Package index • MicrobiomeStat

🚀 Unified Interface

Simplified high-level functions for common analyses

MicrobiomeStat-unified: MicrobiomeStat Unified Interface
plot_alpha(): Unified Alpha Diversity Visualization
plot_beta(): Unified Beta Diversity Visualization
plot_taxa(): Unified Taxa Visualization
test_alpha(): Unified Alpha Diversity Statistical Testing
test_beta(): Unified Beta Diversity Statistical Testing
test_taxa(): Unified Taxa Statistical Testing

📊 Alpha Diversity Analysis

Functions for analyzing within-sample diversity

plot_alpha_diversity(): Plot Alpha Diversity
generate_alpha_boxplot_long(): Generate Alpha Diversity Boxplot (Longitudinal)
generate_alpha_boxplot_single(): Generate Alpha Diversity Boxplot (Single Time Point)
generate_alpha_change_boxplot_pair(): Generate Alpha Diversity Change Boxplot (Paired)
generate_alpha_change_per_time_test_long(): Alpha Diversity Change Test Per Time Point (Longitudinal)
generate_alpha_change_test_pair(): Alpha Diversity Change Test (Paired)
generate_alpha_per_time_dotplot_long(): Alpha Diversity Test Results Dot Plot (Longitudinal)
generate_alpha_per_time_test_long(): Alpha Diversity Test Per Time Point (Longitudinal)
generate_alpha_spaghettiplot_long(): Generate Alpha Diversity Spaghetti Plot (Longitudinal)
generate_alpha_test_pair(): Alpha Diversity Association Test (Paired)
generate_alpha_test_single(): Alpha Diversity Association Test (Single Time Point)
generate_alpha_trend_test_long(): Alpha Diversity Trend Test (Longitudinal)
generate_alpha_volatility_test_long(): Alpha Diversity Volatility Test (Longitudinal)
mStat_calculate_alpha_diversity(): Calculate alpha diversity indices
mStat_calculate_adjusted_alpha_diversity(): Adjust Alpha Diversity Indices Based on Covariates
is_rarefied(): Check if Data has been Rarefied

🌐 Beta Diversity Analysis

Functions for analyzing between-sample diversity

plot_beta_diversity(): Plot Beta Diversity
generate_beta_change_boxplot_long(): Generate Beta Diversity Change Boxplot for Longitudinal Data
generate_beta_change_boxplot_pair(): Generate Beta Diversity Change Boxplot for Paired Samples
generate_beta_change_per_time_test_long(): Beta Diversity Change Tests Per Time Point
generate_beta_change_spaghettiplot_long(): Generate Beta Diversity Change Spaghetti Plot for Longitudinal Data
generate_beta_change_test_pair(): Test Beta Diversity Change Between Time Points
generate_beta_ordination_long(): Generate Beta Diversity Ordination Plots for Longitudinal Data
generate_beta_ordination_pair(): Generate Beta Diversity Ordination Plots for Paired Samples
generate_beta_ordination_single(): Generate Beta Diversity Ordination Plot for Cross-Sectional Data
generate_beta_pc_boxplot_long(): Generate PC Boxplots for Beta Diversity Over Time
generate_beta_pc_change_boxplot_pair(): Generate PC Change Boxplots for Paired Samples
generate_beta_pc_spaghettiplot_long(): Generate PC Spaghetti Plots for Longitudinal Data
generate_beta_pc_trend_test_long(): Trend Test on Principal Coordinates for Longitudinal Data
generate_beta_pc_volatility_test_long(): Volatility Test on Principal Coordinates for Longitudinal Data
generate_beta_per_time_dotplot_long(): Dot Plot for Beta Diversity Change Tests Over Time
generate_beta_test_single(): PERMANOVA Test for Beta Diversity
generate_beta_trend_test_long(): Beta Diversity Trend Test for Longitudinal Data
generate_beta_volatility_test_long(): Beta Diversity Volatility Test for Longitudinal Data
mStat_calculate_beta_diversity(): Calculate Beta Diversity Indices
mStat_calculate_adjusted_distance(): Calculate Adjusted Distances for Specified Variables
mStat_calculate_PC(): Calculate Principal Coordinates using MDS, NMDS
mStat_subset_PC(): Subset Principal Coordinates Analysis (PCoA) Results
mStat_subset_alpha(): Subset Alpha Diversity Object
mStat_subset_data(): Subset Data Object by Sample IDs
mStat_subset_dist(): Subset Distance Matrix

