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(v3.0.1.9095) Taxonomy build: fix root causes of missing and misclassified taxa, add unattended run prompt
Review of reproduction_of_microorganisms.R against the 2026 intermediates: - genus homonyms: overrides, LPSN/MycoBank first, status within LPSN/MycoBank, move misplaced protists, remove true homonyms (Necator, Capillaria, Graphium) - keep clinically relevant names that are not validly published (Tropheryma) - one set of relevant genera for all filters; 30 genera added to MO_RELEVANT_GENERA - MycoBank classification parsed from all columns; empty values never overwrite - GBIF synonyms in another genus get the lineage of their own genus - prevalence no longer copied from genus; current names inherit from synonyms - inferred records follow the relevance filters (no more unrelated lichens) - ASCII names before deduplication (12 duplicate full names in 2026) - MO codes: robust code parsing, reserved old codes, single allocator, domain column used directly (2026 rename would now fail) - name clean-up applied to taxonomy before MO codes, BacDive rows filled - unattended running: review() instead of View(), CSV export of reviews, LPSN cache and retries, stops when raw source files are missing - reproduction_of_microorganisms_CLAUDE.md: prompt for an unattended run with findings report and checklist for human review in the PR Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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@@ -30,4 +30,5 @@ data-raw/DSMZ_bactnames.xlsx
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data-raw/country_analysis_url_token.R
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data-raw/country_analysis2.R
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data-raw/taxonomy.csv
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data-raw/lpsn_scrape_cache.rds
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data-raw/WHONET/*
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+1
-1
@@ -1,5 +1,5 @@
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Package: AMR
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Version: 3.0.1.9094
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Version: 3.0.1.9095
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Date: 2026-10-03
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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@@ -1,4 +1,4 @@
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# AMR 3.0.1.9094
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# AMR 3.0.1.9095
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Planned as v3.1.0, mid October 2026.
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@@ -207,17 +207,24 @@ pre_commit_lst$MO_RELEVANT_GENERA <- c(
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"Angiostrongylus",
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"Anisakis",
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"Anopheles",
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"Apiotrichum",
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"Apophysomyces",
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"Arthroderma",
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"Ascaris",
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"Aspergillus",
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"Aureobasidium",
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"Babesia",
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"Balamuthia",
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"Balantioides",
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"Basidiobolus",
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"Beauveria",
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"Bipolaris",
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"Blastobotrys",
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"Blastocystis",
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"Blastomyces",
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"Brugia",
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"Candida",
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"Candidozyma",
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"Capillaria",
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"Chaetomium",
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"Chilomastix",
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@@ -226,6 +233,7 @@ pre_commit_lst$MO_RELEVANT_GENERA <- c(
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"Cladophialophora",
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"Cladosporium",
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"Clavispora",
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"Clonorchis",
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"Coccidioides",
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"Cokeromyces",
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"Conidiobolus",
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@@ -236,21 +244,31 @@ pre_commit_lst$MO_RELEVANT_GENERA <- c(
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"Cryptosporidium",
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"Cunninghamella",
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"Curvularia",
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"Cutaneotrichosporon",
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"Cyberlindnera",
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"Cyclospora",
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"Cystoisospora",
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"Debaryozyma",
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"Demodex",
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"Dermatobia",
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"Dientamoeba",
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"Diphyllobothrium",
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"Dirofilaria",
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"Diutina",
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"Echinococcus",
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"Echinostoma",
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"Emergomyces",
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"Emmonsia",
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"Encephalitozoon",
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"Entamoeba",
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"Enterobius",
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"Enterocytozoon",
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"Epidermophyton",
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"Exidia",
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"Exophiala",
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"Exserohilum",
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"Fasciola",
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"Fasciolopsis",
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"Fonsecaea",
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"Fusarium",
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"Geotrichum",
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@@ -268,17 +286,21 @@ pre_commit_lst$MO_RELEVANT_GENERA <- c(
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"Hymenolepis",
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"Hypomyces",
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"Hysterothylacium",
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"Kazachstania",
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"Kloeckera",
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"Kluyveromyces",
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"Kodamaea",
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"Lacazia",
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"Leishmania",
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"Lichtheimia",
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"Loa",
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"Lodderomyces",
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"Lomentospora",
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"Madurella",
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"Magnusiomyces",
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"Malassezia",
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"Malbranchea",
