NAMESPACE 17 KB
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# Generated by roxygen2: do not edit by hand

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S3method("$",robiseq)
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S3method("$<-",robimotu)
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S3method("$<-",robisample)
S3method("[",robiseq)
S3method("[",robiseq_db)
S3method("[[",robiseq)
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S3method("[[<-",robimotu)
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S3method("[[<-",robisample)
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S3method(alternative_names,robitaxonomy)
S3method(alternative_taxids,robitaxonomy)
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S3method(as_robidata,default)
S3method(as_robidata,robidata)
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S3method(as_robilca,default)
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S3method(as_robimotu,default)
S3method(as_robimotu,robimotu)
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S3method(as_robimutation,default)
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S3method(as_robiobject,default)
S3method(as_robiobject,robiobject)
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S3method(as_robipath,default)
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S3method(as_robisample,default)
S3method(as_robisample,robisample)
S3method(as_robitaxid,default)
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S3method(as_robitaxid,robitaxonomy)
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S3method(as_robitaxid_master,default)
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S3method(as_robitaxid_master,robitaxonomy)
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S3method(as_robitaxonomy,robilca)
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S3method(as_robitaxonomy,robitaxid)
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S3method(as_robiuniqueid,character)
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S3method(c,robiatomic)
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S3method(categories,default)
S3method(categories,robimetabar)
S3method(categories,robisample)
S3method(categories_colname,robimetabar)
S3method(categories_colname,robisample)
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S3method(clean_tagjump,robimetabar)
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S3method(clone,robimetabar)
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S3method(decostand,"NULL")
S3method(decostand,default)
S3method(decostand,robimetabar)
S3method(dim,robimetabar)
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S3method(dim,robitaxonomy)
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S3method(dimnames,robidata)
S3method(dimnames,robimetabar)
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S3method(ecofind,robitaxonomy)
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S3method(ecotag_best_identity,robimetabar)
S3method(ecotag_best_identity,robimotu)
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S3method(format,robimutation)
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S3method(format,robitaxid)
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S3method(forward_tags,default)
S3method(forward_tags,robimetabar)
S3method(forward_tags,robisample)
S3method(forward_tags_colname,robimetabar)
S3method(forward_tags_colname,robisample)
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S3method(full_taxonomy,robitaxonomy)
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S3method(ids,default)
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S3method(ids,robidata)
S3method(ids_colname,robidata)
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S3method(is_full_taxonomy,robitaxonomy)
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S3method(is_subclade_of,numeric)
S3method(is_subclade_of,robimetabar)
S3method(is_subclade_of,robimotu)
S3method(is_subclade_of,robitaxid)
S3method(is_subclade_of,tbl)
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S3method(left_parse_sample_ids,robidata)
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S3method(left_parse_sample_ids,robimetabar)
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S3method(lowest_common_ancestor,robitaxonomy)
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S3method(master_taxids,default)
S3method(master_taxids,robimetabar)
S3method(master_taxids,robimotu)
S3method(master_taxids_colname,robimetabar)
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S3method(master_taxids_colname,tbl)
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S3method(max,robitaxonomy)
S3method(min,robitaxonomy)
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S3method(motus,robimetabar)
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S3method(motus_ids,robimetabar)
S3method(motus_ids_colname,robimetabar)
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S3method(names,robimetabar)
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S3method(names,robiseq)
S3method(nmotus,robimetabar)
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S3method(nodes,robitaxonomy)
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S3method(nsamples,robimetabar)
S3method(pillar_shaft,robicategory)
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S3method(pillar_shaft,robimutation)
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S3method(pillar_shaft,robitag)
S3method(pillar_shaft,robitaxid)
S3method(pillar_shaft,robiuniqueid)
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S3method(rbind,robidata)
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S3method(reference_taxonomy,robitaxid)
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S3method(reference_taxonomy,robitaxonomy)
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S3method(reverse_tags,default)
S3method(reverse_tags,robimetabar)
S3method(reverse_tags,robisample)
S3method(reverse_tags_colname,robimetabar)
S3method(reverse_tags_colname,robisample)
S3method(right_parse_sample_ids,robimetabar)
S3method(right_parse_sample_ids,robisample)
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S3method(samples,robimetabar)
