Ecosyste.ms: Issues

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

GitHub / katiesaund/hogwash issues and pull requests

#95 - attempt to set an attribute on NULL

Issue - State: open - Opened by samuelbloomfield 6 months ago - 1 comment

#94 - Error with printing of the continuous test results

Issue - State: open - Opened by kylegontjes 7 months ago

#93 - Eccmid

Pull Request - State: closed - Opened by 4C554D43 10 months ago

#90 - gene-based analysis?

Issue - State: open - Opened by Shicheng-Guo almost 3 years ago

#89 - Jelly group bug

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

#88 - ERROR: Tree edge lengths are unreasonably long

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

#87 - How exactly does the p-value calculation work?

Issue - State: open - Opened by MikiSchikora about 3 years ago - 5 comments

#85 - Add paragraph to wiki

Issue - State: open - Opened by katiesaund over 3 years ago

#84 - Ability to take in NA

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

#83 - Tiered approach to p-values

Issue - State: open - Opened by katiesaund over 3 years ago

#82 - check_if_g_mat_can_be_plotted issue

Issue - State: closed - Opened by annarerra almost 4 years ago - 1 comment

#81 - update DESCRIPTION

Issue - State: open - Opened by katiesaund almost 4 years ago

#81 - update DESCRIPTION

Issue - State: open - Opened by katiesaund almost 4 years ago

#79 - Add check for contiguity

Issue - State: open - Opened by katiesaund almost 4 years ago
Labels: enhancement

#78 - Add stochastic mapping

Issue - State: open - Opened by katiesaund almost 4 years ago
Labels: enhancement

#77 - Share AR data

Issue - State: open - Opened by katiesaund over 4 years ago
Labels: enhancement

#76 - Add option for maximum parsimony ancestral reconstruction

Issue - State: open - Opened by zenalapp over 4 years ago
Labels: enhancement

#75 - Return raw delta(phenotype)

Issue - State: open - Opened by katiesaund over 4 years ago
Labels: enhancement

#74 - Add phenotype/genotype to tree with phenotype/genotypes transitions in output pdf

Issue - State: open - Opened by zenalapp over 4 years ago
Labels: enhancement

#73 - Add epsilon vs. p-value plot to the hogwash pdf output

Issue - State: open - Opened by zenalapp over 4 years ago
Labels: enhancement

#72 - Return more objects

Issue - State: open - Opened by katiesaund over 4 years ago - 1 comment
Labels: enhancement

#71 - More updates on ancestral reconstruction (and other steps)

Issue - State: closed - Opened by zenalapp over 4 years ago - 1 comment
Labels: enhancement, good first issue

#70 - Add function to estimate run time

Issue - State: open - Opened by katiesaund over 4 years ago
Labels: enhancement

#69 - Make faster/parallelize where possible

Issue - State: open - Opened by zenalapp over 4 years ago - 1 comment
Labels: enhancement

#68 - Phenotype doesn't map correctly on tree

Issue - State: closed - Opened by zenalapp over 4 years ago - 1 comment
Labels: bug

#67 - Return raw p-values

Issue - State: closed - Opened by katiesaund over 4 years ago - 1 comment
Labels: enhancement

#66 - Better plotting for large trees

Issue - State: closed - Opened by katiesaund over 4 years ago - 1 comment
Labels: enhancement, good first issue

#65 - Also output plots as .tiff or .svg

Issue - State: closed - Opened by katiesaund over 4 years ago - 1 comment
Labels: wontfix

#64 - Object must be a character string

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

#63 - grouped genotype transition plots

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

#62 - Add feature in hogwash where genotypes are printed to PDF by rank rather than by original order

Issue - State: closed - Opened by katiesaund over 4 years ago - 2 comments
Labels: enhancement

#61 - Implement intermediate data saves

Issue - State: open - Opened by katiesaund over 4 years ago - 1 comment
Labels: enhancement

#60 - Add progress statements

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

#59 - Stop running binary tests if sum(beta(phenotype)) == 1

Issue - State: open - Opened by katiesaund almost 5 years ago
Labels: enhancement, good first issue

#58 - Report phylogenetic signal in output

Issue - State: closed - Opened by katiesaund almost 5 years ago - 1 comment
Labels: enhancement

#56 - reorder phenotype/genotypes when midpoint rooting

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

#54 - Heatmap legends

Issue - State: closed - Opened by katiesaund almost 5 years ago
Labels: bug

#53 - Increase histogram bar size

Issue - State: closed - Opened by katiesaund almost 5 years ago - 1 comment
Labels: bug

#52 - Create check_phenotype_normality() function

Issue - State: closed - Opened by katiesaund almost 5 years ago
Labels: enhancement

#51 - Create fit_phenotype_model() function

Issue - State: closed - Opened by katiesaund almost 5 years ago
Labels: enhancement

#50 - Add user input/flag to run either PhyC or Sync instead of both

Issue - State: closed - Opened by katiesaund almost 5 years ago - 1 comment
Labels: enhancement

#49 - How many high confidence transition edges should be required to proceed to permutation testing?

Issue - State: closed - Opened by katiesaund about 5 years ago - 1 comment
Labels: question

#48 - Should I remove variants if they are monophyletic (when not grouping)?

Issue - State: closed - Opened by katiesaund about 5 years ago - 1 comment

#46 - consider if this should be used if grouping == TRUE

Issue - State: closed - Opened by katiesaund about 5 years ago - 1 comment

#45 - missing information in inputs

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#44 - Check fails on r-dev version

Issue - State: closed - Opened by katiesaund over 5 years ago - 2 comments
Labels: bug

#43 - check on windows and mac

Issue - State: closed - Opened by katiesaund over 5 years ago - 2 comments

#42 - fix qpdf error during package check()

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

#41 - Decrease example time for hogwash() function

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#40 - Replace -1 assignment with NA

Issue - State: closed - Opened by katiesaund over 5 years ago - 2 comments

#39 - Make sure that order doesn't matter for cbind

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#38 - Use the annotation function here instead of this redundant code

Issue - State: closed - Opened by katiesaund over 5 years ago - 2 comments

#37 - Add p-value rank to plot?

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#36 - Create contingency/check if there are no genotypes to test.

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#35 - Check assumptions for synchronous test

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#34 - Account for inputs lacking sufficient data to run ks test

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#32 - Add checks to inputs

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

#31 - Remove genotype_reconstruction from input

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#30 - Speed up ancestral reconstruction

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#28 - Remove this function

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#27 - Add check input for uni_genes variable

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#26 - Add input checks

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#23 - Decide to keep or remove check_if_convergence_occurs()

Issue - State: closed - Opened by katiesaund over 5 years ago - 2 comments

#22 - Add check for object input

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

#20 - Check inclusion/exclusion of low confidence edges in trans_edge_mat

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#19 - Bootstrap support value

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#18 - shorten overly long function names

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

#16 - Write a vignette.

Issue - State: closed - Opened by katiesaund over 5 years ago - 3 comments
Labels: documentation

#15 - Add citation

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment
Labels: documentation

#14 - Check() issues

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#13 - Wiki

Issue - State: closed - Opened by katiesaund over 5 years ago
Labels: documentation

#11 - Check issues

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#10 - remove temp object

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#9 - Building package error message

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#8 - Testing

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#7 - Documentation

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

#6 - Fix output object names

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

#5 - Cleaning up output plots

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

#4 - grouping genotypes

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#3 - standardize output file names

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

#2 - Grab bag todo list

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment

#1 - relative paths in test

Issue - State: closed - Opened by katiesaund over 5 years ago - 1 comment