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Code Releases Activity

(v3.0.1.9098) Approve name of species group B_MYCBC_AVIM-C as 'Mycobacterium avium complex'

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As curated in data-raw/Species groups.xlsx since July 2023; the released v3.0.1 data still
used 'Mycobacterium avium-intracellulare complex' for the same group of organisms.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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dr. M.S. (Matthijs) BerendsandClaude Opus 5.5 committed 2026-10-03 14:16:47 +02:00
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commit 6ab8ff8c33
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DESCRIPTION
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Package: AMR
Version: 3.0.1.9097
Version: 3.0.1.9098
Date: 2026-10-03
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
NEWS.md
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# AMR 3.0.1.9097
# AMR 3.0.1.9098
Planned as v3.1.0, mid October 2026.
data-raw/microorganisms_files/mo_code_renames.csv
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"mo","registry_name","new_name","reason","approved_by","approved_date"
"B_MYCBC_AVIM-C","Mycobacterium avium-intracellulare complex","Mycobacterium avium complex","Species group renamed in the development version of 2026; same group of organisms","",""
"B_MYCBC_AVIM-C","Mycobacterium avium-intracellulare complex","Mycobacterium avium complex","Same group of organisms; name as curated in data-raw/Species groups.xlsx since July 2023","Matthijs S. Berends","2026-10-03"
1 mo registry_name new_name reason approved_by approved_date
2 B_MYCBC_AVIM-C Mycobacterium avium-intracellulare complex Mycobacterium avium complex Species group renamed in the development version of 2026; same group of organisms Same group of organisms; name as curated in data-raw/Species groups.xlsx since July 2023 Matthijs S. Berends 2026-10-03
tests/testthat/microorganisms_known_defects.csv
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"registered_code_with_other_taxon","F_LCNLL (Lecaniella)"
"registered_code_with_other_taxon","F_LECID_GLMR (Lecidea glomerella)"
"registered_code_with_other_taxon","F_LECID_SBLT (Lecidea subuletorum)"
"registered_code_with_other_taxon","B_MYCBC_AVIM-C (Mycobacterium avium complex)"
"registered_code_with_other_taxon","B_MYCBC_NNSE (Mycobacterium holstebronense)"
"registered_code_with_other_taxon","F_NMSPR (Naemaspora)"
"registered_code_with_other_taxon","F_NCNTH (Neoconiothyrium)"
@@ -1706,7 +1705,6 @@
"released_taxon_missing","B_MWSNL (Mawsoniella)"
"released_taxon_missing","B_MWSNL_ASTR (Mawsoniella australis)"
"released_taxon_missing","B_MYCBC_AHVZ (Mycobacterium ahvazicum)"
"released_taxon_missing","B_MYCBC_AVIM-C (Mycobacterium avium-intracellulare complex)"
"released_taxon_missing","B_MYCBC_CNTT (Mycobacterium canettii)"
"released_taxon_missing","B_MYCBC_DXNT (Mycobacterium dioxanotrophicus)"
"released_taxon_missing","B_MYCBC_GLLN (Mycobacterium gallinarum)"
1 rule record
378 registered_code_with_other_taxon F_LCNLL (Lecaniella)
379 registered_code_with_other_taxon F_LECID_GLMR (Lecidea glomerella)
380 registered_code_with_other_taxon F_LECID_SBLT (Lecidea subuletorum)
registered_code_with_other_taxon B_MYCBC_AVIM-C (Mycobacterium avium complex)
381 registered_code_with_other_taxon B_MYCBC_NNSE (Mycobacterium holstebronense)
382 registered_code_with_other_taxon F_NMSPR (Naemaspora)
383 registered_code_with_other_taxon F_NCNTH (Neoconiothyrium)
1705 released_taxon_missing B_MWSNL (Mawsoniella)
1706 released_taxon_missing B_MWSNL_ASTR (Mawsoniella australis)
1707 released_taxon_missing B_MYCBC_AHVZ (Mycobacterium ahvazicum)
released_taxon_missing B_MYCBC_AVIM-C (Mycobacterium avium-intracellulare complex)
1708 released_taxon_missing B_MYCBC_CNTT (Mycobacterium canettii)
1709 released_taxon_missing B_MYCBC_DXNT (Mycobacterium dioxanotrophicus)
1710 released_taxon_missing B_MYCBC_GLLN (Mycobacterium gallinarum)