/DAISIE/blob/master/NEWS.md#daisie-402) for DAISIE v4.0.0, v4.0.1 and v4.0.2 patch notes for details on the changes. | ||
|
|
||
| # DAISIErobustness 2.1.0 | ||
|
|
||
| * RNG is no longer seeded it `1L` by default. The seed used for each parameter set is now chosen from the current system time and parameter set index. | ||
| * ML runs again fail when computed loglikelihood is `Inf`. | ||
| * Depend on DAISIE v3.2.1. | ||
| * Add a number of plotting functions and scripts, which live on `scripts/plots/`. | ||
| * Change traits, nonoceanic (termed continental island on the paper), and nonoceanic sea-level parameter spaces. | ||
| * Add better metadata on HPCC log files. | ||
| * Move analysis scripts files from `scripts/` to `scripts/analysis/`. | ||
|
|
||
| # DAISIErobustness 2.0.0 | ||
|
|
||
| * Rework pipeline flow. `pipeline`, `load_from_file`, `replicate_range` removed as arguments from `run_robustness()`. No longer possible to run the simulation part of the pipeline separately from the analysis part. | ||
| * Failed ML runs will now result in a new generating simulation being run to overcome numerical issues in MLE. This results in the output of `run_robustness()` directly matching the number of replicates (barring run time constraints). | ||
| * New traits parameter space. These are now split into two files called `trait_CES.csv` and `trait_trans.csv`. | ||
| * Add regular partition job scripts for Peregrine HPCC. | ||
| * Improved geodynamics plots in `scripts/`. | ||
| * Add new `calc_stat_diff()` unexported function in `scripts/`for data analysis. | ||
| * Add new `extract_error_metrics()` unexported function in `scripts/`for data analysis. | ||
| * Fix bug in calculation of number of mainland species in the traits model. | ||
| * Minor documentation improvements. | ||
|
|
||
| # DAISIErobustness 1.1.2 | ||
|
|
||
| * Rework `decide_best_pars()` to intelligently salvage failed ML convergence whenever possible. | ||
| * Request less memory from the Peregrine HPCC. | ||
|
|
||
| # DAISIErobustness 1.1.1 | ||
|
|
||
| * Pipeline now conditions all simulations and MLE on a minimum of 5 colonising | ||
| lineages. | ||
| * Removed `sim_constraints()`. | ||
| * New traits parameter space. | ||
|
|
||
| # DAISIErobustness 1.1.0 | ||
|
|
||
| * Rework [Peregrine HPC](https://www.rug.nl/society-business/centre-for-information-technology/research/services/hpc/facilities/peregrine-hpc-cluster?lang=en) job submission. Job submissions done by calling `sbatch` | ||
| on `/DAISIErobustness/bash/submit_run_robustness_peregrine.sh`. | ||
| * `run_robustness_peregrine.R` is no longer a function, but an R script that | ||
| runs the pipeline on Peregrine. | ||
| * Include improved DAISIE traits parameter space. | ||
| * Depend on rsetienne/[email protected] (which is also the CRAN release). | ||
|
|
||
| # DAISIErobustness 1.0.3 | ||
|
|
||
| * Use correct diversity-dependence settings when estimating using `calc_ml()`. | ||
| See #43. | ||
| * Depend on rsetienne/DAISIE@25d0285, which is DAISIE v3.0.0 but prior to CRAN | ||
| release. | ||
|
|
||
| # DAISIErobustness 1.0.2 | ||
|
|
||
| * Finalize nonoceanic land bridge parameter space. | ||
| * Improve Peregrine HPCC job submission scripts `simulation_run_script` and add | ||
| `analysis_run_script`. Can now choose number of max concurrent jobs. | ||
| Improvements to parameter set range selection. | ||
| * Remove deprecated code from scripts folder. | ||
| * Move and add images to `/pics/`. | ||
|
|
||
| # DAISIErobustness 1.0.1 | ||
|
|
||
| * Fix bug in `ml_constraints` when one of the `initpars` attempts in | ||
| `run_analysis()` did not converge, which prevented some `failed_cond_` results | ||
| from being saved on Peregrine. | ||
| * Depend on rsetienne/DAISIE@dd54db2. | ||
| * Add revised geodynamics parameter spaces for robustness study. | ||
| * Slightly better test coverage in the pipeline when ML convergence fails. | ||
| * Vignette is in correct location. | ||
|
|
||
| # DAISIErobustness 1.0.0 | ||
|
|
||
| * Package to test the robustness of island biogeography models. | ||
