dendextend

Package: dendextend
Type: Package
Title: Extending R's Dendrogram Functionality
Version: 1.2.0
Date: 2016-06-21
Authors@R: c(person("Tal", "Galili", role = c("aut", "cre", "cph"), email =
"tal.galili@gmail.com", comment = "http://www.r-statistics.com"),
person("Gavin", "Simpson", role = "ctb"), person("Gregory","Jefferis", role
= c("aut", "ctb"), email = "jefferis@gmail.com",
comment ="imported code from his dendroextras package"),
person("Marco", "Gallotta", role = "ctb", comment =
"a.k.a: marcog") , person("Johan", "Renaudie", role = "ctb", comment =
"https://github.com/plannapus"), person("The R Core Team", role = "ctb",
comment = "Thanks for the Infastructure, and code in the examples"),
person("Kurt", "Hornik", role = "ctb"), person("Uwe", "Ligges",
role = "ctb"), person("Andrej-Nikolai", "Spiess", role = "ctb"),
person("Steve", "Horvath",email = "SHorvath@mednet.ucla.edu", role =
"ctb"), person("Peter", "Langfelder",email = "Peter.Langfelder@gmail.com",
role = "ctb"), person("skullkey", role = "ctb"), person("Mark",
"Van Der Loo", email = "mark.vanderloo@gmail.com", comment =
"https://github.com/markvanderloo d3dendrogram", role = "ctb"),
person("Andrie",
"de Vries", email = "apdevries@gmail.com", comment =
"ggdendro author", role = "ctb"),
person("Zuguang",
"Gu", email = "z.gu@dkfz-heidelberg.de", comment =
"circlize author", role = "ctb"),
person("Yoav", "Benjamini", role = "ths"))
Description: Offers a set of functions for extending
dendrogram objects in R, letting you visualize and compare trees of
hierarchical clusterings. You can (1) Adjust a tree's graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different dendrograms to one another.
Depends: R (>= 3.0.0)
Imports: utils, stats, magrittr (>= 1.0.1), ggplot2, fpc, whisker
Suggests: dendextendRcpp (>= 0.5.0), knitr, rmarkdown, testthat,
seriation, colorspace, plyr, ape, profdpm, microbenchmark,
gplots, NMF, heatmaply, d3heatmap, dynamicTreeCut, pvclust,
corrplot, DendSer, MASS, cluster, circlize (>= 0.2.5), covr
Enhances: ggdendro, labeltodendro,dendroextras, data.table, rpart
VignetteBuilder: knitr
LazyData: true
License: GPL-2 | GPL-3
URL: https://cran.r-project.org/package=dendextend,
https://github.com/talgalili/dendextend/,
http://www.r-statistics.com/tag/dendextend/,
https://bioinformatics.oxfordjournals.org/content/31/22/3718
BugReports: https://github.com/talgalili/dendextend/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-22 04:21:48 UTC; junior
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Gavin Simpson [ctb],
Gregory Jefferis [aut, ctb] (imported code from his dendroextras
package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
The R Core Team [ctb] (Thanks for the Infastructure, and code in the
examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),
Andrie de Vries [ctb] (ggdendro author),
Zuguang Gu [ctb] (circlize author),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-22 10:15:48

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'dendextend' ...
** package 'dendextend' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'dendextend'
    finding HTML links ... done
    Bk                                      html  
    Bk_permutations                         html  
    Bk_plot                                 html  
    DendSer.dendrogram                      html  
    FM_index                                html  
    FM_index_R                              html  
    FM_index_permutation                    html  
    FM_index_profdpm                        html  
    all.equal.dendrogram                    html  
    all_couple_rotations_at_k               html  
    all_unique                              html  
    as.dendlist                             html  
    as.phylo.dendrogram                     html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/as.phylo.dendrogram.Rd:18: missing file link 'as.phylo.hclust'
    as_hclust_fixed                         html  
    assign_dendextend_options               html  
    assign_values_to_branches_edgePar       html  
    assign_values_to_leaves_edgePar         html  
    assign_values_to_leaves_nodePar         html  
    assign_values_to_nodes_nodePar          html  
    bakers_gamma_for_2_k_matrix             html  
    branches_attr_by_clusters               html  
    branches_attr_by_labels                 html  
    circlize_dendrogram                     html  
    click_rotate                            html  
    collapse_branch                         html  
    color_branches                          html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/color_branches.Rd:58: missing file link 'cutree'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/color_branches.Rd:26: missing file link 'cutree'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/color_branches.Rd:28: missing file link 'cutree'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/color_branches.Rd:9: missing file link 'color_clusters'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/color_branches.Rd:13: missing file link 'cutree.dendrogram'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/color_branches.Rd:193: missing file link 'cutree'
    color_labels                            html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/color_labels.Rd:44: missing file link 'cutree'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/color_labels.Rd:18: missing file link 'cutree'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/color_labels.Rd:20: missing file link 'cutree'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/color_labels.Rd:74: missing file link 'cutree'
    color_unique_labels                     html  
    colored_bars                            html  
    common_subtrees_clusters                html  
    cor.dendlist                            html  
    cor_FM_index                            html  
    cor_bakers_gamma                        html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/cor_bakers_gamma.Rd:21: missing file link 'cutree'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/cor_bakers_gamma.Rd:35: missing file link 'cutree'
    cor_common_nodes                        html  
    cor_cophenetic                          html  
    count_terminal_nodes                    html  
    cut_lower_fun                           html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/cut_lower_fun.Rd:31: missing file link 'cutree.dendrogram'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/cut_lower_fun.Rd:63: missing file link 'cutree.dendrogram'
    cutree-methods                          html  
    cutree_1h.dendrogram                    html  
    cutree_1k.dendrogram                    html  
    d3dendro_options                        html  
    d3dendrogram                            html  
    dend_diff                               html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/dend_diff.Rd:56: missing file link 'distinct.edges'
    dendextend-package                      html  
    dendextend_labels.dendrogram            html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/dendextend_labels.dendrogram.Rd:18: missing file link 'labels.dendrogram'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/dendextend_labels.dendrogram.Rd:28: missing file link 'labels.dendrogram'
    dendextend_options                      html  
    dendlist                                html  
    dist.dendlist                           html  
    dist_long                               html  
    distinct_edges                          html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/distinct_edges.Rd:7: missing file link 'distinct.edges'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/distinct_edges.Rd:38: missing file link 'distinct.edges'
    duplicate_leaf                          html  
    entanglement                            html  
    fac2num                                 html  
    find_k                                  html  
    fix_members_attr.dendrogram             html  
    flatten.dendrogram                      html  
    flip_leaves                             html  
    get_branches_heights                    html  
    get_childrens_heights                   html  
    get_leaves_attr                         html  
    get_leaves_branches_attr                html  
    get_leaves_branches_col                 html  
    get_leaves_edgePar                      html  
    get_leaves_nodePar                      html  
    get_nodes_attr                          html  
    get_nodes_xy                            html  
    get_root_branches_attr                  html  
    ggdend                                  html  
    hang.dendrogram                         html  
    heights_per_k.dendrogram                html  
    highlight_distinct_edges                html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/highlight_distinct_edges.Rd:77: missing file link 'distinct.edges'
    identify.dendrogram                     html  
    intersect_trees                         html  
    is.dendlist                             html  
    is.dendrogram                           html  
    is.dist                                 html  
    is.hclust                               html  
    is.natural.number                       html  
    is.phylo                                html  
    is_null_list                            html  
    khan                                    html  
    labels-assign                           html  
    labels_cex                              html  
    labels_colors                           html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/labels_colors.Rd:67: missing file link 'cutree'
    ladderize                               html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/ladderize.Rd:19: missing file link 'phylo'
    leaf_Colors                             html  
    lowest_common_branch                    html  
    match_order_by_labels                   html  
    match_order_dendrogram_by_old_order     html  
    na_locf                                 html  
    nleaves                                 html  
    nnodes                                  html  
    noded_with_condition                    html  
    order.dendrogram-assign                 html  
    order.hclust                            html  
    partition_leaves                        html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/partition_leaves.Rd:7: missing file link 'partition.leaves'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/partition_leaves.Rd:44: missing file link 'partition.leaves'
    plot_horiz.dendrogram                   html  
    prune                                   html  
    prune_common_subtrees.dendlist          html  
    prune_leaf                              html  
    pvclust_show_signif                     html  
    pvclust_show_signif_gradient            html  
    raise.dendrogram                        html  
    rank_branches                           html  
    rank_order.dendrogram                   html  
    rank_values_with_clusters               html  
    rect.dendrogram                         html  
    reexports                               html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/reexports.Rd:13: missing file link '%>%'
    remove_branches_edgePar                 html  
    remove_leaves_nodePar                   html  
    remove_nodes_nodePar                    html  
    rllply                                  html  
    rotate                                  html  
    rotate_DendSer                          html  
    sample.dendrogram                       html  
    seriate_dendrogram                      html  
    set                                     html  
    shuffle                                 html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/shuffle.Rd:39: missing file link 'phylo'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/shuffle.Rd:23: missing file link 'phylo'
    sort_2_clusters_vectors                 html  
    sort_dist_mat                           html  
    sort_levels_values                      html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/sort_levels_values.Rd:39: missing file link 'cutree'
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/sort_levels_values.Rd:68: missing file link 'cutree'
    tanglegram                              html  
    theme_dendro                            html  
    unbranch                                html  
Rd warning: /tmp/Rtmpya2WL0/R.INSTALL104f72961103/dendextend/man/unbranch.Rd:45: missing file link 'unroot'
    unclass_dend                            html  
    untangle                                html  
    untangle_DendSer                        html  
    untangle_random_search                  html  
    untangle_step_rotate_1side              html  
    untangle_step_rotate_2side              html  
    which_leaf                              html  
    which_node                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dendextend)
Making 'packages.html' ... done