GuangchuangYu authored on 20/12/2016 16:39:07
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: ggtree |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data |
| 4 |
-Version: 1.7.4 |
|
| 4 |
+Version: 1.7.5 |
|
| 5 | 5 |
Authors@R: c( |
| 6 | 6 |
person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph")),
|
| 7 | 7 |
person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")),
|
| ... | ... |
@@ -11,8 +11,9 @@ Maintainer: Guangchuang Yu <guangchuangyu@gmail.com> |
| 11 | 11 |
Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. |
| 12 | 12 |
'ggtree' is designed for visualization and annotation of phylogenetic trees with their covariates and other associated data. |
| 13 | 13 |
Depends: |
| 14 |
- R (>= 3.3.1), |
|
| 15 |
- ggplot2 (>= 2.2.0) |
|
| 14 |
+ R (>= 3.3.2), |
|
| 15 |
+ ggplot2 (>= 2.2.0), |
|
| 16 |
+ treeio |
|
| 16 | 17 |
Imports: |
| 17 | 18 |
ape, |
| 18 | 19 |
grDevices, |
| ... | ... |
@@ -33,7 +33,6 @@ export(Date2decimal) |
| 33 | 33 |
export(MRCA) |
| 34 | 34 |
export(StatBalance) |
| 35 | 35 |
export(StatHilight) |
| 36 |
-export(add_colorbar) |
|
| 37 | 36 |
export(annotation_image) |
| 38 | 37 |
export(apeBoot) |
| 39 | 38 |
export(as.binary) |
| ... | ... |
@@ -41,7 +40,6 @@ export(as.polytomy) |
| 41 | 40 |
export(collapse) |
| 42 | 41 |
export(decimal2Date) |
| 43 | 42 |
export(download.phylopic) |
| 44 |
-export(drop.tip) |
|
| 45 | 43 |
export(expand) |
| 46 | 44 |
export(facet_plot) |
| 47 | 45 |
export(flip) |
| ... | ... |
@@ -64,29 +62,17 @@ export(geom_tippoint) |
| 64 | 62 |
export(geom_tree) |
| 65 | 63 |
export(geom_tree2) |
| 66 | 64 |
export(geom_treescale) |
| 67 |
-export(get.fields) |
|
| 68 | 65 |
export(get.offspring.tip) |
| 69 | 66 |
export(get.path) |
| 70 | 67 |
export(get.phylopic) |
| 71 |
-export(get.placements) |
|
| 72 |
-export(get.subs) |
|
| 73 |
-export(get.tipseq) |
|
| 74 |
-export(get.tree) |
|
| 75 |
-export(get.treeinfo) |
|
| 76 |
-export(get.treetext) |
|
| 77 |
-export(getNodeNum) |
|
| 78 |
-export(getRoot) |
|
| 79 | 68 |
export(get_balance_position) |
| 80 | 69 |
export(get_clade_position) |
| 81 | 70 |
export(get_heatmap_column_position) |
| 82 | 71 |
export(get_taxa_name) |
| 83 | 72 |
export(ggtree) |
| 84 | 73 |
export(gheatmap) |
| 85 |
-export(groupClade) |
|
| 86 |
-export(groupOTU) |
|
| 87 | 74 |
export(gzoom) |
| 88 | 75 |
export(inset) |
| 89 |
-export(is.ggtree) |
|
| 90 | 76 |
export(mask) |
| 91 | 77 |
export(merge_tree) |
| 92 | 78 |
export(msaplot) |
| ... | ... |
@@ -95,32 +81,16 @@ export(nodebar) |
| 95 | 81 |
export(nodeid) |
| 96 | 82 |
export(nodepie) |
| 97 | 83 |
export(open_tree) |
| 98 |
-export(phyPML) |
|
| 99 | 84 |
export(phylopic) |
| 100 | 85 |
export(plot) |
| 101 |
-export(pmlToSeq) |
|
| 102 | 86 |
export(raxml2nwk) |
| 103 |
-export(read.baseml) |
|
| 104 |
-export(read.beast) |
|
| 105 |
-export(read.codeml) |
|
| 106 |
-export(read.codeml_mlc) |
|
| 107 |
-export(read.hyphy) |
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| 108 |
-export(read.jplace) |
|
| 109 |
-export(read.nhx) |
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| 110 |
-export(read.paml_rst) |
|
| 111 |
-export(read.phylip) |
|
| 112 | 87 |
export(read.phyloT) |
| 113 |
-export(read.r8s) |
|
| 114 |
-export(read.raxml) |
|
| 115 |
-export(read.tree) |
|
| 116 | 88 |
export(reroot) |
| 117 | 89 |
export(rescale_tree) |
| 118 | 90 |
export(revts) |
| 119 | 91 |
export(rotate) |
| 120 | 92 |
export(rotate_tree) |
| 121 |
-export(rtree) |
|
| 122 | 93 |
export(scaleClade) |
| 123 |
-export(scale_color) |
|
| 124 | 94 |
export(scale_x_ggtree) |
| 125 | 95 |
export(stat_balance) |
| 126 | 96 |
export(stat_hilight) |
| ... | ... |
@@ -130,46 +100,20 @@ export(theme_transparent) |
| 130 | 100 |
export(theme_tree) |
| 131 | 101 |
export(theme_tree2) |
| 132 | 102 |
export(viewClade) |
| 133 |
-export(write.jplace) |
|
| 134 | 103 |
export(xlim_expand) |
| 135 | 104 |
export(xlim_tree) |
| 136 |
-exportClasses(apeBootstrap) |
|
| 137 |
-exportClasses(beast) |
|
| 138 |
-exportClasses(codeml) |
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| 139 |
-exportClasses(codeml_mlc) |
|
| 140 |
-exportClasses(hyphy) |
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| 141 |
-exportClasses(jplace) |
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| 142 |
-exportClasses(nhx) |
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| 143 |
-exportClasses(paml_rst) |
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| 144 |
-exportClasses(phangorn) |
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| 145 |
-exportClasses(phylip) |
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| 146 |
-exportClasses(r8s) |
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| 147 |
-exportClasses(raxml) |
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| 148 |
-exportMethods(drop.tip) |
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| 149 |
-exportMethods(get.fields) |
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| 150 |
-exportMethods(get.placements) |
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| 151 |
-exportMethods(get.subs) |
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| 152 |
-exportMethods(get.tipseq) |
|
| 153 |
-exportMethods(get.tree) |
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| 154 |
-exportMethods(get.treeinfo) |
|
| 155 |
-exportMethods(get.treetext) |
|
| 156 | 105 |
exportMethods(groupClade) |
| 157 | 106 |
exportMethods(groupOTU) |
| 158 | 107 |
exportMethods(gzoom) |
| 159 | 108 |
exportMethods(plot) |
| 160 | 109 |
exportMethods(reroot) |
| 161 |
-exportMethods(scale_color) |
|
| 162 |
-exportMethods(show) |
|
| 163 | 110 |
importFrom(ape,di2multi) |
| 164 | 111 |
importFrom(ape,extract.clade) |
| 165 | 112 |
importFrom(ape,getMRCA) |
| 166 | 113 |
importFrom(ape,is.binary.tree) |
| 167 | 114 |
importFrom(ape,ladderize) |
| 168 |
-importFrom(ape,print.phylo) |
|
| 169 |
-importFrom(ape,read.nexus) |
|
| 170 | 115 |
importFrom(ape,read.tree) |
| 171 | 116 |
importFrom(ape,reorder.phylo) |
| 172 |
-importFrom(ape,which.edge) |
|
| 173 | 117 |
importFrom(ape,write.tree) |
| 174 | 118 |
importFrom(ggplot2,GeomCurve) |
| 175 | 119 |
importFrom(ggplot2,GeomLabel) |
| ... | ... |
@@ -235,20 +179,15 @@ importFrom(grid,pushViewport) |
| 235 | 179 |
importFrom(grid,rasterGrob) |
| 236 | 180 |
importFrom(grid,unit) |
| 237 | 181 |
importFrom(grid,viewport) |
| 238 |
-importFrom(jsonlite,fromJSON) |
|
| 239 | 182 |
importFrom(magrittr,"%<>%") |
| 240 | 183 |
importFrom(magrittr,"%>%") |
| 241 | 184 |
importFrom(magrittr,add) |
| 242 | 185 |
importFrom(magrittr,equals) |
| 243 |
-importFrom(methods,"slot<-") |
|
| 244 |
-importFrom(methods,.hasSlot) |
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| 245 |
-importFrom(methods,is) |
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| 246 |
-importFrom(methods,missingArg) |
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| 247 |
-importFrom(methods,new) |
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| 248 |
-importFrom(methods,show) |
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| 249 |
-importFrom(methods,slot) |
|
| 250 | 186 |
importFrom(stats4,plot) |
| 251 | 187 |
importFrom(tidyr,gather) |
| 188 |
+importFrom(treeio,as.treedata) |
|
| 189 |
+importFrom(treeio,groupClade) |
|
| 190 |
+importFrom(treeio,groupOTU) |
|
| 252 | 191 |
importFrom(utils,download.file) |
| 253 | 192 |
importFrom(utils,modifyList) |
| 254 | 193 |
importFrom(utils,packageDescription) |
| ... | ... |
@@ -1,3 +1,7 @@ |
| 1 |
+CHANGES IN VERSION 1.7.5 |
|
| 2 |
+------------------------ |
|
| 3 |
+ o remove codes that move to treeio and now ggtree depends treeio <2016-12-20, Tue> |
|
| 4 |
+ |
|
| 1 | 5 |
CHANGES IN VERSION 1.7.4 |
| 2 | 6 |