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S3method(samples_ids,robimetabar)
S3method(samples_ids_colname,robimetabar)
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S3method(scientific_name,numeric)
S3method(scientific_name,robimetabar)
S3method(scientific_name,robimotu)
S3method(scientific_name,robitaxid)
S3method(scientific_name,tbl)
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S3method(seek_contaminents,robimetabar)
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S3method(sort,robipath)
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S3method(store_into,robimotu)
S3method(store_into,robisample)
S3method(store_into_motus,data.frame)
S3method(store_into_motus,robimotu)
S3method(store_into_samples,robisample)
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S3method(tagjump,robimetabar)
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S3method(tags,default)
S3method(tags,robimetabar)
S3method(tags,robisample)
S3method(tags_colname,robimetabar)
S3method(tags_colname,robisample)
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S3method(tags_positive_ctrls,robimetabar)
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S3method(taxids,default)
S3method(taxids,robimetabar)
S3method(taxids,robimotu)
S3method(taxids_colname,robimetabar)
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S3method(taxids_colname,tbl)
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S3method(taxon_at_rank,numeric)
S3method(taxon_at_rank,robimetabar)
S3method(taxon_at_rank,robimotu)
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S3method(taxon_at_rank,robitaxid)
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S3method(taxon_at_rank,tbl)
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S3method(taxonomic_parent,numeric)
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S3method(taxonomic_parent,robimetabar)
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S3method(taxonomic_parent,robimotu)
S3method(taxonomic_parent,robitaxid)
S3method(taxonomic_parent,tbl)
S3method(taxonomic_rank,numeric)
S3method(taxonomic_rank,robimetabar)
S3method(taxonomic_rank,robimotu)
S3method(taxonomic_rank,robitaxid)
S3method(taxonomic_rank,tbl)
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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,robiuniqueid)
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S3method(unique,robicategory)
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S3method(validate_object,default)
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S3method(validate_object,robi4mer)
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S3method(validate_object,robiatomic)
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S3method(validate_object,robicategory)
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S3method(validate_object,robidata)
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S3method(validate_object,robimetabar)
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S3method(validate_object,robimotu)
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S3method(validate_object,robimutation)
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S3method(validate_object,robisample)
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S3method(validate_object,robitag)
S3method(validate_object,robitaxid)
S3method(validate_object,robiuniqueid)
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S3method(validate_robitaxonomy,robitaxonomy)
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S3method(vec_cast,character.robicategory)
S3method(vec_cast,character.robilca)
S3method(vec_cast,character.robimutation)
S3method(vec_cast,character.robipath)
S3method(vec_cast,character.robitag)
S3method(vec_cast,character.robitag_forward)
S3method(vec_cast,character.robitag_reverse)
S3method(vec_cast,character.robitaxid)
S3method(vec_cast,character.robitaxid_master)
S3method(vec_cast,character.robiuniqueid)
S3method(vec_cast,double.robicategory)
S3method(vec_cast,double.robilca)
S3method(vec_cast,double.robimutation)
S3method(vec_cast,double.robipath)
S3method(vec_cast,double.robitaxid)
S3method(vec_cast,double.robitaxid_master)
S3method(vec_cast,factor.robicategory)
S3method(vec_cast,integer.robicategory)
S3method(vec_cast,integer.robilca)
S3method(vec_cast,integer.robimutation)
S3method(vec_cast,integer.robipath)
S3method(vec_cast,integer.robitaxid)
S3method(vec_cast,integer.robitaxid_master)
S3method(vec_cast,logical.robimutation)
S3method(vec_cast,robicategory.character)
S3method(vec_cast,robicategory.default)
S3method(vec_cast,robicategory.factor)
S3method(vec_cast,robicategory.robicategory)
S3method(vec_cast,robilca.character)
S3method(vec_cast,robilca.double)
S3method(vec_cast,robilca.integer)
S3method(vec_cast,robilca.robilca)
S3method(vec_cast,robilca.robitaxid)
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S3method(vec_cast,robilca.robitaxid_master)
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S3method(vec_cast,robimutation.default)
S3method(vec_cast,robimutation.double)
S3method(vec_cast,robimutation.integer)
S3method(vec_cast,robimutation.robimutation)
S3method(vec_cast,robipath.character)
S3method(vec_cast,robipath.double)
S3method(vec_cast,robipath.integer)
S3method(vec_cast,robipath.robipath)
S3method(vec_cast,robipath.robitaxid)
S3method(vec_cast,robitag.character)
S3method(vec_cast,robitag.robitag)
S3method(vec_cast,robitag.robitag_forward)
S3method(vec_cast,robitag.robitag_reverse)
S3method(vec_cast,robitag_forward.character)
S3method(vec_cast,robitag_forward.robitag)
S3method(vec_cast,robitag_forward.robitag_forward)
S3method(vec_cast,robitag_reverse.character)
S3method(vec_cast,robitag_reverse.robitag)
S3method(vec_cast,robitag_reverse.robitag_reverse)
S3method(vec_cast,robitaxid.character)
S3method(vec_cast,robitaxid.double)
S3method(vec_cast,robitaxid.integer)
S3method(vec_cast,robitaxid.robilca)
S3method(vec_cast,robitaxid.robipath)
S3method(vec_cast,robitaxid.robitaxid)
S3method(vec_cast,robitaxid.robitaxid_master)
S3method(vec_cast,robitaxid_master.character)
S3method(vec_cast,robitaxid_master.double)
S3method(vec_cast,robitaxid_master.integer)