| * Simulate new geodynamics and trait dependent models using the | ||
| DAISIE model. | ||
| * Pipeline to analyse the robustness of the DAISIE ML inference to the newly | ||
| implemented models. | ||
| * Can read any new model input in the DAISIE format regardless of generating | ||
| model from a file. | ||
| * Store intermediate simulation output and read said output to finish analyses | ||
| and save to file. | ||
| * Interact and submit jobs to the Peregrine HPCC at the RUG. | ||
| * Generate parameter spaces used for geodynamics and trait dependence robustness | ||
| studies. | ||
| # DAISIErobustness (development version) | ||
|
|
||
| * Remove unused argument `replicates` from `calc_error()`. #68, thanks @Yangshen0325 | ||
| * Depend on production version of `DAISIE`, not on v4.3.0 installed from rsetienne/[email protected]. | ||
|
|
||
| # DAISIErobustness 2.6.0 | ||
|
|
||
| * Depend on DAISIE v4.3.0. | ||
| * New traits parameter space considering different carrying capacity among | ||
| states, as well as the case without asymmetric transitions. The parameter sets | ||
| are recorded in two files called `trait_CES_2K.csv` and `trait_no_trans.csv`. | ||
| * Update data analysis files for trait-dependent simulations. | ||
|
|
||
| # DAISIErobustness 2.5.0 | ||
|
|
||
| * Suggest `'patchwork'` to assist in figure layout. Used in conjunction with | ||
| previous package `'cowplot'` for generating publication ready figures. | ||
| * Update layout of faceted plots to comply with journal requirements. | ||
|
|
||
| # DAISIErobustness 2.4.0 | ||
|
|
||
| * Update and tweak visuals of figures for publication as requested by journal. | ||
| * Minor style and linting. | ||
|
|
||
| # DAISIErobustness 2.3.0 | ||
|
|
||
| * Depend on DAISIE v4.1.1. | ||
| * Restructured parameter spaces using scripts in `/data-raw/`. | ||
| * Changes to summary metrics. | ||
| * Added new diagnostic functions that use generated log files. | ||
|
|
||
| # DAISIErobustness 2.2.1 | ||
|
|
||
| * Change plot legend to read "colonisation multiplier" rather than "immigration multiplier". | ||
|
|
||
| # DAISIErobustness 2.2.0 | ||
|
|
||
| * Completely rework all plotting functions for Santos Neves, Lambert, Valente, and Etienne 2021. Scripts associated with the paper can be found in the `scripts/folder/` and the necessary functions are found in the sub directory `scripts/folder/functions`. | ||
| * Add functions for reading log files and checking checking correlations between error and run time. Functions are `calc_ed95_param_set()`, `read_runtime_log()`, `read_param_space_log()`, `read_param_set_log()`, `get_runtime_params()`, `calc_runtime_ed95_cor()`, and `plot_cor()`. | ||
| * Rename `calc_stat_diff()` to `calc_ed_95_for_plot()`. This is the function upon which | ||
| the plotting functions for publications rely. Add tests for this function. | ||
| * `load_param_space()` no longer uses the function `read_csv2()` from the `readr` package in favour of base R `read.csv2()`. This change was prompted by the release of `readr` v2.0.0, which parses column types in a different way, resulting in the incorrect reading of `K` from the parameter spaces. Either character vectors or `NA`s were returned due to a combination of ',' as decimal and `Inf` in the data set. The change to `read.csv()` is functionally the same. | ||
| * Improve `run_robustness()` documentation. | ||
|
|
||
|
|
||
| # DAISIErobustness 2.1.1 | ||
|
|
||
| * Depend on DAISIE v4.0.2 to make use of all of it's corrections. See [here](https://github.com/rsetienne/DAISIE/blob/master/NEWS.md#daisie-402) for DAISIE v4.0.0, v4.0.1 and v4.0.2 patch notes for details on the changes. | ||
|
|
||
| # DAISIErobustness 2.1.0 | ||
|
|
||
| * RNG is no longer seeded it `1L` by default. The seed used for each parameter set is now chosen from the current system time and parameter set index. | ||
| * ML runs again fail when computed loglikelihood is `Inf`. | ||
| * Depend on DAISIE v3.2.1. | ||
| * Add a number of plotting functions and scripts, which live on `scripts/plots/`. | ||
| * Change traits, nonoceanic (termed continental island on the paper), and nonoceanic sea-level parameter spaces. | ||