------------------------ |
| 3 | 7 |
o is.ggtree function to test whether object is produced by ggtree <2016-12-06, Tue> |
| ... | ... |
@@ -1,9 +1,9 @@ |
| 1 |
-setOldClass("phylo")
|
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| 2 |
-setOldClass("multiPhylo")
|
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| 3 |
-setOldClass("ggtree")
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| 1 |
+## setOldClass("phylo")
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| 2 |
+## setOldClass("multiPhylo")
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| 3 |
+## setOldClass("ggtree")
|
|
| 4 | 4 |
|
| 5 | 5 |
|
| 6 |
-setClassUnion("phyloOrmultiPhylo", c("phylo", "multiPhylo"))
|
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| 6 |
+## setClassUnion("phyloOrmultiPhylo", c("phylo", "multiPhylo"))
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|
| 7 | 7 |
|
| 8 | 8 |
|
| 9 | 9 |
supported_tree_object <- function() {
|
| ... | ... |
@@ -21,367 +21,367 @@ supported_tree_object <- function() {
|
| 21 | 21 |
"raxml") |
| 22 | 22 |
} |
| 23 | 23 |
|
| 24 |
-##' Class "apeBootstrap" |
|
| 25 |
-##' This class stores ape bootstrapping analysis result |
|
| 26 |
-##' |
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| 27 |
-##' |
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| 28 |
-##' @name apeBootstrap-class |
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| 29 |
-##' @docType class |
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| 30 |
-##' @slot phylo phylo object of treetext |
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| 31 |
-##' @slot fields available features |
|
| 32 |
-##' @slot bootstrap bootstrap value |
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| 33 |
-##' @slot extraInfo extra information |
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| 34 |
-##' @exportClass apeBootstrap |
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| 35 |
-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
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| 36 |
-##' @keywords classes |
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| 37 |
-setClass("apeBootstrap",
|
|
| 38 |
- representation = representation( |
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| 39 |
- phylo = "phylo", |
|
| 40 |
- fields = "character", |
|
| 41 |
- bootstrap = "data.frame", |
|
| 42 |
- extraInfo = "data.frame" |
|
| 43 |
- ) |
|
| 44 |
- ) |
|
| 24 |
+## ##' Class "apeBootstrap" |
|
| 25 |
+## ##' This class stores ape bootstrapping analysis result |
|
| 26 |
+## ##' |
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| 27 |
+## ##' |
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| 28 |
+## ##' @name apeBootstrap-class |
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| 29 |
+## ##' @docType class |
|
| 30 |
+## ##' @slot phylo phylo object of treetext |
|
| 31 |
+## ##' @slot fields available features |
|
| 32 |
+## ##' @slot bootstrap bootstrap value |
|
| 33 |
+## ##' @slot extraInfo extra information |
|
| 34 |
+## ##' @exportClass apeBootstrap |
|
| 35 |
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 36 |
+## ##' @keywords classes |
|
| 37 |
+## setClass("apeBootstrap",
|
|
| 38 |
+## representation = representation( |
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| 39 |
+## phylo = "phylo", |
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| 40 |
+## fields = "character", |
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| 41 |
+## bootstrap = "data.frame", |
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| 42 |
+## extraInfo = "data.frame" |
|
| 43 |
+## ) |
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| 44 |
+## ) |
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| 45 | 45 |
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| 46 |
-##' Class "beast" |
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| 47 |
-##' This class stores information of beast output |
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| 48 |
-##' |
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| 49 |
-##' |
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| 50 |
-##' @name beast-class |
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| 51 |
-##' @aliases beast-class |
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| 52 |
-##' get.tree,beast-method |
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| 53 |
-##' |
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| 54 |
-##' @docType class |
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| 55 |
-##' @slot fields beast statistic variables |
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| 56 |
-##' @slot treetext tree text in beast file |
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| 57 |
-##' @slot phylo tree phylo object |
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| 58 |
-##' @slot translation tip number to name translation in beast file |
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| 59 |
-##' @slot stats beast statistics |
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| 60 |
-##' @slot file beast file, nexus format |
|
| 61 |
-##' @slot extraInfo extra information |
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| 62 |
-##' @exportClass beast |
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| 63 |
-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 64 |
-##' @seealso \code{\link{show}} \code{\link{get.fields}}
|
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| 65 |
-##' \code{\link{ggtree}}
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|
| 66 |
-##' @keywords classes |
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| 67 |
-setClass("beast",
|
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| 68 |
- representation = representation( |
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| 69 |
- fields = "character", |
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| 70 |
- treetext = "character", |
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| 71 |
- phylo = "phylo", |
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| 72 |
- translation = "matrix", |
|
| 73 |
- stats = "data.frame", |
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| 74 |
- file = "character", |
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| 75 |
- extraInfo = "data.frame" |
|
| 76 |
- ) |
|
| 77 |
- ) |
|
| 46 |
+## ##' Class "beast" |
|
| 47 |
+## ##' This class stores information of beast output |
|
| 48 |
+## ##' |
|
| 49 |
+## ##' |
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| 50 |
+## ##' @name beast-class |
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| 51 |
+## ##' @aliases beast-class |
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| 52 |
+## ##' get.tree,beast-method |
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| 53 |
+## ##' |
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| 54 |
+## ##' @docType class |
|
| 55 |
+## ##' @slot fields beast statistic variables |
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| 56 |
+## ##' @slot treetext tree text in beast file |
|
| 57 |
+## ##' @slot phylo tree phylo object |
|
| 58 |
+## ##' @slot translation tip number to name translation in beast file |
|
| 59 |
+## ##' @slot stats beast statistics |
|
| 60 |
+## ##' @slot file beast file, nexus format |
|
| 61 |
+## ##' @slot extraInfo extra information |
|
| 62 |
+## ##' @exportClass beast |
|
| 63 |
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 64 |
+## ##' @seealso \code{\link{show}} \code{\link{get.fields}}
|
|
| 65 |
+## ##' \code{\link{ggtree}}
|
|
| 66 |
+## ##' @keywords classes |
|
| 67 |
+## setClass("beast",
|
|
| 68 |
+## representation = representation( |
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| 69 |