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S3method(vec_cast,robitaxid_master.robilca)
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S3method(vec_cast,robitaxid_master.robitaxid)
S3method(vec_cast,robitaxid_master.robitaxid_master)
S3method(vec_cast,robiuniqueid.character)
S3method(vec_cast,robiuniqueid.default)
S3method(vec_cast,robiuniqueid.robiuniqueid)
S3method(vec_ptype2,character.robicategory)
S3method(vec_ptype2,character.robitag)
S3method(vec_ptype2,character.robitag_forward)
S3method(vec_ptype2,character.robitag_reverse)
S3method(vec_ptype2,character.robiuniqueid)
S3method(vec_ptype2,double.robicategory)
S3method(vec_ptype2,double.robilca)
S3method(vec_ptype2,double.robimutation)
S3method(vec_ptype2,double.robipath)
S3method(vec_ptype2,double.robitaxid)
S3method(vec_ptype2,double.robitaxid_master)
S3method(vec_ptype2,factor.robicategory)
S3method(vec_ptype2,integer.robicategory)
S3method(vec_ptype2,integer.robilca)
S3method(vec_ptype2,integer.robimutation)
S3method(vec_ptype2,integer.robipath)
S3method(vec_ptype2,integer.robitaxid)
S3method(vec_ptype2,integer.robitaxid_master)
S3method(vec_ptype2,robicategory.character)
S3method(vec_ptype2,robicategory.default)
S3method(vec_ptype2,robicategory.double)
S3method(vec_ptype2,robicategory.factor)
S3method(vec_ptype2,robicategory.integer)
S3method(vec_ptype2,robicategory.robicategory)
S3method(vec_ptype2,robilca.double)
S3method(vec_ptype2,robilca.integer)
S3method(vec_ptype2,robilca.robilca)
S3method(vec_ptype2,robilca.robitaxid)
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S3method(vec_ptype2,robilca.robitaxid_master)
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S3method(vec_ptype2,robimutation.default)
S3method(vec_ptype2,robimutation.double)
S3method(vec_ptype2,robimutation.integer)
S3method(vec_ptype2,robimutation.robimutation)
S3method(vec_ptype2,robipath.double)
S3method(vec_ptype2,robipath.integer)
S3method(vec_ptype2,robipath.robipath)
S3method(vec_ptype2,robipath.robitaxid)
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S3method(vec_ptype2,robipath.robitaxid_master)
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S3method(vec_ptype2,robitag.character)
S3method(vec_ptype2,robitag.robitag)
S3method(vec_ptype2,robitag.robitag_forward)
S3method(vec_ptype2,robitag.robitag_reverse)
S3method(vec_ptype2,robitag_forward.character)
S3method(vec_ptype2,robitag_forward.robitag)
S3method(vec_ptype2,robitag_forward.robitag_forward)
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S3method(vec_ptype2,robitag_forward.robitag_reverse)
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S3method(vec_ptype2,robitag_reverse.character)
S3method(vec_ptype2,robitag_reverse.robitag)
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S3method(vec_ptype2,robitag_reverse.robitag_forward)
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S3method(vec_ptype2,robitag_reverse.robitag_reverse)
S3method(vec_ptype2,robitaxid.double)
S3method(vec_ptype2,robitaxid.integer)
S3method(vec_ptype2,robitaxid.robilca)
S3method(vec_ptype2,robitaxid.robipath)
S3method(vec_ptype2,robitaxid.robitaxid)
S3method(vec_ptype2,robitaxid.robitaxid_master)
S3method(vec_ptype2,robitaxid_master.double)
S3method(vec_ptype2,robitaxid_master.integer)
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S3method(vec_ptype2,robitaxid_master.robilca)
S3method(vec_ptype2,robitaxid_master.robipath)
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S3method(vec_ptype2,robitaxid_master.robitaxid)
S3method(vec_ptype2,robitaxid_master.robitaxid_master)
S3method(vec_ptype2,robiuniqueid.character)
S3method(vec_ptype2,robiuniqueid.default)
S3method(vec_ptype2,robiuniqueid.robiuniqueid)
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S3method(vec_ptype_abbr,robicategory)
S3method(vec_ptype_abbr,robilca)
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S3method(vec_ptype_abbr,robimutation)
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S3method(vec_ptype_abbr,robipath)
S3method(vec_ptype_abbr,robitag)
S3method(vec_ptype_abbr,robitag_forward)
S3method(vec_ptype_abbr,robitag_reverse)
S3method(vec_ptype_abbr,robitaxid)
S3method(vec_ptype_abbr,robitaxid_master)
S3method(vec_ptype_abbr,robiuniqueid)
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S3method(vec_ptype_full,robitaxid)
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S3method(vec_ptype_full,robitaxid_master)
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S3method(write_xlsx,default)
S3method(write_xlsx,robimetabar)
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export("levels <- .robicategory")
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export("motus<-")
export("samples<-")
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export(D_q)
export(H_q)
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export(aggregate_robidata)
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export(alternative_names)
export(alternative_taxids)
export(as.robimetabar.robiseq_db)
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export(as_motus_matrix)
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export(as_robi4mer)
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export(as_robiatomic)
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export(as_robicategory)
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export(as_robidata)
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export(as_robilca)
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export(as_robimetabar)
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export(as_robimotu)
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export(as_robimutation)
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export(as_robiobject)
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export(as_robipath)
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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)
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export(bezier3)
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export(build.robiseq)
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export(build_motu_names)
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export(build_sample_names)
