[med-svn] [r-bioc-phyloseq] 10/11: Updated version 1.19.1 from 'upstream/1.19.1'
Andreas Tille
tille at debian.org
Fri Sep 22 20:52:53 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-phyloseq.
commit 551ae95f95b3bab4733a15a8b2dc207540121462
Merge: 41ef25b bab0860
Author: Andreas Tille <tille at debian.org>
Date: Fri Sep 22 22:47:52 2017 +0200
Updated version 1.19.1 from 'upstream/1.19.1'
with Debian dir f049912f1c02768739c959bd8db8c79bae41c0cd
DESCRIPTION | 41 +
NAMESPACE | 272 ++
R/IO-methods.R | 2431 +++++++++++++++
R/allClasses.R | 295 ++
R/allData.R | 213 ++
R/allPackage.R | 24 +
R/almostAllAccessors.R | 554 ++++
R/as-methods.R | 34 +
R/assignment-methods.R | 375 +++
R/deprecated_functions.R | 130 +
R/distance-methods.R | 690 +++++
R/extend_DESeq2.R | 72 +
R/extend_metagenomeSeq.R | 68 +
R/extend_vegan.R | 274 ++
R/extract-methods.R | 74 +
R/merge-methods.R | 600 ++++
R/multtest-wrapper.R | 173 ++
R/network-methods.R | 171 ++
R/ordination-methods.R | 642 ++++
R/otuTable-class.R | 145 +
R/phylo-class.R | 26 +
R/phyloseq-class.R | 400 +++
R/plot-methods.R | 2857 ++++++++++++++++++
R/sampleData-class.R | 149 +
R/show-methods.R | 82 +
R/taxonomyTable-class.R | 132 +
R/transform_filter-methods.R | 1187 ++++++++
R/validity-methods.R | 117 +
README.html | 102 +
README.md | 54 +
TODO.txt | 5 +
build/vignette.rds | Bin 0 -> 349 bytes
data/GlobalPatterns.RData | Bin 0 -> 435652 bytes
data/datalist | 4 +
data/enterotype.RData | Bin 0 -> 195260 bytes
data/esophagus.RData | Bin 0 -> 1840 bytes
data/soilrep.RData | Bin 0 -> 107392 bytes
inst/CITATION | 13 +
inst/NEWS | 1659 +++++++++++
inst/doc/Unweighted_UniFrac.RData | Bin 0 -> 2785 bytes
inst/doc/phyloseq-FAQ.R | 31 +
inst/doc/phyloseq-FAQ.Rmd | 562 ++++
inst/doc/phyloseq-FAQ.html | 347 +++
inst/doc/phyloseq-analysis.R | 208 ++
inst/doc/phyloseq-analysis.Rmd | 506 ++++
inst/doc/phyloseq-analysis.html | 463 +++
inst/doc/phyloseq-basics.R | 112 +
inst/doc/phyloseq-basics.Rmd | 600 ++++
inst/doc/phyloseq-basics.html | 509 ++++
inst/doc/phyloseq-mixture-models.R | 74 +
inst/doc/phyloseq-mixture-models.Rmd | 191 ++
inst/doc/phyloseq-mixture-models.html | 302 ++
inst/extdata/GP_otu_table_rand_short.txt.gz | Bin 0 -> 13316 bytes
inst/extdata/GP_tree_rand_short.newick.gz | Bin 0 -> 7183 bytes
inst/extdata/biom-refseq.fasta | 29 +
inst/extdata/biom-tree.phy | 1 +
inst/extdata/esophagus.fn.list.gz | Bin 0 -> 4578 bytes
inst/extdata/esophagus.fn.shared.gz | Bin 0 -> 2362 bytes
inst/extdata/esophagus.good.groups.gz | Bin 0 -> 1347 bytes
inst/extdata/esophagus.tree.gz | Bin 0 -> 4989 bytes
inst/extdata/gg13-5-73.tree.gz | Bin 0 -> 3512 bytes
inst/extdata/gp500-pycogent.py | 19 +
inst/extdata/gp500-uuf.csv | 28 +
inst/extdata/gp500-wuf.csv | 28 +
inst/extdata/gp500-wufu.csv | 28 +
