Remove legacy functions and related code #126
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* Add zenodo badge [skip ci] * Test cond on constant rate * test constant_rate_shift with cond * Add test sim_time_dependent * Add sim_trait_dependent cond test * Fix sim_constant_rate_shift cond test * Lint * More stringent constant_rate test * Better test title * fix constant_rate_shift test * Typo * More sim_time_dep cond test * More trait_dependent sim cond tests * test conditioning in relaxed rate * Remove duplicated tests * Add 2 type cond warning. Closes #123 * Fix cond relaxed rate gam test * Better warning text. Closes #123 * Lint * Move over tests from DAISIEtesting * No lintrbot * Increase travis wait time * Test warning of cond with 2 types * Split format_CS_sampled_stt and format_CS_trait files * abuse split-rate model with gamma = 0 * abuse time dependent model with gamma = 0 * Remove some input checks * Better tests sim_core_1_4a * test abuse and verbose DAISIE sim time dep * test abuse sim_core_trait_dependent * test no colonization happening returining 0 on stt * trait sims don't take nonoceanic pars * Delete DAISIE_single_branch * Add are_rates test * Better check format tests * Fix typo * Remove lingering nonoceanic pars in traits tests * Better is_simulation_outputs name checking * added higher subdivisions limit to integral_peak * added rel.tol to integral_peak * changed abs.tol to 1e-10 * changed integration to catch errors and return -Inf * changed rho to log gamma distribution and integrand to sum * removed if statement to catch integration errors * removed stop.on.error in integration * manual merge with 'hanno' Signed-off-by: Hanno <h.hildenbrandt@rug.nl> * builds,install & runs on Linux source package added Signed-off-by: Hanno <h.hildenbrandt@rug.nl> * Updated version and documentation * useDynLib in DAISIE-package.R, renewed documentation * useDynLib in DAISIE-package.R, renewed documentation * useDynLib in DAISIE-package.R, renewed documentation * No export pipe just import from magrittr * Correct appveyor.yml * logos and AppVeyor status in README * indent * lint * Progress correct brts ONEcolonist #125 * Only remove youngest_col if in vector. Progress #125 * Assert that youngest_col_time must be in btimes_all_clado_desc. Progress #125 * Format * Add comments and asserts. Remove else * Adjust refernce progress #125 * Add /pics to .Rbuildignore * Try adding col times, removing youngest. Progress #125 * Remove appveyor setup * Go GHA * GHA on onecolonist_fix * Switch to else if. Progress #125 * Fix references after testing. Progress #125 * Rename other_clades_same_ancestor to all_colonisations. Lint. Progress #125 * Better CI checks for testing * seq_along() not seq_len(). Progress #125 * Better doc. Progress #125 * Fix reference test CS_full_stt. Progress #125 * other_clades_same_ancestor -> all_colonisations. Progress #125 * other_clades_same_ancestor -> all_colonisations in core_1_4. Consider removing, changed to pass tests. Progress #125 * Better skips * Expand ONEcolonist hedge case coverage. Progress #125 * Comment temp code * Fix reference. Progress #125 * use NULL stt_table for testing. Progress #125 * Remove 1_4 and 1_5 functions and tests * Legacy functions removed from tests. Progress #126 * Remove more legacy code and tests. Progress #126 * V with single string w/ all times. Progress #125 * DAISIE_ONEcolonist returns all_event_times. Closes #125 * Update test-format_CS references. Progress #125 * Add $all_colonisations reference tests. Progress #125 * Add and rearrange ONEcolonist tests. Progress #125 * Remove unnecessary section. Close #125 * Sort all_colonisations from oldest to youngest. #125 * Expand tests and add test for 2 clado 1 nonendemic. #125 * Remove get_brts_mya(). Progress #126 * create_island() is internal. Progress #126 * Don't export DAISIE_make_global(). Progress #126 * Fix ONEcolonist documentation * Minor formatting * Use improved GHA yaml * Remove travis * Faster example in constant_rate * MinAge and better input support in DAISIE_dataprep * Fix table * Format pic * Try travis again * No roxygen doc on .Rproj * Travis in right place * Don't depend on Rcpp, RcppEigen, BH * Delete top level files * Buiild on Windows R4.0.2, Rtools40 Signed-off-by: Hanno <h.hildenbrandt@rug.nl> * Windows binary package added Signed-off-by: Hanno <h.hildenbrandt@rug.nl> * Linux: devtools::check pass Signed-off-by: Hanno <h.hildenbrandt@rug.nl> * Try Rcpp, RcppEigen, BH on imports * Rcpp, RcppEigen, BH on Imports * Don't run on PR. Install doMC on unix * Rcpp, RcppEigen, BH on Depends * still trying * R CMD check passes on Windows (R 3.6.3) R CMD check passes on Linux (R 3.6.3) Signed-off-by: Hanno <h.hildenbrandt@rug.nl> * Install ggtree * biocViews: to install ggtree instead * No longer use travis * date change * invoke_IW to test * Bug fix dopri5 and documentation * documentation * Solve Error: function 'enterRNGScope' not provided by package 'Rcpp' as outlined on https://github.com/immunogenomics/LISI/blob/master/NAMESPACE * Depend on specific setup-r tag See similar issue rsetienne/DDD#29 * GHA on macOS_fix * Use full SHA * Check if new test breaks covr * Add skip message * Don't define functions in tests * lint 2 integration tests * lint rate-shift and IW vs CS integration tests * Tweak time_dep ML WIP test * 2 type integration test lint * Remove redundant test-integration_tests * Informative comment on parallel test fix * Try loading Rcpp in tests * Avoid coverage check on solver test * Change flag location * Correct nocov flags * Split loglik_IW_solver and add to .covrignore * covr output in GHA output * Fix syntax * Remove Rcpp library call * skip_on_covr() and remove #nocov flags * Just run codecov * Delete wrong argument * Add @xieshu95's ORCID * Add @joshwlambert's ORCID * Add a NEWS.md file to track changes to the package * Add DAISIE_macOS instructions * Update NEWS.md to match v3.2.0 release notes * Add Big Sur note on README.md * Typo * setup-r@v1 again See Neves-P/DAISIErobustness/cb6ae80f545f01e8a2ebe0c134f915d8f804c7b4 * Add LICENSE file * arrows instead of = * Solving numerical problems with logcondprob * Improving numerical accuracy logcond * Modified test to conform to new logcond * cleaning up logcond * Improving logcond * bug fix * Resolving numerical issues near 0 in integration across parameters * passing mean and sd * fixed bug * Correctly format doi * relaxed rate in NEWS.md * Add note on logcondprob fix * Update date * updated relaxed_rate loglik * Use midpoint of function for better approximation * reduce approx threshold to 0.01 for relaxed-rate * Add @rscherrer's ORCID * Touch up references and authors * @HHildenbrandt is an author * changed approx threshold to 1 and change approximation to DAISIE_loglik * added tests for DAISIE_loglik_integrate * tidy DAISIE_loglik_integrate Co-authored-by: Pedro Neves <10762799+Neves-P@users.noreply.github.com> Co-authored-by: Neves-P <p.m.santos.neves@rug.nl> Co-authored-by: joshwlambert <j.w.l.lambert@rug.nl> Co-authored-by: rsetienne <rampaletienne@gmail.com> Co-authored-by: = <=>
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Legacy functions such as
DAISIE_sim_core_1_4(),DAISIE_sim_core_1_4a()andDAISIE_sim_core_1_5()can now be removed from the package.These will still be available in older releases of the package, such as v2.0 (e7a41da).
Make sure to remove all tests and related documentation associated with these legacy functions.
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