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"Mansonella",
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"Metagonimus",
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"Meyerozyma",
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"Microascus",
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@@ -288,15 +310,20 @@ pre_commit_lst$MO_RELEVANT_GENERA <- c(
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"Mortierella",
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"Mucor",
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"Mycocentrospora",
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"Naegleria",
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"Nakaseomyces",
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"Nannizzia",
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"Necator",
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"Nectria",
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"Neocosmospora",
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"Ochroconis",
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"Oesophagostomum",
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"Oidiodendron",
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"Onchocerca",
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"Opisthorchis",
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"Paecilomyces",
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"Paracoccidioides",
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"Paragonimus",
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"Pediculus",
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"Penicillium",
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"Phaeoacremonium",
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@@ -316,6 +343,7 @@ pre_commit_lst$MO_RELEVANT_GENERA <- c(
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"Pulex",
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"Purpureocillium",
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"Quambalaria",
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"Rasamsonia",
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"Rhinocladiella",
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"Rhizomucor",
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"Rhizopus",
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@@ -323,6 +351,7 @@ pre_commit_lst$MO_RELEVANT_GENERA <- c(
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"Saccharomyces",
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"Saksenaea",
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"Saprochaete",
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"Sarcocystis",
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"Sarcoptes",
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"Scedosporium",
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"Schistosoma",
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@@ -344,6 +373,7 @@ pre_commit_lst$MO_RELEVANT_GENERA <- c(
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"Talaromyces",
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"Teleomorph",
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"Toxocara",
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"Toxoplasma",
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"Trichinella",
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"Trichobilharzia",
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"Trichoderma",
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File diff suppressed because it is too large.
Load diff
@@ -0,0 +1,284 @@
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# Unattended update of the `microorganisms` data set
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You are updating the taxonomy of the AMR package for R: the `microorganisms` data set, built by
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`data-raw/_reproduction_scripts/reproduction_of_microorganisms.R`. Hundreds of thousands of people
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rely on this data set, in clinical microbiology, surveillance and research. An error here, such as a
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pathogen in the wrong kingdom, a missing genus or an MO code that changes meaning, propagates into
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patient-related analyses worldwide. Work like a senior clinical microbiologist who is also a
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meticulous data engineer: careful, sceptical of every source, and never satisfied with "it ran
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without errors".
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Work autonomously from start to finish. Only stop early for the reasons listed under
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"When to stop". Everything you do ends up in one new pull request.
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**A human is in the loop.** You do the work, a human decides. Every finding, every decision you
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took and every point you could not resolve must be written to the repository (git-tracked) and to the
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pull request as a checklist, so that the human can review each point separately before merging. You
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never merge the PR yourself. In the text below, `YYYY-MM` is the year and month of this update, and
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`<review dir>` is `data-raw/taxonomy_review/YYYY-MM`.
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## Non-negotiable rules
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- **Never download the source files yourself.** GBIF/COL, LPSN, MycoBank and BacDive require
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registration or manual export buttons, so a human downloads them. If the script stops because
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files are missing, report exactly which files are missing, with the steps at the top of the
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script, and stop.
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- **Never edit `data/*.rda` by hand** and never patch individual records afterwards. Every fix goes
|
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into the script, so that next year's run includes it. The script is the product, the data set is
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its output.
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- **Fix root causes, not symptoms.** If a genus has the wrong family, find out why (source data,
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parser, priority rule, homonym) and fix that mechanism. Only use the explicit override lists in
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the script (`genus_domain_override`, the Plasmodium and Leishmania blocks) when the cause is a
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genuine flaw in the source data that no rule can resolve, and explain each addition in a code comment.
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- **Never fabricate.** No invented species names, citations, release dates or test results. If you
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cannot verify something, say so in the PR.
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- **Never commit to or push to `main`.** Work on a new branch and open a new PR.
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- Follow `CLAUDE.md` in the repository root: tidyverse style, `%like%`/`%like_case%` instead of
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`grepl()`, British English, zero dependencies (packages used only in `data-raw/` are fine).
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- Never write to or modify anything under `/etc`.
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## Step 0: preflight
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1. Check the working tree is clean, `git fetch --tags` and update `main`, then create a branch
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`taxonomy-update-YYYY-MM` (current year and month) from `origin/main`.
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2. Check resources: at least 16 GB RAM (`free -g`) and 10 GB free disk space. If not, stop.
