Ecosyste.ms: Issues

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

GitHub / traitecoevo/modeladequacy issues and pull requests

#107 - Update remake.yml folder names to source

Pull Request - State: closed - Opened by Rekyt over 8 years ago

#106 - Reproduction error in fits_ml

Issue - State: open - Opened by nuest over 8 years ago - 3 comments

#105 - Question about directory "analysis/docker"

Issue - State: open - Opened by nuest over 8 years ago - 1 comment

#104 - Data missing

Issue - State: closed - Opened by nuest almost 9 years ago - 4 comments

#103 - update readme to reflect this is now published.

Issue - State: open - Opened by wcornwell over 9 years ago

#102 - Use spermatophyta_synonyms_PLANTLIST.csv from wood

Issue - State: open - Opened by richfitz about 10 years ago

#101 - Re-create cached version of Kew data

Issue - State: open - Opened by richfitz about 10 years ago

#100 - simulation cleanup

Issue - State: open - Opened by mwpennell about 10 years ago - 1 comment

#99 - updates to arbutus

Issue - State: closed - Opened by mwpennell over 10 years ago - 1 comment

#98 - Read xls file with openxlsx

Issue - State: open - Opened by richfitz over 10 years ago - 2 comments

#97 - Set up minimal reproducible component

Issue - State: open - Opened by richfitz over 10 years ago - 1 comment

#96 - Main README needs to link to the the one in analysis

Issue - State: closed - Opened by richfitz over 10 years ago - 3 comments

#95 - Manuscript is not built by any make target

Issue - State: open - Opened by richfitz over 10 years ago

#94 - please make repo public and set up releases

Issue - State: closed - Opened by mwpennell over 10 years ago - 4 comments

#93 - rewrite fxns in model-adequacy-helper.R

Issue - State: closed - Opened by mwpennell over 10 years ago - 1 comment

#92 - make data-process

Issue - State: closed - Opened by mwpennell over 10 years ago - 4 comments

#91 - DICw = DIC$_w$ ?

Issue - State: closed - Opened by wcornwell over 10 years ago - 3 comments

#90 - is "subclade" a word or do we need a hyphen?

Issue - State: closed - Opened by wcornwell over 10 years ago - 1 comment

#89 - README file for package

Issue - State: closed - Opened by mwpennell over 10 years ago - 1 comment

#88 - Big tree figure

Issue - State: closed - Opened by richfitz over 10 years ago - 2 comments

#86 - remove phytools dependency

Issue - State: closed - Opened by mwpennell over 10 years ago - 2 comments

#85 - Rationalise R directory

Issue - State: closed - Opened by richfitz over 10 years ago - 2 comments

#84 - these files can be removed from the repo

Issue - State: closed - Opened by mwpennell over 10 years ago - 2 comments

#83 - Weird datasets

Issue - State: closed - Opened by mwpennell over 10 years ago - 3 comments

#82 - clunkiness in analysis

Issue - State: closed - Opened by mwpennell over 10 years ago - 3 comments

#81 - Turn down warnings on treedata when building angio-trait-data-all

Issue - State: closed - Opened by richfitz over 10 years ago - 2 comments

#80 - get.sla.data and similar functions are duplicated

Issue - State: closed - Opened by richfitz over 10 years ago - 2 comments

#79 - Kew data is a moving target

Issue - State: closed - Opened by richfitz over 10 years ago - 3 comments
Labels: wontfix

#78 - spermatophyta_synonyms_PLANTLIST.csv

Issue - State: open - Opened by richfitz over 10 years ago - 5 comments

#77 - Remove bootstrap trees and repush?

Issue - State: closed - Opened by richfitz over 10 years ago - 1 comment

#76 - structure of code/data dump for suppmat

Issue - State: closed - Opened by mwpennell over 10 years ago - 4 comments

#75 - finish bayesian analyses/make plots

Issue - State: closed - Opened by mwpennell over 10 years ago

#74 - clean up analyses and plotting scripts for submission

Issue - State: closed - Opened by mwpennell over 10 years ago - 1 comment

#73 - code for downloading and cleaning data

Issue - State: closed - Opened by mwpennell over 10 years ago - 4 comments

#72 - grid and gridExtra

Issue - State: closed - Opened by mwpennell almost 11 years ago - 1 comment
Labels: migrate_to_arbutus

#71 - Convergence problems apparent in Figure 4?