inst/extdata/gp500test.env.txt | 3093 ++++++++++++++++++++
inst/extdata/gp500test.tree | 1 +
inst/extdata/master_map.txt | 29 +
inst/extdata/min_dense_otu_table.biom | 32 +
inst/extdata/min_sparse_otu_table.biom | 43 +
inst/extdata/mothur_example.cons.taxonomy.gz | Bin 0 -> 565 bytes
inst/extdata/qiime500-refseq.fasta | 3070 +++++++++++++++++++
inst/extdata/rformat_dist_0.03.txt.gz | Bin 0 -> 26684 bytes
inst/extdata/rich_dense_otu_table.biom | 56 +
inst/extdata/rich_sparse_otu_table.biom | 66 +
.../study_1457_split_library_seqs_and_mapping.zip | Bin 0 -> 161176 bytes
...study_816_split_library_seqs_and_mapping.tar.gz | Bin 0 -> 4991 bytes
.../study_816_split_library_seqs_and_mapping.zip | Bin 0 -> 5191 bytes
inst/extdata/study_gp.txt | 29 +
inst/extdata/usearch.uc | 100 +
inst/scripts/installer.R | 49 +
man/DPCoA.Rd | 91 +
man/JSD.Rd | 60 +
man/UniFrac-methods.Rd | 174 ++
man/access.Rd | 49 +
man/assign-otu_table.Rd | 46 +
man/assign-phy_tree.Rd | 35 +
man/assign-sample_data.Rd | 48 +
man/assign-sample_names.Rd | 51 +
man/assign-tax_table.Rd | 53 +
man/assign-taxa_are_rows.Rd | 33 +
man/assign-taxa_names.Rd | 57 +
man/build_tax_table.Rd | 43 +
man/capscale-phyloseq-methods.Rd | 70 +
man/cca-rda-phyloseq-methods.Rd | 60 +
man/chunkReOrder.Rd | 35 +
man/data-GlobalPatterns.Rd | 50 +
man/data-enterotype.Rd | 48 +
man/data-esophagus.Rd | 49 +
man/data-soilrep.Rd | 84 +
man/decorana.Rd | 27 +
man/dist-class.Rd | 13 +
man/distance.Rd | 110 +
man/distanceMethodList.Rd | 76 +
man/envHash2otu_table.Rd | 47 +
man/estimate_richness.Rd | 64 +
man/export_env_file.Rd | 36 +
man/export_mothur_dist.Rd | 40 +
man/extract-methods.Rd | 80 +
man/filter_taxa.Rd | 55 +
man/filterfun_sample.Rd | 37 +
man/fix_phylo.Rd | 18 +
man/gapstat_ord.Rd | 70 +
man/genefilter_sample-methods.Rd | 73 +
man/get.component.classes.Rd | 22 +
man/get_sample-methods.Rd | 40 +
man/get_taxa-methods.Rd | 41 +
man/get_taxa_unique.Rd | 39 +
man/get_variable.Rd | 35 +
man/getslots.phyloseq.Rd | 34 +
man/import.Rd | 73 +
man/import_RDP_cluster.Rd | 49 +
man/import_RDP_otu.Rd | 44 +
man/import_biom.Rd | 171 ++
man/import_env_file.Rd | 42 +
man/import_mothur.Rd | 121 +
man/import_mothur_constaxonomy.Rd | 36 +
man/import_mothur_dist.Rd | 32 +
man/import_mothur_groups.Rd | 32 +
man/import_mothur_otu_table.Rd | 41 +
man/import_mothur_otulist.Rd | 43 +
man/import_mothur_shared.Rd | 24 +
man/import_pyrotagger_tab.Rd | 67 +
man/import_qiime.Rd | 156 +
man/import_qiime_otu_tax.Rd | 83 +
man/import_qiime_sample_data.Rd | 49 +
man/import_uparse.Rd | 69 +
man/import_usearch_uc.Rd | 89 +
man/index_reorder.Rd | 30 +
man/intersect_taxa.Rd | 33 +
man/make_network.Rd | 97 +
man/merge_phyloseq.Rd | 67 +
man/merge_phyloseq_pair-methods.Rd | 79 +