🦠 Taxonomic Analysis

Functions for taxonomic composition and differential abundance

plot_feature_diversity(): Visualize Feature Diversity
generate_taxa_areaplot_long(): Generate Taxa Area Plots for Longitudinal Data
generate_taxa_association_test_long(): Longitudinal Taxa Association Test
generate_taxa_barplot_long(): Generate Taxa Barplots for Longitudinal Data
generate_taxa_barplot_pair(): Generate Pairwise Taxa Barplots
generate_taxa_barplot_single(): Generate Taxa Barplots for Single Time Point
generate_taxa_boxplot_long(): Generate Taxa Boxplots for Longitudinal Data
generate_taxa_boxplot_single(): Generate Taxa Boxplots for Single Time Point
generate_taxa_change_boxplot_pair(): Generate Taxa Change Boxplots for Paired Data
generate_taxa_change_dotplot_pair(): Generate Taxa Change Dotplot for Paired Data
generate_taxa_change_heatmap_long(): Generate Taxonomic Change Heatmap for Longitudinal Data
generate_taxa_change_heatmap_pair(): Generate Taxa Change Heatmap for Paired Data
generate_taxa_change_per_time_test_long(): Longitudinal Change-From-Baseline Taxa Test
generate_taxa_change_scatterplot_pair(): Generate Taxa Change Scatterplot for Paired Data
generate_taxa_change_test_pair(): Taxa Change Test for Paired Data
generate_taxa_cladogram_single(): Generate Circular Cladogram with Heatmap for Taxonomic Data
generate_taxa_dotplot_pair(): Generate Taxa Dotplot for Paired Samples
generate_taxa_dotplot_single(): Generate Taxa Dotplot for Single Time Point
generate_taxa_heatmap_long(): Generate Taxa Heatmap for Longitudinal Data
generate_taxa_heatmap_pair(): Generate Taxa Heatmap for Paired Samples
generate_taxa_heatmap_single(): Generate Taxa Heatmap for Single Time Point
generate_taxa_indiv_boxplot_long(): Generate Individual Taxa Boxplots for Longitudinal Data
generate_taxa_indiv_boxplot_single(): Generate Individual Taxa Boxplots for Single Time Point
generate_taxa_indiv_change_boxplot_pair(): Generate Individual Change Boxplots for Paired Samples
generate_taxa_indiv_change_scatterplot_pair(): Generate Individual Change Scatterplots for Paired Samples
generate_taxa_indiv_spaghettiplot_long(): Generate Individual Taxa Spaghetti Plots for Longitudinal Data
generate_taxa_ma_plot_single(): Generate MA Plots for Taxa Differential Abundance Test
generate_taxa_per_time_dotplot_long(): Longitudinal Taxa Dot Plot
generate_taxa_per_time_test_long(): Longitudinal Per-Time-Point Differential Abundance Test
generate_taxa_spaghettiplot_long(): Generate Longitudinal Spaghetti Plots of Taxonomic Composition
generate_taxa_test_pair(): Paired/Longitudinal Taxa Differential Abundance Test
generate_taxa_test_single(): Differential Abundance Testing for Single Time Point
generate_taxa_trend_test_long(): Longitudinal Taxa Trend Test
generate_taxa_trend_volcano_long(): Generate Volcano Plots for Longitudinal Taxa Trend Test
generate_taxa_volatility_test_long(): Longitudinal Taxa Abundance Volatility Test
generate_taxa_volatility_volcano_long(): Generate Volcano Plots for Taxa Volatility Test
generate_taxa_volcano_single(): Generate Volcano Plots for Single Time Point Taxa Test
mStat_aggregate_by_taxonomy(): Aggregate Feature Table by Taxonomy Level
mStat_aggregate_by_taxonomy2(): Aggregate Feature Table by Taxonomy Level (Low-Level Interface)
mStat_aggregate_data(): Aggregate Data by Subject
build_mStat_tax_table(): Build mStat tax table