+## fields = "character", |
|
| 70 |
+## treetext = "character", |
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| 71 |
+## phylo = "phylo", |
|
| 72 |
+## translation = "matrix", |
|
| 73 |
+## stats = "data.frame", |
|
| 74 |
+## file = "character", |
|
| 75 |
+## extraInfo = "data.frame" |
|
| 76 |
+## ) |
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| 77 |
+## ) |
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| 78 | 78 |
|
| 79 | 79 |
|
| 80 |
-##' Class "codeml_mlc" |
|
| 81 |
-##' This class stores information of mlc file frm codeml output |
|
| 82 |
-##' |
|
| 83 |
-##' |
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| 84 |
-##' @name codeml_mlc-class |
|
| 85 |
-##' @docType class |
|
| 86 |
-##' @slot fields available features |
|
| 87 |
-##' @slot treetext tree text |
|
| 88 |
-##' @slot phylo phylo object |
|
| 89 |
-##' @slot dNdS dN dS information |
|
| 90 |
-##' @slot mlcfile mlc file |
|
| 91 |
-##' @slot extraInfo extra information |
|
| 92 |
-##' @exportClass codeml_mlc |
|
| 93 |
-##' @author Guangchuang Yu |
|
| 94 |
-##' @seealso \linkS4class{paml_rst} \linkS4class{codeml}
|
|
| 95 |
-##' @keywords classes |
|
| 96 |
-setClass("codeml_mlc",
|
|
| 97 |
- representation = representation( |
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| 98 |
- fields = "character", |
|
| 99 |
- treetext = "character", |
|
| 100 |
- phylo = "phylo", |
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| 101 |
- dNdS = "matrix", |
|
| 102 |
- ## seq_type = "character", |
|
| 103 |
- ## tip_seq = "character", |
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| 104 |
- mlcfile = "character", |
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| 105 |
- extraInfo = "data.frame" |
|
| 106 |
- ) |
|
| 107 |
- ) |
|
| 80 |
+## ##' Class "codeml_mlc" |
|
| 81 |
+## ##' This class stores information of mlc file frm codeml output |
|
| 82 |
+## ##' |
|
| 83 |
+## ##' |
|
| 84 |
+## ##' @name codeml_mlc-class |
|
| 85 |
+## ##' @docType class |
|
| 86 |
+## ##' @slot fields available features |
|
| 87 |
+## ##' @slot treetext tree text |
|
| 88 |
+## ##' @slot phylo phylo object |
|
| 89 |
+## ##' @slot dNdS dN dS information |
|
| 90 |
+## ##' @slot mlcfile mlc file |
|
| 91 |
+## ##' @slot extraInfo extra information |
|
| 92 |
+## ##' @exportClass codeml_mlc |
|
| 93 |
+## ##' @author Guangchuang Yu |
|
| 94 |
+## ##' @seealso \linkS4class{paml_rst} \linkS4class{codeml}
|
|
| 95 |
+## ##' @keywords classes |
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| 96 |
+## setClass("codeml_mlc",
|
|
| 97 |
+## representation = representation( |
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| 98 |
+## fields = "character", |
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| 99 |
+## treetext = "character", |
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| 100 |
+## phylo = "phylo", |
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| 101 |
+## dNdS = "matrix", |
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| 102 |
+## ## seq_type = "character", |
|
| 103 |
+## ## tip_seq = "character", |
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| 104 |
+## mlcfile = "character", |
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| 105 |
+## extraInfo = "data.frame" |
|
| 106 |
+## ) |
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| 107 |
+## ) |
|
| 108 | 108 |
|
| 109 |
-##' Class "paml_rst" |
|
| 110 |
-##' This class stores information of rst file from PAML output |
|
| 111 |
-##' |
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| 112 |
-##' |
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| 113 |
-##' @name paml_rst-class |
|
| 114 |
-##' @aliases paml_rst-class |
|
| 115 |
-##' set.subs,paml_rst-method |
|
| 116 |
-##' set.subs<-,paml_rst-method |
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| 117 |
-##' |
|
| 118 |
-##' @docType class |
|
| 119 |
-##' @slot fields availabel attributes |
|
| 120 |
-##' @slot treetext tree text |
|
| 121 |
-##' @slot phylo phylo object |
|
| 122 |
-##' @slot seq_type one of "NT" and "AA" |
|
| 123 |
-##' @slot tip_seq sequences of tips |
|
| 124 |
-##' @slot marginal_ancseq Marginal reconstruction of ancestral sequences |
|
| 125 |
-##' @slot joint_ancseq Joint reconstruction of ancestral sequences |
|
| 126 |
-##' @slot marginal_subs sequence substitutions based on marginal_ancseq |
|
| 127 |
-##' @slot joint_subs sequence substitutions based on joint_ancseq |
|
| 128 |
-##' @slot marginal_AA_subs Amino acid sequence substitutions based on marginal_ancseq |
|
| 129 |
-##' @slot joint_AA_subs Amino acid sequence substitutions based on joint_ancseq |
|
| 130 |
-##' @slot rstfile rst file |
|
| 131 |
-##' @slot extraInfo extra information |
|
| 132 |
-##' @exportClass paml_rst |
|
| 133 |
-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 134 |
-##' @seealso \linkS4class{codeml} \linkS4class{codeml_mlc}
|
|
| 135 |
-##' @keywords classes |
|
| 136 |
-setClass("paml_rst",
|
|
| 137 |
- representation = representation( |
|
| 138 |
- fields = "character", |
|
| 139 |
- treetext = "character", |
|
| 140 |
- phylo = "phylo", |
|
| 141 |
- seq_type = "character", |
|
| 142 |
- tip_seq = "character", |
|
| 143 |
- marginal_ancseq = "character", |
|
| 144 |
- joint_ancseq = "character", |
|
| 145 |
- marginal_subs = "data.frame", |
|
| 146 |
- joint_subs = "data.frame", |
|
| 147 |
- marginal_AA_subs = "data.frame", |
|
| 148 |
- joint_AA_subs = "data.frame", |
|
| 149 |
- rstfile = "character", |
|
| 150 |
- extraInfo = "data.frame" |
|
| 151 |
- ) |
|
| 152 |
- ) |
|
| 109 |
+## ##' Class "paml_rst" |
|
| 110 |
+## ##' This class stores information of rst file from PAML output |
|
| 111 |
+## ##' |
|
| 112 |
+## ##' |
|
| 113 |
+## ##' @name paml_rst-class |
|
| 114 |
+## ##' @aliases paml_rst-class |
|
| 115 |
+## ##' set.subs,paml_rst-method |
|
| 116 |
+## ##' set.subs<-,paml_rst-method |
|
| 117 |
+## ##' |
|
| 118 |
+## ##' @docType class |
|
| 119 |
+## ##' @slot fields availabel attributes |
|
| 120 |
+## ##' @slot treetext tree text |
|
| 121 |
+## ##' @slot phylo phylo object |
|
| 122 |
+## ##' @slot seq_type one of "NT" and "AA" |
|
| 123 |
+## ##' @slot tip_seq sequences of tips |
|
| 124 |
+## ##' @slot marginal_ancseq Marginal reconstruction of ancestral sequences |
|
| 125 |
+## ##' @slot joint_ancseq Joint reconstruction of ancestral sequences |
|
| 126 |
+## ##' @slot marginal_subs sequence substitutions based on marginal_ancseq |
|
| 127 |
+## ##' @slot joint_subs sequence substitutions based on joint_ancseq |
|
| 128 |
+## ##' @slot marginal_AA_subs Amino acid sequence substitutions based on marginal_ancseq |
|
| 129 |
+## ##' @slot joint_AA_subs Amino acid sequence substitutions based on joint_ancseq |
|
| 130 |
+## ##' @slot rstfile rst file |
|
| 131 |
+## ##' @slot extraInfo extra information |
|
| 132 |
+## ##' @exportClass paml_rst |
|
| 133 |
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 134 |
+## ##' @seealso \linkS4class{codeml} \linkS4class{codeml_mlc}
|
|
| 135 |
+## ##' @keywords classes |
|
| 136 |
+## setClass("paml_rst",
|
|
| 137 |
+## representation = representation( |
|
| 138 |
+## fields = "character", |
|
| 139 |
+## treetext = "character", |
|
| 140 |
+## phylo = "phylo", |
|
| 141 |
+## seq_type = "character", |
|
| 142 |
+## tip_seq = "character", |
|
| 143 |
+## marginal_ancseq = "character", |
|
| 144 |
+## joint_ancseq = "character", |
|
| 145 |
+## marginal_subs = "data.frame", |
|
| 146 |
+## joint_subs = "data.frame", |
|
| 147 |
+## marginal_AA_subs = "data.frame", |
|
| 148 |
+## joint_AA_subs = "data.frame", |
|
| 149 |
+## rstfile = "character", |
|
| 150 |
+## extraInfo = "data.frame" |
|
| 151 |
+## ) |
|
| 152 |
+## ) |
|
| 153 | 153 |
|
| 154 |
-##' Class "codeml" |
