Ecosyste.ms: Issues

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

GitHub / grunwaldlab/poppr issues and pull requests

#261 - [chore] Update Continuous Integration

Pull Request - State: closed - Opened by zkamvar 6 months ago

#260 - do not accidentally set seed on package load

Pull Request - State: closed - Opened by zkamvar 8 months ago - 1 comment

#259 - Preserve state of random number generator in .onAttach()

Issue - State: closed - Opened by TimTaylor 8 months ago - 6 comments

#258 - release 2.9.5 (CRAN chore)

Pull Request - State: closed - Opened by zkamvar 12 months ago

#257 - Fix cran bug 256

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

#256 - CRAN Errors to fix by 2023-03-22

Issue - State: closed - Opened by zkamvar over 1 year ago - 2 comments
Labels: bug :bug: :skull_and_crossbones:, CRAN maintenance :construction_worker_man:, High Priority :rotating_light:, C-level :nut_and_bolt:

#255 - add markdown rendering for diversity_ci

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

#254 - Error Message from R using read.genalex

Issue - State: closed - Opened by Tsholo243 about 2 years ago - 1 comment

#252 - [read.genalex()]: Detect semicolon-separated files and throw error with correct command

Issue - State: open - Opened by zkamvar over 2 years ago
Labels: enhancement

#251 - Find All Duplicate MLGs

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

#250 - PAIRWISE FST Calculation

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

#249 - threads not being respected and defaulting to 1

Issue - State: open - Opened by pdimens about 3 years ago - 1 comment

#248 - Optional disabling of statistics in poppr table

Issue - State: open - Opened by Neato-Nick about 3 years ago - 6 comments

#247 - Feature request: separation/removal of sf package requirement

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

#246 - move all headers to the top of the file

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

#245 - DUE 2021-09-21: Packages including omp.h after Rincludes.h

Issue - State: closed - Opened by zkamvar about 3 years ago
Labels: CRAN maintenance :construction_worker_man:, High Priority :rotating_light:, C-level :nut_and_bolt:

#244 - Cannot re-level strata of a snpclone object

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

#243 - add the universe

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

#242 - Fix `bruvo.between()` test fixture

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

#241 - CRAN test failure in R-devel on Debian

Issue - State: closed - Opened by zkamvar over 3 years ago
Labels: CRAN maintenance :construction_worker_man:

#240 - Error in bruvo.boot

Issue - State: closed - Opened by zhangqingah over 3 years ago - 4 comments

#239 - Clade rooting abnormally with updated

Issue - State: closed - Opened by mandiedriskill over 3 years ago - 4 comments

#238 - Cran release 2021 03 21

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

#237 - remove phangorn dependency and add upgma

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

#236 - CRAN submission version 2.9.0

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

#235 - update denominator for bitwise.ia to be int64_t

Pull Request - State: closed - Opened by zkamvar almost 4 years ago - 2 comments

#234 - bitwise.ia() degraded performance on windows

Issue - State: closed - Opened by zkamvar almost 4 years ago - 1 comment
Labels: bug :bug: :skull_and_crossbones:, C-level :nut_and_bolt:

#233 - Fix genind2genalex() error with SNP data

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

#232 - poppr 2.8.7 (cran maintenance)

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

#231 - genind2genalex() produces all zero genotypes with some SNP data.

Issue - State: closed - Opened by zkamvar almost 4 years ago - 1 comment
Labels: bug :bug: :skull_and_crossbones:

#230 - Error with reverse dependency checks for phangorn

Issue - State: closed - Opened by KlausVigo almost 4 years ago - 12 comments

#229 - Interpretation of negative values in AMOVA

Issue - State: closed - Opened by GrimPerez about 4 years ago - 3 comments
Labels: duplicate

#228 - change check to main branch

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

#227 - use github actions

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

#226 - Fix inefficient implementation of boot.bruvo

Issue - State: open - Opened by StaffanBetner about 4 years ago - 3 comments

#225 - Genetic distance calculation yields NAs

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

#224 - export bruvo.between

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

#223 - 220 add bruvos between

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

#222 - Create FUNDING.yml

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

#221 - use gh actions for website

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

#220 - Bruvos Distance function comparing n individuals to a reference set.

