[med-svn] [r-bioc-phyloseq] branch upstream updated (2cdbfe7 -> 47aabbd)
Andreas Tille
tille at debian.org
Sat Nov 11 07:43:03 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository r-bioc-phyloseq.
from 2cdbfe7 New upstream version 1.20.0
new 47aabbd New upstream version 1.22.3
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.travis.yml | 15 +++
DESCRIPTION | 28 ++---
NAMESPACE | 2 +
R/distance-methods.R | 7 +-
R/phylo-class.R | 9 --
R/plot-methods.R | 28 ++---
build/vignette.rds | Bin 347 -> 349 bytes
inst/doc/phyloseq-FAQ.R | 8 +-
inst/doc/phyloseq-FAQ.html | 147 ++++++++++++++++++----
inst/doc/phyloseq-analysis.R | 74 +++++------
inst/doc/phyloseq-analysis.html | 230 ++++++++++++++++++++++++----------
inst/doc/phyloseq-basics.R | 50 ++++----
inst/doc/phyloseq-basics.html | 127 ++++++++++++++++---
inst/doc/phyloseq-mixture-models.R | 24 ++--
inst/doc/phyloseq-mixture-models.html | 137 ++++++++++++++++----
man/DPCoA.Rd | 35 +++---
man/JSD.Rd | 9 +-
man/UniFrac-methods.Rd | 1 -
man/access.Rd | 1 -
man/assign-otu_table.Rd | 5 +-
man/assign-phy_tree.Rd | 3 +-
man/assign-sample_data.Rd | 3 +-
man/assign-sample_names.Rd | 5 +-
man/assign-tax_table.Rd | 7 +-
man/assign-taxa_are_rows.Rd | 3 +-
man/assign-taxa_names.Rd | 7 +-
man/build_tax_table.Rd | 1 -
man/capscale-phyloseq-methods.Rd | 3 +-
man/cca-rda-phyloseq-methods.Rd | 5 +-
man/chunkReOrder.Rd | 1 -
man/data-GlobalPatterns.Rd | 9 +-
man/data-enterotype.Rd | 7 +-
man/data-esophagus.Rd | 7 +-
man/data-soilrep.Rd | 7 +-
man/decorana.Rd | 1 -
man/dist-class.Rd | 1 -
man/distance.Rd | 3 +-
man/distanceMethodList.Rd | 1 -
man/envHash2otu_table.Rd | 1 -
man/estimate_richness.Rd | 1 -
man/export_env_file.Rd | 1 -
man/export_mothur_dist.Rd | 1 -
man/extract-methods.Rd | 3 +-
man/filter_taxa.Rd | 1 -
man/filterfun_sample.Rd | 1 -
man/fix_phylo.Rd | 1 -
man/gapstat_ord.Rd | 1 -
man/genefilter_sample-methods.Rd | 1 -
man/get.component.classes.Rd | 1 -
man/get_sample-methods.Rd | 1 -
man/get_taxa-methods.Rd | 1 -
man/get_taxa_unique.Rd | 1 -
man/get_variable.Rd | 1 -
man/getslots.phyloseq.Rd | 1 -
man/import.Rd | 1 -
man/import_RDP_cluster.Rd | 1 -
man/import_RDP_otu.Rd | 1 -
man/import_biom.Rd | 1 -
man/import_env_file.Rd | 1 -
man/import_mothur.Rd | 1 -
man/import_mothur_constaxonomy.Rd | 1 -
man/import_mothur_dist.Rd | 1 -
man/import_mothur_groups.Rd | 1 -
man/import_mothur_otu_table.Rd | 1 -
man/import_mothur_otulist.Rd | 1 -
man/import_mothur_shared.Rd | 1 -
man/import_pyrotagger_tab.Rd | 1 -
man/import_qiime.Rd | 1 -