|
| 155 |
-##' This class stores information of output from codeml |
|
| 156 |
-##' |
|
| 157 |
-##' |
|
| 158 |
-##' @name codeml-class |
|
| 159 |
-##' @docType class |
|
| 160 |
-##' @slot mlc A \code{code_mlc} object
|
|
| 161 |
-##' @slot rst A \code{paml_rst} object
|
|
| 162 |
-##' @slot extraInfo extra information |
|
| 163 |
-##' @exportClass codeml |
|
| 164 |
-##' @seealso \linkS4class{codeml_mlc} \linkS4class{paml_rst}
|
|
| 165 |
-##' @keywords codeml |
|
| 166 |
-setClass("codeml",
|
|
| 167 |
- representation = representation( |
|
| 168 |
- mlc = "codeml_mlc", |
|
| 169 |
- rst = "paml_rst", |
|
| 170 |
- extraInfo = "data.frame" |
|
| 171 |
- ) |
|
| 172 |
- ) |
|
| 154 |
+## ##' Class "codeml" |
|
| 155 |
+## ##' This class stores information of output from codeml |
|
| 156 |
+## ##' |
|
| 157 |
+## ##' |
|
| 158 |
+## ##' @name codeml-class |
|
| 159 |
+## ##' @docType class |
|
| 160 |
+## ##' @slot mlc A \code{code_mlc} object
|
|
| 161 |
+## ##' @slot rst A \code{paml_rst} object
|
|
| 162 |
+## ##' @slot extraInfo extra information |
|
| 163 |
+## ##' @exportClass codeml |
|
| 164 |
+## ##' @seealso \linkS4class{codeml_mlc} \linkS4class{paml_rst}
|
|
| 165 |
+## ##' @keywords codeml |
|
| 166 |
+## setClass("codeml",
|
|
| 167 |
+## representation = representation( |
|
| 168 |
+## mlc = "codeml_mlc", |
|
| 169 |
+## rst = "paml_rst", |
|
| 170 |
+## extraInfo = "data.frame" |
|
| 171 |
+## ) |
|
| 172 |
+## ) |
|
| 173 | 173 |
|
| 174 | 174 |
|
| 175 | 175 |
|
| 176 |
-##' Class "hyphy" |
|
| 177 |
-##' This class stores information of HYPHY output |
|
| 178 |
-##' |
|
| 179 |
-##' |
|
| 180 |
-##' @name hyphy-class |
|
| 181 |
-##' @docType class |
|
| 182 |
-##' @slot fields available features |
|
| 183 |
-##' @slot treetext tree text |
|
| 184 |
-##' @slot phylo phylo object |
|
| 185 |
-##' @slot seq_type one of "NT" and "AA" |
|
| 186 |
-##' @slot subs sequence substitutions |
|
| 187 |
-##' @slot AA_subs Amino acid sequence substitution |
|
| 188 |
-##' @slot ancseq ancestral sequences |
|
| 189 |
-##' @slot tip_seq tip sequences |
|
| 190 |
-##' @slot tip.fasfile fasta file of tip sequences |
|
| 191 |
-##' @slot tree.file tree file |
|
| 192 |
-##' @slot ancseq.file ancestral sequence file, nexus format |
|
| 193 |
-##' @slot extraInfo extra information |
|
| 194 |
-##' @exportClass hyphy |
|
| 195 |
-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 196 |
-##' @seealso \linkS4class{paml_rst}
|
|
| 197 |
-##' @keywords classes |
|
| 198 |
-setClass("hyphy",
|
|
| 199 |
- representation = representation( |
|
| 200 |
- fields = "character", |
|
| 201 |
- treetext = "character", |
|
| 202 |
- phylo = "phylo", |
|
| 203 |
- seq_type = "character", |
|
| 204 |
- subs = "data.frame", |
|
| 205 |
- AA_subs = "data.frame", |
|
| 206 |
- ancseq = "character", |
|
| 207 |
- tip_seq = "character", |
|
| 208 |
- tip.fasfile = "character", |
|
| 209 |
- tree.file = "character", |
|
| 210 |
- ancseq.file = "character", |
|
| 211 |
- extraInfo = "data.frame" |
|
| 212 |
- ) |
|
| 213 |
- ) |
|
| 176 |
+## ##' Class "hyphy" |
|
| 177 |
+## ##' This class stores information of HYPHY output |
|
| 178 |
+## ##' |
|
| 179 |
+## ##' |
|
| 180 |
+## ##' @name hyphy-class |
|
| 181 |
+## ##' @docType class |
|
| 182 |
+## ##' @slot fields available features |
|
| 183 |
+## ##' @slot treetext tree text |
|
| 184 |
+## ##' @slot phylo phylo object |
|
| 185 |
+## ##' @slot seq_type one of "NT" and "AA" |
|
| 186 |
+## ##' @slot subs sequence substitutions |
|
| 187 |
+## ##' @slot AA_subs Amino acid sequence substitution |
|
| 188 |
+## ##' @slot ancseq ancestral sequences |
|
| 189 |
+## ##' @slot tip_seq tip sequences |
|
| 190 |
+## ##' @slot tip.fasfile fasta file of tip sequences |
|
| 191 |
+## ##' @slot tree.file tree file |
|
| 192 |
+## ##' @slot ancseq.file ancestral sequence file, nexus format |
|
| 193 |
+## ##' @slot extraInfo extra information |
|
| 194 |
+## ##' @exportClass hyphy |
|
| 195 |
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 196 |
+## ##' @seealso \linkS4class{paml_rst}
|
|
| 197 |
+## ##' @keywords classes |
|
| 198 |
+## setClass("hyphy",
|
|
| 199 |
+## representation = representation( |
|
| 200 |
+## fields = "character", |
|
| 201 |
+## treetext = "character", |
|
| 202 |
+## phylo = "phylo", |
|
| 203 |
+## seq_type = "character", |
|
| 204 |
+## subs = "data.frame", |
|
| 205 |
+## AA_subs = "data.frame", |
|
| 206 |
+## ancseq = "character", |
|
| 207 |
+## tip_seq = "character", |
|
| 208 |
+## tip.fasfile = "character", |
|
| 209 |
+## tree.file = "character", |
|
| 210 |
+## ancseq.file = "character", |
|
| 211 |
+## extraInfo = "data.frame" |
|
| 212 |
+## ) |
|
| 213 |
+## ) |
|
| 214 | 214 |
|
| 215 |
-##' Class "jplace" |
|
| 216 |
-##' This class stores information of jplace file. |
|
| 217 |
-##' |
|
| 218 |
-##' |
|
| 219 |
-##' @name jplace-class |
|
| 220 |
-##' @aliases jplace-class |
|
| 221 |
-##' show,jplace-method |
|
| 222 |
-##' get.placements,jplace-method |
|
| 223 |
-##' get.treeinfo,jplace-method |
|
| 224 |
-##' get.fields,jplace-method |
|
| 225 |
-##' get.treetext,jplace-method |
|
| 226 |
-##' |
|
| 227 |
-##' @docType class |
|
| 228 |
-##' @slot fields colnames of first variable of placements |
|
| 229 |
-##' @slot treetext tree text |
|
| 230 |
-##' @slot phylo tree phylo object |
|
| 231 |
-##' @slot placements placement information |
|
| 232 |
-##' @slot version version |
|
| 233 |
-##' @slot metadata metadata |
|
| 234 |
-##' @slot file jplace file |
|
| 235 |
-##' @slot extraInfo extra information |
|
| 236 |
-##' @exportClass jplace |
|
| 237 |
-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 238 |
-##' @seealso \code{\link{show}} \code{\link{get.tree}}
|
|
| 239 |
-##' \code{\link{ggtree}}
|
|
| 240 |
-##' @keywords classes |
|
| 241 |
-setClass("jplace",
|
|
| 242 |
- representation = representation( |
|
| 243 |
- fields = "character", |
|
| 244 |
- treetext = "character", |
|
| 245 |
- phylo = "phylo", |
|
| 246 |
- placements = "data.frame", |
|
| 247 |
- version = "numeric", |
|
| 248 |
- metadata = "list", |
|
| 249 |
- file = "character", |
|
| 250 |
- extraInfo = "data.frame" |
|
| 251 |
- ) |
|
| 252 |
- ) |
|
| 215 |
+## ##' Class "jplace" |
|
| 216 |
+## ##' This class stores information of jplace file. |
|
| 217 |
+## ##' |
|
| 218 |
+## ##' |
|
| 219 |
+## ##' @name jplace-class |
|
| 220 |
+## ##' @aliases jplace-class |
|
| 221 |
+## ##' show,jplace-method |
|
| 222 |
+## ##' get.placements,jplace-method |
|
| 223 |
+## ##' get.treeinfo,jplace-method |
|
| 224 |
+## ##' get.fields,jplace-method |
|
| 225 |
+## ##' get.treetext,jplace-method |
|
| 226 |
+## ##' |
|
| 227 |
+## ##' @docType class |
|
| 228 |
+## ##' @slot fields colnames of first variable of placements |
|
| 229 |
+## ##' @slot treetext tree text |
|
| 230 |
+## ##' @slot phylo tree phylo object |
|
| 231 |
+## ##' @slot placements placement information |
|
| 232 |
+## ##' @slot version version |
|
| 233 |
+## ##' @slot metadata metadata |
|
| 234 |
+## ##' @slot file jplace file |
|
| 235 |
+## ##' @slot extraInfo extra information |
|
| 236 |
+## ##' @exportClass jplace |
|
| 237 |
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 238 |
+## ##' @seealso \code{\link{show}} \code{\link{get.tree}}
|
|
| 239 |
+## ##' \code{\link{ggtree}}
|
|
| 240 |
+## ##' @keywords classes |
|
| 241 |
+## setClass("jplace",
|
|
| 242 |
+## representation = representation( |
|
| 243 |
+## fields = "character", |
|
| 244 |
+## treetext = "character", |
|
| 245 |
+## phylo = "phylo", |
|
| 246 |
+## placements = "data.frame", |
|
| 247 |
+## version = "numeric", |
|
| 248 |
+## metadata = "list", |
|
| 249 |
+## file = "character", |
|
| 250 |
+## extraInfo = "data.frame" |
|
| 251 |
+## ) |
