Package index • pctax

All functions
`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()` `easy_tree()`	Annotate a tree
`aor()` `plot(<AOR>)`	Calculate Abundance-occupancy_relationship
`as.b_dist()` `plot(<dist>)` `plot(<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
`bbtt()`	ggdotchart for diff analysis
`before_tree()`	Before df2tree check
`plot(<time_cm>)`	Plot time_cm
`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
`envfitt()`	Envfit test for RDA result
`gene2id()`	Gene symbolid transfer to entrezIDs (human gene)
`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
`m_group_env()` `plot(<mant_g>)`	Multi-table test with env
`mat_dist()`	Calculate distance for otutab
`micro_sbatch()`	Microbiome sbatch
`multi_bar()`	Difference analysis
`myRDA()` `myCCA()` `myCAP()`	RDA
`name_or_id2df()`	Transfer taxon name or taxid to the lineage dataframe
`ncm()` `plot(<ncm_res>)`	Sloan Neutral Model
`nst()`	Calculate NST for each group
`nti_rc()` `plot(<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_N_cycle()`	Plot the N-cycling pathway and genes
`plot_element_cycle()`	Plot element cycle
`plot_two_tree()`	Plot two trees in one plot
`pre_GEO()`	prepare the GEO data
`pre_fastp()`	Prepare the result from fastp (.json file)
`pre_tax_table()`	Complete a taxonomy table
`print(<pc_otu>)`	Print
`procrustes_analyse()`	Procrustes Rotation of Two Configurations and PROTEST
`rare_curve_sample()` `plot(<rare_res>)`	Rare the sample
`rare_curve_species()`	Rare the species
`rarefaction()`	Rarefy a otutab
`sangji_plot()`	Plot a sankey
`suijisenlin()`	RandomForest
`summary(<pc_otu>)`	Summary pc_otu
`sunburst()`	Plot a sunburst
`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()` `plot(<zeta_res>)`	Calculate Zeta Diversity
`z_diversity_decay()` `plot(<zeta_decay>)`	Calculate Zeta Diversity with Distance

Reference

All functions