Files in schuyler-smith/phylosmith
Functions to help analyze data as phyloseq objects

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
Dockerfile
JOSS_paper/paper.bib
JOSS_paper/paper.md
LICENSE
NAMESPACE
Notes.txt
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
doc_elements.txt
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
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docs/site_libs/bootstrap-3.3.5/css/fonts/RalewayBold.ttf
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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
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docs/site_libs/jqueryui-1.11.4/jquery-ui.js
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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
makefile
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
schuyler-smith/phylosmith documentation built on Aug. 17, 2024, 10:19 a.m.