| HEAD | d39a692 | typos | 26 October 2020, 15:18:34 UTC |
| refs/heads/master | d39a692 | typos | 26 October 2020, 15:18:34 UTC |
| refs/tags/0.3.5 | e8d06fb | edit link for vignette | 07 November 2016, 20:19:46 UTC |
| refs/tags/0.3.6 | 0049e03 | edits | 14 November 2016, 07:09:39 UTC |
| refs/tags/0.3.7 | 27eae1d | **v.0.3.7** * `assigner::fst_WC84` is 30% faster! | 23 November 2016, 03:43:18 UTC |
| refs/tags/0.3.9 | 1643330 | **v.0.3.9** * I'm pleased to announce that `assigner` now works in parallel with **Windows** * bug fix introduce in last commit in `write_gsi_sim` where the file was not created properly from an internal module. | 28 November 2016, 23:13:45 UTC |
| refs/tags/0.4.0 | a4a0c16 | **v.0.4.0** * `assignment_ngs` and `assignment_mixture` code cleaning to prep for CRAN and make them easier to debug. | 08 December 2016, 23:21:23 UTC |
| refs/tags/v.0.1.0 | 6ac915e | edits | 19 December 2015, 19:39:04 UTC |
| refs/tags/v.0.1.1 | 402deb2 | Merge branch 'master' of https://github.com/thierrygosselin/assigner | 29 January 2016, 16:44:25 UTC |
| refs/tags/v.0.1.2 | 5927fec | new version to update with gsi_sim new install instruction for Linux and Mac. After re-installing assigner package, follow the instruction to re-install the new [gsi_sim] (https://github.com/eriqande/gsi_sim). And delete the old binary 'gsisim' in the /usr/local/bin folder with the following Terminal command: `sudo rm /usr/local/bin/gsisim` | 04 February 2016, 20:21:31 UTC |
| refs/tags/v.0.1.3 | 75cdf34 | fixing bug in snp.ld and changing arguments naming to avoid confusion or respect naming convention | 05 February 2016, 07:14:56 UTC |
| refs/tags/v.0.1.4 | 252d9e0 | v.0.1.4 Introducing 2 new arguments: strata and df.file. Bug fixe. | 10 February 2016, 18:52:48 UTC |
| refs/tags/v.0.1.5 | 7a3d97c | better coding for imputations bug fix in the random method section | 11 February 2016, 07:15:47 UTC |
| refs/tags/v.0.1.6 | 5f51974 | edit | 24 February 2016, 06:06:59 UTC |
| refs/tags/v.0.1.7 | 2d4250e | **v.0.1.7** * New input file: Re-introduced the haplotype data frame file from stacks. * Argument name change: `imputations` is now `impute.method`. * New argument: `impute` with 2 options: `impute = "genotype"` or `impute = "allele"`. | 25 February 2016, 22:10:52 UTC |
| refs/tags/v.0.1.8 | 034d4de | edit | 29 February 2016, 15:51:19 UTC |
| refs/tags/v.0.1.9 | e8793c7 | edits | 12 March 2016, 18:48:30 UTC |
| refs/tags/v.0.2.1 | 4a1b9a4 | **v.0.2.1** * updated the function `assignment_mixture` with `sampling.method = "ranked"` and `assignment.analysis = "adegenet"`. | 09 April 2016, 22:16:59 UTC |
| refs/tags/v.0.2.2 | ed74974 | v.0.2.2 using consistent naming output files for assignment_ngs | 15 April 2016, 11:21:03 UTC |
| refs/tags/v.0.2.3 | 0cc864a | bug fix in the compilation results section when not using pop.id.start and pop.id.end (bug introduced in version 0.2.2) | 22 April 2016, 21:23:56 UTC |
| refs/tags/v.0.2.4 | 685977d | v.0.2.4 introducing a new function `import_subsamples_fst` | 26 April 2016, 12:58:24 UTC |
| refs/tags/v.0.2.5 | 583d5c9 | v.0.2.5 bug fix see readme | 03 May 2016, 15:43:26 UTC |
| refs/tags/v.0.2.6 | 04bbd8e | edit | 15 May 2016, 02:02:52 UTC |
| refs/tags/v.0.2.7 | 4b836ab | **v.0.2.7** * you need to update [stackr] (https://github.com/thierrygosselin/stackr) to v.0.2.7 to appreciate this new version of assigner. * updated `assignment_ngs` with the separate stackr module to simplify the function. * new arguments in `assignment_ngs`. The assignment using dapc can now use the optimized alpha score `adegenet.dapc.opt == "optim.a.score"` or the cross-validation `adegenet.dapc.opt == "xval"`. This is useful for fine tuning the trade-off between power of discrimination and over-fitting (for stability of group membership probabilities). Cross validation with `adegenet.dapc.opt == "xval"` doesn't work with missing data, so it's only available with *imputed data* (i.e. `imputation.method == "rf" or "max"`). With non imputed data or the default: the optimized alpha-score is used (`adegenet.dapc.opt == "optim.a.score"`). When using `adegenet.dapc.opt == "xval"`, 2 new arguments are available: (1) `adegenet.n.rep` and (2) `adegenet.training`. See documentation for details. * removed arguments in `assignment_ngs`. Removed the `pop.id.start` and `pop.id.end` arguments that were confusing people. For those used to these arguments, they are now recycled in the new function `individuals2strata` in [stackr] (https://github.com/thierrygosselin/stackr). The strata file created by this function can be used with the `strata` argument in `assignment_ngs`. * 2 modified arguments in `assignment_ngs`: (1) `gsi_sim.filename` is now `filename`; and (2) if you didn't use the imputation argument, replace `imputation.method = FALSE` to `imputation.method = NULL` or leave the argument missing. * simplified sections of codes in `assignment_ngs` that dealt with `strata`, `pop.levels` and `pop.labels`. * new function: `write_gsi_sim`. Write a gsi_sim file from a data frame (wide or long/tidy). Used internally in [assigner] (https://github.com/thierrygosselin/assigner) and might be of interest for users. | 26 May 2016, 13:11:29 UTC |
| refs/tags/v.0.2.8 | 860e055 | **v.0.2.8** * While changing some lines with `tidyr::spread` and `tidyr::gather` for `data.table::dcast.data.table` and `data.table::melt.data.table` to make the code faster, I forgot to split genotype into alleles for `gsi_sim`. * please update both **stackr** and **assigner** * the build error from Travis will be fixed soon. It should not affect the package "experience"" in any way. | 27 May 2016, 11:48:27 UTC |
| refs/tags/v.0.2.9 | 97d189a | edit | 31 May 2016, 07:58:38 UTC |
| refs/tags/v.0.3.3 | 9142ae9 | Merge branch 'master' of https://github.com/thierrygosselin/assigner | 22 September 2016, 12:46:16 UTC |
| refs/tags/v.0.3.4 | d0a8fae | **v.0.3.4** * `fst_NEI87`: very fast function that can compute: the overall and pairwise Nei's (1987) fst and f'st (prime). Bootstrap resampling of markers is avalaible to build Confidence Intervals. The estimates are available as a data frame and a matrix with upper diagonal filled with Fst values and lower diagonal filled with the confidence intervals. Jost's D is also given ;) | 26 September 2016, 16:02:14 UTC |
| refs/tags/v.0.5.6 | 5936459 | # assigner 0.5.6 2019-05-01 * included 2 simulated datasets * updated documentation of `assignment_ngs` * vignette to get started with assigner, finally! * this is really starting to smell like a CRAN release * work on travis CI * work on pkgdown | 01 May 2019, 20:13:48 UTC |