|
| 252 |
+## ) |
|
| 253 | 253 |
|
| 254 | 254 |
|
| 255 |
-##' Class "nhx" |
|
| 256 |
-##' This class stores nhx tree |
|
| 257 |
-##' |
|
| 258 |
-##' |
|
| 259 |
-##' @name nhx-class |
|
| 260 |
-##' @rdname nhx-class |
|
| 261 |
-##' @docType class |
|
| 262 |
-##' @slot file input file |
|
| 263 |
-##' @slot fields available feature |
|
| 264 |
-##' @slot phylo phylo object |
|
| 265 |
-##' @slot nhx_tags tag information in nhx file |
|
| 266 |
-##' @slot extraInfo extra information |
|
| 267 |
-##' @exportClass nhx |
|
| 268 |
-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 269 |
-##' @keywords classes |
|
| 270 |
-setClass("nhx",
|
|
| 271 |
- representation = representation( |
|
| 272 |
- file = "character", |
|
| 273 |
- fields = "character", |
|
| 274 |
- phylo = "phylo", |
|
| 275 |
- nhx_tags = "data.frame", |
|
| 276 |
- extraInfo = "data.frame" |
|
| 277 |
- ) |
|
| 278 |
- ) |
|
| 255 |
+## ##' Class "nhx" |
|
| 256 |
+## ##' This class stores nhx tree |
|
| 257 |
+## ##' |
|
| 258 |
+## ##' |
|
| 259 |
+## ##' @name nhx-class |
|
| 260 |
+## ##' @rdname nhx-class |
|
| 261 |
+## ##' @docType class |
|
| 262 |
+## ##' @slot file input file |
|
| 263 |
+## ##' @slot fields available feature |
|
| 264 |
+## ##' @slot phylo phylo object |
|
| 265 |
+## ##' @slot nhx_tags tag information in nhx file |
|
| 266 |
+## ##' @slot extraInfo extra information |
|
| 267 |
+## ##' @exportClass nhx |
|
| 268 |
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 269 |
+## ##' @keywords classes |
|
| 270 |
+## setClass("nhx",
|
|
| 271 |
+## representation = representation( |
|
| 272 |
+## file = "character", |
|
| 273 |
+## fields = "character", |
|
| 274 |
+## phylo = "phylo", |
|
| 275 |
+## nhx_tags = "data.frame", |
|
| 276 |
+## extraInfo = "data.frame" |
|
| 277 |
+## ) |
|
| 278 |
+## ) |
|
| 279 | 279 |
|
| 280 | 280 |
|
| 281 |
-##' Class "phangorn" |
|
| 282 |
-##' This class stores ancestral sequences inferred from 'phangorn' |
|
| 283 |
-##' |
|
| 284 |
-##' |
|
| 285 |
-##' @name phangorn-class |
|
| 286 |
-##' @docType class |
|
| 287 |
-##' @slot fields available attributes |
|
| 288 |
-##' @slot phylo phylo object |
|
| 289 |
-##' @slot seq_type one of "NT" and "AA" |
|
| 290 |
-##' @slot tip_seq sequences of tips |
|
| 291 |
-##' @slot ancseq ancenstral sequences |
|
| 292 |
-##' @slot subs sequence substitution |
|
| 293 |
-##' @slot AA_subs Amino acid sequence substitution |
|
| 294 |
-##' @slot extraInfo extra information |
|
| 295 |
-##' @exportClass phangorn |
|
| 296 |
-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 297 |
-##' @seealso \linkS4class{paml_rst}
|
|
| 298 |
-##' @keywords classes |
|
| 299 |
-setClass("phangorn",
|
|
| 300 |
- representation = representation( |
|
| 301 |
- fields = "character", |
|
| 302 |
- phylo = "phylo", |
|
| 303 |
- seq_type = "character", |
|
| 304 |
- tip_seq = "character", |
|
| 305 |
- ancseq = "character", |
|
| 306 |
- subs = "data.frame", |
|
| 307 |
- AA_subs = "data.frame", |
|
| 308 |
- extraInfo = "data.frame") |
|
| 309 |
- ) |
|
| 281 |
+## ##' Class "phangorn" |
|
| 282 |
+## ##' This class stores ancestral sequences inferred from 'phangorn' |
|
| 283 |
+## ##' |
|
| 284 |
+## ##' |
|
| 285 |
+## ##' @name phangorn-class |
|
| 286 |
+## ##' @docType class |
|
| 287 |
+## ##' @slot fields available attributes |
|
| 288 |
+## ##' @slot phylo phylo object |
|
| 289 |
+## ##' @slot seq_type one of "NT" and "AA" |
|
| 290 |
+## ##' @slot tip_seq sequences of tips |
|
| 291 |
+## ##' @slot ancseq ancenstral sequences |
|
| 292 |
+## ##' @slot subs sequence substitution |
|
| 293 |
+## ##' @slot AA_subs Amino acid sequence substitution |
|
| 294 |
+## ##' @slot extraInfo extra information |
|
| 295 |
+## ##' @exportClass phangorn |
|
| 296 |
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 297 |
+## ##' @seealso \linkS4class{paml_rst}
|
|
| 298 |
+## ##' @keywords classes |
|
| 299 |
+## setClass("phangorn",
|
|
| 300 |
+## representation = representation( |
|
| 301 |
+## fields = "character", |
|
| 302 |
+## phylo = "phylo", |
|
| 303 |
+## seq_type = "character", |
|
| 304 |
+## tip_seq = "character", |
|
| 305 |
+## ancseq = "character", |
|
| 306 |
+## subs = "data.frame", |
|
| 307 |
+## AA_subs = "data.frame", |
|
| 308 |
+## extraInfo = "data.frame") |
|
| 309 |
+## ) |
|
| 310 | 310 |
|
| 311 | 311 |
|
| 312 | 312 |
|
| 313 |
-##' Class "phylip" |
|
| 314 |
-##' This class stores phylip tree(s) |
|
| 315 |
-##' |
|
| 316 |
-##' |
|
| 317 |
-##' @name phylip-class |
|
| 318 |
-##' @docType class |
|
| 319 |
-##' @slot file input file |
|
| 320 |
-##' @slot fields available feature |
|
| 321 |
-##' @slot phylo phylo or multiPhylo |
|
| 322 |
-##' @slot ntree number of trees |
|
| 323 |
-##' @slot sequence sequences |
|
| 324 |
-##' @slot extraInfo extra information |
|
| 325 |
-##' @exportClass phylip |
|
| 326 |
-##' @author Guangchuang Yu |
|
| 327 |
-##' @keywords classes |
|
| 328 |
-setClass("phylip",
|
|
| 329 |
- representation = representation( |
|
| 330 |
- file = "character", |
|
| 331 |
- fields = "character", |
|
| 332 |
- phylo = "phyloOrmultiPhylo", |
|
| 333 |
- ntree = "numeric", |
|
| 334 |
- sequence = "character", |
|
| 335 |
- extraInfo = "data.frame") |
|
| 336 |
- ) |
|
| 313 |
+## ##' Class "phylip" |
|
| 314 |
+## ##' This class stores phylip tree(s) |
|
| 315 |
+## ##' |
|
| 316 |
+## ##' |
|
| 317 |
+## ##' @name phylip-class |
|
| 318 |
+## ##' @docType class |
|
| 319 |
+## ##' @slot file input file |
|
| 320 |
+## ##' @slot fields available feature |
|
| 321 |
+## ##' @slot phylo phylo or multiPhylo |
|
| 322 |
+## ##' @slot ntree number of trees |
|
| 323 |
+## ##' @slot sequence sequences |
|
| 324 |
+## ##' @slot extraInfo extra information |
|
| 325 |
+## ##' @exportClass phylip |
|
| 326 |
+## ##' @author Guangchuang Yu |
|
| 327 |
+## ##' @keywords classes |
|
| 328 |
+## setClass("phylip",
|
|
| 329 |
+## representation = representation( |
|
| 330 |
+## file = "character", |
|
| 331 |
+## fields = "character", |
|
| 332 |
+## phylo = "phyloOrmultiPhylo", |
|
| 333 |
+## ntree = "numeric", |
|
| 334 |
+## sequence = "character", |
|
| 335 |
+## extraInfo = "data.frame") |
|
| 336 |
+## ) |
|
| 337 | 337 |
|
| 338 | 338 |
|
| 339 |
-##' Class "r8s" |
|
| 340 |
-##' This class stores output info from r8s |
|
| 341 |
-##' |
|
| 342 |
-##' |
|
| 343 |
-##' @name r8s-class |
|
| 344 |
-##' @docType class |
|
| 345 |
-##' @slot file input file |
|
| 346 |
-##' @slot fields available feature |
|
| 347 |
-##' @slot treetext tree text |
|
| 348 |
-##' @slot phylo multiPhylo, time tree, rate tree and absolute substitution tree |
|
| 349 |
-##' @slot extraInfo extra information |
|
| 350 |
-##' @exportClass r8s |
|
| 351 |
-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 352 |
-##' @keywords classes |
|
| 353 |
-setClass("r8s",
|
|
| 354 |
- representation = representation( |
|
| 355 |
- file = "character", |
|
| 356 |
- fields = "character", |
|
| 357 |
- treetext = "character", |
|
| 358 |
- phylo = "multiPhylo", |
|
| 359 |
- extraInfo = "data.frame" |
|
| 360 |
- ) |
|
| 361 |
- ) |
|
| 339 |
+## ##' Class "r8s" |
|
| 340 |
+## ##' This class stores output info from r8s |
|
| 341 |
+## ##' |
|
| 342 |
+## ##' |
|
| 343 |
+## ##' @name r8s-class |
|
| 344 |
+## ##' @docType class |
|
| 345 |
+## ##' @slot file input file |
|
| 346 |
+## ##' @slot fields available feature |
|
| 347 |
+## ##' @slot treetext tree text |
|
| 348 |
+## ##' @slot phylo multiPhylo, time tree, rate tree and absolute substitution tree |
|
| 349 |
+## ##' @slot extraInfo extra information |
|
| 350 |
+## ##' @exportClass r8s |
|
| 351 |
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 352 |
+## ##' @keywords classes |
|
| 353 |
+## setClass("r8s",