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export(categories)
export(categories_colname)
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export(clean_tagjump)
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export(clique_tag)
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export(clone)
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export(colors_tol)
export(combine_LETTERS)
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export(cum_hill)
export(cum_relative_frequencies)
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export(d_exp_q)
export(d_log_q)
export(dd_exp_q)
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export(decostand)
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export(download_ncbi_taxdump)
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export(ecofind)
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export(ecotag_best_identity)
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export(every_oligo)
export(exp_q)
export(expand_names)
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export(family)
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export(feature_as_matrix)
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export(filter_motus)
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export(filter_motus_empty)
export(filter_sample_category)
export(filter_sample_empty)
export(filter_sample_max_diversity)
export(filter_sample_max_read)
export(filter_sample_min_diversity)
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export(filter_sample_min_read)
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export(filter_tag_gcmax)
export(filter_tag_homopolymere)
export(filter_tag_homopolymere_min)
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export(forward_tags)
export(forward_tags_colname)
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export(fourMerTable)
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export(full_taxonomy)
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export(genus)
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export(get_default_taxonomy)
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export(gradient_tol1)
export(gradient_tol2)
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export(hellinger)
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export(hist_tag_jumps)
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export(ids)
export(ids_colname)
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export(import_motus_matrix)
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export(int2nuc)
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export(is_dist_1_or_0)
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export(is_full_taxonomy)
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export(is_robi4mer)
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export(is_robi_verbose)
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export(is_robiatomic)
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export(is_robicategory)
export(is_robidata)
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export(is_robimetabar)
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export(is_robimotu)
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export(is_robimutation)
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export(is_robiobject)
export(is_robisample)
export(is_robitag)
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export(is_robitag_forward)
export(is_robitag_reverse)
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export(is_robitaxid)
export(is_robitaxonomy)
export(is_robiuniqueid)
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export(is_subclade_of)
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export(kingdom)
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export(lcs_score)
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export(left_parse_sample_ids)
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export(log_q)
export(lowest_common_ancestor)
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export(master_taxids)
export(master_taxids_colname)
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export(motus)
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export(motus_average)
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export(motus_ids)
export(motus_ids_colname)
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export(motus_ranks)
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export(motus_read_count)
export(motus_sample_count)
export(motus_sample_max)
export(motus_sample_min)
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export(mutated_site)
export(mutation_position)
export(new_robi4mer)
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export(new_robiatomic)
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export(new_robicategory)
export(new_robidata)
export(new_robilca)
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export(new_robimetabar)
export(new_robimotu)
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export(new_robimutation)
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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)
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export(origin_site)
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export(parent.robitaxonomy)
export(plot_read_x_hill)
export(plot_read_x_pcr_tags)
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export(rainbow_tol)
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export(rank.list)
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export(rbarcode)
export(read.sequence)
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export(read_ecopcr)
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export(read_metabar)
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export(read_ncbi_taxdump)
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export(read_ngsfilter)
export(read_obifasta)
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export(read_obitab)
export(read_obitools_taxonomy)
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export(read_robitaxonomy)
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export(reference_taxonomy)
