Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add inference #79

Merged
merged 59 commits into from
Oct 16, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
59 commits
Select commit Hold shift + click to select a range
6e06a50
Add inference and testing
ejd99 Feb 23, 2023
b38d7df
remove test/
ejd99 Feb 24, 2023
ffd9c50
add phylolm
ejd99 Feb 24, 2023
513a817
add inference example
ejd99 Feb 28, 2023
c182e11
hopefully will now pass tests
ejd99 Mar 1, 2023
e8538ee
include global skipR
ejd99 Mar 1, 2023
d613aa1
added estimaterates!
ejd99 Mar 14, 2023
5a80d0a
Updated estimaterates, all info is on the tree
ejd99 Mar 29, 2023
0e9c10a
add lambda calcs
ejd99 Apr 5, 2023
4343a8c
Merge branch 'rr/getnodesfix' into ejd/inference
richardreeve Apr 16, 2023
3831094
Merge branch 'rr/getnodesfix' into ejd/inference
richardreeve Apr 16, 2023
6bf55c6
Fix inference testing
richardreeve Apr 16, 2023
104b55d
examples folder needs manifest
richardreeve Apr 16, 2023
6e50f57
Only compare to R if packages are installed
richardreeve Apr 16, 2023
dbe4eb4
Update workflows
richardreeve Apr 16, 2023
96b3fb6
Merge branch 'rr/getnodesfix' into ejd/inference
richardreeve Apr 23, 2023
91ef1f1
Minor fixes to type stability
richardreeve Apr 24, 2023
0ca9405
Switch from Dict to a struct for trait storage
richardreeve Apr 24, 2023
b222e81
Merge branch 'dev' into ejd/inference
richardreeve Apr 26, 2023
3a69b38
fix problems with estimaterates and clean examples
ejd99 Aug 2, 2023
17e4fc1
mult lambda
ejd99 Oct 27, 2023
2fb70f1
manifest and project
ejd99 Oct 27, 2023
2cc9515
Merge branch 'dev' into ejd/inference
richardreeve Oct 30, 2023
acdc530
Merge branch 'dev' into ejd/inference
richardreeve Nov 25, 2023
5be7ee4
Merge branch 'dev' into ejd/inference
richardreeve Dec 7, 2023
b8fd52e
Fix authorship list
richardreeve Dec 7, 2023
4e2bd92
multi lambda
ejd99 Dec 7, 2023
46e8efe
Merge branch 'ejd/inference' of https://github.com/EcoJulia/Phylo.jl …
ejd99 Dec 7, 2023
4613b05
fix tests
ejd99 Dec 7, 2023
3386210
add orcid
ejd99 Dec 7, 2023
aee5098
Merge branch 'dev' into ejd/inference
richardreeve Dec 20, 2023
646264d
Merge branch 'dev' into ejd/inference
richardreeve Jan 6, 2024
067c76b
export traitdata
ejd99 Mar 21, 2024
b1f64f8
create distribution for bayesian analysis
ejd99 Mar 21, 2024
1114e0f
example baysian analysis
ejd99 Mar 21, 2024
8d9ce33
Change Float to Number, add bayes method for signal
ejd99 Mar 27, 2024
fd30793
example for Bayes method to calculate signal
ejd99 Mar 27, 2024
0aa896a
include chain and plottinng
ejd99 Mar 27, 2024
b8ce796
change to d.tree
ejd99 Mar 27, 2024
55665a3
Fixing node data types to allow Duals in a small union
richardreeve Apr 2, 2024
c869a14
Whitespace and name fixes
richardreeve Apr 2, 2024
57d3ff7
Update manifest to Julia 1.10
richardreeve Apr 2, 2024
8d206dc
Update Bayesian inference testing
richardreeve Apr 2, 2024
c6f13f7
Whitespace fixes
richardreeve Apr 2, 2024
32136f6
Whitespace fixes
richardreeve Apr 3, 2024
e0a800b
Bugfix in threepoint!() lambda calculation and speed up
richardreeve Apr 3, 2024
b41f8e0
Clean up code for Bayesian example
richardreeve Apr 3, 2024
ae5c3f9
Removed redundant upper calculation
richardreeve Apr 3, 2024
60f037f
Clean demo code
richardreeve Apr 6, 2024
4de1d89
Claire Analysis
ejd99 Jun 11, 2024
1f288d2
Merge commit '4de1d89bce3f63f1d84ccaa1ba84549636efaa6f' into ejd/infe…
richardreeve Jun 11, 2024
b3c139a
Merge branch 'dev' into ejd/inference
richardreeve Jul 18, 2024
e879ed5
Fix case issue
richardreeve Jul 18, 2024
f97553f
Inference fixes
richardreeve Jul 18, 2024
514d584
Merge branch 'dev' into ejd/inference
richardreeve Jul 22, 2024
c688663
Fix for dropping no tips, metadata fix
richardreeve Oct 13, 2024
9830223
Allow retention of internal nodes with only one outbound connection a…
richardreeve Oct 14, 2024
18f7c51
keep_tips!() can have keep argument
richardreeve Oct 14, 2024
f641458
Report on whether R ran
richardreeve Oct 14, 2024
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions .github/workflows/testing.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,7 @@ jobs:
if: ${{ matrix.r-testing }}
run: |
install.packages("ape", repos="http://cran.r-project.org")
install.packages("phylolm", repos="http://cran.r-project.org")
shell: R --vanilla --file={0}
- name: Cache
uses: julia-actions/cache@v2
Expand Down
6 changes: 6 additions & 0 deletions .zenodo.json
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,12 @@
"affiliation": "University of Glasgow",
"ror": "00vtgdb53"
},
{
"name": "Davison, Emily",
"orcid": "0009-0000-3656-8309",
"affiliation": "University of Glasgow",
"ror": "00vtgdb53"
},
{
"name": "Borregaard, Michael",
"orcid": "0000-0002-8146-8435",
Expand Down
Loading
Loading