| * Add better metadata on HPCC log files. | ||
| * Move analysis scripts files from `scripts/` to `scripts/analysis/`. | ||
|
|
||
| # DAISIErobustness 2.0.0 | ||
|
|
||
| * Rework pipeline flow. `pipeline`, `load_from_file`, `replicate_range` removed as arguments from `run_robustness()`. No longer possible to run the simulation part of the pipeline separately from the analysis part. | ||
| * Failed ML runs will now result in a new generating simulation being run to overcome numerical issues in MLE. This results in the output of `run_robustness()` directly matching the number of replicates (barring run time constraints). | ||
| * New traits parameter space. These are now split into two files called `trait_CES.csv` and `trait_trans.csv`. | ||
| * Add regular partition job scripts for Peregrine HPCC. | ||
| * Improved geodynamics plots in `scripts/`. | ||
| * Add new `calc_stat_diff()` unexported function in `scripts/`for data analysis. | ||
| * Add new `extract_error_metrics()` unexported function in `scripts/`for data analysis. | ||
| * Fix bug in calculation of number of mainland species in the traits model. | ||
| * Minor documentation improvements. | ||
|
|
||
| # DAISIErobustness 1.1.2 | ||
|
|
||
| * Rework `decide_best_pars()` to intelligently salvage failed ML convergence whenever possible. | ||
| * Request less memory from the Peregrine HPCC. | ||
|
|
||
| # DAISIErobustness 1.1.1 | ||
|
|
||
| * Pipeline now conditions all simulations and MLE on a minimum of 5 colonising | ||
| lineages. | ||
| * Removed `sim_constraints()`. | ||
| * New traits parameter space. | ||
|
|
||
| # DAISIErobustness 1.1.0 | ||
|
|
||
| * Rework [Peregrine HPC](https://www.rug.nl/society-business/centre-for-information-technology/research/services/hpc/facilities/peregrine-hpc-cluster?lang=en) job submission. Job submissions done by calling `sbatch` | ||
| on `/DAISIErobustness/bash/submit_run_robustness_peregrine.sh`. | ||
| * `run_robustness_peregrine.R` is no longer a function, but an R script that | ||
| runs the pipeline on Peregrine. | ||
| * Include improved DAISIE traits parameter space. | ||
| * Depend on rsetienne/[email protected] (which is also the CRAN release). | ||
|
|
||
| # DAISIErobustness 1.0.3 | ||
|
|
||
| * Use correct diversity-dependence settings when estimating using `calc_ml()`. | ||
| See #43. | ||
| * Depend on rsetienne/DAISIE@25d0285, which is DAISIE v3.0.0 but prior to CRAN | ||
| release. | ||
|
|
||
| # DAISIErobustness 1.0.2 | ||
|
|
||
| * Finalize nonoceanic land bridge parameter space. | ||
| * Improve Peregrine HPCC job submission scripts `simulation_run_script` and add | ||
| `analysis_run_script`. Can now choose number of max concurrent jobs. | ||
| Improvements to parameter set range selection. | ||
| * Remove deprecated code from scripts folder. | ||
| * Move and add images to `/pics/`. | ||
|
|
||
| # DAISIErobustness 1.0.1 | ||
|
|
||
| * Fix bug in `ml_constraints` when one of the `initpars` attempts in | ||
| `run_analysis()` did not converge, which prevented some `failed_cond_` results | ||
| from being saved on Peregrine. | ||
| * Depend on rsetienne/DAISIE@dd54db2. | ||
| * Add revised geodynamics parameter spaces for robustness study. | ||
| * Slightly better test coverage in the pipeline when ML convergence fails. | ||
| * Vignette is in correct location. | ||
|
|
||
| # DAISIErobustness 1.0.0 | ||
|
|
||
| * Package to test the robustness of island biogeography models. | ||
| * Simulate new geodynamics and trait dependent models using the | ||
| DAISIE model. | ||
| * Pipeline to analyse the robustness of the DAISIE ML inference to the newly | ||
| implemented models. | ||
| * Can read any new model input in the DAISIE format regardless of generating | ||
| model from a file. | ||
| * Store intermediate simulation output and read said output to finish analyses | ||
| and save to file. | ||
| * Interact and submit jobs to the Peregrine HPCC at the RUG. | ||
| * Generate parameter spaces used for geodynamics and trait dependence robustness | ||
| studies. |
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