Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / joshwlambert/DAISIEmainland issues and pull requests

#81 - Package update for Habrok HPC

Pull Request - State: closed - Opened by joshwlambert over 1 year ago

#80 - Test PR to check which changes need to merged into main for Habrok

Pull Request - State: closed - Opened by joshwlambert over 1 year ago

#79 - Package maintenance

Pull Request - State: closed - Opened by joshwlambert over 1 year ago - 1 comment

#78 - Change label, fix #77

Pull Request - State: closed - Opened by richelbilderbeek almost 3 years ago - 2 comments

#77 - Island plot legend

Issue - State: closed - Opened by richelbilderbeek almost 3 years ago - 1 comment

#76 - Load the library secretly to omit explicit namespace usage

Pull Request - State: closed - Opened by richelbilderbeek almost 3 years ago - 1 comment

#75 - Changes to bookdown

Pull Request - State: closed - Opened by Neves-P almost 3 years ago - 1 comment
Labels: documentation

#74 - Numerical integrator use

Issue - State: closed - Opened by Neves-P almost 3 years ago - 1 comment

#73 - Recolonisations are plotted prettily as well

Pull Request - State: closed - Opened by richelbilderbeek almost 3 years ago - 1 comment

#72 - No branching for colonist that underwent anagenesis?

Issue - State: closed - Opened by richelbilderbeek almost 3 years ago - 2 comments

#71 - Vertical lines are at correct time

Pull Request - State: closed - Opened by richelbilderbeek almost 3 years ago - 1 comment

#70 - Plot branches connected correctly by `plot_daisie_data`

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 5 comments

#69 - Issue #68: plot recolonisations

Pull Request - State: closed - Opened by richelbilderbeek about 3 years ago - 1 comment

#68 - Plot all recolonisations in 'plot_daisie_mainland_data'

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 23 comments

#67 - Use 'Time before present' in 'plot_mainland', fix #63

Pull Request - State: closed - Opened by richelbilderbeek about 3 years ago - 1 comment

#66 - Joss

Pull Request - State: closed - Opened by joshwlambert about 3 years ago - 1 comment

#65 - Use correct X axis

Pull Request - State: closed - Opened by richelbilderbeek about 3 years ago - 2 comments

#64 - plot_daisie_mainland_data: reverse time axis

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 5 comments

#63 - Changing `plot_mainland` x-axis to time before present

Issue - State: closed - Opened by joshwlambert about 3 years ago - 8 comments

#62 - Use time before present + plot recolonisations

Issue - State: closed - Opened by joshwlambert about 3 years ago - 7 comments

#61 - Color clades based on stac_str

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 1 comment

#60 - Add plotting

Pull Request - State: closed - Opened by richelbilderbeek about 3 years ago - 1 comment

#59 - Add `plot_daisie_mainland_data`

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 4 comments

#58 - add tidyverse style check to tests

Issue - State: closed - Opened by joshwlambert about 3 years ago - 1 comment

#57 - Reconclude some scenarios

Pull Request - State: closed - Opened by joshwlambert about 3 years ago

#56 - Resurrect island_to_tables and daisie_data_to_tables for V2?

Issue - State: closed - Opened by joshwlambert about 3 years ago - 3 comments

#54 - add labels argument to plots

Issue - State: closed - Opened by joshwlambert about 3 years ago

#52 - fix the build on fix_check branch

Issue - State: closed - Opened by joshwlambert about 3 years ago - 1 comment

#51 - Finish plot_island_tbl on tree_plots branch

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 7 comments

#49 - Write read_results function

Issue - State: closed - Opened by joshwlambert about 3 years ago
Labels: enhancement

#48 - Remove link to Tidyverse coding standard?

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 1 comment

#47 - Better document `island_replicates`, remove `sim_island_and_mainland`

Pull Request - State: closed - Opened by richelbilderbeek about 3 years ago - 1 comment

#46 - Suggest: uniform 'island_replicates' datatype

Issue - State: closed - Opened by richelbilderbeek about 3 years ago

#45 - Clean up within-function checks when done

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 2 comments

#44 - Delete sim_island_and_mainland in future

Issue - State: closed - Opened by joshwlambert about 3 years ago - 1 comment

#43 - Param plots

Pull Request - State: closed - Opened by joshwlambert about 3 years ago

#42 - Create `plot_daisie_data`

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 11 comments

#41 - Fix `plot_mainland`

Pull Request - State: closed - Opened by richelbilderbeek about 3 years ago - 2 comments

#40 - Create plot with phylogenies for mainland

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 9 comments

#39 - Restructure param plotting functions to make it more modular

Issue - State: closed - Opened by joshwlambert about 3 years ago - 1 comment
Labels: enhancement

