dr. M.S. (Matthijs) Berends b63263cc56 (v3.0.1.9150) Add the open issues found while correcting the WHONET codes to the taxonomy report

2026-10-15 21:31:28 +02:00

..

changed_mo_codes_of_existing_names.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

checks_sentinels_comparison.R

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

codes_without_a_match_in_amr_clinical_breakpoints_mo.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

codes_without_a_match_in_amr_example_isolates_mo.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

codes_without_a_match_in_amr_intrinsic_resistant_mo.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

codes_without_a_match_in_amr_microorganisms_codes_mo.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

codes_without_a_match_in_amr_microorganisms_groups_mo.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

codes_without_a_match_in_microorganisms_groups_mo_group.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

comparison_per_domain_rank_status.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

comparison_per_domain.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

cycles_of_synonyms.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

duplicate_full_names_after_adding_missing_parents.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

duplicate_full_names_after_adding_mo_codes.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

duplicate_full_names.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

duplicate_mo_codes.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

genera_that_moved_to_another_domain.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

genera_with_multiple_families.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

genera_without_a_family_that_get_a_family_from_gbif_or_the_override_list.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

homonyms_decided_by_the_domain_of_the_last_release.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

homonyms_of_relevant_genera_check_best_domain.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

lichens_and_their_synonyms_these_will_be_removed.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

lpsn_genera_with_multiple_lineages.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

lpsn_higher_taxa_that_could_not_be_downloaded.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

missing_parent_records_that_were_added_or_moved.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

mo_codes_with_repeated_elements_after_fixing.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

mo_codes_with_repeated_elements.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

most_relevant_new_taxa.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

most_relevant_removed_taxa.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

names_that_moved_to_another_domain.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

new_records_per_domain_and_kind.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

new_taxa.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

not_validly_published_or_unknown_status_but_kept_as_clinically_relevant.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

orthographic_variants_linked_to_their_accepted_name.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

prevalence_by_rank.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

previously_manually_added_taxa_that_are_not_in_the_new_data_set.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

records_removed_as_homonyms_of_a_genus_in_another_domain.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

records_that_shared_a_source_identifier_one_kept_as_the_current_name.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

records_whose_higher_taxonomy_was_harmonised_with_the_record_of_their_parent.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

records_without_a_valid_mo_code_these_will_be_removed.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

registered_codes_with_another_name.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

released_mo_codes_that_are_retired_since_a_more_recent_release_has_their_name_in_another_domain.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

released_mo_codes_that_are_retired_since_their_genus_is_now_only_known_in_another_domain.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

released_mo_codes_that_are_retired_since_their_taxon_is_another_organism_with_the_same_genus_name.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

released_mo_codes_that_are_retired_since_their_taxon_was_a_synonym_without_a_current_name.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

released_taxa_that_are_retired_by_a_human_decision_these_will_be_removed.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

released_taxa_that_were_missing_and_are_restored_by_domain_rank_and_status.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

relevant_genera_with_a_new_or_empty_family.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

removed_taxa_that_were_clinically_relevant_prevalence_2.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

removed_taxa.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

REPORT.md

(v3.0.1.9150) Add the open issues found while correcting the WHONET codes to the taxonomy report

2026-10-15 21:31:28 +02:00

restored_released_taxa_that_are_clinically_relevant.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

salmonella_species_synonyms_that_are_serovars_in_this_data_set_these_will_be_removed.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

sentinel_organisms.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

synonym_genera_with_accepted_species_these_will_become_accepted.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

synonyms_without_a_current_name_and_their_outcome.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

synonyms_without_a_current_name.csv

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00