|
|
| 354 |
+## representation = representation( |
|
| 355 |
+## file = "character", |
|
| 356 |
+## fields = "character", |
|
| 357 |
+## treetext = "character", |
|
| 358 |
+## phylo = "multiPhylo", |
|
| 359 |
+## extraInfo = "data.frame" |
|
| 360 |
+## ) |
|
| 361 |
+## ) |
|
| 362 | 362 |
|
| 363 | 363 |
|
| 364 |
-##' Class "raxml" |
|
| 365 |
-##' This class stores RAxML bootstrapping analysis result |
|
| 366 |
-##' |
|
| 367 |
-##' |
|
| 368 |
-##' @name raxml-class |
|
| 369 |
-##' @docType class |
|
| 370 |
-##' @slot file input file |
|
| 371 |
-##' @slot fields available features |
|
| 372 |
-##' @slot treetext tree text |
|
| 373 |
-##' @slot phylo phylo object of treetext |
|
| 374 |
-##' @slot bootstrap bootstrap value |
|
| 375 |
-##' @slot extraInfo extra information |
|
| 376 |
-##' @exportClass raxml |
|
| 377 |
-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 378 |
-##' @keywords classes |
|
| 379 |
-setClass("raxml",
|
|
| 380 |
- representation = representation( |
|
| 381 |
- file = "character", |
|
| 382 |
- treetext = "character" |
|
| 383 |
- ), |
|
| 384 |
- contains = "apeBootstrap" |
|
| 385 |
- ) |
|
| 364 |
+## ##' Class "raxml" |
|
| 365 |
+## ##' This class stores RAxML bootstrapping analysis result |
|
| 366 |
+## ##' |
|
| 367 |
+## ##' |
|
| 368 |
+## ##' @name raxml-class |
|
| 369 |
+## ##' @docType class |
|
| 370 |
+## ##' @slot file input file |
|
| 371 |
+## ##' @slot fields available features |
|
| 372 |
+## ##' @slot treetext tree text |
|
| 373 |
+## ##' @slot phylo phylo object of treetext |
|
| 374 |
+## ##' @slot bootstrap bootstrap value |
|
| 375 |
+## ##' @slot extraInfo extra information |
|
| 376 |
+## ##' @exportClass raxml |
|
| 377 |
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
|
|
| 378 |
+## ##' @keywords classes |
|
| 379 |
+## setClass("raxml",
|
|
| 380 |
+## representation = representation( |
|
| 381 |
+## file = "character", |
|
| 382 |
+## treetext = "character" |
|
| 383 |
+## ), |
|
| 384 |
+## contains = "apeBootstrap" |
|
| 385 |
+## ) |
|
| 386 | 386 |
|
| 387 | 387 |
|
| ... | ... |
@@ -33,124 +33,124 @@ if ( !isGeneric("plot") )
|
| 33 | 33 |
##' @export |
| 34 | 34 |
setGeneric("reroot", function(object, node, ...) standardGeneric("reroot"))
|
| 35 | 35 |
|
| 36 |
-##' @docType methods |
|
| 37 |
-##' @name get.tree |
|
| 38 |
-##' @rdname get.tree-methods |
|
| 39 |
-##' @title get.tree method |
|
| 40 |
-##' @param object one of \code{phylo}, \code{jplace}, \code{nhx}, \code{phangorn}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object
|
|
| 41 |
-##' @param ... additional parameter |
|
| 42 |
-##' @return phylo object |
|
| 43 |
-##' @export |
|
| 44 |
-setGeneric("get.tree", function(object, ...) standardGeneric("get.tree"))
|
|
| 45 |
- |
|
| 46 |
-##' @docType methods |
|
| 47 |
-##' @name get.treetext |
|
| 48 |
-##' @rdname get.treetext-methods |
|
| 49 |
-##' @title get.treetext method |
|
| 50 |
-##' @param object one of \code{phylo}, \code{jplace}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object
|
|
| 51 |
-##' @param ... additional parameter |
|
| 52 |
-##' @return phylo object |
|
| 53 |
-##' @export |
|
| 54 |
-setGeneric("get.treetext", function(object, ...) standardGeneric("get.treetext"))
|
|
| 55 |
- |
|
| 56 |
- |
|
| 57 |
-##' @docType methods |
|
| 58 |
-##' @name get.treeinfo |
|
| 59 |
-##' @rdname get.treeinfo-methods |
|
| 60 |
-##' @title get.treeinfo method |
|
| 61 |
-##' @param object jplace object |
|
| 62 |
-##' @param layout layout |
|
| 63 |
-##' @param ladderize ladderize, logical |
|
| 64 |
-##' @param right logical, parameter for ladderize |
|
| 65 |
-##' @param ... additional parameter |
|
| 66 |
-##' @return data.frame |
|
| 67 |
-##' @export |
|
| 68 |
-setGeneric("get.treeinfo", function(object, layout="phylogram", ladderize=TRUE, right=FALSE, ...) standardGeneric("get.treeinfo"))
|
|
| 69 |
- |
|
| 70 |
- |
|
| 71 |
-##' @docType methods |
|
| 72 |
-##' @name get.fields |
|
| 73 |
-##' @rdname get.fields-methods |
|
| 74 |
-##' @title get.fields method |
|
| 75 |
-##' @param object one of \code{jplace}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object
|
|
| 76 |
-##' @param ... additional parameter |
|
| 77 |
-##' @return available annotation variables |
|
| 78 |
-##' @export |
|
| 79 |
-setGeneric("get.fields", function(object, ...) standardGeneric("get.fields"))
|
|
| 80 |
- |
|
| 81 |
- |
|
| 82 |
-##' @docType methods |
|
| 83 |
-##' @name get.placements |
|
| 84 |
-##' @rdname get.placements-methods |
|
| 85 |
-##' @title get.placements method |
|
| 86 |
-##' @param object jplace object |
|
| 87 |
-##' @param by get best hit or others |
|
| 88 |
-##' @param ... additional parameter |
|
| 89 |
-##' @return data.frame |
|
| 90 |
-##' @export |
|
| 91 |
-setGeneric("get.placements", function(object, by, ...) standardGeneric("get.placements"))
|
|
| 92 |
- |
|
| 93 |
-##' @docType methods |
|
| 94 |
-##' @name get.subs |
|
| 95 |
-##' @rdname get.subs-methods |
|
| 96 |
-##' @title get.subs method |
|
| 97 |
-##' @param object paml_rst object |
|
| 98 |
-##' @param type one of 'marginal_subs', 'marginal_AA_subs', |
|
| 99 |
-##' 'joint_subs' or 'joint_AA_subs'. |
|
| 100 |
-##' @param ... additional parameter |
|
| 101 |
-##' @return data.frame |
|
| 102 |
-##' @export |
|
| 103 |
-setGeneric("get.subs", function(object, type, ...) standardGeneric("get.subs"))
|
|
| 104 |
- |
|
| 105 |
- |
|
| 106 |
-##' @docType methods |
|
| 107 |
-##' @name get.tipseq |
|
| 108 |
-##' @rdname get.tipseq-methods |
|
| 109 |
-##' @title get.tipseq method |
|
| 110 |
-##' @param object one of paml_rst or codeml object |
|
| 111 |
-##' @param ... additional parameter |
|
| 112 |
-##' @return character |
|
| 113 |
-##' @export |
|
| 114 |
-setGeneric("get.tipseq", function(object, ...) standardGeneric("get.tipseq"))
|
|
| 115 |
- |
|
| 116 |
-##' @docType methods |
|
| 117 |
-##' @name groupOTU |
|
| 118 |
-##' @rdname groupOTU-methods |
|
| 119 |
-##' @title groupOTU method |
|
| 120 |
-##' @param object supported objects, including phylo, paml_rst, |
|
| 121 |
-##' codeml_mlc, codeml, jplace, beast, hyphy |
|
| 122 |
-##' @param focus a vector of tip (label or number) or a list of tips. |
|
| 123 |
-##' @param group_name name of the group, 'group' by default |
|
| 124 |
-##' @param ... additional parameter |
|
| 125 |
-##' @return group index |
|
| 126 |
-##' @export |
|
| 127 |
-setGeneric("groupOTU", function(object, focus, group_name="group", ...) standardGeneric("groupOTU"))
|
|
| 128 |
- |
|
| 129 |
-##' @docType methods |
|
| 130 |
-##' @name groupClade |
|
| 131 |
-##' @rdname groupClade-methods |
|
| 132 |
-##' @title groupClade method |
|
| 133 |
-##' @param object supported objects, including phylo, paml_rst, |
|
| 134 |
-##' codeml_mlc, codeml, jplace, beast, hyphy |
|
| 135 |
-##' @param node a internal node or a vector of internal nodes |
|
| 136 |
-##' @param group_name name of the group, 'group' by default |
|
| 137 |
-##' @param ... additional parameter |
|
| 138 |
-##' @return group index |
|
| 139 |
-##' @export |
|
| 140 |
-setGeneric("groupClade", function(object, node, group_name="group", ...) standardGeneric("groupClade"))
|
|
| 141 |
- |
|
| 142 |
- |
|
| 143 |
-##' @docType methods |
|
| 144 |
-##' @name scale_color |
|
| 145 |
-##' @rdname scale_color-methods |
|
| 146 |
-##' @title scale_color method |
|
| 147 |
-##' @param object supported objects, including phylo, paml_rst, |
|
| 148 |
-##' codeml_mlc, codeml, jplace, beast, hyphy |
|
| 149 |
-##' @param by one of numerical attributes |
|
| 150 |
-##' @param ... additional parameter |
|
| 151 |
-##' @return color vector |
|
| 152 |
-##' @export |
|
| 153 |
-setGeneric("scale_color", function(object, by, ...) standardGeneric("scale_color"))
