| adiv_boxplot | Visualize alpha diversity with boxplots. |
| adiv_corrplot | Visualize alpha diversity with scatterplots and trendlines. |
| adiv_matrix | Create a matrix of samples x alpha diversity metrics. |
| adiv_stats | Test alpha diversity for associations with metadata. |
| adiv_table | Calculate the alpha diversity of each sample. |
| as.list.rbiom | Convert an rbiom object to a base R list. |
| as.matrix.rbiom | Convert an rbiom object to a simple count matrix. |
| as_rbiom | Convert a variety of data types to an rbiom object. |
| babies | Longitudinal Stool Samples from Infants (n = 2,684) |
| bdiv_boxplot | Visualize BIOM data with boxplots. |
| bdiv_clusters | Cluster samples by beta diversity k-means. |
| bdiv_corrplot | Visualize beta diversity with scatterplots and trendlines. |
| bdiv_heatmap | Display beta diversities in an all vs all grid. |
| bdiv_ord_plot | Ordinate samples and taxa on a 2D plane based on beta... |
| bdiv_ord_table | Calculate PCoA and other ordinations, including taxa biplots... |
| bdiv_stats | Test beta diversity for associations with metadata. |
| bdiv_table | Distance / dissimilarity between samples. |
| bdply | Apply a function to each subset of an rbiom object. |
| biom_merge | Combine several rbiom objects into one. |
| convert_to | Convert biom data to an external package class. |
| distmat_ord_table | Run ordinations on a distance matrix. |
| distmat_stats | Run statistics on a distance matrix vs a categorical or... |
| documentation_biom.rbiom | documentation_biom.rbiom |
| documentation_clusters | documentation_clusters |
| documentation_cmp | documentation_cmp |
| documentation_default | documentation_default |
| documentation_dist_test | documentation_dist_test |
| documentation_heatmap | documentation_heatmap |
| documentation_plot_return | documentation_plot_return |
| documentation_rank.2 | documentation_rank.2 |
| documentation_rank.NULL | documentation_rank.NULL |
| documentation_return.biom | documentation_return.biom |
| documentation_taxa.4 | documentation_taxa.4 |
| export | Export data to QIIME 2 or mothur. |
| gems | Global Enteric Multicenter Study (n = 1,006) |
| glimpse.rbiom | Get a glimpse of your metadata. |
| hmp50 | Human Microbiome Project - demo dataset (n = 50) |
| modify_metadata | Create, modify, and delete metadata fields. |
| plot_heatmap | Create a heatmap with tracks and dendrograms from any matrix. |
| pull.rbiom | Map sample names to metadata field values. |
| rare_corrplot | Visualize rarefaction curves with scatterplots and... |
| rarefy | Rarefy OTU counts. |
| rarefy_cols | Transform a counts matrix. |
| rare_multiplot | Combines rare_corrplot and rare_stacked into a single figure. |
| rare_stacked | Visualize the number of observations per sample. |
| rbiom-deprecated | Deprecated functions in package 'rbiom'. |
| rbiom_objects | Working with rbiom Objects. |
| rbiom-package | rbiom: Read/Write, Transform, and Summarize BIOM Data |
| read_biom | Parse counts, metadata, taxonomy, and phylogeny from a BIOM... |
| read_fasta | Parse a fasta file into a named character vector. |
| read_tree | Read a newick formatted phylogenetic tree. |
| reexports | Objects exported from other packages |
| sample_sums | Summarize the taxa observations in each sample. |
| slice_metadata | Subset to a specific number of samples. |
| speed | Speed Ups. |
| stats_boxplot | Visualize categorical metadata effects on numeric values. |
| stats_corrplot | Visualize regression with scatterplots and trendlines. |
| stats_table | Run non-parametric statistics on a data.frame. |
| subset | Subset an rbiom object by sample names, OTU names, metadata,... |
| taxa_boxplot | Visualize BIOM data with boxplots. |
| taxa_clusters | Cluster samples by taxa abundances k-means. |
| taxa_corrplot | Visualize taxa abundance with scatterplots and trendlines. |
| taxa_heatmap | Display taxa abundances as a heatmap. |
| taxa_map | Map OTUs names to taxa names at a given rank. |
| taxa_matrix | Taxa abundances per sample. |
| taxa_stacked | Display taxa abundances as a stacked bar graph. |
| taxa_stats | Test taxa abundances for associations with metadata. |
| taxa_sums | Get summary taxa abundances. |
| tree_subset | Create a subtree by specifying tips to keep. |
| with | Evaluate expressions on metadata. |
| write_biom | Save an rbiom object to a file. |
