# Generated by roxygen2: do not edit by hand

S3method("$",robimetabar)
S3method("$",robiseq)
S3method("$<-",robimetabar)
S3method("$<-",robisample)
S3method("[",robicategory)
S3method("[",robiseq)
S3method("[",robiseq_db)
S3method("[",robitag)
S3method("[",robitag_forward)
S3method("[",robitag_reverse)
S3method("[",robitaxid)
S3method("[",robitaxid_master)
S3method("[",robiuniqueid)
S3method("[<-",robicategory)
S3method("[<-",robitag)
S3method("[<-",robitag_forward)
S3method("[<-",robitag_reverse)
S3method("[<-",robitaxid)
S3method("[<-",robitaxid_master)
S3method("[<-",robiuniqueid)
S3method("[[",robimetabar)
S3method("[[",robiseq)
S3method("[[<-",robimetabar)
S3method("[[<-",robisample)
S3method("motus<-",robimetabar)
S3method("samples<-",robimetabar)
S3method(alternative_names,robitaxonomy)
S3method(alternative_taxids,robitaxonomy)
S3method(as_robicategory,character)
S3method(as_robicategory,default)
S3method(as_robicategory,factor)
S3method(as_robicategory,robicategory)
S3method(as_robiobject,default)
S3method(as_robiobject,robiobject)
S3method(as_robisample,default)
S3method(as_robisample,robisample)
S3method(as_robitag,character)
S3method(as_robitag,default)
S3method(as_robitag,robitag)
S3method(as_robitag_forward,character)
S3method(as_robitag_forward,default)
S3method(as_robitag_forward,robitag)
S3method(as_robitag_reverse,character)
S3method(as_robitag_reverse,default)
S3method(as_robitag_reverse,robitag)
S3method(as_robitaxid,default)
S3method(as_robitaxid,robitaxid)
S3method(as_robitaxid,robitaxonomy)
S3method(as_robitaxid_master,default)
S3method(as_robitaxid_master,robitaxid)
S3method(as_robitaxid_master,robitaxonomy)
S3method(as_robitaxonomy,robilca)
S3method(as_robiuniqueid,character)
S3method(as_robiuniqueid,default)
S3method(as_robiuniqueid,robiuniqueid)
S3method(c,robicategory)
S3method(c,robitag)
S3method(c,robitag_forward)
S3method(c,robitag_reverse)
S3method(c,robitaxid)
S3method(c,robitaxid_master)
S3method(c,robiuniqueid)
S3method(decostand,"NULL")
S3method(decostand,default)
S3method(decostand,robimetabar)
S3method(dim,robimetabar)
S3method(dim,robitaxonomy)
S3method(dimnames,robidata)
S3method(dimnames,robimetabar)
S3method(ecofind,robitaxonomy)
S3method(expand_names,robitaxonomy)
S3method(format,robicategory)
S3method(full_taxonomy,robitaxonomy)
S3method(ids,default)
S3method(ids,robisample)
S3method(ids_colname,robisample)
S3method(is_full_taxonomy,robitaxonomy)
S3method(lowest_common_ancestor,robitaxonomy)
S3method(max,robitaxonomy)
S3method(min,robitaxonomy)
S3method(motu_ids_name,robimetabar)
S3method(motus,robimetabar)
S3method(names,robimetabar)
S3method(names,robiseq)
S3method(nmotus,robimetabar)
S3method(nodes,robitaxonomy)
S3method(nsamples,robimetabar)
S3method(parent,robitaxonomy)
S3method(pillar_shaft,robicategory)
S3method(pillar_shaft,robitag)
S3method(pillar_shaft,robitaxid)
S3method(pillar_shaft,robiuniqueid)
S3method(print,robicategory)
S3method(reference_taxonomy,robilca)
S3method(reference_taxonomy,robitaxid)
S3method(reference_taxonomy,robitaxonomy)
S3method(rep,robicategory)
S3method(rep,robitag)
S3method(rep,robitag_forward)
S3method(rep,robitag_reverse)
S3method(rep,robitaxid)
S3method(rep,robitaxid_master)
S3method(sample_ids_name,robimetabar)
S3method(samples,robimetabar)
S3method(scientific_name,robitaxonomy)
S3method(sort,robipath)
S3method(tags_positive_ctrls,robimetabar)