|
|
| 36 |
+## ##' @docType methods |
|
| 37 |
+## ##' @name get.tree |
|
| 38 |
+## ##' @rdname get.tree-methods |
|
| 39 |
+## ##' @title get.tree method |
|
| 40 |
+## ##' @param object one of \code{phylo}, \code{jplace}, \code{nhx}, \code{phangorn}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object
|
|
| 41 |
+## ##' @param ... additional parameter |
|
| 42 |
+## ##' @return phylo object |
|
| 43 |
+## ##' @export |
|
| 44 |
+## setGeneric("get.tree", function(object, ...) standardGeneric("get.tree"))
|
|
| 45 |
+ |
|
| 46 |
+## ##' @docType methods |
|
| 47 |
+## ##' @name get.treetext |
|
| 48 |
+## ##' @rdname get.treetext-methods |
|
| 49 |
+## ##' @title get.treetext method |
|
| 50 |
+## ##' @param object one of \code{phylo}, \code{jplace}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object
|
|
| 51 |
+## ##' @param ... additional parameter |
|
| 52 |
+## ##' @return phylo object |
|
| 53 |
+## ##' @export |
|
| 54 |
+## setGeneric("get.treetext", function(object, ...) standardGeneric("get.treetext"))
|
|
| 55 |
+ |
|
| 56 |
+ |
|
| 57 |
+## ##' @docType methods |
|
| 58 |
+## ##' @name get.treeinfo |
|
| 59 |
+## ##' @rdname get.treeinfo-methods |
|
| 60 |
+## ##' @title get.treeinfo method |
|
| 61 |
+## ##' @param object jplace object |
|
| 62 |
+## ##' @param layout layout |
|
| 63 |
+## ##' @param ladderize ladderize, logical |
|
| 64 |
+## ##' @param right logical, parameter for ladderize |
|
| 65 |
+## ##' @param ... additional parameter |
|
| 66 |
+## ##' @return data.frame |
|
| 67 |
+## ##' @export |
|
| 68 |
+## setGeneric("get.treeinfo", function(object, layout="phylogram", ladderize=TRUE, right=FALSE, ...) standardGeneric("get.treeinfo"))
|
|
| 69 |
+ |
|
| 70 |
+ |
|
| 71 |
+## ##' @docType methods |
|
| 72 |
+## ##' @name get.fields |
|
| 73 |
+## ##' @rdname get.fields-methods |
|
| 74 |
+## ##' @title get.fields method |
|
| 75 |
+## ##' @param object one of \code{jplace}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object
|
|
| 76 |
+## ##' @param ... additional parameter |
|
| 77 |
+## ##' @return available annotation variables |
|
| 78 |
+## ##' @export |
|
| 79 |
+## setGeneric("get.fields", function(object, ...) standardGeneric("get.fields"))
|
|
| 80 |
+ |
|
| 81 |
+ |
|
| 82 |
+## ##' @docType methods |
|
| 83 |
+## ##' @name get.placements |
|
| 84 |
+## ##' @rdname get.placements-methods |
|
| 85 |
+## ##' @title get.placements method |
|
| 86 |
+## ##' @param object jplace object |
|
| 87 |
+## ##' @param by get best hit or others |
|
| 88 |
+## ##' @param ... additional parameter |
|
| 89 |
+## ##' @return data.frame |
|
| 90 |
+## ##' @export |
|
| 91 |
+## setGeneric("get.placements", function(object, by, ...) standardGeneric("get.placements"))
|
|
| 92 |
+ |
|
| 93 |
+## ##' @docType methods |
|
| 94 |
+## ##' @name get.subs |
|
| 95 |
+## ##' @rdname get.subs-methods |
|
| 96 |
+## ##' @title get.subs method |
|
| 97 |
+## ##' @param object paml_rst object |
|
| 98 |
+## ##' @param type one of 'marginal_subs', 'marginal_AA_subs', |
|
| 99 |
+## ##' 'joint_subs' or 'joint_AA_subs'. |
|
| 100 |
+## ##' @param ... additional parameter |
|
| 101 |
+## ##' @return data.frame |
|
| 102 |
+## ##' @export |
|
| 103 |
+## setGeneric("get.subs", function(object, type, ...) standardGeneric("get.subs"))
|
|
| 104 |
+ |
|
| 105 |
+ |
|
| 106 |
+## ##' @docType methods |
|
| 107 |
+## ##' @name get.tipseq |
|
| 108 |
+## ##' @rdname get.tipseq-methods |
|
| 109 |
+## ##' @title get.tipseq method |
|
| 110 |
+## ##' @param object one of paml_rst or codeml object |
|
| 111 |
+## ##' @param ... additional parameter |
|
| 112 |
+## ##' @return character |
|
| 113 |
+## ##' @export |
|
| 114 |
+## setGeneric("get.tipseq", function(object, ...) standardGeneric("get.tipseq"))
|
|
| 115 |
+ |
|
| 116 |
+## ##' @docType methods |
|
| 117 |
+## ##' @name groupOTU |
|
| 118 |
+## ##' @rdname groupOTU-methods |
|
| 119 |
+## ##' @title groupOTU method |
|
| 120 |
+## ##' @param object supported objects, including phylo, paml_rst, |
|
| 121 |
+## ##' codeml_mlc, codeml, jplace, beast, hyphy |
|
| 122 |
+## ##' @param focus a vector of tip (label or number) or a list of tips. |
|
| 123 |
+## ##' @param group_name name of the group, 'group' by default |
|
| 124 |
+## ##' @param ... additional parameter |
|
| 125 |
+## ##' @return group index |
|
| 126 |
+## ##' @export |
|
| 127 |
+## setGeneric("groupOTU", function(object, focus, group_name="group", ...) standardGeneric("groupOTU"))
|
|
| 128 |
+ |
|
| 129 |
+## ##' @docType methods |
|
| 130 |
+## ##' @name groupClade |
|
| 131 |
+## ##' @rdname groupClade-methods |
|
| 132 |
+## ##' @title groupClade method |
|
| 133 |
+## ##' @param object supported objects, including phylo, paml_rst, |
|
| 134 |
+## ##' codeml_mlc, codeml, jplace, beast, hyphy |
|
| 135 |
+## ##' @param node a internal node or a vector of internal nodes |
|
| 136 |
+## ##' @param group_name name of the group, 'group' by default |
|
| 137 |
+## ##' @param ... additional parameter |
|
| 138 |
+## ##' @return group index |
|
| 139 |
+## ##' @export |
|
| 140 |
+## setGeneric("groupClade", function(object, node, group_name="group", ...) standardGeneric("groupClade"))
|
|
| 141 |
+ |
|
| 142 |
+ |
|
| 143 |
+## ##' @docType methods |
|
| 144 |
+## ##' @name scale_color |
|
| 145 |
+## ##' @rdname scale_color-methods |
|
| 146 |
+## ##' @title scale_color method |
|
| 147 |
+## ##' @param object supported objects, including phylo, paml_rst, |
|
| 148 |
+## ##' codeml_mlc, codeml, jplace, beast, hyphy |
|
| 149 |
+## ##' @param by one of numerical attributes |
|
| 150 |
+## ##' @param ... additional parameter |
|
| 151 |
+## ##' @return color vector |
|
| 152 |
+## ##' @export |
|
| 153 |
+## setGeneric("scale_color", function(object, by, ...) standardGeneric("scale_color"))
|
|
| 154 | 154 |
|
| 155 | 155 |
##' @docType methods |
| 156 | 156 |
##' @name gzoom |
| ... | ... |
@@ -166,17 +166,17 @@ setGeneric("scale_color", function(object, by, ...) standardGeneric("scale_color
|
| 166 | 166 |
setGeneric("gzoom", function(object, focus, subtree=FALSE, widths=c(.3, .7), ...) standardGeneric("gzoom"))
|
| 167 | 167 |
|
| 168 | 168 |
|
| 169 |
-##' @docType methods |
|
| 170 |
-##' @name drop.tip |
|
| 171 |
-##' @rdname drop.tip-methods |
|
| 172 |
-##' @title drop.tip method |
|
| 173 |
-##' @param object An nhx or phylo object |
|
| 174 |
-##' @param tip a vector of mode numeric or character specifying the tips to delete |
|
| 175 |
-##' @param ... additional parameters |
|
| 176 |
-##' @return updated object |
|
| 177 |
-##' @export |
|
| 178 |
-setGeneric ( |
|
| 179 |
- name = "drop.tip", |
|
| 180 |
- def = function( object, tip, ... ) |
|
| 181 |
- { standardGeneric("drop.tip") }
|
|
| 182 |
-) |
|
| 169 |
+## ##' @docType methods |
|
| 170 |
+## ##' @name drop.tip |
|
| 171 |
+## ##' @rdname drop.tip-methods |
|
| 172 |
+## ##' @title drop.tip method |
|
| 173 |
+## ##' @param object An nhx or phylo object |
|
| 174 |
+## ##' @param tip a vector of mode numeric or character specifying the tips to delete |
|
| 175 |
+## ##' @param ... additional parameters |
|
| 176 |
+## ##' @return updated object |
|
| 177 |
+## ##' @export |
|
| 178 |
+## setGeneric ( |
|
| 179 |
+## name = "drop.tip", |
|
| 180 |
+## def = function( object, tip, ... ) |
|
| 181 |
+## { standardGeneric("drop.tip") }
|
|
| 182 |
+## ) |
| ... | ... |
@@ -1,95 +1,95 @@ |
| 1 |
-##' parse RAxML bootstrapping analysis output |
|
| 2 |
-##' |
|
| 3 |
-##' |
|
| 4 |
-##' @title read.raxml |
|
| 5 |
-##' @param file RAxML bootstrapping analysis output |
|
| 6 |
-##' @return raxml object |
|
| 7 |
-##' @export |
|
| 8 |
-##' @author Guangchuang Yu |
|
| 9 |
-read.raxml <- function(file) {
|
|
| 10 |
- tree.text <- readLines(file) |
