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Alpha Diversity

plot_alpha_diversity()
Plot Alpha Diversity
generate_alpha_boxplot_single()
Generate boxplot for alpha diversity index at a single time point
generate_alpha_boxplot_long()
Generate boxplot for specified alpha diversity index
generate_alpha_per_time_dotplot_long()
Longitudinal Alpha Diversity Dot Plot for Microbiome Data
generate_alpha_spaghettiplot_long()
Generate an alpha diversity line plot for longitudinal data
generate_alpha_change_boxplot_pair()
Generate boxplot comparing change in specified alpha diversity index
generate_alpha_change_test_pair()
Compare alpha diversity between time points
generate_alpha_change_per_time_test_long()
Compare alpha diversity between time points
generate_alpha_test_pair()
Alpha Diversity Association Test
generate_alpha_per_time_test_long()
Longitudinal Alpha Diversity Test in Microbiome Data
generate_alpha_test_single()
Perform alpha diversity association tests using linear models
generate_alpha_trend_test_long()
Longitudinal Alpha Diversity Trend Test in MicrobiomeStat
generate_alpha_volatility_test_long()
Longitudinal Alpha Diversity Volatility Test in MicrobiomeStat
mStat_calculate_adjusted_alpha_diversity()
Adjust Alpha Diversity Indices Based on Covariates
is_rarefied()
Check if the data has been rarefied

Beta Diversity

plot_beta_diversity()
Plot Beta Diversity
generate_beta_change_boxplot_pair()
Compare beta diversity between time points
generate_beta_change_boxplot_long()
Compare within-group and between-group beta diversity across time points
generate_beta_change_spaghettiplot_long()
Generate beta diversity change spaghetti plot for longitudinal data
generate_beta_ordination_long()
Generate Beta Ordination Plots
generate_beta_ordination_pair()
Generate beta ordination plots for paired samples
generate_beta_ordination_single()
Generate Beta Diversity Ordination Plot
generate_beta_pc_change_boxplot_pair()
Visualize Beta Diversity Changes Over Time
generate_beta_change_test_pair()
Compute and analyze changes in beta diversity
generate_beta_change_per_time_test_long()
Generate Beta Change Tests for Longitudinal Data
generate_beta_per_time_dotplot_long()
Longitudinal Beta Diversity Dot Plot for Microbiome Data
generate_beta_pc_boxplot_long()
Create Boxplots for Beta Diversity Metrics
generate_beta_pc_spaghettiplot_long()
Generate spaghetti plots of beta diversity over time
generate_beta_pc_trend_test_long()
Trend Test on Principal Coordinates of Beta Diversity Metrics Over Time
generate_beta_pc_volatility_test_long()
Generate Beta PC Volatility Test in Long Format
generate_beta_test_single()
Calculate Beta Diversity Indices and Perform PERMANOVA Tests
generate_beta_trend_test_long()
Generate Beta Diversity Trend Test for Longitudinal Data
generate_beta_volatility_test_long()
Generate Beta Diversity Volatility Test for Longitudinal Data
mStat_calculate_adjusted_distance()
Calculate Adjusted Distances for Specified Variables
mStat_calculate_PC()
Calculate Principal Coordinates using MDS, NMDS

