NEWS.md

In thierrygosselin/grur: Imputations of RADseq data

grur 0.1.4 2020-10-21

• Version bump because it updates numerous packages: tidyr, readr.
• using future and carrier.
• Switched to GitHub actions to run the R-CMD-check on the 3 OS instead of Travis CI and AppVeyor.
• Further testing are required to highlight breaking change.

grur 0.1.3 2020-08-31

• grur_imputations: tidyr::spread and tidyr::gather are now deprecated in favor of (pivot_) functions. These are actually a lot slower than gather and spread (https://github.com/tidyverse/tidyr/issues/613). No thank you. They are now replaced in grur by the data.table equivalent verbs.

grur 0.1.2 2020-02-13

• lots of works on simulate_rad and missing_distributions from Eric Archer.

grur 0.1.1 2019-05-01

• pkgdown website
• better function doc
• vignettes
• work on dependencies
• work on travis CI

grur 0.1.0 2019-03-15

• several commits will come with this in the next 2 weeks
• missing_visualization: is getting an upgrade. Will work with GDS file/object.
• grur_imputations: will be fully reviewed and updated to work with GDS.
• radiator::genomic_converter: is now integrated at the end of the imputation module, instead of the later. This will reduce duplication codes for me, and help pass CRAN...
• New documentations.
• Several arguments are now deprecated or moved to the advance section. Read documentation.
• new life cycle section in grur_imputations
• Requirement to pass some test before imputations will be generated so that user with bad data don't waist time with imputations!

grur 0.0.11 2018-07-09

• grur ready for R 3.5.1 "Feather Spray" released on 2018/07/05
• grur updated to work with ggplot2 v.3.0.0

grur 0.0.10 2018-04-26

grur's dependencies:

• I transferred to Suggests section these packages: lightgbm, missRanger, randomForestSRC, ranger, rmarkdown, rmetasim, strataG, xgboost.
• Functions thate requires specific package will now say so.
• Reason: people only interested in missing_visualization don't have to install all the required packages required for imputations or simulations.

simulate_rad: with the latest R release (3.5.0), Check now throw a new note: Note: next used in wrong context: no loop is visible at simulate_rad.R:189 I replaced next inside sapply with while.

grur 0.0.9 2017-10-27

• lightGBM option to conduct the imputations is fully functional

grur 0.0.8 2017-10-24

• worked on missing_visualization to get better output figures with large number of pop
• worked on imputation algorithm to prep for the use of lightGBM package

grur 0.0.7 2017-10-02

worked on missing_visualization added Eric Archer's work on detecting patterns figures are now combined under themes (e.g. all PCoA for the same strata are together, etc)

grur 0.0.6 2017-08-18

• several typos fixed
• work on missing_visualization

grur 0.0.5 2017-08-15

• restored progress bar when using parallel computing by installing the new dev version of pbmcapply package.

grur 0.0.5 2017-08-15

• restored progress bar when using parallel computing by installing the new dev version of pbmcapply package.

grur 0.0.4 2017-08-15

• bug fix: removed the progress bar when using parallel computing. This is temporary, while waiting for a fix with pbmcapply package.

grur 0.0.3 2017-06-17

• simulate_rad: a new function developed by Eric Archer to simulate populations of RADseq data following island or stepping stone models.
• grur works with dplyr v.0.7.0

grur 0.0.2 2017-04-23

• Work on generate_missing function.
• Still not as I wish. But getting there.
• 2 new functions: imputations_accuracy and memorize_missing. Check functions documentations for more info.

grur 0.0.1 2017-04-07

New package is out!

thierrygosselin/grur documentation built on Oct. 28, 2020, 5:48 p.m.