Ecosyste.ms: Issues

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

GitHub / thibautjombart/adegenet issues and pull requests

#365 - LOOCV option for DAPC

Issue - State: open - Opened by carlaperezmon 15 days ago - 1 comment

#363 - bug in genlight filtering

Issue - State: open - Opened by maxecoulter 2 months ago - 1 comment

#362 - find.clusters() scale default value different for data.frame

Issue - State: open - Opened by cassondranewman 3 months ago - 1 comment

#361 - Error in DAPC while selecting DAs

Issue - State: closed - Opened by massub 6 months ago - 1 comment

#360 - Strata problem

Issue - State: open - Opened by laiajulianamu 7 months ago - 7 comments
Labels: not adegenet

#359 - Geographic Distance (IBD)

Issue - State: closed - Opened by isapetitta 7 months ago - 2 comments

#358 - Error in fstat(b, fstonly = T) : could not find function "fstat"

Issue - State: open - Opened by nicolashazzi23 10 months ago - 3 comments

#357 - SNP weight values

Issue - State: open - Opened by Tannervanorden 12 months ago

#356 - How to migrate genind objects to newer version of adegenet?

Issue - State: closed - Opened by romunov about 1 year ago - 1 comment

#352 - scatter error

Issue - State: open - Opened by cfz1998 over 1 year ago

#351 - genet.dist not working for populations with large difference in sample size

Issue - State: closed - Opened by georgeomics over 1 year ago - 3 comments

#350 - permutations running gene.dist

Issue - State: open - Opened by Humminglipe over 1 year ago

#349 - Screeplot() function for sPCA is extremely slow.

Issue - State: open - Opened by cms2775 over 1 year ago

#347 - Majority of variance explained by LA1

Issue - State: open - Opened by Repti34 over 1 year ago

#346 - fix cran again

Pull Request - State: closed - Opened by zkamvar almost 2 years ago

#345 - fix short bool

Issue - State: closed - Opened by zkamvar almost 2 years ago
Labels: check: error

#344 - attempt to update C functions

Pull Request - State: closed - Opened by zkamvar almost 2 years ago - 1 comment

#343 - Compoplot of DPAC assigning individuals complete membership of clusters issue

Issue - State: closed - Opened by mattbareno almost 2 years ago - 4 comments

#342 - adegenate

Issue - State: closed - Opened by zinstan almost 2 years ago - 1 comment

#341 - failing CRAN check in C23 mode

Issue - State: closed - Opened by zkamvar almost 2 years ago - 2 comments
Labels: priority

#340 - vcfR2genlight does not calculate loc.all field

Issue - State: closed - Opened by frederikvand almost 2 years ago - 1 comment

#339 - Parallel option for find.clusters and dapc?

Issue - State: open - Opened by ac-harris about 2 years ago - 1 comment

#338 - fix CRAN warnings

Pull Request - State: closed - Opened by zkamvar about 2 years ago - 1 comment

#337 - CRAN Errors 2022-09

Issue - State: closed - Opened by zkamvar about 2 years ago

#336 - DNAbin2genind and ambiguity codes from Fasta

Issue - State: open - Opened by burbrink about 2 years ago - 1 comment

#335 - Not reproducible results with find.clusters

Issue - State: open - Opened by Deepak12Kaushik over 2 years ago - 1 comment

#334 - Expected heterozygosity

Issue - State: open - Opened by ettorefedele over 2 years ago

#333 - CRAN release 2022 06

Pull Request - State: closed - Opened by zkamvar over 2 years ago

#332 - RIPLEY: remove tripack and akima from Suggests

Issue - State: closed - Opened by zkamvar over 2 years ago

#331 - as.matrix.genind: NA.method="mean" doesn't work

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

#330 - xval error object 'out' not found

Issue - State: closed - Opened by nlv209 over 2 years ago - 1 comment

#329 - summmary.spca bug fix for matrices and data frames

Pull Request - State: closed - Opened by lvclark over 2 years ago - 2 comments

#328 - `summary.spca` not working when `spca` run on matrices

Issue - State: closed - Opened by lvclark over 2 years ago - 2 comments
Labels: bug

#327 - PCA result of glPca is quite different from plink

Issue - State: open - Opened by cpwater over 2 years ago - 1 comment

#326 - Does read.genepop really needs `ncode`?

Issue - State: open - Opened by courtiol over 2 years ago

#325 - Strata for running AMOVA

Issue - State: closed - Opened by laiajulianamu over 2 years ago - 1 comment

#324 - PCoA plot problems

Issue - State: closed - Opened by laiajulianamu over 2 years ago - 1 comment

#323 - add sanity check to n.pca.max to default to max value if vector

Pull Request - State: closed - Opened by pdimens over 2 years ago - 2 comments

#322 - cross validation is slow

Issue - State: open - Opened by pdimens almost 3 years ago - 3 comments

#320 - genind2df() doesn't work for 'rupica' when 'oneColPerAll = TRUE'

Issue - State: open - Opened by dfriend21 almost 3 years ago - 1 comment

#319 - the obtained graph doesn't represent individuals as dots in DAPC

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

#318 - CRAN release 2021-10

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

#317 - fix bug in hybridize via tab method for genpop

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

#316 - move spdep to suggests

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

#315 - Move spdep to suggests

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

#314 - Set all parallel = FALSE

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

#313 - Better handling of parallel computation (or lack of) for Windows users

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

#312 - ERROR: number of cluster centres must lie between 1 and nrow(x)

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

#311 - Remove exportPattern() from NAMESPACE

Issue - State: open - Opened by zkamvar over 3 years ago - 1 comment
Labels: documentation, development status

#310 - prepare for CRAN release

Pull Request - State: closed - Opened by zkamvar over 3 years ago

#309 - New release to add missing doc on snapclust

Issue - State: closed - Opened by thibautjombart over 3 years ago - 1 comment
Labels: development status

#308 - `dim()` primitive behavior change with dist objects on load

Issue - State: closed - Opened by zkamvar over 3 years ago - 4 comments
Labels: bug, help wanted, priority

#307 - Issues with June 5, 2021 Tutorial

Issue - State: closed - Opened by neellab-umd over 3 years ago - 8 comments

#306 - Update tutorials; add script

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

#304 - glPca and dapc freezing -- am I picking the wrong nf?

