Tidying

thibautjombart · Nov 17, 2020 · c9138de · c9138de
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -6,7 +6,6 @@ Authors@R: c(TJ = person("Thibaut", "Jombart", email="[email protected]",
  	     MK = person("Michelle", "Kendall", email="[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7344-7071")),
 	     JAG = person("Jacob", "Almagro-Garcia", role = "aut", comment = c(ORCID = "0000-0002-0595-7333")),
 	     CC = person("Caroline", "Colijn", role = "aut", comment = c(ORCID = "0000-0001-6097-6708")))
-Maintainer: Michelle Kendall <[email protected]>
 Description: Tools for the exploration of distributions of phylogenetic trees.
     This package includes a 'shiny' interface which can be started from R using
     treespaceServer(). 
@@ -31,9 +30,5 @@ URL: https://cran.r-project.org/package=treespace,
 BugReports: https://github.com/thibautjombart/treespace/issues
 NeedsCompilation: yes
 Packaged: 2019-12-05
-Author: Thibaut Jombart [aut],
-  Michelle Kendall [aut, cre],
-  Jacob Almagro-Garcia [aut],
-  Caroline Colijn [aut]
 Repository: CRAN
 Date/Publication: 2019-04-07 11:21:55 UTC
diff --git a/docs/articles/DengueVignette.html b/docs/articles/DengueVignette.html
diff --git a/docs/articles/TransmissionTreesVignette.html b/docs/articles/TransmissionTreesVignette.html
diff --git a/docs/articles/TransmissionTreesVignette_files/figure-html/igraph_tree1-1.png b/docs/articles/TransmissionTreesVignette_files/figure-html/igraph_tree1-1.png
diff --git a/docs/articles/TransmissionTreesVignette_files/figure-html/trees2_and_3-1.png b/docs/articles/TransmissionTreesVignette_files/figure-html/trees2_and_3-1.png
diff --git a/docs/articles/TransmissionTreesVignette_files/figure-html/trees2_and_3-2.png b/docs/articles/TransmissionTreesVignette_files/figure-html/trees2_and_3-2.png
diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html
diff --git a/docs/articles/tipCategories.html b/docs/articles/tipCategories.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -6,5 +6,5 @@ articles:
   TransmissionTreesVignette: TransmissionTreesVignette.html
   introduction: introduction.html
   tipCategories: tipCategories.html
-last_built: 2020-11-13T21:23Z
+last_built: 2020-11-17T10:41Z
 
diff --git a/images/svg/main-images.svg b/images/svg/main-images.svg
diff --git a/vignettes/introduction.R b/vignettes/introduction.R
@@ -122,7 +122,7 @@ wm3.groves <- findGroves(woodmiceTrees,nf=3,nclust=6,emphasise.tips=c("No1007S",
 plotGrovesD3(wm3.groves)
 
 ## ----figure_construction, echo=FALSE, fig.retina = NULL-----------------------
-knitr::include_graphics("construction.png", dpi=72)
+knitr::include_graphics("construction.png")
 
 ## ----treevec------------------------------------------------------------------
 # generate a random tree:

diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd
@@ -289,10 +289,10 @@ Conversely, where the structure of a particular clade is not of interest (for ex
 
 Method: characterising a tree by a vector
 --------------
-Kendall and Colijn proposed a [metric](http://dx.doi.org/10.1093/molbev/msw124) for comparing rooted phylogenetic trees (Kendall and COlijn, 2016). Each tree is characterised by a vector which notes the placement of the most recent common ancestor (MRCA) of each pair of tips, as demonstrated in this example:
+Kendall and Colijn proposed a [metric](http://dx.doi.org/10.1093/molbev/msw124) for comparing rooted phylogenetic trees (Kendall and Colijn, 2016). Each tree is characterised by a vector which notes the placement of the most recent common ancestor (MRCA) of each pair of tips, as demonstrated in this example:
 
 ```{r figure_construction, echo=FALSE, fig.retina = NULL}
-knitr::include_graphics("construction.png", dpi=72)
+knitr::include_graphics("construction.png")
 ```
 
 Specifically, it records the distance between the MRCA of a pair of tips $(i,j)$ and the root in two ways: the number of edges $m_{i,j}$, and the path length $M_{i,j}$. It also records the length $p_i$ of each 'pendant' edge between a tip $i$ and its immediate ancestor. This procedure results in two vectors for a tree $T$: