Bayesian vignette (#22)

.gitignore

@@ -1,7 +1,9 @@
 Meta
 doc
+/doc/
 docs
 gen-*
+/Meta/
 src-*
 src/*.o
 src/*.so

DESCRIPTION

@@ -40,6 +40,8 @@ Imports:
   TreeTools (>= 1.6.0),
   utils,
 Suggests:
+  knitr,
+  rmarkdown,
   spelling,
   testthat,
 Config/Needs/github-actions:
@@ -55,5 +57,6 @@ SystemRequirements: C99
 ByteCompile: true
 Encoding: UTF-8
 Language: en-GB
+VignetteBuilder: knitr
 RoxygenNote: 7.1.2
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -8,6 +8,8 @@
 
 - Improve support for `multiPhylo` objects.
 
+- Vignette detailing rogue detection with Bayesian tree samples.
+
 
 # Rogue v2.0.0
 

codemeta.json

@@ -61,6 +61,30 @@
     }
   ],
   "softwareSuggestions": [
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "knitr",
+      "name": "knitr",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=knitr"
+    },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "rmarkdown",
+      "name": "rmarkdown",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "spelling",
@@ -211,7 +235,7 @@
     },
     "SystemRequirements": "C99"
   },
-  "fileSize": "2256.334KB",
+  "fileSize": "2288.327KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

inst/REFERENCES.bib

@@ -42,6 +42,15 @@ @article{Holder2008
   doi = {10.1080/10635150802422308}
 }
 
+@article{Hulsenbeck2001,
+  title={MrBayes: Bayesian inference of phylogeny},
+  author={Hulsenbeck, JP and Ronquist, F},
+  journal={Bioinformatics},
+  volume={17},
+  pages={754--755},
+  year={2001}
+}
+
 @article{Kearney2002,
   title = {Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions},
   author = {Kearney, Maureen},
@@ -116,6 +125,17 @@ @article{SmithCons
   year = {2022}
 }
 
+@article{Sun2018,
+  title={Hyoliths with pedicles illuminate the origin of the brachiopod body plan},
+  author={Sun, Haijing and Smith, Martin R and Zeng, Han and Zhao, Fangchen and Li, Guoxiang and Zhu, Maoyan},
+  journal={Proceedings of the Royal Society B: Biological Sciences},
+  volume={285},
+  number={1887},
+  pages={20181780},
+  year={2018},
+  doi = {10.1098/rspb.2018.1780},
+}
+
 @article{Thomson2010,
   title = {Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles},
   author = {Thomson, Robert C. and Shaffer, H. Bradley},

inst/WORDLIST

@@ -10,6 +10,7 @@ dropset
 durham
 googlemail
 Krompass
+MrBayes
 ORCID
 Paradis
 Pattengale's