Issue - State: closed - Opened by wcornwell almost 11 years ago - 1 comment

#70 - summary stats

Issue - State: closed - Opened by mwpennell almost 11 years ago - 3 comments

#69 - Sending the ms to other people?

Issue - State: closed - Opened by wcornwell almost 11 years ago

#68 - title for paper

Issue - State: closed - Opened by mwpennell almost 11 years ago - 6 comments

#67 - good names for summary stats

Issue - State: closed - Opened by mwpennell almost 11 years ago

#66 - figures

Issue - State: closed - Opened by mwpennell almost 11 years ago - 5 comments

#65 - bayesian analysis getting stuck

Issue - State: closed - Opened by mwpennell almost 11 years ago - 6 comments

#64 - build.tree.data issues

Issue - State: closed - Opened by richfitz almost 11 years ago - 1 comment

#63 - two versions of OU in phylolm

Issue - State: closed - Opened by mwpennell almost 11 years ago - 3 comments
Labels: migrate_to_arbutus

#62 - Package dependencies

Issue - State: closed - Opened by richfitz almost 11 years ago - 4 comments

#61 - converting from reml to ml estimate

Issue - State: closed - Opened by mwpennell almost 11 years ago - 1 comment

#60 - caper with multiple rescaling

Issue - State: closed - Opened by mwpennell almost 11 years ago - 2 comments

#59 - Write model.phylo.trend()

Issue - State: closed - Opened by richfitz almost 11 years ago - 3 comments
Labels: migrate_to_arbutus

#58 - Delta transform disagrees with geiger

Issue - State: closed - Opened by richfitz almost 11 years ago - 4 comments
Labels: migrate_to_arbutus

#57 - Correct way of using geiger::rescale.phylo with SE

Issue - State: closed - Opened by richfitz almost 11 years ago - 2 comments

#56 - Extraction of ML and REML s2 estimates from gls models

Issue - State: closed - Opened by richfitz almost 11 years ago - 4 comments
Labels: migrate_to_arbutus

#55 - Caper interface?

Issue - State: closed - Opened by richfitz almost 11 years ago - 2 comments

#54 - model.data for pgls is tricky

Issue - State: closed - Opened by richfitz almost 11 years ago - 2 comments

#53 - Decide to change diversitree to save likelihood functions with fitted objects

Issue - State: closed - Opened by richfitz almost 11 years ago - 3 comments

#52 - Need tests for phylolm internals

Issue - State: closed - Opened by richfitz almost 11 years ago - 3 comments

#51 - Should we assess model adequacy for linear part of PGLS

Issue - State: closed - Opened by richfitz almost 11 years ago - 3 comments

#50 - Should we return parameters for linear part of PGLS models

Issue - State: closed - Opened by richfitz almost 11 years ago - 1 comment
Labels: migrate_to_arbutus

#49 - model.info for constrained fits

Issue - State: closed - Opened by mwpennell about 11 years ago - 1 comment

#48 - PGLS description in manuscript

Issue - State: closed - Opened by mwpennell about 11 years ago - 1 comment

#47 - Problems with diversitree and OU models

Issue - State: closed - Opened by mwpennell about 11 years ago - 12 comments

#45 - Sampling pars from mcmcsamples

Issue - State: closed - Opened by mwpennell about 11 years ago - 1 comment

#44 - direction of pgls

Issue - State: closed - Opened by mwpennell about 11 years ago - 6 comments

#43 - SE for leafN?

Issue - State: closed - Opened by mwpennell about 11 years ago - 3 comments

#42 - Angiosperms or vascular plants?

Issue - State: closed - Opened by wcornwell about 11 years ago - 2 comments

#41 - Original plan was also to do leaf N--do we still care?

