Files in schuyler-smith/phyloschuyler
Functions to help analyze data as phyloseq objects
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
JOSS_paper/paper.bib
JOSS_paper/paper.md
LICENSE
NAMESPACE
R/RcppExports.R
R/abundance_heatmap.R
R/abundance_lines.R
R/alpha_diversity_graph.R
R/argument_rules.R
R/co_occurrence.R
R/co_occurrence_network.R
R/common_taxa.R
R/conglomerate_samples.R
R/conglomerate_taxa.R
R/curate_co_occurrence.R
R/datasets.R
R/dendrogram_phyloseq.R
R/histogram_permuted_rhos.R
R/internal.R
R/library_size.R
R/melt_phyloseq.R
R/merge_treatments.R
R/network_layout_ps.R
R/network_ps.R
R/new.R
R/nmds_phyloseq.R
R/pcoa_phyloseq.R
R/permute_rho.R
R/phylogeny_profile.R
R/phylosmith_package.R
R/quantile_permuted_rhos.R
R/relative_abundance.R
R/set_sample_order.R
R/set_treatment_levels.R
R/sysdata.rda
R/taxa_abundance_bars.R
R/taxa_core.R
R/taxa_core_graph.R
R/taxa_extract.R
R/taxa_filter.R
R/taxa_proportions.R
R/taxa_prune.R
R/theme_schuy.R
R/tsne_phyloseq.R
R/unique_taxa.R
R/variable_correlation.R
R/variable_correlation_heatmap.R
R/variable_correlation_network.R
README.md
cleanup
configure
configure.ac
data/ia_lakes.rda
data/mock_phyloseq.rda
data/mock_phyloseq_2.rda
data/soil_column.rda
docs/analytics.html
docs/calculations.html
docs/calculations_files/figure-html/histogram_permuted_rhos-1.png
docs/graphics.html
docs/graphics_files/figure-html/abundance_heatmap-1.png
docs/graphics_files/figure-html/abundance_lines-1.png
docs/graphics_files/figure-html/alpha_diversity_graph-1.png
docs/graphics_files/figure-html/dendrogram_phyloseq-1.png
docs/graphics_files/figure-html/nmds_phyloseq-1.png
docs/graphics_files/figure-html/pcoa_phyloseq-1.png
docs/graphics_files/figure-html/phylogeny_profile-1.png
docs/graphics_files/figure-html/taxa_abundance_bars-1.png
docs/graphics_files/figure-html/taxa_core_graph-1.png
docs/graphics_files/figure-html/tsne_phyloseq-1.png
docs/graphics_files/figure-html/variable_correlation_heatmap-1.png
docs/index.html
docs/networks.html
docs/networks_files/figure-html/co_occurrence_network-1.png
docs/networks_files/figure-html/variable_correlation_network-1.png
docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.css
docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.css.map
docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.min.css
docs/site_libs/bootstrap-3.3.5/css/bootstrap.css
docs/site_libs/bootstrap-3.3.5/css/bootstrap.css.map
docs/site_libs/bootstrap-3.3.5/css/bootstrap.min.css
docs/site_libs/bootstrap-3.3.5/css/cerulean.min.css
docs/site_libs/bootstrap-3.3.5/css/cosmo.min.css
docs/site_libs/bootstrap-3.3.5/css/darkly.min.css
docs/site_libs/bootstrap-3.3.5/css/flatly.min.css
docs/site_libs/bootstrap-3.3.5/css/fonts/Lato.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/LatoBold.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/LatoItalic.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/NewsCycle.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/NewsCycleBold.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/OpenSans.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/OpenSansBold.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/OpenSansBoldItalic.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/OpenSansItalic.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/OpenSansLight.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/OpenSansLightItalic.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/Raleway.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/RalewayBold.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/Roboto.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/RobotoBold.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/RobotoLight.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/RobotoMedium.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/SourceSansPro.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/SourceSansProBold.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/SourceSansProItalic.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/SourceSansProLight.ttf
docs/site_libs/bootstrap-3.3.5/css/fonts/Ubuntu.ttf
docs/site_libs/bootstrap-3.3.5/css/journal.min.css
docs/site_libs/bootstrap-3.3.5/css/lumen.min.css
docs/site_libs/bootstrap-3.3.5/css/paper.min.css
docs/site_libs/bootstrap-3.3.5/css/readable.min.css
docs/site_libs/bootstrap-3.3.5/css/sandstone.min.css
docs/site_libs/bootstrap-3.3.5/css/simplex.min.css
docs/site_libs/bootstrap-3.3.5/css/spacelab.min.css
docs/site_libs/bootstrap-3.3.5/css/united.min.css
docs/site_libs/bootstrap-3.3.5/css/yeti.min.css
docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.eot
