ALDEX                   ALDEX
RCbray1                 Calculate RCbray-curtis
RDA_plot                Plot RDA res
a_diversity             Calculate a_diversity of otutab
add_strip               add strips for a tree plot
add_tax                 Add taxonomy for a pc_otu object
all_ec_info             all element cycle information.
all_sp_la_zh_name       all species latin names and chinese names
ann_tree                Annotate a tree
aor                     Calculate Abundance-occupancy_relationship
as.b_dist               Transfer dist to b_dist
as.dist.b_dist          Transfer b_dist to dist
b_NTI1                  Calculate beta_NTI
b_analyse               Beta_diversity Ordination: dimensionality
                        reduction
b_res_3d                3D plot for b_res
batch_mediate           Batch mediate
bbtt                    ggdotchart for diff analysis
before_tree             Before df2tree check
check_taxonkit          Check taxonkit
convert_taxon_name      Convert taxon names between Chinese and Latin
cor_net                 Correlation network, species-interaction
                        network for omics
df2tree                 From a dataframe to construct a phylo
df2tree1                From a dataframe to construct a phylo (save
                        nwk)
diff_da                 Difference analysis
download_taxonkit_dataset
                        Download taxonkit dataset
drop_tips_update        Drop Tips and Update a Phylogenetic Tree
envfitt                 Envfit test for RDA result
geo_sim                 Lm for sample similarity and geographical
                        distance
get_all_sp_la_zh_name   get all species Latin and Chinese name from the
                        CCTCC database
get_diff_type           Get mean and type
gp_dis_density          Group inter-intra density
grap_p_test             Performs graph-based permutation tests
install_taxonkit        Install taxonkit
kwtest                  KW test
load_N_data             Load N-cycle data
load_mpa_df             Load a metaphlan format data.frame
mat_dist                Calculate distance for otutab
micro_sbatch            Microbiome sbatch
multi_bar               Difference analysis
multi_conf              Difference analysis
myRDA                   RDA
name_or_id2df           Transfer taxon name or taxid to the lineage
                        dataframe
ncm                     Sloan Neutral Model
nst                     Calculate NST for each group
nti_rc                  Calculate b_NTI and RC_bray for each group
pc_otu                  Create a pc_otu class object
pc_tax1                 test data (pc_otu class) for pc_tax package.
pc_valid                Judge pc_otu is valid or not
permanova               Permanova between a otutab and a variable
plot.a_res              Plot a_res object
plot.b_res              Plot a b_res
plot.g_test             Plot g_test
plot.pro_res            Plot pro_res
plot.time_cm            Plot time_cm
plot_N_cycle            Plot the N-cycling pathway and genes
plot_checkm2_res        Visualize CheckM2 Genome Quality Assessment
                        Results
plot_contigs_quality    Visualize Contigs Quality Metrics
plot_element_cycle      Plot element cycle
plot_gtdb_tr            Plot GTDB-Tk Phylogenetic Tree with Taxonomic
                        Coloring
plot_one_phage          Plot Individual Phage Genome Structure with
                        Annotations
plot_two_tree           Plot two trees in one plot
pre_assembly_stats      Prepare the result from assembly_stats (.json
                        file)
pre_fastp               Prepare the result from fastp (.json file)
pre_format_report       Preprocess MPA Species Abundance and Taxonomy
                        Data
pre_genomad             Preprocess geNomad and CheckV Output Results
pre_gtdb_tk             Preprocess GTDB-Tk Classification Results
pre_tax_table           Complete a taxonomy table
print.pc_otu            Print
print.virus_res         Print method for virus_res objects
procrustes_analyse      Procrustes Rotation of Two Configurations and
                        PROTEST
rare_curve_sample       Rare the sample
rare_curve_species      Rare the species
rarefaction             Rarefy a otutab
stamp_plot              Stamp style plot
suijisenlin             RandomForest
summary.pc_otu          Summary pc_otu
tax_lca                 Calculate the lowest common ancestor (LCA) of a
                        set of taxa
taxonkit_filter         Filter TaxIDs based on Taxonomic Ranks
taxonkit_lca            Compute Lowest Common Ancestor (LCA) of TaxIDs
taxonkit_lineage        Retrieve Taxonomic Lineage using taxonkit
taxonkit_list           Taxonkit list
taxonkit_name2taxid     Convert Taxonomic Names to TaxIDs
taxonkit_reformat       Reformat Taxonomic Lineage using taxonkit
time_by_cm              Time series analysis
volcano_p               Volcano plot for difference analysis
z_diversity             Calculate Zeta Diversity
z_diversity_decay       Calculate Zeta Diversity with Distance
