image for example added

bug fixed in vignette

vignettes/phyloraster-vignette.Rmd

@@ -182,7 +182,7 @@ names(dataprep$x) == tree$tip.label
 The user also has the option to compute branch length and descendant number using the full supplied tree or the tree subsetted by the species present in the raster. Notice the implications of using the full or the subsetted tree. Consider, for instance, a scenario where a clade comprises four species (A, B, C and D - Figure 1a), and the particular area of study involves two of these species (A and B, in blue- Figure 1). Furthermore, let's assume that species A and B share a branch, denoted as D (in red- Figure 1). Using the full phylogenetic tree will estimate the whole length of branches for these two species, including the branch shared between them (D), that connects them with the ancestor shared with the species absent from that specific region (Figure 1b). On the other hand, when using the subsetted tree (Figure 1c), branch D will be disregarded and only the terminal branches will be used to calculate branch length, so that the calculated branch lengths of the species A and B will be shorter (Figure 1c). 
 
 ```{r, fig.height = 5, fig.width = 7, fig.align = 'center', warning= FALSE, echo = FALSE}
-knitr::include_graphics("/media/gabriela/HDD/Documents/Doutorado_UESC/Artigo_phylogrid/submissao Ecography/Revisao 3 Ecography Minor/tree.jpg")
+knitr::include_graphics("/home/gabriela/Documents/phyloraster/inst/extdata/tree.jpg")
 ```
 Figure 1. Phylogenetic tree for tree frogs denoting the implications of using the full or the subsetted tree in the phylo.pres function. Figure a) demonstrates the full phylogenetic tree for some tree frog species. In figure b), we have the full tree considering species A and B that are present in the region (blue), as well as the common ancestor between the two species (red). In figure c) we only have the species present in the region.