📈 Statistical Testing

Core statistical methods including LinDA

linda(): Linear (Lin) model for differential abundance (DA) analysis
linda2(): Linear Model for Differential Abundance Analysis with Sample Weighting (Experimental)
linda.plot(): Plot linda results

📁 Data Import & Conversion

Import data from various microbiome analysis platforms

mStat_import_biom_as_data_obj(): Import a BIOM formatted data file into an mStat data object
mStat_import_dada2_as_data_obj(): Convert DADA2 Data into MicrobiomeStat's Data Object
mStat_import_mothur_as_data_obj(): Convert Mothur Data into MicrobiomeStat's Data Object
mStat_import_qiime2_as_data_obj(): Convert Qiime2 Data into MicrobiomeStat's Data Object
mStat_convert_DESeqDataSet_to_data_obj(): Convert a DESeqDataSet Object to a MicrobiomeStat Data Object
mStat_convert_DGEList_to_data_obj(): Convert a DGEList Object to a MicrobiomeStat Data Object
mStat_convert_MRExperiment_to_data_obj(): Convert a MRExperiment Object to a MicrobiomeStat Data Object
mStat_convert_MultiAssayExperiment_to_data_obj(): Convert MultiAssayExperiment Object to a Data Object
mStat_convert_SummarizedExperiment_to_data_obj(): Convert SummarizedExperiment Object to a MicrobiomeStat Data Object
mStat_convert_phyloseq_to_data_obj(): Convert a Phyloseq Object to a MicrobiomeStat's Data Object

🔧 Data Processing

Data manipulation and preprocessing utilities

mStat_normalize_data(): Normalize a MicrobiomeStat Data Object
mStat_rarefy_data(): Rarefy Data to Specified Sampling Depth
mStat_filter(): Filter a Microbiome Data Matrix by Prevalence and Average Abundance
mStat_subset_data(): Subset Data Object by Sample IDs
mStat_remove_feature(): Remove Specific Features from Data Object
mStat_validate_data(): Validate and Adjust a MicrobiomeStat Data Object
mStat_update_meta_data(): Update Metadata in a MicrobiomeStat Data Object
mStat_update_sample_name(): Update Sample Names in Data Object
mStat_combine_data(): mStat_combine_data
mStat_process_time_variable(): Process Time Variable in Metadata
mStat_identify_time_varying_vars(): Identify Time-Varying Variables within Subjects
mStat_summarize_data_obj(): Summarize a MicrobiomeStat Data Object

📝 Automated Reports

Generate comprehensive analysis reports

mStat_generate_report_single(): Generate Single Time Point Microbiome Analysis Report
mStat_generate_report_pair(): Generate Paired Microbiome Analysis Report
mStat_generate_report_long(): Generate Longitudinal Microbiome Analysis Report

🎨 Visualization Utilities

Helper functions for customizing plots

mStat_get_palette(): Retrieve Custom Color Palettes for Data Visualization
mStat_get_theme(): Get ggplot2 Theme for Plots
is_categorical(): Determine if a variable is categorical
is_continuous_numeric(): Check if a Variable is Continuous Numeric

📚 Example Datasets

Built-in datasets for testing and learning

ecam.obj: Data from the Early Childhood Antibiotics and the Microbiome (ECAM) study
peerj32.obj: Probiotics Intervention Data from the PeerJ32 Study
smokers: Smokers Microbiome Data from the Human Upper Respiratory Tract
subset_T2D.obj: Subset T2D Microbiome Data from the HMP2 Study
subset_pairs.obj: Paired Sample 16S Sequencing Data from the MiPair Study