phylotastic/datelife issues and pull requests

#96 - Do all summaries require bladj?

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

#95 - Run bladj from calibrations

Issue - State: open - Opened by snacktavish 7 months ago - 4 comments

#94 - Error in phylo_median

Issue - State: open - Opened by snacktavish 7 months ago - 1 comment

#93 - query fails due to unmatched names

Issue - State: open - Opened by snacktavish 7 months ago - 2 comments

#92 - print method for chronogram database

Issue - State: open - Opened by LunaSare 11 months ago

#91 - chronogram database update

Pull Request - State: closed - Opened by LunaSare 11 months ago - 1 comment

#90 - Documentations tweaks

Issue - State: closed - Opened by snacktavish 11 months ago - 2 comments

#89 - citation not getting rebuilt via pkgdown

Issue - State: open - Opened by snacktavish 11 months ago

#88 - Reltime fix

Pull Request - State: closed - Opened by snacktavish 12 months ago - 1 comment

#87 - Ott names

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

#86 - No species found in homo

Issue - State: open - Opened by snacktavish 12 months ago - 3 comments

#85 - OTT name search failing

Issue - State: closed - Opened by snacktavish 12 months ago - 1 comment

#84 - fix various bugs

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

#83 - add score to hard-coded Mus

Pull Request - State: closed - Opened by fmichonneau over 1 year ago - 4 comments

#82 - fix bug

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

#81 - Summarising chronograms fails

Issue - State: open - Opened by irmoodie almost 2 years ago - 2 comments

#80 - elephas datelife query returning 7 species instead of 8

Issue - State: open - Opened by LunaSare almost 2 years ago

#79 - managing subspecies when making a datelife query

Issue - State: open - Opened by LunaSare almost 2 years ago

#78 - Database update

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

#77 - Getting dated OpenTree induced synthetic subtree fails

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

#76 - warning: lazy data db without compression

Issue - State: closed - Opened by LunaSare almost 3 years ago - 1 comment

#75 - Testing

Pull Request - State: closed - Opened by LunaSare almost 3 years ago

#74 - Adding Vignettes

Pull Request - State: closed - Opened by LunaSare almost 3 years ago

#73 - Relative time

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

#72 - Datelife plots

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

#71 - tnrs_match batch function fix

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

#70 - Issue with DESCRIPTION prevents installation

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

#69 - catsanddogs_bold

Issue - State: open - Opened by LunaSare over 4 years ago

#68 - a solution for packages on imports that got kicked out of CRAN

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

#67 - add some S3 methods

Issue - State: open - Opened by LunaSare over 5 years ago

#66 - tree from taxonomy reticulates and gives fatal memory error with ape::write.tree

Issue - State: open - Opened by LunaSare over 5 years ago

#65 - datelife testing data sets

Issue - State: open - Opened by LunaSare over 5 years ago

#64 - Get a TLS cert so people can connect via https

Issue - State: open - Opened by bomeara almost 6 years ago

#63 - add dropped taxa to get_dated_otol_induced_subtree output

Issue - State: open - Opened by LunaSare almost 6 years ago

#62 - summarize trees with hierarchical clustering method used for timetree

Issue - State: open - Opened by LunaSare almost 6 years ago

#61 - allow tree grafting when n_overlap = 1

Issue - State: open - Opened by LunaSare about 6 years ago

#60 - standardize names below species level (eliminate var, subsp, etc.)

Issue - State: open - Opened by LunaSare about 6 years ago

#59 - Use common names

Issue - State: open - Opened by bomeara about 6 years ago

#58 - optimize get_datelife_result speed

Issue - State: open - Opened by LunaSare over 6 years ago

#57 - topology change induced by median scaling

Issue - State: closed - Opened by arlin over 6 years ago - 1 comment

#56 - enable higher-taxon search on web page

Issue - State: closed - Opened by LunaSare over 6 years ago - 1 comment

#55 - webpage need some improvements

Issue - State: closed - Opened by LunaSare over 6 years ago - 1 comment

#54 - datelifeweb page seems to be using an old datelife version

Issue - State: open - Opened by LunaSare over 6 years ago - 2 comments

#53 - test that tree_fix_brlen with mrbayes works with large trees

Issue - State: open - Opened by LunaSare over 6 years ago

#52 - profile sdm

Issue - State: open - Opened by LunaSare over 6 years ago

#51 - what happens when we have no overlapping taxa in multiple chronograms?

Issue - State: open - Opened by LunaSare over 6 years ago - 1 comment

#50 - using hclust with mean linkage clustering

Issue - State: closed - Opened by LunaSare over 6 years ago - 1 comment

#49 - in studies with several trees from the same group, identify the tree with median depth

Issue - State: open - Opened by LunaSare over 6 years ago

#48 - identify units in return value of scaling service

Issue - State: open - Opened by arlin over 6 years ago

#47 - Future-proof DOI reg-ex by broadening pattern

Pull Request - State: closed - Opened by katrinleinweber almost 7 years ago - 4 comments