Issue - State: closed - Opened by davefol over 4 years ago - 5 comments
Labels: Feature Request :bulb:

#219 - update non-package links for R-devel

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

#218 - Change branch name; rename option

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

#217 - Cran release 2020 05 26

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

#216 - Import progressr package over the dplyr bars

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

#215 - force read.genalex() to read in character data

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

#214 - Issue when reading in GenAlEx csv

Issue - State: closed - Opened by blex-max over 4 years ago - 3 comments
Labels: bug :bug: :skull_and_crossbones:

#213 - Update poppr() to output strings, not factors

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

#212 - R 4.0.0 will change behavior of poppr()

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

#211 - Update unique.MLG documentation for CRAN

Pull Request - State: closed - Opened by zkamvar over 4 years ago - 1 comment
Labels: CRAN maintenance :construction_worker_man:, Documentation :memo:

#210 - Error with custom distance in aboot with PA data

Issue - State: open - Opened by zkamvar almost 5 years ago - 2 comments
Labels: wontfix

#208 - Allow users to allow zero alleles

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

#207 - add distenv slot and accessor to mlg class

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

#206 - Remove .GlobalEnv search in mlg.filter methods

Issue - State: closed - Opened by zkamvar over 5 years ago
Labels: CRAN maintenance :construction_worker_man:

#205 - Cran release 2.8.3

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

#204 - News update

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

#203 - Nodes of single population improved

Pull Request - State: closed - Opened by fdchevalier over 5 years ago - 3 comments

#202 - Fix readgenalex numeric inds

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

#201 - Single population nodes as circles, not pies

Issue - State: closed - Opened by fdchevalier over 5 years ago - 1 comment
Labels: Feature Request :bulb:

#200 - Duplicate word on string 134

Pull Request - State: closed - Opened by kant over 5 years ago - 1 comment

#199 - Cran 2.8.2 rc

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

#198 - Fix testing and travis

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

#197 - R 3.6.0 changes default randomization scheme.

Issue - State: closed - Opened by zkamvar over 5 years ago - 2 comments
Labels: CRAN maintenance :construction_worker_man:, High Priority :rotating_light:

#196 - add libudunits2 to .travis.yml

Issue - State: closed - Opened by zkamvar over 5 years ago

#195 - rarefaction in private_alleles function

Issue - State: open - Opened by afontcub almost 6 years ago - 2 comments
Labels: enhancement, Feature Request :bulb:

#194 - Simpson index

Issue - State: open - Opened by grunwald about 6 years ago - 3 comments
Labels: High Priority :rotating_light:, Documentation :memo:

#193 - Update aboot doc

Pull Request - State: closed - Opened by zkamvar about 6 years ago

#192 - 'shufflepop' methods

Issue - State: closed - Opened by dionnecargy over 6 years ago - 2 comments
Labels: question, Documentation :memo:

#191 - Use vdiffr for testing plots

Issue - State: open - Opened by zkamvar over 6 years ago
Labels: nitpick :thinking: :thinking: :thinking:, Travis maintenance :construction_worker_woman:

#190 - get_local_ploidy() throws an error with non-SSR loci

Issue - State: closed - Opened by zkamvar over 6 years ago
Labels: bug :bug: :skull_and_crossbones:

#189 - Error with poppr() when when population information is missing

Issue - State: closed - Opened by zkamvar over 6 years ago - 6 comments
Labels: bug :bug: :skull_and_crossbones:, fix upstream :ocean:

#188 - Hyperlink DOIs against preferred resolver

Pull Request - State: closed - Opened by katrinleinweber over 6 years ago - 2 comments

#187 - Add RClone to suggests

Issue - State: closed - Opened by zkamvar over 6 years ago
Labels: CRAN maintenance :construction_worker_man:

