ImportDada2             Import function to load the feature table and
                        taxonomy table of dada2
ImportQiime2            Import function to load the output of qiime2.
MPSE                    Construct a MPSE object
MPSE-accessors          MPSE accessors
MPSE-class              MPSE class
alphasample-class       alphasample class
as.MPSE                 as.MPSE method
as.phyloseq             convert to phyloseq object.
as.treedata.taxonomyTable
                        as.treedata
build_tree              building tree
convert_to_treedata     convert dataframe contained hierarchical
                        relationship or other classes to treedata class
data-hmp_aerobiosis_small
                        (Data) Small subset of the HMP 16S dataset
data-kostic2012crc      (Data) Genomic analysis identifies association
                        of Fusobacterium with colorectal carcinoma
                        (2012)
data-test_otu_data      (Data) simulated dataset.
diffAnalysisClass-class
                        diffAnalysisClass class
diff_analysis           Differential expression analysis
dr_extract              Extracting the internal tbl_df attribute of
                        tibble.
drop_taxa               Dropping Species with Few abundance and Few
                        Occurrences
extract_binary_offspring
                        extract the binary offspring of the specified
                        internal nodes
generalizedFC           generalized fold change
get_NRI_NTI             calculating related phylogenetic alpha metric
get_alphaindex          alpha index
get_clust               Hierarchical cluster analysis for the samples
get_coord.pcoa          get ordination coordinates.
get_count               calculate the count or relative abundance of
                        replicate element with a speficify column
get_dist                calculate distance
get_mean_median         get the mean and median of specific feature.
get_pca                 Performs a principal components analysis
get_pcoa                performs principal coordinate analysis (PCoA)
get_pvalue              Methods for computation of the p-value
get_rarecurve           obtain the result of rare curve
get_sampledflist        Generate random data list from a original data.
get_taxadf              get the data of specified taxonomy
get_upset               generate the dataset for upset of UpSetR
get_varct.pcoa          get the contribution of variables
get_vennlist            generate a vennlist for VennDiagram
ggbartax                taxonomy barplot
ggbox                   A box or violin plot with significance test
ggclust                 plot the result of hierarchical cluster
                        analysis for the samples
ggdiffbox               boxplot for the result of diff_analysis
ggdiffclade             plot the clade tree with highlight
ggdifftaxbar            significantly discriminative feature barplot
ggeffectsize            visualization of effect size by the Linear
                        Discriminant Analysis or randomForest
ggordpoint              ordination plotter based on ggplot2.
ggrarecurve             Rarefaction alpha index
mouse.time.mpse         (Data) An example data
mp_adonis               Permutational Multivariate Analysis of Variance
                        Using Distance Matrices for MPSE or tbl_mpse
                        object
mp_aggregate            aggregate the assays with the specific group of
                        sample and fun.
mp_aggregate_clade      calculate the mean/median (relative) abundance
                        of internal nodes according to their children
                        tips.
mp_anosim               Analysis of Similarities (ANOSIM) with MPSE or
                        tbl_mpse object
mp_balance_clade        Calculating the balance score of internal nodes
                        (clade) according to the
                        geometric.mean/mean/median abundance of their
                        binary children tips.
mp_cal_abundance        Calculate the (relative) abundance of each
                        taxonomy class for each sample or group.
mp_cal_alpha            calculate the alpha index with MPSE or tbl_mpse
mp_cal_cca              [Partial] [Constrained] Correspondence Analysis
                        with MPSE or tbl_mpse object
mp_cal_clust            Hierarchical cluster analysis for the samples
                        with MPSE or tbl_mpse object
mp_cal_dca              Detrended Correspondence Analysis with MPSE or
                        tbl_mpse object
mp_cal_dist             Calculate the distances between the samples or
                        features with specified abundance.
