add inference (#79)

* Add inference and testing
* remove test/
* add phylolm
* add inference example
* hopefully will now pass tests
* include global skipR
* added estimaterates!
* Updated estimaterates, all info is on the tree
* add lambda calcs
* Fix inference testing
* examples folder needs manifest
* Only compare to R if packages are installed
* Update workflows
* Minor fixes to type stability
* Switch from Dict to a struct for trait storage
* fix problems with estimaterates and clean examples
* mult lambda
* manifest and project
* Fix authorship list
* multi lambda
* fix tests
* add orcid
* export traitdata
* create distribution for bayesian analysis
* example baysian analysis
* Change Float to Number, add bayes method for signal
* example for Bayes method to calculate signal
* include chain and plottinng
* change to d.tree
* Fixing node data types to allow Duals in a small union
* Whitespace and name fixes
* Update manifest to Julia 1.10
* Update Bayesian inference testing
* Whitespace fixes
* Whitespace fixes
* Bugfix in threepoint!() lambda calculation and speed up
* Clean up code for Bayesian example
* Removed redundant upper calculation
* Clean demo code
* Claire Analysis
* Fix case issue
* Inference fixes
* Fix for dropping no tips, metadata fix
* Allow retention of internal nodes with only one outbound connection after droptips!().
* keep_tips!() can have keep argument
* Report on whether R ran

.github/workflows/testing.yaml

@@ -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

.zenodo.json

@@ -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",