├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── addins.R ├── data_release.R ├── datasets.R ├── deprecated.R ├── microbiota2.R ├── yingtools2-package.R └── yingtools2.R ├── README.Rmd ├── README.md ├── common.R ├── data-raw └── cli_reference.R ├── data ├── 4_plot_klebsiella_pts.png ├── 5_klebsiella_abundance.png ├── CID94_lefse.png ├── cid.bsi.rda ├── cid.cdiff.rda ├── cid.hosp.rda ├── cid.meds.rda ├── cid.patients.rda ├── cid.phy.rda ├── fig1.png ├── ggstack_sample.png ├── stcox_firstexample.png ├── stcox_multivariate.png └── univariate_manyvars.png ├── examples ├── cid.diversity.Rmd ├── cid.diversity.md ├── cid.diversity_files │ └── figure-markdown_github │ │ ├── unnamed-chunk-3-1.png │ │ ├── unnamed-chunk-4-1.png │ │ └── unnamed-chunk-5-1.png ├── cid.hclust.Rmd ├── cid.hclust.md ├── cid.hclust_files │ └── figure-markdown_github │ │ ├── unnamed-chunk-2-1.png │ │ ├── unnamed-chunk-3-1.png │ │ └── unnamed-chunk-4-1.png ├── commands.Rmd ├── commands.knit.md ├── commands.md ├── commands.utf8.md ├── curriculum.Rmd ├── curriculum.html ├── curriculum.md ├── curriculum_files │ └── figure-gfm │ │ ├── fig-margin-1.png │ │ ├── ggplot-1.png │ │ ├── ggplot-2.png │ │ ├── ggplot-3.png │ │ ├── ggplot-4.png │ │ ├── ggplot-5.png │ │ ├── ggplot-6.png │ │ ├── ggplot-7.png │ │ ├── ggplot-8.png │ │ ├── ggplot2-1.png │ │ ├── ggplot2-2.png │ │ ├── ggplot2-3.png │ │ ├── ggplot2-4.png │ │ ├── ggplot2-5.png │ │ ├── ggplot2-6.png │ │ ├── ggplot2-7.png │ │ ├── ggplot2-8.png │ │ ├── ggplot_1b-1.png │ │ ├── ggplot_1b-10.png │ │ ├── ggplot_1b-2.png │ │ ├── ggplot_1b-3.png │ │ ├── ggplot_1b-4.png │ │ ├── ggplot_1b-5.png │ │ ├── ggplot_1b-6.png │ │ ├── ggplot_1b-7.png │ │ ├── ggplot_1b-8.png │ │ ├── ggplot_1b-9.png │ │ ├── ggplot_2-1.png │ │ ├── ggplot_2-10.png │ │ ├── ggplot_2-2.png │ │ ├── ggplot_2-3.png │ │ ├── ggplot_2-4.png │ │ ├── ggplot_2-5.png │ │ ├── ggplot_2-6.png │ │ ├── ggplot_2-7.png │ │ ├── ggplot_2-8.png │ │ ├── ggplot_2-9.png │ │ ├── ggplot_2b-1.png │ │ ├── ggplot_2b-2.png │ │ ├── mychunk-1.png │ │ ├── mychunk-10.png │ │ ├── mychunk-2.png │ │ ├── mychunk-3.png │ │ ├── mychunk-4.png │ │ ├── mychunk-5.png │ │ ├── mychunk-6.png │ │ ├── mychunk-7.png │ │ ├── mychunk-8.png │ │ ├── mychunk-9.png │ │ ├── score_table2-1.png │ │ ├── score_table2-2.png │ │ ├── score_table2-3.png │ │ ├── score_table2-4.png │ │ ├── score_table2-5.png │ │ ├── score_table2-6.png │ │ ├── score_table2-7.png │ │ ├── score_table2x-1.png │ │ ├── score_table2x-2.png │ │ ├── score_table2x-3.png │ │ ├── score_table2x-4.png │ │ ├── score_table2x-5.png │ │ ├── score_table2x-6.png │ │ ├── score_table2x-7.png │ │ ├── score_table2x-8.png │ │ ├── score_table2xxx-1.png │ │ ├── score_table2xxx-2.png │ │ ├── score_table2xxx-3.png │ │ ├── score_table2xxx-4.png │ │ ├── score_table2xxx-5.png │ │ ├── score_table2xxx-6.png │ │ ├── score_table2xxx-7.png │ │ ├── score_table2xxx-8.png │ │ ├── score_tablex-1.png │ │ ├── score_tablex-2.png │ │ ├── score_tablex-3.png │ │ ├── unnamed-chunk-10-1.png │ │ ├── unnamed-chunk-10-2.png │ │ ├── unnamed-chunk-10-3.png │ │ ├── unnamed-chunk-10-4.png │ │ ├── unnamed-chunk-10-5.png │ │ ├── unnamed-chunk-10-6.png │ │ ├── unnamed-chunk-10-7.png │ │ ├── unnamed-chunk-10-8.png │ │ ├── unnamed-chunk-11-1.png │ │ ├── unnamed-chunk-11-2.png │ │ ├── unnamed-chunk-11-3.png │ │ ├── unnamed-chunk-11-4.png │ │ ├── unnamed-chunk-11-5.png │ │ ├── unnamed-chunk-11-6.png │ │ ├── unnamed-chunk-11-7.png │ │ ├── unnamed-chunk-11-8.png │ │ ├── unnamed-chunk-6-1.png │ │ ├── unnamed-chunk-6-10.png │ │ ├── unnamed-chunk-6-11.png │ │ ├── unnamed-chunk-6-2.png │ │ ├── unnamed-chunk-6-3.png │ │ ├── unnamed-chunk-6-4.png │ │ ├── unnamed-chunk-6-5.png │ │ ├── unnamed-chunk-6-6.png │ │ ├── unnamed-chunk-6-7.png │ │ ├── unnamed-chunk-6-8.png │ │ ├── unnamed-chunk-6-9.png │ │ ├── unnamed-chunk-7-1.png │ │ ├── unnamed-chunk-7-10.png │ │ ├── unnamed-chunk-7-11.png │ │ ├── unnamed-chunk-7-2.png │ │ ├── unnamed-chunk-7-3.png │ │ ├── unnamed-chunk-7-4.png │ │ ├── unnamed-chunk-7-5.png │ │ ├── unnamed-chunk-7-6.png │ │ ├── unnamed-chunk-7-7.png │ │ ├── unnamed-chunk-7-8.png │ │ ├── unnamed-chunk-7-9.png │ │ ├── unnamed-chunk-8-1.png │ │ ├── unnamed-chunk-8-10.png │ │ ├── unnamed-chunk-8-11.png │ │ ├── unnamed-chunk-8-2.png │ │ ├── unnamed-chunk-8-3.png │ │ ├── unnamed-chunk-8-4.png │ │ ├── unnamed-chunk-8-5.png │ │ ├── unnamed-chunk-8-6.png │ │ ├── unnamed-chunk-8-7.png │ │ ├── unnamed-chunk-8-8.png │ │ ├── unnamed-chunk-8-9.png │ │ ├── unnamed-chunk-9-1.png │ │ ├── unnamed-chunk-9-2.png │ │ ├── unnamed-chunk-9-3.png │ │ ├── unnamed-chunk-9-4.png │ │ ├── unnamed-chunk-9-5.png │ │ ├── unnamed-chunk-9-6.png │ │ ├── unnamed-chunk-9-7.png │ │ └── unnamed-chunk-9-8.png ├── exercises.Rmd ├── exercises.md ├── exercises_files │ ├── figure-gfm │ │ ├── unnamed-chunk-10-1.png │ │ ├── unnamed-chunk-11-1.png │ │ ├── unnamed-chunk-12-1.png │ │ ├── unnamed-chunk-13-1.png │ │ ├── unnamed-chunk-20-1.png │ │ ├── unnamed-chunk-22-1.png │ │ └── unnamed-chunk-23-1.png │ └── figure-markdown_github │ │ ├── unnamed-chunk-10-1.png │ │ ├── unnamed-chunk-11-1.png │ │ ├── unnamed-chunk-12-1.png │ │ ├── unnamed-chunk-13-1.png │ │ ├── unnamed-chunk-20-1.png │ │ └── unnamed-chunk-22-1.png ├── features.Rmd ├── features.md ├── features_files │ ├── figure-gfm │ │ ├── unnamed-chunk-4-1.png │ │ └── unnamed-chunk-5-1.png │ └── figure-markdown_github │ │ ├── unnamed-chunk-4-1.png │ │ └── unnamed-chunk-5-1.png ├── patients.pdf ├── pcoa.Rmd ├── pcoa.md ├── pcoa_files │ └── figure-gfm │ │ ├── unnamed-chunk-2-1.png │ │ ├── unnamed-chunk-3-1.png │ │ ├── unnamed-chunk-4-1.png │ │ └── unnamed-chunk-5-1.png ├── phylotree.Rmd ├── phylotree.md ├── phylotree_files │ └── figure-gfm │ │ ├── unnamed-chunk-2-1.png │ │ ├── unnamed-chunk-3-1.png │ │ ├── unnamed-chunk-4-1.png │ │ ├── unnamed-chunk-4-2.png │ │ ├── unnamed-chunk-4-3.png │ │ ├── unnamed-chunk-6-1.png │ │ ├── unnamed-chunk-7-1.png │ │ ├── unnamed-chunk-8-1.png │ │ └── unnamed-chunk-9-1.png ├── regex.Rmd ├── regex.md ├── taxbar.Rmd ├── taxbar.md ├── taxbar_files │ └── figure-gfm │ │ ├── unnamed-chunk-3-1.png │ │ └── unnamed-chunk-4-1.png ├── taxhclust.Rmd └── xcommands.Rmd ├── inst └── rstudio │ └── addins.dcf ├── man ├── GeomTaxonomy.Rd ├── GuideTaxonomy.Rd ├── LayerTaxonomy.Rd ├── StatTaxonomy.Rd ├── age.years.Rd ├── all.grepl.Rd ├── all.same.Rd ├── annotation_ruler.Rd ├── any_overlap.Rd ├── as.Date2.Rd ├── as.mrn.Rd ├── as.phylo.formula2.Rd ├── as_date_fractional.Rd ├── bracketGrob.Rd ├── calc.distance.Rd ├── calc.mean.distance.Rd ├── calc.pairwise.Rd ├── calc.taxhorn.distance.Rd ├── chop.endpoint.Rd ├── cid.bsi.Rd ├── cid.cdiff.Rd ├── cid.colors.Rd ├── cid.hosp.Rd ├── cid.meds.Rd ├── cid.patients.Rd ├── cid.phy.Rd ├── cleanup.data.Rd ├── cli_table.Rd ├── coalesce_indicators.Rd ├── coalesce_values.Rd ├── color2hex.Rd ├── compare.Rd ├── compare_relationship.Rd ├── convert.dates.Rd ├── copy.as.select.Rd ├── copy.as.tribble.Rd ├── copy.to.clipboard.Rd ├── cox.Rd ├── cox.old.Rd ├── createSurvivalFrame.Rd ├── cummax.Rd ├── cut2.Rd ├── date.regex.Rd ├── declare.args.Rd ├── deparse2.Rd ├── draw_key_polygon_close.Rd ├── dt.OLD.Rd ├── dt.Rd ├── dt_subset_data_for_viewing.Rd ├── fan.angle.Rd ├── fct_reordern.Rd ├── figures │ ├── lifecycle-archived.svg │ ├── lifecycle-defunct.svg │ ├── lifecycle-deprecated.svg │ ├── lifecycle-experimental.svg │ ├── lifecycle-maturing.svg │ ├── lifecycle-questioning.svg │ ├── lifecycle-stable.svg │ ├── lifecycle-superseded.svg │ └── unnamed-chunk-1-1.png ├── file_activity_status.Rd ├── fill_in_blanks.Rd ├── find.all.distinct.vars.Rd ├── fungal.palette.Rd ├── geom_bracket.Rd ├── geom_hilight.Rd ├── geom_kaplanmeier.Rd ├── geom_logrank.Rd ├── geom_taxonomy.Rd ├── geom_taxonomy_interactive.Rd ├── geom_timeline.Rd ├── geom_timeline_interactive.Rd ├── get.abundance.Rd ├── get.all.dependencies.Rd ├── get.code.info.Rd ├── get.dist.Rd ├── get.environment.locations.Rd ├── get.otu.Rd ├── get.otu.melt.Rd ├── get.pairwise.Rd ├── get.phyloseq.from.melt.Rd ├── get.row.OLD.Rd ├── get.row.Rd ├── get.samp.Rd ├── get.tax.Rd ├── get.tax.legend.Rd ├── get.tax.legend2.Rd ├── get.tax.palette.Rd ├── get.taxonomy.colordata.Rd ├── get.time.Rd ├── get.yt.palette.Rd ├── get.yt.palette2.Rd ├── get_epsilon.Rd ├── get_gitdir_info.Rd ├── gg.align.xlim.Rd ├── gg.axis.limits.Rd ├── gg.colors.Rd ├── gg.legend.Rd ├── gg.stack.Rd ├── gg.stack2.Rd ├── git_release.Rd ├── grapes-allin-grapes.Rd ├── grapes-find-grapes.Rd ├── grapes-grapes.Rd ├── grapes-notin-grapes.Rd ├── group_by_all_distinct.Rd ├── group_by_time.Rd ├── group_by_time_streaks.Rd ├── group_split_named.Rd ├── guide_gengrob.taxonomy.Rd ├── guide_geom.taxonomy.Rd ├── guide_taxonomy.Rd ├── guide_train.taxonomy.Rd ├── highlight_grep.OLD.Rd ├── highlight_grep.Rd ├── highlight_text.Rd ├── hilight.clade.Rd ├── inline.Rd ├── inner_join_fuzzy.Rd ├── inner_join_replace.Rd ├── inner_join_replace_old.Rd ├── ir_dist.Rd ├── is.between.Rd ├── is.distinct.Rd ├── is.mrn.Rd ├── is.pattern.Rd ├── is.same.Rd ├── is.wholenumber.Rd ├── kill_port_process.Rd ├── lda.clado.Rd ├── lda.effect.Rd ├── lda.plot.Rd ├── lefse.prep.Rd ├── like.Rd ├── list.all.exported.functions.Rd ├── list.gg.items.Rd ├── locs2irl.Rd ├── log_epsilon_trans.Rd ├── log_epsilon_trans_breaks.Rd ├── logistic.Rd ├── logistic_trans.Rd ├── logistic_trans_breaks.Rd ├── logit.Rd ├── lookahead.Rd ├── ls.object.sizes.Rd ├── make.datetime.Rd ├── make.names.Rd ├── make.surv.endpt.Rd ├── make.table.Rd ├── makeContent.taxfittexttree.Rd ├── make_table.Rd ├── make_taxonomy_distinct.Rd ├── max2.Rd ├── middle.pattern.Rd ├── midpoint.Rd ├── mix.colors.Rd ├── mutate.phyloseq.Rd ├── occurs.within.Rd ├── old3.phy.collapse.bins.Rd ├── ordering.Rd ├── overlaps.Rd ├── paste2.Rd ├── pca.plot.Rd ├── phy.calc.relative.abundance.Rd ├── phy.collapse.Rd ├── phy.collapse.bins.Rd ├── phy.collapse.bins.old.Rd ├── phy.unfold.taxranks.Rd ├── phy.use.tax.tree.Rd ├── pipe.Rd ├── pivot_wider_recode.Rd ├── pretty_number.Rd ├── pretty_scientific.Rd ├── prune_unused_taxa.Rd ├── read.blastn.file.Rd ├── read.clipboard.Rd ├── read.mothur.taxfile.Rd ├── read.oligos.Rd ├── read.otu.table.Rd ├── read.tree.uparse.Rd ├── read.uparse.data.Rd ├── read_all_excel.Rd ├── read_excel2.Rd ├── recode2.Rd ├── regex.widget.OLD.Rd ├── regex.widget.Rd ├── regex.widget0.Rd ├── remove.na.cols.Rd ├── remove.na.rows.Rd ├── replace.grep.Rd ├── replace.grep.data.Rd ├── replace_grep_data.Rd ├── runGadget_bg.Rd ├── run_r.Rd ├── sample_groups.Rd ├── sample_n_groups_OLD.Rd ├── scale_fill_taxonomy.Rd ├── scale_sample.colour_discrete.Rd ├── scale_x_timebars.Rd ├── search.data.columns.Rd ├── select2.Rd ├── set.otu.Rd ├── set.samp.Rd ├── set.tax.Rd ├── set_precedence.Rd ├── shades.Rd ├── shell.exec.Rd ├── short_number.Rd ├── show_linetypes.Rd ├── show_shapes.Rd ├── stcox.Rd ├── str_extract_all_quotes.Rd ├── str_locate_all_df.Rd ├── str_locate_all_irl.Rd ├── str_protect_escape_characters.Rd ├── 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