Issue - State: open - Opened by konradtaube over 3 years ago - 1 comment

#302 - there is no package called ‘units’

Issue - State: closed - Opened by patrilia001 over 3 years ago - 1 comment

#301 - Function for observed heterozygosity per pop?

Issue - State: closed - Opened by courtiol over 3 years ago - 5 comments

#299 - pairwise.fast(sim2pop) function not working ?

Issue - State: open - Opened by sunnyEV over 3 years ago - 7 comments

#298 - Documentation bug: glPca parallel is FALSE by default, docs say it's TRUE

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

#296 - method for sorting compoplot by population?

Issue - State: open - Opened by MycoPunk almost 4 years ago - 3 comments

#295 - no need to escape "|" as a separator in df2genind

Issue - State: open - Opened by jean-baka almost 4 years ago - 2 comments

#294 - legend disappear when i export pdf

Issue - State: open - Opened by zxy1555847 about 4 years ago - 1 comment

#293 - sPCA colorplot with more than 3 significant PCs

Issue - State: open - Opened by Katrinhoh about 4 years ago - 1 comment

#292 - add support for parallel in find.clusters

Pull Request - State: open - Opened by timflutre about 4 years ago - 2 comments

#291 - Negative BIC values from find.clusters

Issue - State: closed - Opened by mep19 about 4 years ago - 1 comment

#290 - Variance explained by PCA does NOT reach a plateau

Issue - State: open - Opened by Carol-Symbiomics over 4 years ago - 1 comment

#289 - find.clusters not working

Issue - State: open - Opened by subha-sorghum over 4 years ago - 3 comments

#288 - How to make find.clusters accepts the principle components?

Issue - State: closed - Opened by NamLQ over 4 years ago - 1 comment

#287 - adding doc for snapclust

Pull Request - State: closed - Opened by thibautjombart over 4 years ago - 3 comments

#286 - Adding doc for snapclust

Issue - State: closed - Opened by thibautjombart over 4 years ago

#285 - Very slow find.clusters and dapc computation

Issue - State: open - Opened by vlattko over 4 years ago - 2 comments

#284 - release version 2.1.3

Pull Request - State: closed - Opened by zkamvar over 4 years ago

#283 - Closing parenthesis in find.clusters() choose the number of clusters

Pull Request - State: closed - Opened by knausb over 4 years ago - 4 comments

#282 - Large dataset syndrome NA values

Issue - State: open - Opened by dmacguigan over 4 years ago - 3 comments

#281 - Reading Triploid VCF in useable adegenet object

Issue - State: open - Opened by laurelfloral over 4 years ago - 2 comments

#280 - nancycats file data inconsistent with .rda

Issue - State: open - Opened by pdimens over 4 years ago - 1 comment

#279 - we should be able to enter distance through an argument

Issue - State: closed - Opened by romunov over 4 years ago - 1 comment

#278 - Basic tutorial uses hierfstat::pairwise.fst, which no longer exists

Issue - State: closed - Opened by plantarum over 4 years ago - 7 comments

#277 - Error with splitStrata(x) <- value

Issue - State: closed - Opened by Barsha-P over 4 years ago - 1 comment

#276 - update warning messages to be clearer

Pull Request - State: closed - Opened by zkamvar over 4 years ago

#275 - use inherits instead of class(x) ==

Pull Request - State: closed - Opened by zkamvar over 4 years ago - 1 comment

#274 - "entirely non-type individual(s) deleted" warning is unclear

Issue - State: closed - Opened by plantarum over 4 years ago - 4 comments

#273 - Fix scaleGen example and use Authors@R

Pull Request - State: closed - Opened by courtiol over 4 years ago - 5 comments

#272 - issues installing adeneget

Issue - State: closed - Opened by taniachavarria79 over 4 years ago - 2 comments

#271 - Add pop argument to genlight bracket accessor

Pull Request - State: closed - Opened by zkamvar almost 5 years ago - 3 comments

#270 - seppop doesn't work on genlight objects in latest version

Issue - State: closed - Opened by rdinnager almost 5 years ago - 1 comment

#269 - Cannot load adegenet

Issue - State: closed - Opened by gibedini almost 5 years ago - 6 comments

#268 - CRAN release

Pull Request - State: closed - Opened by zkamvar almost 5 years ago

#267 - Znk fix 265

Pull Request - State: closed - Opened by zkamvar almost 5 years ago - 1 comment

#266 - This function is now deprecated. please use multispati...

Issue - State: open - Opened by Katrinhoh almost 5 years ago - 1 comment

#265 - export_to_mvmapper causing NOTE on CRAN

Issue - State: closed - Opened by zkamvar almost 5 years ago - 1 comment
Labels: check: Warnings / NOTES, priority

#264 - update maintainer

Pull Request - State: closed - Opened by zkamvar almost 5 years ago