%+>%                    %+>%
%<%                     %<%
%<+%                    %<+%
%>%                     pipe
.                       .
Date2decimal            Date2decimal
MRCA                    MRCA
NJ                      NJ
StatBalance             StatBalance
add_colorbar            add_colorbar
annotation_image        annotation_image
apeBoot                 apeBoot
apeBootstrap-class      Class "apeBootstrap" This class stores ape
                        bootstrapping analysis result
as.binary               as.binary
as.data.frame.phylo     as.data.frame
as.polytomy             as.polytomy
beast-class             Class "beast" This class stores information of
                        beast output
codeml-class            Class "codeml" This class stores information of
                        output from codeml
codeml_mlc-class        Class "codeml_mlc" This class stores
                        information of mlc file frm codeml output
collapse                collapse
decimal2Date            decimal2Date
download.phylopic       download.phylopic
expand                  expand
facet_plot              facet_plot
flip                    flip
fortify.phylo           fortify
geom_aline              geom_aline
geom_balance            geom_balance
geom_cladelabel         geom_cladelabel
geom_hilight            geom_hilight
geom_label2             geom_text2
geom_nodepoint          geom_nodepoint
geom_point2             geom_point2
geom_range              geom_range
geom_rootpoint          geom_rootpoint
geom_segment2           geom_segment2
geom_strip              geom_strip
geom_taxalink           geom_taxalink
geom_text2              geom_text2
geom_tiplab             geom_tiplab
geom_tiplab2            geom_tiplab2
geom_tippoint           geom_tippoint
geom_tree               geom_tree
geom_tree2              geom_tree2
geom_treescale          geom_treescale
get.fields              get.fields method
get.offspring.tip       get.offspring.tip
get.path                get.path
get.phylopic            get.phylopic
get.placements          get.placements method
get.subs                get.subs method
get.tipseq              get.tipseq method
get.tree                get.tree method
get.treeinfo            get.treeinfo method
get.treetext            get.treetext method
getNodeNum              getNodeNum
getRoot                 getRoot
get_balance_position    get_balance_position
get_clade_position      get_clade_position
get_heatmap_column_position
                        get_heatmap_column_position
get_taxa_name           get_taxa_name
ggtree                  visualizing phylogenetic tree and heterogenous
                        associated data based on grammar of graphics
                        'ggtree' provides functions for visualizing
                        phylogenetic tree and its associated data in R.
gheatmap                gheatmap
groupClade              groupClade method
groupOTU                groupOTU method
groupOTU.phylo          groupOTU.phylo
gzoom                   gzoom method
gzoom.phylo             gzoom
hyphy-class             Class "hyphy" This class stores information of
                        HYPHY output
identify.gg             identify
inset                   inset
jplace-class            Class "jplace" This class stores information of
                        jplace file.
mask                    mask
merge_tree              merge_tree
msaplot                 msaplot
multiplot               multiplot
nhx-class               Class "nhx" This class stores nhx tree
nodebar                 nodebar
nodeid                  nodeid
nodepie                 nodepie
open_tree               open_tree
paml_rst-class          Class "paml_rst" This class stores information
                        of rst file from PAML output
phangorn-class          Class "phangorn" This class stores ancestral
                        sequences inferred from 'phangorn'
phyPML                  treeAnno.pml
phylip-class            Class "phylip" This class stores phylip tree(s)
phylopic                phylopic
plot                    plot method
pmlToSeq                pmlToSeq
print.beastList         print
r8s-class               Class "r8s" This class stores output info from
                        r8s
raxml-class             Class "raxml" This class stores RAxML
                        bootstrapping analysis result
raxml2nwk               raxml2nwk
read.baseml             read.baseml
read.beast              read.beast
read.codeml             read.codeml
read.codeml_mlc         read.codeml_mlc
read.hyphy              read.hyphy
read.jplace             read.jplace
read.nhx                read.nhx
read.paml_rst           read.paml_rst
read.phylip             read.phylip
read.phyloT             read.phyloT
read.r8s                read.r8s
read.raxml              read.raxml
reroot                  reroot method
rescale_tree            rescale_tree
rm.singleton.newick     rm.singleton.newick
rotate                  rotate
rotate_tree             rotate_tree
rtree                   generate random tree
scaleClade              scaleClade
scale_color             scale_color method
scale_x_ggtree          scale_x_ggtree
show,raxml-method       show method
stat_balance            stat_balance
stat_hilight            stat_hilight
subview                 subview
theme_inset             theme_inset
theme_transparent       theme_transparent
theme_tree              theme_tree
theme_tree2             theme_tree2
viewClade               viewClade
write.jplace            write.jplace