#46 - install packages with datelife

Issue - State: closed - Opened by LunaSare almost 7 years ago - 2 comments

#45 - Export total time in tree

Issue - State: open - Opened by bomeara almost 7 years ago
Labels: enhancement

#44 - Recommend tree

Issue - State: open - Opened by bomeara almost 7 years ago
Labels: enhancement

#43 - Convert rphylotastic fns to match new names

Issue - State: closed - Opened by bomeara almost 7 years ago - 1 comment

#42 - Fix negative branch lengths inside GetBoldOToLTree function

Issue - State: open - Opened by LunaSare almost 7 years ago

#41 - adopt ropensci style for datelife

Issue - State: closed - Opened by LunaSare almost 7 years ago - 1 comment

#40 - make datelife_results object

Issue - State: closed - Opened by LunaSare almost 7 years ago
Labels: in review

#39 - query of >250 spp names not supported by rotl::tnrs_match_names fn

Issue - State: closed - Opened by LunaSare almost 7 years ago - 1 comment
Labels: question

#38 - install mrBayes with datelife

Issue - State: open - Opened by LunaSare almost 7 years ago - 1 comment

#37 - allow different dating methods in GetBoldOToLTree function

Issue - State: open - Opened by LunaSare about 7 years ago

#36 - add dating with treePL as an alternative to PATHd8

Issue - State: closed - Opened by LunaSare about 7 years ago - 3 comments

#35 - Unable to scale tree for Red Lion fish list from wikipedia

Issue - State: open - Opened by ducvan0212 about 7 years ago - 2 comments

#34 - shut up, geiger

Issue - State: open - Opened by bomeara about 7 years ago

#33 - Include tree name (esp in case of multiple returned trees per study)

Issue - State: open - Opened by bomeara about 7 years ago
Labels: enhancement

#32 - Show matching chronograms with only 2 species when output is in the appropriate format

Issue - State: closed - Opened by LunaSare about 7 years ago - 1 comment
Labels: help wanted

#31 - allow multiple markers in GetBoldOToLTree

Issue - State: open - Opened by LunaSare about 7 years ago - 1 comment
Labels: in progress

#30 - Implement other methods for congruification

Issue - State: open - Opened by LunaSare about 7 years ago - 1 comment

#29 - Dating with MrBayes

Issue - State: closed - Opened by LunaSare about 7 years ago - 1 comment

#28 - Allow clade names as input

Issue - State: closed - Opened by LunaSare about 7 years ago

#27 - Make up missing taxa branch lengths with bd with our own function

Issue - State: open - Opened by LunaSare about 7 years ago - 1 comment

#26 - Making up missing taxa branch lengths under bd with pastis and mrbayes

Issue - State: closed - Opened by LunaSare about 7 years ago - 1 comment

#25 - Making up missing taxa branch lengths with congruify

Issue - State: open - Opened by LunaSare about 7 years ago
Labels: invalid

#24 - Get info for named taxon

Issue - State: open - Opened by bomeara about 7 years ago
Labels: enhancement

#23 - indicate in the output which species are not found in opentree chronograms

Issue - State: closed - Opened by LunaSare about 7 years ago - 4 comments

#22 - choose longer bold sequences, not first ones in list

Issue - State: closed - Opened by LunaSare over 7 years ago - 1 comment
Labels: enhancement

#21 - allow users to input species names with spaces or underscores between names

Issue - State: open - Opened by LunaSare over 7 years ago - 4 comments

#20 - update opentree_chronograms cache

Issue - State: closed - Opened by LunaSare over 7 years ago
Labels: enhancement

#19 - describe each output.format on EstimateDates function

Issue - State: closed - Opened by LunaSare over 7 years ago

#18 - Pull in dates from paleoDB or similar

Issue - State: open - Opened by bomeara over 7 years ago - 2 comments

#17 - Create DB of fossil calibrations

Issue - State: open - Opened by bomeara over 7 years ago - 1 comment

#16 - Go Bayesian

Issue - State: open - Opened by bomeara over 7 years ago

#15 - Compare a given tree with datelife tree

Issue - State: open - Opened by bomeara over 7 years ago

#14 - Autopull with new opentree submissions

Issue - State: open - Opened by bomeara over 7 years ago

#13 - Add taxa w/o brlen

Issue - State: closed - Opened by bomeara over 7 years ago - 2 comments

#12 - Keep node labels

Issue - State: closed - Opened by bomeara over 7 years ago - 2 comments
Labels: enhancement, wontfix

#11 - Negative brlen in returned tree

Issue - State: closed - Opened by bomeara over 7 years ago - 1 comment
Labels: bug

#10 - broken links on main page?

Issue - State: closed - Opened by arlin almost 8 years ago - 1 comment
Labels: bug

#9 - Datelife not using all OToL trees

Issue - State: closed - Opened by hdliv about 8 years ago - 4 comments

#8 - ProcessResultsList deal with taxa=NULL

Issue - State: closed - Opened by bomeara over 8 years ago - 1 comment
Labels: bug

#7 - Fix pulling from OToL

Issue - State: closed - Opened by bomeara over 8 years ago - 2 comments
Labels: bug

#6 - Auto-updating chronogram for life (using opentree synthetic tree + chronograms)

Issue - State: open - Opened by bomeara over 8 years ago
Labels: enhancement

#5 - Create function to automatically bind the chronogram patristic matrices

Issue - State: open - Opened by bomeara over 8 years ago
Labels: enhancement

#4 - Add measurement of unit testing coverage

Issue - State: closed - Opened by bomeara over 8 years ago - 2 comments

#3 - Add unit testing

Issue - State: closed - Opened by bomeara over 8 years ago - 8 comments

#2 - Clean up OToL human names

Issue - State: open - Opened by bomeara over 8 years ago
Labels: enhancement

#1 - Output format json

Issue - State: open - Opened by bomeara over 8 years ago
Labels: enhancement

GitHub / phylotastic/datelife issues and pull requests