man/import_qiime_otu_tax.Rd | 1 -
man/import_qiime_sample_data.Rd | 1 -
man/import_uparse.Rd | 1 -
man/import_usearch_uc.Rd | 1 -
man/index_reorder.Rd | 1 -
man/intersect_taxa.Rd | 1 -
man/make_network.Rd | 1 -
man/merge_phyloseq.Rd | 1 -
man/merge_phyloseq_pair-methods.Rd | 7 +-
man/merge_samples-methods.Rd | 3 +-
man/merge_taxa-methods.Rd | 7 +-
man/metaMDS.Rd | 1 -
man/microbio_me_qiime.Rd | 1 -
man/mt-methods.Rd | 9 +-
man/nodeplotblank.Rd | 1 -
man/nodeplotboot.Rd | 1 -
man/nodeplotdefault.Rd | 1 -
man/nsamples-methods.Rd | 3 +-
man/ntaxa-methods.Rd | 7 +-
man/ordinate.Rd | 1 -
man/otu_table-class.Rd | 1 -
man/otu_table-methods.Rd | 9 +-
man/parseTaxonomy-functions.Rd | 3 +-
man/pcoa.Rd | 1 -
man/phy_tree-methods.Rd | 1 -
man/phylo-class.Rd | 1 -
man/phylo.Rd | 1 -
man/phyloseq-class.Rd | 1 -
man/phyloseq-deprecated.Rd | 59 +++++----
man/phyloseq-package.Rd | 7 +-
man/phyloseq.Rd | 1 -
man/phyloseq_to_deseq2.Rd | 1 -
man/phyloseq_to_metagenomeSeq.Rd | 1 -
man/plot_bar.Rd | 1 -
man/plot_clusgap.Rd | 1 -
man/plot_heatmap.Rd | 1 -
man/plot_net.Rd | 1 -
man/plot_network.Rd | 1 -
man/plot_ordination.Rd | 1 -
man/plot_phyloseq-methods.Rd | 1 -
man/plot_richness.Rd | 1 -
man/plot_scree.Rd | 1 -
man/plot_tree.Rd | 1 -
man/prune_samples-methods.Rd | 3 +-
man/prune_taxa-methods.Rd | 9 +-
man/psmelt.Rd | 1 -
man/rank_names.Rd | 1 -
man/rarefy_even_depth.Rd | 1 -
man/read_tree.Rd | 1 -
man/read_tree_greengenes.Rd | 1 -
man/reconcile_categories.Rd | 1 -
man/refseq-methods.Rd | 1 -
man/rm_outlierf.Rd | 1 -
man/sample_data-class.Rd | 1 -
man/sample_data-methods.Rd | 1 -
man/sample_names-methods.Rd | 3 +-
man/sample_sums.Rd | 1 -
man/sample_variables.Rd | 1 -
man/show-methods.Rd | 3 +-
man/show_mothur_cutoffs.Rd | 1 -
man/splat.phyloseq.objects.Rd | 1 -
man/subset_ord_plot.Rd | 1 -
man/subset_samples-methods.Rd | 1 -
man/subset_taxa-methods.Rd | 1 -
man/tax_glom.Rd | 1 -
man/tax_table-methods.Rd | 3 +-
man/taxa_are_rows-methods.Rd | 1 -
man/taxa_names-methods.Rd | 9 +-
man/taxa_sums.Rd | 1 -
man/taxonomyTable-class.Rd | 1 -
man/threshrank.Rd | 1 -
man/threshrankfun.Rd | 1 -
man/tip_glom.Rd | 1 -
man/topf.Rd | 1 -
man/topk.Rd | 1 -
man/topp.Rd | 1 -
man/transformcounts.Rd | 4 +-
man/transpose-methods.Rd | 1 -
man/tree_layout.Rd | 1 -
tests/testthat/test-IO.R | 5 +-
148 files changed, 753 insertions(+), 505 deletions(-)
create mode 100644 .travis.yml
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-phyloseq.git
More information about the debian-med-commit
mailing list