#186 - Size legend in plot_poppr_msn does not scale well with large nodes

Issue - State: open - Opened by Neato-Nick over 6 years ago - 10 comments
Labels: lots of refactoring :sweat_smile:

#185 - Add genlight/snpclone support to poppr.amova()

Pull Request - State: closed - Opened by zkamvar over 6 years ago

#184 - add cutoff_predictor to mlg vignette

Pull Request - State: closed - Opened by zkamvar over 6 years ago

#183 - Add p-values to pair.ia

Pull Request - State: closed - Opened by zkamvar over 6 years ago

#182 - update filter_stats

Pull Request - State: closed - Opened by zkamvar over 6 years ago

#181 - Change win.ia algorithm

Pull Request - State: closed - Opened by zkamvar over 6 years ago - 1 comment

#180 - pair.ia calculating p-values?

Issue - State: closed - Opened by ktiedje over 6 years ago - 14 comments
Labels: Feature Request :bulb:

#179 - Error using win.ia function in poppr

Issue - State: closed - Opened by MarisaMiller over 6 years ago - 10 comments
Labels: bug :bug: :skull_and_crossbones:

#178 - Allow plot_filter_stats to take list of thresholds instead of nested list

Issue - State: closed - Opened by zkamvar over 6 years ago
Labels: bug :bug: :skull_and_crossbones:

#177 - add cutoff_predictor in mlg vignette

Issue - State: closed - Opened by zkamvar over 6 years ago
Labels: Documentation :memo:

#176 - Add euclidean option and missing correction to bitwise.dist

Pull Request - State: closed - Opened by zkamvar over 6 years ago

#175 - Change default of write.genalex() to tempfile() and document

Issue - State: closed - Opened by zkamvar over 6 years ago
Labels: CRAN maintenance :construction_worker_man:

#174 - Fix site

Pull Request - State: closed - Opened by zkamvar over 6 years ago

#173 - Update AMOVA

Pull Request - State: closed - Opened by zkamvar over 6 years ago
Labels: enhancement

#172 - Add euclidean distance calculation option for bitwise.dist

Issue - State: closed - Opened by zkamvar over 6 years ago - 2 comments
Labels: enhancement, C-level :nut_and_bolt:

#171 - Use euclidean distance for AMOVA if `within = FALSE`

Issue - State: closed - Opened by zkamvar almost 7 years ago
Labels: bug :bug: :skull_and_crossbones:

#170 - Prevent fencepost errors in bitwise.dist memory access

Pull Request - State: closed - Opened by zkamvar almost 7 years ago
Labels: CRAN maintenance :construction_worker_man:, High Priority :rotating_light:, C-level :nut_and_bolt:

#161 - Add size legend to MSN

Pull Request - State: closed - Opened by zkamvar almost 7 years ago

#159 - Change ISSUES.md

Issue - State: closed - Opened by zkamvar almost 7 years ago - 1 comment
Labels: nitpick :thinking: :thinking: :thinking:

#139 - allow for binomial expansion estimations for polyploidy in Bruvo's distance

Issue - State: closed - Opened by zkamvar over 7 years ago - 2 comments
Labels: enhancement, High Priority :rotating_light:, C-level :nut_and_bolt:

#133 - protect warnings

Issue - State: closed - Opened by zkamvar over 7 years ago
Labels: C-level :nut_and_bolt:

#86 - Allow for interruptions in C functions

Issue - State: closed - Opened by zkamvar over 8 years ago - 2 comments
Labels: C-level :nut_and_bolt:

#75 - make C function neighbor_clustering return list instead of pairlist

Issue - State: closed - Opened by zkamvar almost 9 years ago
Labels: enhancement, nitpick :thinking: :thinking: :thinking:, C-level :nut_and_bolt:

#72 - Allow genlight/snpclone objects for AMOVA

Issue - State: closed - Opened by zkamvar almost 9 years ago - 3 comments
Labels: enhancement, lots of refactoring :sweat_smile:

#33 - ensure bitwise.IA can handle missing data.

Issue - State: closed - Opened by zkamvar over 9 years ago - 2 comments
Labels: C-level :nut_and_bolt: