RAM

Package: RAM
Type: Package
Title: R for Amplicon-Sequencing-Based Microbial-Ecology
Version: 1.2.1.3
Date: 2016-01-02
Author: Wen Chen, Joshua Simpson, C. Andre Levesque
Maintainer: Wen Chen <Wen.Chen@agr.gc.ca>
Description: Characterizing environmental microbiota diversity using amplicon-based next generation sequencing (NGS) data. Functions are developed to manipulate operational taxonomic unit (OTU) table, perform descriptive and inferential statistics, and generate publication-quality plots.
License: MIT + file LICENSE
Copyright: Government of Canada
Depends: vegan, ggplot2, stats
Imports: RColorBrewer, gplots, plyr, reshape2, scales, labdsv, grid,
gridExtra, ggmap, permute, VennDiagram, data.table, FD, MASS,
RgoogleMaps, lattice, reshape, ade4, phangorn, phytools, utils,
graphics, grDevices, ape
Suggests: testthat, mapproj, gtable, indicspecies, Heatplus
Repository: CRAN
URL: http://cran.r-project.org/package=RAM
https://bitbucket.org/Wen_Chen/ram_releases/src/
BugReports: https://bitbucket.org/Wen_Chen/ram_releases/issues/
NeedsCompilation: no
Packaged: 2016-01-02 08:49:12 UTC; chenw
Date/Publication: 2016-01-02 16:06:23

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'RAM' ...
** package 'RAM' successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
Warning in readLines(tmpcon) : incomplete final line found on ''
*** installing help indices
  converting help for package 'RAM'
    finding HTML links ... done
    ITS1_and_ITS2                           html  
    LCA.OTU                                 html  
    META.clust                              html  
    finding level-2 HTML links ... done

    OTU.diversity                           html  
    OTU.ord                                 html  
Rd warning: /tmp/RtmpNSEz0I/R.INSTALL69cb7e6420eb/RAM/man/OTU.ord.Rd:12: missing file link 'rda'
    OTU.rarefy                              html  
    OTU.recap                               html  
    OTU.subsets                             html  
    RAM-package                             html  
    RAM.dates                               html  
    RAM.factors                             html  
    RAM.input.formatting                    html  
    RAM.pal                                 html  
    RAM.plotting                            html  
    RAM.rank.formatting                     html  
    Taxa.ord                                html  
    alignment                               html  
    assist.NB                               html  
    assist.ado                              html  
    assist.ordination                       html  
    col.splitup                             html  
    combine.OTU                             html  
    core.OTU                                html  
    core.OTU.rank                           html  
    core.Taxa                               html  
    correlation                             html  
    data.clust                              html  
    data.revamp                             html  
    dissim                                  html  
    dissim.heatmap                          html  
    dissim.plot                             html  
    diversity.indices                       html  
    envis.NB                                html  
    factor.abundance                        html  
    filter.META                             html  
    filter.OTU                              html  
    filter.Taxa                             html  
    fread.OTU                               html  
    fread.meta                              html  
    get.rank                                html  
    group.OTU                               html  
    group.Taxa.bar                          html  
    group.Taxa.box                          html  
    group.abund.Taxa                        html  
    group.abundance                         html  
    group.abundance.meta                    html  
    group.diversity                         html  
    group.heatmap                           html  
    group.heatmap.simple                    html  
    group.indicators                        html  
    group.rich                              html  
    group.spatial                           html  
    group.spec                              html  
    group.temporal                          html  
    group.venn                              html  
    location.formatting                     html  
    match.data                              html  
    meta                                    html  
    network_data                            html  
    pcoa.plot                               html  
    percent.classified                      html  
    phylo_taxonomy                          html  
    phylog_taxonomy                         html  
    read.OTU                                html  
    read.meta                               html  
    reset.META                              html  
    sample.locations                        html  
    sample.map                              html  
    sample.sites                            html  
    seq_var                                 html  
    shared.OTU                              html  
    shared.Taxa                             html  
    tax.abund                               html  
    tax.fill                                html  
    tax.split                               html  
    theme_ggplot                            html  
    top.groups.plot                         html  
    transpose.LCA                           html  
    transpose.OTU                           html  
    valid.OTU                               html  
    valid.taxonomy                          html  
    write.data                              html  
** building package indices
** testing if installed package can be loaded
* DONE (RAM)
Making 'packages.html' ... done