mp_cal_divergence       calculate the divergence with MPSE or tbl_mpse
mp_cal_nmds             Nonmetric Multidimensional Scaling Analysis
                        with MPSE or tbl_mpse object
mp_cal_pca              Principal Components Analysis with MPSE or
                        tbl_mpse object
mp_cal_pcoa             Principal Coordinate Analysis with MPSE or
                        tbl_mpse object
mp_cal_pd_metric        Calculating related phylogenetic alpha metric
                        with MPSE or tbl_mpse object
mp_cal_rarecurve        Calculating the different alpha diversities
                        index with different depth
mp_cal_rda              [Partial] [Constrained] Redundancy Analysis
                        with MPSE or tbl_mpse object
mp_cal_upset            Calculating the samples or groups for each OTU,
                        the result can be visualized by 'ggupset'
mp_cal_venn             Calculating the OTU for each sample or group,
                        the result can be visualized by 'ggVennDiagram'
mp_decostand            This Function Provideds Several Standardization
                        Methods for Community Data
mp_diff_analysis        Differential expression analysis for MPSE or
                        tbl_mpse object
mp_diff_clade           Differential internal and tip nodes (clades)
                        analysis for MPSE or tbl_mpse object
mp_dmn                  Fit Dirichlet-Multinomial models to MPSE or
                        tbl_mpse
mp_dmngroup             Dirichlet-Multinomial generative classifiers to
                        MPSE or tbl_mpse
mp_envfit               Fits an Environmental Vector or Factor onto an
                        Ordination With MPSE or tbl_mpse Object
mp_extract_abundance    Extracting the abundance metric from MPSE or
                        tbl_mpse object
mp_extract_assays       extract the abundance matrix from MPSE object
                        or tbl_mpse object
mp_extract_dist         extract the dist object from MPSE or tbl_mpse
                        object
mp_extract_feature      extract the feature (OTU) information in MPSE
                        object
mp_extract_internal_attr
                        Extracting the PCA, PCoA, etc results from MPSE
                        or tbl_mpse object
mp_extract_rarecurve    Extract the result of mp_cal_rarecurve with
                        action="add" from MPSE or tbl_mpse object
mp_extract_refseq       Extract the representative sequences from MPSE
                        object
mp_extract_sample       extract the sample information in MPSE object
mp_extract_tree         extract the taxonomy tree in MPSE object
mp_filter_taxa          Filter OTU (Features) By Abundance Level
mp_fortify              mp_fortify
mp_import_biom          building MPSE object from biom-format file.
mp_import_metaphlan     Import function to load the output of
                        MetaPhlAn.
mp_import_qiime         Import function to load the output of qiime.
mp_mantel               Mantel and Partial Mantel Tests for MPSE or
                        tbl_mpse Object
mp_mrpp                 Analysis of Multi Response Permutation
                        Procedure (MRPP) with MPSE or tbl_mpse object
mp_plot_abundance       plotting the abundance of taxa via specified
                        taxonomy class
mp_plot_alpha           Plotting the alpha diversity between samples or
                        groups.
mp_plot_diff_boxplot    displaying the differential result contained
                        abundance and LDA with boxplot (abundance) and
                        error bar (LDA).
mp_plot_diff_cladogram
                        Visualizing the result of mp_diff_analysis with
                        cladogram.
mp_plot_diff_manhattan
                        displaying the differential result contained
                        abundance and LDA with manhattan plot.
mp_plot_diff_res        The visualization of result of mp_diff_analysis
mp_plot_dist            Plotting the distance between the samples with
                        heatmap or boxplot.
mp_plot_ord             Plotting the result of PCA, PCoA, CCA, RDA,
                        NDMS or DCA
mp_plot_rarecurve       Rarefaction alpha index with MPSE
mp_plot_upset           Plotting the different number of OTU between
                        group via UpSet plot
mp_plot_venn            Plotting the different number of OTU between
                        groups with Venn Diagram.
mp_rrarefy              mp_rrarefy method
mp_select_as_tip        select specific taxa level as rownames of MPSE
mp_stat_taxa            Count the number and total number taxa for each
                        sample at different taxonomy levels
multi_compare           a container for performing two or more sample
                        test.
ordplotClass-class      ordplotClass class
pcasample-class         pcasample class
print                   print some objects
read_qza                read the qza file, output of qiime2.
scale_fill_diff_cladogram
                        Create the scale of mp_plot_diff_cladogram.
set_diff_boxplot_color
                        set the color scale of plot generated by
                        mp_plot_diff_boxplot
set_scale_theme         adjust the color of heatmap of mp_plot_dist
show,diffAnalysisClass-method
                        method extensions to show for diffAnalysisClass
                        or alphasample objects.
split_data              Split Large Vector or DataFrame
split_str_to_list       split a dataframe contained one column
taxonomy                extract the taxonomy annotation in MPSE object
theme_taxbar            theme_taxbar