S3method(type_sum,robicategory)
S3method(type_sum,robilca)
S3method(type_sum,robipath)
S3method(type_sum,robitag)
S3method(type_sum,robitag_forward)
S3method(type_sum,robitag_reverse)
S3method(type_sum,robitaxid)
S3method(type_sum,robitaxid_master)
S3method(type_sum,robiuniqueid)
S3method(validate_robisample,robisample)
S3method(validate_robitaxonomy,robitaxonomy)
S3method(write.xlsx,default)
S3method(write.xlsx,robimetabar)
export("levels <- .robicategory")
export("motus<-")
export("samples<-")
export(D_q)
export(H_q)
export(alternative_names)
export(alternative_taxids)
export(as.robimetabar.robiseq_db)
export(as_robicategory)
export(as_robimetabar)
export(as_robiobject)
export(as_robisample)
export(as_robitag)
export(as_robitag_forward)
export(as_robitag_reverse)
export(as_robitaxid)
export(as_robitaxid_master)
export(as_robitaxonomy)
export(as_robiuniqueid)
export(build.robiseq)
export(build_sample_names)
export(clique_tag)
export(colors_tol)
export(combine_LETTERS)
export(d_exp_q)
export(d_log_q)
export(dd_exp_q)
export(decostand)
export(download_ncbi_taxdump)
export(ecofind)
export(every_oligo)
export(exp_q)
export(expand_names)
export(family)
export(feature_as_matrix)
export(filter_tag_gcmax)
export(filter_tag_homopolymere)
export(filter_tag_homopolymere_min)
export(full_taxonomy)
export(genus)
export(get_default_taxonomy)
export(gradient_tol1)
export(gradient_tol2)
export(ids)
export(ids_colname)
export(int2nuc)
export(is.subcladeof)
export(is_full_taxonomy)
export(is_robi_verbose)
export(is_robicategory)
export(is_robidata)
export(is_robiobject)
export(is_robisample)
export(is_robitag)
export(is_robitaxid)
export(is_robitaxonomy)
export(is_robiuniqueid)
export(kingdom)
export(log_q)
export(lowest_common_ancestor)
export(motu_ids_name)
export(motus)
export(new_robicategory)
export(new_robidata)
export(new_robilca)
export(new_robiobject)
export(new_robipath)
export(new_robisample)
export(new_robitag)
export(new_robitag_forward)
export(new_robitag_reverse)
export(new_robitaxid)
export(new_robitaxid_master)
export(new_robitaxonomy)
export(new_robiuniqueid)
export(nmotus)
export(nodes)
export(nsamples)
export(nuc2int)
export(parent)
export(rainbow_tol)
export(rank.list)
export(rbarcode)
export(read.sequence)
export(read_fasta)
export(read_ncbi_taxdump)
export(read_obitab)
export(read_obitools_taxonomy)
export(read_robitaxonomy)
export(reference_taxonomy)
export(resets_category_tags)
export(rkmer)
export(rnuc)
export(robiassert)
export(robiassert_arg)
export(robicategory)
export(robilca)
export(robimetabar)
export(robipath)
export(robisample)
export(robitag)
export(robitag_forward)
export(robitag_reverse)
export(robitaxid)
export(robitaxid_master)
export(robiuniqueid)
export(rseq)
export(sample_ids_name)
export(samples)
export(scientific_name)
export(set_default_taxonomy)
export(species)
export(superkingdom)
export(tags_positive_ctrls)
export(taxid.validate)
export(taxon.at.rank)
export(taxon.path)
export(taxonomic.rank)
export(unclass_robiobject)
export(validate_robisample)
export(validate_robitaxonomy)
export(write.xlsx)
export(write_robitaxonomy)
import(R6)
import(doParallel)
import(dplyr)
import(foreach)
import(readr)
import(stringr)
import(tibble)
import(utils)
import(vegan)
import(xlsx)
importFrom(Rdpack,reprompt)
importFrom(glue,glue)
importFrom(pillar,pillar_shaft)
importFrom(pillar,type_sum)
useDynLib(ROBITools2)