Feature-level Analysis

plot_feature_diversity()
Visualize the relative abundance of selected taxa or functions
generate_taxa_cladogram_single()
Generate a Circular Cladogram with Heatmap for Taxa
generate_taxa_barplot_pair()
Generate Pairwise Taxa Barplots for Longitudinal Data
generate_taxa_barplot_single()
Generate Stacked Taxa Barplots for Single or Longitudinal Data
generate_taxa_boxplot_long()
Generate Taxa Boxplots for Longitudinal Data
generate_taxa_boxplot_single()
Generate Single Time Point Taxa Boxplots
generate_taxa_change_dotplot_pair()
Generate Taxa Stack Dotplot Pair
generate_taxa_change_heatmap_long()
Generate Taxonomic Change Heatmap Long
generate_taxa_change_heatmap_pair()
Generate Taxa Change Heatmap Pair
generate_taxa_change_scatterplot_pair()
Generate taxa-level difference scatterplot pairs
generate_taxa_dotplot_pair()
Generate Taxa Stack Dotplot Pair
generate_taxa_dotplot_single()
Generate Taxonomic Dotplot Single
generate_taxa_heatmap_long()
Generate Taxonomic Heatmap Long
generate_taxa_heatmap_pair()
Generate Taxonomic Heatmap Pair
generate_taxa_heatmap_single()
Generate Taxonomic Heatmap Single
generate_taxa_areaplot_long()
Generate taxa area plots over time
generate_taxa_barplot_long()
Generate Taxa Barplots for Longitudinal Data
generate_taxa_per_time_dotplot_long()
Longitudinal Taxa Dot Plot for Microbiome Data
generate_taxa_change_boxplot_pair()
Generate Individual Taxa Change Boxplot Pair
generate_taxa_change_test_pair()
Compute taxa changes and analyze differential abundance
generate_taxa_change_per_time_test_long()
Longitudinal Taxa Test in Microbiome Data
generate_taxa_indiv_boxplot_long()
Generate Boxplot of Individual Taxa Abundance Over Time
generate_taxa_indiv_boxplot_single()
Generate Taxa Boxplots for Single Time Point
generate_taxa_indiv_change_boxplot_pair()
Generate Individual Change Boxplot Pairs for Taxonomic Composition Data
generate_taxa_indiv_change_scatterplot_pair()
Generate Individual Change Scatterplot Pairs for Taxonomic Composition Data
generate_taxa_indiv_spaghettiplot_long()
Generate longitudinal line plots of taxonomic composition
generate_taxa_spaghettiplot_long()
Generate longitudinal spaghettiplot plots of taxonomic composition
generate_taxa_test_pair()
Generate Taxa Test Pair
generate_taxa_per_time_test_long()
Longitudinal Differential Abundance Test in Microbiome Data
generate_taxa_test_single()
Conduct Differential Abundance Testing Using LinDA Method in MicrobiomeStat Package
generate_taxa_volcano_single()
Generate Volcano Plots for Taxa Differential Test for a Single Time Point
generate_taxa_association_test_long()
Longitudinal Taxa Association Test Generation
generate_taxa_trend_test_long()
Longitudinal Taxa Trend Test Generation
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 Longitudinal Taxa Abundance Volatility Test
mStat_aggregate_by_taxonomy()
Aggregate OTU Table by Taxonomy Level
mStat_aggregate_by_taxonomy2()
Aggregate OTU Table by Taxonomy Level

Data Management

mStat_subset_alpha()
Subset Alpha Diversity Object
mStat_subset_dist()
Subset Distance Matrix
mStat_subset_PC()
Subset Principal Coordinates Analysis (PCoA) Results
mStat_summarize_data_obj()
Summarize a MicrobiomeStat Data Object
mStat_process_time_variable()
Handle Time Variable in Meta Data Table
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_phyloseq_to_data_obj()
Convert a Phyloseq Object to a MicrobiomeStat's Data Object
mStat_convert_SummarizedExperiment_to_data_obj()
Convert SummarizedExperiment Object to a MicrobiomeStat Data Object
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_normalize_data()
Normalize a MicrobiomeStat Data Object
mStat_rarefy_data()
Rarefy data to a specified sampling depth
mStat_filter()
Filter a Microbiome Data Matrix by Prevalence and Average Abundance
mStat_remove_feature()
Remove Specific Features from a MicrobiomeStat Data Object
mStat_subset_data()
Subset Data Object by Sample IDs in MicrobiomeStat
mStat_update_meta_data()
Update Metadata in a MicrobiomeStat Data Object
mStat_update_sample_name()
Update Sample Names in MicrobiomeStat Data Object
mStat_validate_data()
Validate and Adjust a MicrobiomeStat Data Object
mStat_identify_time_varying_vars()
Identify Time-Varying Variables within Subjects

Reports

mStat_generate_report_long()
Generate Comprehensive Longitudinal Microbiome Analysis Report for MicrobiomeStat
mStat_generate_report_pair()
Generate a report for microbial ecology analysis of paired data
mStat_generate_report_single()
Generate a report for microbial ecology analysis of cross-sectional, longitudinal or paired data at a single time point

Data Sets

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

Miscellaneous

mStat_get_palette()
Retrieve Custom Color Palettes for Data Visualization
mStat_get_theme()
Get the ggplot2 Theme for Plots
is_categorical()
Determine if a variable is categorical
is_continuous_numeric()
Check if a Variable is Continuous Numeric
linda.plot()
Plot linda results
build_mStat_tax_table()
Build mStat tax table
mStat_aggregate_data()
Aggregate Data Function
linda()
Linear (Lin) model for differential abundance (DA) analysis
mStat_calculate_alpha_diversity()
Calculate alpha diversity indices
mStat_calculate_beta_diversity()
Calculate various beta diversity indices
mStat_combine_data()
mStat_combine_data