|
| 11 |
- tree_text <- gsub('(:[0-9\\.eE+\\-]+)\\[(\\d+)\\]', '\\@\\2\\1', tree.text)
|
|
| 12 |
- phylo <- read.tree(text=tree_text) |
|
| 13 |
- if(any(grepl('@', phylo$node.label))) {
|
|
| 14 |
- bootstrap <- as.numeric(gsub("[^@]*@(\\d+)", "\\1", phylo$node.label))
|
|
| 15 |
- phylo$node.label <- gsub("@\\d+", "", phylo$node.label)
|
|
| 16 |
- } |
|
| 1 |
+## ##' parse RAxML bootstrapping analysis output |
|
| 2 |
+## ##' |
|
| 3 |
+## ##' |
|
| 4 |
+## ##' @title read.raxml |
|
| 5 |
+## ##' @param file RAxML bootstrapping analysis output |
|
| 6 |
+## ##' @return raxml object |
|
| 7 |
+## ##' @export |
|
| 8 |
+## ##' @author Guangchuang Yu |
|
| 9 |
+## read.raxml <- function(file) {
|
|
| 10 |
+## tree.text <- readLines(file) |
|
| 11 |
+## tree_text <- gsub('(:[0-9\\.eE+\\-]+)\\[(\\d+)\\]', '\\@\\2\\1', tree.text)
|
|
| 12 |
+## phylo <- read.tree(text=tree_text) |
|
| 13 |
+## if(any(grepl('@', phylo$node.label))) {
|
|
| 14 |
+## bootstrap <- as.numeric(gsub("[^@]*@(\\d+)", "\\1", phylo$node.label))
|
|
| 15 |
+## phylo$node.label <- gsub("@\\d+", "", phylo$node.label)
|
|
| 16 |
+## } |
|
| 17 | 17 |
|
| 18 |
- if (all(phylo$node.label == "")) {
|
|
| 19 |
- phylo$node.label <- NULL |
|
| 20 |
- } |
|
| 18 |
+## if (all(phylo$node.label == "")) {
|
|
| 19 |
+## phylo$node.label <- NULL |
|
| 20 |
+## } |
|
| 21 | 21 |
|
| 22 |
- bootstrap <- data.frame(node = Ntip(phylo) + 1:phylo$Nnode, |
|
| 23 |
- bootstrap = bootstrap) |
|
| 22 |
+## bootstrap <- data.frame(node = Ntip(phylo) + 1:phylo$Nnode, |
|
| 23 |
+## bootstrap = bootstrap) |
|
| 24 | 24 |
|
| 25 |
- new("raxml",
|
|
| 26 |
- file = file, |
|
| 27 |
- fields = "bootstrap", |
|
| 28 |
- treetext = tree.text, |
|
| 29 |
- phylo = phylo, |
|
| 30 |
- bootstrap = bootstrap |
|
| 31 |
- ) |
|
| 32 |
-} |
|
| 25 |
+## new("raxml",
|
|
| 26 |
+## file = file, |
|
| 27 |
+## fields = "bootstrap", |
|
| 28 |
+## treetext = tree.text, |
|
| 29 |
+## phylo = phylo, |
|
| 30 |
+## bootstrap = bootstrap |
|
| 31 |
+## ) |
|
| 32 |
+## } |
|
| 33 | 33 |
|
| 34 | 34 |
|
| 35 |
-##' @rdname show-methods |
|
| 36 |
-##' @importFrom ape print.phylo |
|
| 37 |
-##' @exportMethod show |
|
| 38 |
-setMethod("show", signature(object = "raxml"),
|
|
| 39 |
- function(object) {
|
|
| 40 |
- cat("'raxml' S4 object that stored information of\n\t",
|
|
| 41 |
- paste0("'", object@file, "'.\n\n"))
|
|
| 42 |
- cat("...@ tree: ")
|
|
| 43 |
- print.phylo(get.tree(object)) |
|
| 44 |
- cat("\nwith the following features available:\n")
|
|
| 45 |
- print_fields(object) |
|
| 46 |
- }) |
|
| 35 |
+## ##' @rdname show-methods |
|
| 36 |
+## ##' @importFrom ape print.phylo |
|
| 37 |
+## ##' @exportMethod show |
|
| 38 |
+## setMethod("show", signature(object = "raxml"),
|
|
| 39 |
+## function(object) {
|
|
| 40 |
+## cat("'raxml' S4 object that stored information of\n\t",
|
|
| 41 |
+## paste0("'", object@file, "'.\n\n"))
|
|
| 42 |
+## cat("...@ tree: ")
|
|
| 43 |
+## print.phylo(get.tree(object)) |
|
| 44 |
+## cat("\nwith the following features available:\n")
|
|
| 45 |
+## print_fields(object) |
|
| 46 |
+## }) |
|
| 47 | 47 |
|
| 48 |
-##' @rdname groupOTU-methods |
|
| 49 |
-##' @exportMethod groupOTU |
|
| 50 |
-setMethod("groupOTU", signature(object="raxml"),
|
|
| 51 |
- function(object, focus, group_name="group") {
|
|
| 52 |
- groupOTU_(object, focus, group_name) |
|
| 53 |
- } |
|
| 54 |
- ) |
|
| 48 |
+## ##' @rdname groupOTU-methods |
|
| 49 |
+## ##' @exportMethod groupOTU |
|
| 50 |
+## setMethod("groupOTU", signature(object="raxml"),
|
|
| 51 |
+## function(object, focus, group_name="group") {
|
|
| 52 |
+## groupOTU_(object, focus, group_name) |
|
| 53 |
+## } |
|
| 54 |
+## ) |
|
| 55 | 55 |
|
| 56 |
-##' @rdname groupClade-methods |
|
| 57 |
-##' @exportMethod groupClade |
|
| 58 |
-setMethod("groupClade", signature(object="raxml"),
|
|
| 59 |
- function(object, node, group_name="group") {
|
|
| 60 |
- groupClade_(object, node, group_name) |
|
| 61 |
- }) |
|
| 56 |
+## ##' @rdname groupClade-methods |
|
| 57 |
+## ##' @exportMethod groupClade |
|
| 58 |
+## setMethod("groupClade", signature(object="raxml"),
|
|
| 59 |
+## function(object, node, group_name="group") {
|
|
| 60 |
+## groupClade_(object, node, group_name) |
|
| 61 |
+## }) |
|
| 62 | 62 |
|
| 63 |
-##' @rdname scale_color-methods |
|
| 64 |
-##' @exportMethod scale_color |
|
| 65 |
-setMethod("scale_color", signature(object="raxml"),
|
|
| 66 |
- function(object, by="bootstrap", ...) {
|
|
| 67 |
- scale_color_(object, by, ...) |
|
| 68 |
- }) |
|
| 63 |
+## ##' @rdname scale_color-methods |
|
| 64 |
+## ##' @exportMethod scale_color |
|
| 65 |
+## setMethod("scale_color", signature(object="raxml"),
|
|
| 66 |
+## function(object, by="bootstrap", ...) {
|
|
| 67 |
+## scale_color_(object, by, ...) |
|
| 68 |
+## }) |
|
| 69 | 69 |
|
| 70 | 70 |
|
| 71 |
-##' @rdname gzoom-methods |
|
| 72 |
-##' @exportMethod gzoom |
|
| 73 |
-setMethod("gzoom", signature(object="raxml"),
|
|
| 74 |
- function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
|
|
| 75 |
- gzoom.phylo(get.tree(object), focus, subtree, widths) |
|
| 76 |
- }) |
|
| 71 |
+## ##' @rdname gzoom-methods |
|
| 72 |
+## ##' @exportMethod gzoom |
|
| 73 |
+## setMethod("gzoom", signature(object="raxml"),
|
|
| 74 |
+## function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
|
|
| 75 |
+## gzoom.phylo(get.tree(object), focus, subtree, widths) |
|
| 76 |
+## }) |
|
| 77 | 77 |
|
| 78 | 78 |
|
| 79 |
-##' @rdname get.tree-methods |
|
| 80 |
-##' @exportMethod get.tree |
|
| 81 |
-setMethod("get.tree", signature(object="raxml"),
|
|
| 82 |
- function(object,...) {
|
|
| 83 |
- object@phylo |
|
| 84 |
- } |
|
| 85 |
- ) |
|
| 79 |
+## ##' @rdname get.tree-methods |
|
| 80 |
+## ##' @exportMethod get.tree |
|
| 81 |
+## setMethod("get.tree", signature(object="raxml"),
|
|
| 82 |
+## function(object,...) {
|
|
| 83 |
+## object@phylo |
|
| 84 |
+## } |
|
| 85 |
+## ) |
|
| 86 | 86 |
|
| 87 | 87 |
|
| 88 |
-##' @rdname get.fields-methods |
|
| 89 |
-##' @exportMethod get.fields |
|
| 90 |
-setMethod("get.fields", signature(object="raxml"),
|
|
| 91 |
- function(object, ...) {
|
|
| 92 |
- get.fields.tree(object) |
|
| 93 |
- } |
|
| 94 |
- ) |
|
| 88 |
+## ##' @rdname get.fields-methods |
|
| 89 |
+## ##' @exportMethod get.fields |
|
| 90 |
+## setMethod("get.fields", signature(object="raxml"),
|
|
| 91 |
+## function(object, ...) {
|
|
| 92 |
+## get.fields.tree(object) |
|
| 93 |
+## } |
|
| 94 |
+## ) |
|
| 95 | 95 |
|
| ... | ... |
@@ -1,29 +1,29 @@ |
| 1 | 1 |
|
| 2 |
-##' @export |
|
| 3 |
-ape::read.tree |
|
| 2 |
+## ##' @export |
|
| 3 |
+## ape::read.tree |
|
| 4 | 4 |
|
| 5 | 5 |
|
| 6 |
-##' generate random tree |
|
| 7 |
-##' @export |
|
| 8 |
-##' @rdname rtree |
|
| 9 |
-##' @param n number of tips in the tree |
|
| 10 |
-##' @param rooted logcial |
|
| 11 |
-##' @param tip.label tip label |
|
| 12 |
-##' @param br one of the following: (i) an R function used to generate the |
|
| 13 |
-##' branch lengths ('rtree'; use 'NULL' to simulate only a
|
|
| 14 |
-##' topology), or the coalescence times ('rcoal'); (ii) a
|
|
| 15 |
-##' character to simulate a genuine coalescent tree for 'rcoal' |
|
| 16 |
-##' (the default); or (iii) a numeric vector for the branch |
|
| 17 |
-##' lengths or the coalescence times. |
|
| 18 |
-##' @param ... additional parameters to be passed to 'br' |
|
| 19 |
-##' @source |
|
| 20 |
-##' This is just the imported function |
|
| 21 |
-##' from the ape package. The documentation you should |
|
| 22 |
-##' read for the rtree function can be found here: \link[ape]{rtree}
|
|
| 23 |
-##' |
|
| 24 |
-##' @seealso |
|
| 25 |
-##' \link[ape]{rtree}
|
|
| 26 |
-rtree <- ape::rtree |
|
| 6 |
+## ##' generate random tree |
|