Package index • MicrobiomeStat

📊 Alpha Diversity Analysis

Functions for analyzing within-sample diversity

plot_alpha_diversity(): Plot Alpha Diversity
generate_alpha_boxplot_long(): Generate boxplot for specified alpha diversity index
generate_alpha_boxplot_single(): Generate boxplot for alpha diversity index at a single time point
generate_alpha_change_boxplot_pair(): Generate boxplot comparing change in specified alpha diversity index
generate_alpha_change_per_time_test_long(): Compare alpha diversity between time points
generate_alpha_change_test_pair(): Compare alpha diversity between time points
generate_alpha_per_time_dotplot_long(): Longitudinal Alpha Diversity Dot Plot for Microbiome Data
generate_alpha_per_time_test_long(): Longitudinal Alpha Diversity Test in Microbiome Data
generate_alpha_spaghettiplot_long(): Generate an alpha diversity line plot for longitudinal data
generate_alpha_test_pair(): Alpha Diversity Association Test
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_alpha_diversity(): Calculate alpha diversity indices
mStat_calculate_adjusted_alpha_diversity(): Adjust Alpha Diversity Indices Based on Covariates
is_rarefied(): Check if the data has been rarefied

🌐 Beta Diversity Analysis

Functions for analyzing between-sample diversity

plot_beta_diversity(): Plot Beta Diversity
generate_beta_change_boxplot_long(): Compare within-group and between-group beta diversity across time points
generate_beta_change_boxplot_pair(): Compare beta diversity between time points
generate_beta_change_per_time_test_long(): Generate Beta Change Tests for Longitudinal Data
generate_beta_change_spaghettiplot_long(): Generate beta diversity change spaghetti plot for longitudinal data
generate_beta_change_test_pair(): Compute and analyze changes in beta diversity
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_boxplot_long(): Create Boxplots for Beta Diversity Metrics
generate_beta_pc_change_boxplot_pair(): Visualize Beta Diversity Changes Over Time
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_per_time_dotplot_long(): Longitudinal Beta Diversity Dot Plot for Microbiome Data
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_beta_diversity(): Calculate various 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 in MicrobiomeStat
mStat_subset_dist(): Subset Distance Matrix

🦠 Taxonomic Analysis

Functions for taxonomic composition and differential abundance

plot_feature_diversity(): Visualize the relative abundance of selected taxa or functions
generate_taxa_areaplot_long(): Generate taxa area plots over time
generate_taxa_association_test_long(): Longitudinal Taxa Association Test Generation
generate_taxa_barplot_long(): Generate Taxa Barplots for Longitudinal Data
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_boxplot_pair(): Generate Individual Taxa Change Boxplot Pair
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_per_time_test_long(): Longitudinal Taxa Test in Microbiome Data
generate_taxa_change_scatterplot_pair(): Generate taxa-level difference scatterplot pairs
generate_taxa_change_test_pair(): Compute taxa changes and analyze differential abundance
generate_taxa_cladogram_single(): Generate Circular Cladogram with Heatmap for Taxonomic Data
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_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_ma_plot_single(): Generate MA Plots for Taxa Differential Test for a Single Time Point
generate_taxa_per_time_dotplot_long(): Longitudinal Taxa Dot Plot for Microbiome Data
generate_taxa_per_time_test_long(): Longitudinal Differential Abundance Test in Microbiome Data
generate_taxa_spaghettiplot_long(): Generate longitudinal spaghettiplot plots of taxonomic composition
generate_taxa_test_pair(): Generate Taxa Test Pair
generate_taxa_test_single(): Conduct Differential Abundance Testing Using LinDA Method in MicrobiomeStat Package
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
generate_taxa_volcano_single(): Generate Volcano Plots for Taxa Differential Test for a Single Time Point
mStat_aggregate_by_taxonomy(): Aggregate OTU Table by Taxonomy Level
mStat_aggregate_by_taxonomy2(): Aggregate OTU Table by Taxonomy Level
mStat_aggregate_data(): Aggregate Data Function
build_mStat_tax_table(): Build mStat tax table

📈 Statistical Testing

Core statistical methods including LinDA

linda(): Linear (Lin) model for differential abundance (DA) analysis
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 a specified sampling depth
mStat_filter(): Filter a Microbiome Data Matrix by Prevalence and Average Abundance
mStat_subset_data(): Subset Data Object by Sample IDs in MicrobiomeStat
mStat_remove_feature(): Remove Specific Features from a MicrobiomeStat 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 MicrobiomeStat Data Object
mStat_combine_data(): mStat_combine_data
mStat_process_time_variable(): Handle Time Variable in Meta Data Table
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 a report for microbial ecology analysis of cross-sectional, longitudinal or paired data at a single time point
mStat_generate_report_pair(): Generate a report for microbial ecology analysis of paired data
mStat_generate_report_long(): Generate Comprehensive Longitudinal Microbiome Analysis Report for MicrobiomeStat

🎨 Visualization Utilities

Helper functions for customizing plots

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

📚 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