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docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff
docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff2
docs/site_libs/bootstrap-3.3.5/js/bootstrap.js
docs/site_libs/bootstrap-3.3.5/js/bootstrap.min.js
docs/site_libs/bootstrap-3.3.5/js/npm.js
docs/site_libs/bootstrap-3.3.5/shim/html5shiv.min.js
docs/site_libs/bootstrap-3.3.5/shim/respond.min.js
docs/site_libs/font-awesome-5.1.0/css/all.css
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docs/site_libs/highlightjs-9.12.0/default.css
docs/site_libs/highlightjs-9.12.0/highlight.js
docs/site_libs/highlightjs-9.12.0/textmate.css
docs/site_libs/jquery-3.6.0/jquery-3.6.0.js
docs/site_libs/jquery-3.6.0/jquery-3.6.0.min.js
docs/site_libs/jquery-3.6.0/jquery-3.6.0.min.map
docs/site_libs/jqueryui-1.11.4/README
docs/site_libs/jqueryui-1.11.4/images/ui-icons_444444_256x240.png
docs/site_libs/jqueryui-1.11.4/images/ui-icons_555555_256x240.png
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docs/site_libs/jqueryui-1.11.4/images/ui-icons_cc0000_256x240.png
docs/site_libs/jqueryui-1.11.4/images/ui-icons_ffffff_256x240.png
docs/site_libs/jqueryui-1.11.4/index.html
docs/site_libs/jqueryui-1.11.4/jquery-ui.css
docs/site_libs/jqueryui-1.11.4/jquery-ui.js
docs/site_libs/jqueryui-1.11.4/jquery-ui.min.css
docs/site_libs/jqueryui-1.11.4/jquery-ui.min.js
docs/site_libs/jqueryui-1.11.4/jquery-ui.structure.css
docs/site_libs/jqueryui-1.11.4/jquery-ui.structure.min.css
docs/site_libs/jqueryui-1.11.4/jquery-ui.theme.css
docs/site_libs/jqueryui-1.11.4/jquery-ui.theme.min.css
docs/site_libs/navigation-1.1/codefolding-lua.css
docs/site_libs/navigation-1.1/codefolding.js
docs/site_libs/navigation-1.1/sourceembed.js
docs/site_libs/navigation-1.1/tabsets.js
docs/site_libs/pagedtable-1.1/css/pagedtable.css
docs/site_libs/pagedtable-1.1/js/pagedtable.js
docs/site_libs/tocify-1.9.1/jquery.tocify.css
docs/site_libs/tocify-1.9.1/jquery.tocify.js
docs/src/footer.html
docs/src/header.html
docs/src/style.css
docs/wrangling.html
inst/NEWS
inst/include/significance.h
man/CI_ellipse.Rd
man/Correlation.Rd
man/abundance_heatmap.Rd
man/abundance_lines.Rd
man/alpha_diversity_graph.Rd
man/arrange_co_occurrence_table.Rd
man/assign_rank.Rd
man/bin.Rd
man/change_labels.Rd
man/check_TaR.Rd
man/check_index_classification.Rd
man/check_index_treatment.Rd
man/co_occurrence.Rd
man/co_occurrence_network.Rd
man/common_taxa.Rd
man/conglomerate_samples.Rd
man/conglomerate_taxa.Rd
man/create_palette.Rd
man/curate_co_occurrence.Rd
man/dendrogram_phyloseq.Rd
man/histogram_permuted_rhos.Rd
man/ia_lakes.Rd
man/library_size.Rd
man/melt_phyloseq.Rd
man/merge_treatments.Rd
man/mock_phyloseq.Rd
man/mock_phyloseq_2.Rd
man/network_layout_ps.Rd
man/network_ps.Rd
man/nmds_phyloseq.Rd
man/pcoa_phyloseq.Rd
man/permute_rho.Rd
man/permute_rho_Rcpp.Rd
man/phylogeny_profile.Rd
man/phylosmith.Rd
man/quantile_permuted_rhos.Rd
man/relative_abundance.Rd
man/set_sample_order.Rd
man/set_treatment_levels.Rd
man/soil_column.Rd
man/taxa_abundance_bars.Rd
man/taxa_core.Rd
man/taxa_core_graph.Rd
man/taxa_extract.Rd
man/taxa_filter.Rd
man/taxa_proportions.Rd
man/taxa_prune.Rd
man/tsne_phyloseq.Rd
man/unique_taxa.Rd
man/variable_correlation.Rd
man/variable_correlation_heatmap.Rd
man/variable_correlation_network.Rd
src/Makevars
src/Makevars.in
src/Makevars.win
src/RcppExports.cpp
src/correlations_Rcpp.cpp
src/significance.cpp
vignette_site/_site.yml
vignette_site/analytics.Rmd
vignette_site/calculations.Rmd
vignette_site/calculations_files/figure-html/histogram_permuted_rhos-1.png
vignette_site/graphics.Rmd
vignette_site/graphics_files/figure-html/abundance_heatmap-1.png
vignette_site/graphics_files/figure-html/abundance_lines-1.png
vignette_site/graphics_files/figure-html/alpha_diversity_graph-1.png
vignette_site/graphics_files/figure-html/dendrogram_phyloseq-1.png
vignette_site/graphics_files/figure-html/nmds_phyloseq-1.png
vignette_site/graphics_files/figure-html/pcoa_phyloseq-1.png
vignette_site/graphics_files/figure-html/phylogeny_profile-1.png
vignette_site/graphics_files/figure-html/taxa_abundance_bars-1.png
vignette_site/graphics_files/figure-html/taxa_core_graph-1.png
vignette_site/graphics_files/figure-html/tsne_phyloseq-1.png
vignette_site/graphics_files/figure-html/variable_correlation_heatmap-1.png
vignette_site/index.Rmd
vignette_site/networks.Rmd
vignette_site/networks_files/figure-html/co_occurrence_network-1.png
vignette_site/networks_files/figure-html/variable_correlation_network-1.png
vignette_site/src/footer.html
vignette_site/src/header.html
vignette_site/src/style.css
vignette_site/wrangling.Rmd
vignettes/phylosmith.Rmd