Issue - State: closed - Opened by wcornwell about 11 years ago - 4 comments

#40 - we need a logo for arbutus :)

Issue - State: closed - Opened by mwpennell about 11 years ago - 3 comments

#39 - Cornwell 2006

Issue - State: closed - Opened by mwpennell about 11 years ago - 3 comments

#38 - links in example files

Issue - State: closed - Opened by mwpennell about 11 years ago - 1 comment

#37 - R CMD check does not like the functions in internal-diversitree

Issue - State: closed - Opened by mwpennell about 11 years ago - 2 comments

#36 - need to put a version of treedata in arbutus

Issue - State: closed - Opened by mwpennell about 11 years ago - 2 comments

#35 - please invite luke to repository

Issue - State: closed - Opened by mwpennell about 11 years ago - 2 comments

#34 - Seed mass download is redundant

Issue - State: closed - Opened by wcornwell about 11 years ago - 4 comments
Labels: wontfix

#33 - Lamiales seedmass

Issue - State: closed - Opened by mwpennell about 11 years ago - 10 comments

#32 - when there is basically no info in the phylogeny

Issue - State: closed - Opened by mwpennell about 11 years ago - 1 comment

#31 - model selection for bayesian analysis

Issue - State: closed - Opened by mwpennell about 11 years ago

#30 - drop.tip

Issue - State: closed - Opened by mwpennell about 11 years ago - 1 comment

#29 - need to run treedata on data before including in package

Issue - State: closed - Opened by mwpennell about 11 years ago

#28 - geiger dependency removed

Issue - State: closed - Opened by mwpennell about 11 years ago - 4 comments

#27 - use .paths.phylo in geiger.

Issue - State: closed - Opened by mwpennell about 11 years ago - 2 comments

#26 - Removing `geiger` dependency will remove `data(geospiza)`

Issue - State: closed - Opened by richfitz about 11 years ago - 3 comments

#24 - importFrom

Issue - State: closed - Opened by mwpennell about 11 years ago - 4 comments

#23 - Variable SE

Issue - State: closed - Opened by mwpennell about 11 years ago - 5 comments

#22 - MCMC unit tree support

Issue - State: closed - Opened by richfitz about 11 years ago - 2 comments

#21 - Unit tree with arbitrary parameters

Issue - State: closed - Opened by richfitz about 11 years ago - 4 comments
Labels: migrate_to_arbutus

#20 - rd files for internals

Issue - State: closed - Opened by mwpennell about 11 years ago - 1 comment

#15 - testting summary stats

Issue - State: closed - Opened by mwpennell about 11 years ago - 2 comments
Labels: migrate_to_arbutus

#14 - plotting fxns

Issue - State: closed - Opened by mwpennell about 11 years ago - 1 comment

#13 - slopePicNh for non-ultrametric trees

Issue - State: closed - Opened by mwpennell about 11 years ago - 3 comments

#12 - More informative error messages for as.unit.tree

Issue - State: closed - Opened by richfitz about 11 years ago - 1 comment
Labels: migrate_to_arbutus

#10 - Standardised parameter names

Issue - State: closed - Opened by richfitz about 11 years ago - 3 comments

#9 - Diversitree does not return likelihood functions with fitted objects

Issue - State: closed - Opened by richfitz about 11 years ago - 2 comments

#8 - Dealing with additional arguments

Issue - State: closed - Opened by richfitz about 11 years ago - 1 comment

#7 - Note on organization of repository

Issue - State: closed - Opened by richfitz about 11 years ago

#6 - Taxonomic scrubbing

Issue - State: closed - Opened by richfitz about 11 years ago - 2 comments

#5 - Get trait units and error scrubbing correct

Issue - State: closed - Opened by richfitz about 11 years ago - 1 comment

#3 - Models with shift points along branches

Issue - State: closed - Opened by richfitz about 11 years ago - 2 comments
Labels: migrate_to_arbutus

#2 - Computing pics multiple times

Issue - State: closed - Opened by richfitz about 11 years ago - 3 comments

#1 - Multi-optimum OU models

Issue - State: closed - Opened by richfitz about 11 years ago - 2 comments
Labels: migrate_to_arbutus