Files in leffj/mctoolsr
Microbial Community Data Analysis Tools
.Rbuildignore
.Rprofile
.gitignore
DESCRIPTION
NAMESPACE
R/datasets_documentation.R
R/dissimilarity-based.R
R/diversity-based.R
R/initialize.R
R/input_output_filter.R
R/mctoolsr.R
R/misc_analyses.R
R/misc_plots.R
R/normalization.R
R/taxa_by_sample_type_functions.R
R/taxonomy-based.R
R/tree-based.R
R/utils.R
README.Rmd
README.md
README_files/figure-html/unnamed-chunk-11-1.png
README_files/figure-html/unnamed-chunk-12-1.png
README_files/figure-html/unnamed-chunk-13-1.png
README_files/figure-html/unnamed-chunk-15-1.png
README_files/figure-html/unnamed-chunk-9-1.png
data-raw/generate_functions_list.R
data-raw/prep_data.R
data-raw/update_version.R
data/.Rapp.history
data/fruits_veggies.rda
data/fruits_veggies_OTUs_tree.rda
data/sumtax_example_data.rda
function_list.md
inst/extdata/fruits_veggies_dm.txt
inst/extdata/fruits_veggies_metadata.txt
inst/extdata/fruits_veggies_metadata_2col.txt
inst/extdata/fruits_veggies_taxa.tre
inst/extdata/fruits_veggies_taxa_table_wTax.biom
inst/extdata/fruits_veggies_taxa_table_wTax.txt
man/.Rapp.history
man/add_metadata_to_dm_clmns.Rd
man/calc_diversity.Rd
man/calc_dm.Rd
man/calc_mean_dissimilarities.Rd
man/calc_ordination.Rd
man/calc_pairwise_permanovas.Rd
man/calc_prop_shared_taxa.Rd
man/calc_prop_taxa_from_sample_type.Rd
man/calc_taxa_changes.Rd
man/calc_taxa_means.Rd
man/collapse_taxonomy.Rd
man/convert_dm_to_3_column.Rd
man/convert_to_relative_abundances.Rd
man/core_taxa.Rd
man/export_otu_table.Rd
man/export_taxa_table.Rd
man/filter_data.Rd
man/filter_dm.Rd
man/filter_samples_by_counts.Rd
man/filter_taxa_from_input.Rd
man/filter_taxa_from_table.Rd
man/filter_tree.Rd
man/fruits_veggies.Rd
man/fruits_veggies_OTUs_tree.Rd
man/load_2_dms.Rd
man/load_dm.Rd
man/load_taxa_table.Rd
man/load_tree.Rd
man/match_datasets.Rd
man/mctoolsr.Rd
man/plot_dendrogram.Rd
man/plot_diversity.Rd
man/plot_nmds.Rd
man/plot_ordination.Rd
man/plot_taxa_bars.Rd
man/plot_ts_heatmap.Rd
man/plot_venn_diagram.Rd
man/rename_samples.Rd
man/return_top_taxa.Rd
man/single_rarefy.Rd
man/summarize_taxonomy.Rd
man/sumtax_example_data.Rd
man/taxa_summary_by_sample_type.Rd
mctoolsr.Rproj
tests/testthat.R
tests/testthat/test_dissimilarity.R
tests/testthat/test_diversity_calculations.R
tests/testthat/test_filter_data.R
tests/testthat/test_input_output.R
tests/testthat/test_misc_analyses.R
tests/testthat/test_normalization.R
tests/testthat/test_taxonomy.R
tests/testthat/test_taxonomy_plots.R
tutorials/modifying_plots.Rmd
tutorials/modifying_plots.html
tutorials/modifying_plots.md
tutorials/modifying_plots_files/figure-html/unnamed-chunk-4-1.png
tutorials/modifying_plots_files/figure-html/unnamed-chunk-7-1.png
tutorials/modifying_plots_files/figure-html/unnamed-chunk-8-1.png
tutorials/modifying_plots_files/figure-html/unnamed-chunk-8-2.png
vignettes/getting_started.Rmd