man/merge_samples-methods.Rd | 73 +
man/merge_taxa-methods.Rd | 78 +
man/metaMDS.Rd | 27 +
man/microbio_me_qiime.Rd | 99 +
man/mt-methods.Rd | 93 +
man/nodeplotblank.Rd | 40 +
man/nodeplotboot.Rd | 61 +
man/nodeplotdefault.Rd | 48 +
man/nsamples-methods.Rd | 45 +
man/ntaxa-methods.Rd | 48 +
man/ordinate.Rd | 156 +
man/otu_table-class.Rd | 24 +
man/otu_table-methods.Rd | 59 +
man/parseTaxonomy-functions.Rd | 71 +
man/pcoa.Rd | 20 +
man/phy_tree-methods.Rd | 58 +
man/phylo-class.Rd | 14 +
man/phylo.Rd | 36 +
man/phyloseq-class.Rd | 51 +
man/phyloseq-deprecated.Rd | 111 +
man/phyloseq-package.Rd | 28 +
man/phyloseq.Rd | 49 +
man/phyloseq_to_deseq2.Rd | 62 +
man/phyloseq_to_metagenomeSeq.Rd | 42 +
man/plot_bar.Rd | 74 +
man/plot_clusgap.Rd | 59 +
man/plot_heatmap.Rd | 206 ++
man/plot_net.Rd | 117 +
man/plot_network.Rd | 112 +
man/plot_ordination.Rd | 114 +
man/plot_phyloseq-methods.Rd | 48 +
man/plot_richness.Rd | 134 +
man/plot_scree.Rd | 55 +
man/plot_tree.Rd | 185 ++
man/prune_samples-methods.Rd | 50 +
man/prune_taxa-methods.Rd | 71 +
man/psmelt.Rd | 73 +
man/rank_names.Rd | 33 +
man/rarefy_even_depth.Rd | 126 +
man/read_tree.Rd | 51 +
man/read_tree_greengenes.Rd | 57 +
man/reconcile_categories.Rd | 35 +
man/refseq-methods.Rd | 49 +
man/rm_outlierf.Rd | 40 +
man/sample_data-class.Rd | 25 +
man/sample_data-methods.Rd | 53 +
man/sample_names-methods.Rd | 39 +
man/sample_sums.Rd | 31 +
man/sample_variables.Rd | 33 +
man/show-methods.Rd | 34 +
man/show_mothur_cutoffs.Rd | 29 +
man/splat.phyloseq.objects.Rd | 36 +
man/subset_ord_plot.Rd | 70 +
man/subset_samples-methods.Rd | 43 +
man/subset_taxa-methods.Rd | 41 +
man/tax_glom.Rd | 73 +
man/tax_table-methods.Rd | 57 +
man/taxa_are_rows-methods.Rd | 31 +
man/taxa_names-methods.Rd | 55 +
man/taxa_sums.Rd | 30 +
man/taxonomyTable-class.Rd | 16 +
man/threshrank.Rd | 43 +
man/threshrankfun.Rd | 38 +
man/tip_glom.Rd | 70 +
man/topf.Rd | 42 +
man/topk.Rd | 36 +
man/topp.Rd | 38 +
man/transformcounts.Rd | 55 +
man/transpose-methods.Rd | 32 +
man/tree_layout.Rd | 67 +
tests/testthat-phyloseq.R | 13 +
tests/testthat/test-IO.R | 379 +++
tests/testthat/test-distance.R | 118 +
tests/testthat/test-merge.R | 305 ++
tests/testthat/test-phyloseq.R | 140 +
tests/testthat/test-plot.R | 500 ++++
tests/testthat/test-rarefy.R | 61 +
tests/testthat/test-subset.R | 110 +
tests/testthat/test-transform.R | 100 +
vignettes/import_qiime_directory_structure.jpg | Bin 0 -> 24538 bytes
vignettes/phyloseq-FAQ.Rmd | 562 ++++
vignettes/phyloseq-analysis.Rmd | 506 ++++
vignettes/phyloseq-basics.Rmd | 600 ++++
vignettes/phyloseq-mixture-models.Rmd | 191 ++
vignettes/phyloseq_classes_7.png | Bin 0 -> 294387 bytes
228 files changed, 36075 insertions(+)
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