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export(relative_cum_hill)
export(relative_frequencies)
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export(resets_category_tags)
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export(reverse_tags)
export(reverse_tags_colname)
export(right_parse_sample_ids)
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export(rkmer)
export(rnuc)
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export(robi4mer)
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export(robiassert)
export(robiassert_arg)
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export(robiatomic)
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export(robicategory)
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export(robicategory_mapping)
export(robidata)
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export(robidnadist)
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export(robilca)
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export(robimessage)
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export(robimetabar)
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export(robimotu)
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export(robimutation)
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export(robipath)
export(robisample)
export(robitag)
export(robitag_forward)
export(robitag_reverse)
export(robitaxid)
export(robitaxid_master)
export(robiuniqueid)
export(rseq)
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export(samples)
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export(samples_average)
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export(samples_entropy)
export(samples_hill)
export(samples_ids)
export(samples_ids_colname)
export(samples_motu_count)
export(samples_motu_max)
export(samples_motu_min)
export(samples_read_count)
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export(scientific_name)
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export(seek_contaminents)
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export(set_default_taxonomy)
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export(species)
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export(spread_names.robitaxonomy)
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export(store_into)
export(store_into_motus)
export(store_into_sample.data.frame)
export(store_into_samples)
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export(substitution)
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export(superkingdom)
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export(tagjump)
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export(tags)
export(tags_colname)
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export(tags_positive_ctrls)
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export(taxid.validate)
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export(taxids)
export(taxids_colname)
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export(taxon.path)
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export(taxon_at_rank)
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export(taxonomic_parent)
export(taxonomic_rank)
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export(unclass_robiobject)
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export(validate_object)
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export(validate_robitaxonomy)
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export(vec_cast.robicategory)
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export(vec_cast.robimutation)
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export(vec_cast.robiuniqueid)
export(vec_ptype2.robicategory)
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export(vec_ptype2.robimutation)
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export(vec_ptype2.robiuniqueid)
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export(write_obifasta)
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export(write_robitaxonomy)
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export(write_xlsx)
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import(R6)
import(doParallel)
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import(dplyr)
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import(foreach)
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import(openxlsx)
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import(progressr)
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import(purrr)
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import(readr)
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import(rlang)
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import(stringr)
import(tibble)
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import(tidyfast)
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import(tidyr)
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import(utils)
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import(vctrs)
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import(vegan)
importFrom(Rdpack,reprompt)
importFrom(glue,glue)
importFrom(pillar,pillar_shaft)
importFrom(pillar,type_sum)
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importFrom(rlang,abort)
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importFrom(rlang,are_na)
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importFrom(rlang,inform)
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importFrom(rlang,is_atomic)
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importFrom(rlang,warn)
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importFrom(stringr,str_sub)
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importFrom(tibble,as_tibble)
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importFrom(vctrs,new_factor)
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importFrom(vctrs,new_vctr)
importFrom(vctrs,vec_c)
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importFrom(vctrs,vec_cast)
importFrom(vctrs,vec_data)
importFrom(vctrs,vec_default_cast)
importFrom(vctrs,vec_default_ptype2)
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useDynLib(ROBITools2)