Package index • MicrobiomeR

Import
`create_phyloseq()`	Get Phyloseq Object
`create_taxmap()`	Get Taxmap Object
`parse_taxonomy_silva_128()`	Parse elements of a taxonomy vector
`pick_new_outgroup()`	Pick Outgroup for Tree
`root_by_longest_edge()`	Root Phylogenetic Tree
`root_phyloseq_tree()`	Root phyloseq tree.
Formatting
`MicrobiomeR_Formats`	The MicrobiomeR Formats
`as_MicrobiomeR_format()`	As MicrobiomeR Format
`as_analyzed_format()`	As Analyzed MicrobiomeR Format
`as_basic_format()`	As Basic MicrobiomeR Format
`as_custom_format()`	As Custom MicrobiomeR Format
`as_phyloseq_format()`	As Phyloseq MicrobiomeR Format
`as_raw_format()`	As Raw MicrobiomeR Format
`melt_taxmap()`	Melt Taxmap
`treatment_matrix()`	Get Treatment Matrix
Statistics
`alpha_diversity_measures()`	Alpha Diversity Measures
`permanova()`	PERMANOVA
Validation
`is_analyzed_format()`	Is Analyzed MicrobiomeR Format
`is_basic_format()`	Is Basic MicrobiomeR Format
`is_phyloseq_format()`	Is Phyloseq MicrobiomeR Format
`is_raw_format()`	Is Raw MicrobiomeR Format
`order_metacoder_data()`	Order Metacoder Observation Data
`validate_MicrobiomeR_format()`	Validate MicrobiomeR Format
`which_format()`	Which MicrobiomeR Format
Basic Filtering
`otu_id_filter()`	Filter OTU Ids from Taxmap Objects
`sample_id_filter()`	Filter Samples Ids from Taxmap Objects
`taxon_id_filter()`	Filter Taxon Ids from Taxmap Objects
Advanced Filtering
`agglomerate_taxmap()`	Agglomerate taxmap Objects
`cov_filter()`	Coefficient of Variation Filter
`otu_prevalence_filter()`	OTU Prevalence Filter
`otu_proportion_filter()`	OTU Proportion Filter
`taxa_prevalence_filter()`	Taxonomic Prevalence Filter (Metacoder)
Other Filtering
`convert_proportions()`	Convert Proportions
`metacoder_comp_func_1()`	Metacoder Comparison Function #1
`transformer()`	Transforming Tidy Data
`transposer()`	Transposing Tidy Data
`vlookup()`	Mock Excel "VlookUp" Function
Visualization
`output_dir()`	Create an Output Directory
`save_top_coefficients_barplot()`	Save Top Coefficients Barplot
`alpha_diversity_plot()` `alpha_diversity_plots()`	Alpha Diversity Plot
`correlation_data()`	Get Correlation Plot Data
`correlation_plot()`	Correlation Plot
`correlation_plots()`	Get Multiple Correlation Plots
`heat_tree_parameters()`	Get Heat Tree Parameters
`heat_tree_plots()`	Get Heat Tree Plots
`ordination_plot()` `ordination_plots()`	Ordination Plot
`plot_limits()`	Get Plot Limits
`save_alpha_diversity_plots()`	Save Alpha Diversity Plots
`save_correlation_plots()`	Save Correlation Plots
`save_heat_tree_plots()`	Save Heat Tree Plots
`save_ordination_plots()`	Save Ordination Plots
`save_stacked_barplots()`	Save Stacked Barplots
`stacked_barplot()`	Stacked Barplot
`stacked_barplots()`	Stacked Barplots
`top_coefficients_barplot()`	Top Coefficients Barplot
Color Palettes
`combination_palette()`	Combine Color Palettes
`get_color_palette()`	Get a Color Palette
`scico_palette()`	Scico Palette Function
`viridis_magma_palette()`	Viridis-Magma Palette Function
`viridis_palette()`	Viridis Palette Function
Miscellaneous
`MicrobiomeR_Workflow`	The MicrobiomeR Workflow
`create_pub_table()`	Create Publication Table
Example Data
`phyloseq_silva_2`	Phyloseq Data with 2 Treatment Groups
`phyloseq_silva_3`	Phyloseq Data with 3 Treatment Groups
`raw_silva_2`	"raw_format" Data with 2 Treatment Groups
`raw_silva_3`	"raw_format" Data with 3 Treatment Groups

Reference

Import

Formatting

Statistics

Validation

Basic Filtering

Advanced Filtering

Other Filtering

Visualization

Color Palettes

Miscellaneous

Example Data