#38 - Write official DAISIE data standard documentation

Issue - State: closed - Opened by joshwlambert about 3 years ago - 6 comments

#37 - unify naming conventions for data structures

Issue - State: closed - Opened by joshwlambert about 3 years ago
Labels: enhancement

#36 - Data types better checked and documented

Pull Request - State: closed - Opened by richelbilderbeek about 3 years ago - 2 comments

#35 - Revise current vignette to focus on parameter estimation using DAISIE

Issue - State: closed - Opened by joshwlambert about 3 years ago
Labels: documentation, enhancement

#34 - Write vignette on island-mainland visualisation

Issue - State: closed - Opened by joshwlambert about 3 years ago
Labels: documentation, enhancement

#33 - Suggest: try to get DAISIEmainland on rOpenSci

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 1 comment

#32 - Plot mainland and island

Pull Request - State: closed - Opened by richelbilderbeek about 3 years ago - 1 comment

#31 - Fix #27, #28, #29, #30 [do not accept yet]

Pull Request - State: closed - Opened by richelbilderbeek about 3 years ago - 2 comments

#30 - Function housekeeping

Issue - State: closed - Opened by joshwlambert about 3 years ago - 2 comments
Labels: enhancement

#29 - purr and tidyverse

Issue - State: closed - Opened by joshwlambert about 3 years ago - 3 comments
Labels: bug, enhancement

#28 - Example in plot_ideal_island does not run

Issue - State: closed - Opened by joshwlambert about 3 years ago - 4 comments
Labels: bug

#27 - Document ideal_island

Issue - State: closed - Opened by joshwlambert about 3 years ago - 2 comments
Labels: documentation

#26 - stac == 4 is documented correctly, start of plotting of islands

Pull Request - State: closed - Opened by richelbilderbeek about 3 years ago

#25 - stac 1 and stac 4 identical?

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 2 comments

#24 - Note to self: `sim_island` always returns an uninteresting result?

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 1 comment

#23 - `mainland_sample_type` can be nonsense

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 2 comments

#22 - Can plot mainland

Pull Request - State: closed - Opened by richelbilderbeek about 3 years ago - 1 comment

#21 - Suggest: export `sim_mainland`

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 1 comment

#20 - Mainland extinction correct?

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 1 comment

#19 - Feature request: sim_island_with_mainland for t = 0

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 2 comments

#18 - Suggest: show the resulting errors in the vignette

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 1 comment

#17 - Feature request: mainland with 1 clade

Issue - State: closed - Opened by richelbilderbeek about 3 years ago - 4 comments

#16 - Allow transitions between scenarios

Pull Request - State: closed - Opened by richelbilderbeek over 3 years ago - 1 comment

#15 - Fix typo and fresh DESCRIPTION

Pull Request - State: closed - Opened by richelbilderbeek over 3 years ago - 1 comment

#14 - Suggest: add supplemenary materials as PDF

Issue - State: closed - Opened by richelbilderbeek over 3 years ago - 1 comment

#13 - Suggest: use `create_test_island_spec`

Issue - State: closed - Opened by richelbilderbeek over 3 years ago - 1 comment

#12 - Suggest: doc and test `format_to_daisie_data`

Issue - State: closed - Opened by richelbilderbeek over 3 years ago

#11 - Feature request: plot the ontology

Issue - State: closed - Opened by richelbilderbeek over 3 years ago - 7 comments

#10 - Example in `DAISIEmainland` doc does not work

Issue - State: closed - Opened by richelbilderbeek over 3 years ago - 1 comment

#9 - CRAN disallows installing GitHub repos from vignettes

Issue - State: closed - Opened by richelbilderbeek over 3 years ago - 2 comments

#8 - Suggest: remove or activate skipped tests

Issue - State: closed - Opened by richelbilderbeek over 3 years ago - 2 comments

#7 - Suggest: document prerequisites

Issue - State: closed - Opened by richelbilderbeek over 3 years ago - 1 comment

#6 - Suggest: let vignette do actual calculations

Issue - State: closed - Opened by richelbilderbeek over 3 years ago - 1 comment

#5 - Add data documentation

Issue - State: closed - Opened by joshwlambert over 3 years ago - 1 comment
Labels: documentation

#4 - create_island() unit testing

Pull Request - State: closed - Opened by Neves-P almost 4 years ago

#3 - Add PN comments

Pull Request - State: closed - Opened by Neves-P almost 4 years ago - 1 comment

#2 - Review Richel

Pull Request - State: closed - Opened by richelbilderbeek almost 4 years ago - 1 comment

#1 - First review

Pull Request - State: closed - Opened by richelbilderbeek almost 4 years ago