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3. Determine the folder with the raw files. Use the environment variable `AMR_TAXONOMY_SOURCE_DIR` if
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set, otherwise `~/Downloads/`. Run only the guard at the top of the script, from
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`folder_location <- ...` up to and including `rm(raw_missing, raw_downloads, raw_age)`, in a
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separate R process. If it stops, report and stop. If it warns about old files, compare the
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dates with the release dates (step 1) before continuing. If the files are clearly from the
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previous update, stop and report.
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4. Keep the previous release for comparison:
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`git show origin/main:data/microorganisms.rda > <scratch>/microorganisms_old.rda`, where
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`<scratch>` is a folder outside the repository.
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## Step 1: record the source versions
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These are needed for `TAXONOMY_VERSION` in `R/aa_globals.R` later. Write them down now:
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- **GBIF/COL**: read `eml.xml` (or `metadata.yaml`) in the folder of `Taxon.tsv` for the release
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title, date and DOI. The citation format must match the existing one in `R/aa_globals.R`.
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- **LPSN, MycoBank, BacDive**: the accessed date is the modification date of the downloaded file.
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- Do not guess any of these. If a value cannot be found, leave the existing value and list it in the
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PR under "Needs a human".
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## Step 2: run the build
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The script takes several hours (most of it is LPSN scraping, which is cached in
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`data-raw/lpsn_scrape_cache.rds`, so a restart is fast). Run it detached from your tool calls, so that
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it survives time limits, and write everything to a log:
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```bash
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mkdir -p <scratch>/logs
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cd <repo root>
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nohup Rscript -e 'options(AMR_build_view = FALSE, AMR_build_print_rows = 200, AMR_build_review_dir = "<review dir>", warn = 1, width = 200); source("data-raw/_reproduction_scripts/reproduction_of_microorganisms.R", echo = TRUE, max.deparse.length = Inf, keep.source = TRUE)' > <scratch>/logs/build_1.log 2>&1 &
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```
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Monitor the log at sensible intervals (every 10 to 20 minutes, not continuously). Read every
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`>>> REVIEW:` block as soon as it appears; you do not have to wait until the end to start thinking.
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With `AMR_build_review_dir` set, every review block is also saved in full as a CSV file in
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`<review dir>`, named after its title. These files are part of the PR. Set the same option in every
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resumed run.
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### Intermediate results
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The script saves its state at fixed points, exactly as in previous years. Keep this structure intact
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and do not add, rename or remove checkpoints without a clear reason:
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| File in `data-raw/` | Saved after |
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|---|---|
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| `taxonomy_lpsn.rds`, `taxonomy_mycobank.rds`, `taxonomy_gbif.rds` | reading each source |
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| `taxonomy_lpsn_missing.rds` | scraping the LPSN lineage of all genera |
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| `taxonomy0.rds` | combining the sources and resolving homonyms |
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| `taxonomy1.rds` | adding missing parents and deduplication |
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| `taxonomy1b.rds` | LPSN lookup of GBIF records |
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| `taxonomy1c.rds` | fixing GBIF taxonomy with LPSN/MycoBank |
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| `taxonomy2.rds` | prevalence |
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| `taxonomy2b.rds` | removing unwanted records and harmonising taxonomy |
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| `taxonomy2c.rds` | MO codes |
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| `taxonomy3.rds` | integrity checks and parent identifiers |
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| `taxonomy3b.rds` | all additions, just before saving to the package |
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These files are tracked in git and must be committed in the PR, so that the human can inspect every
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stage. The same applies to everything in `<review dir>`. `lpsn_scrape_cache.rds` is ignored by git
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and must not be committed.
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### If the run fails
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1. Read the error and the 100 lines before it. Find the root cause in the script, fix it, and
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check the syntax with `Rscript -e 'invisible(parse("<script>"))'`.
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2. Do not start from scratch if a checkpoint exists. Write a resume script in `<scratch>` (never in
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the repository) that contains, in this order:
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- the script from the top up to (not including) `# Read LPSN data ---`: setup, guard, helpers,
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clinically relevant genera;
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- `taxonomy_lpsn`, `taxonomy_mycobank` and `taxonomy_gbif` from their `.rds` files;
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- if resuming at or after `taxonomy0.rds`: the two lines that read the raw GBIF file
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(`taxonomy_gbif.bak <- vroom(...)` and the `colnames()` line after it) and the definition of
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`current_gbif` (needed by `add_missing_parents()`);
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- if resuming at or after `taxonomy2.rds`: the section `# Add prevalence ---` up to and including
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the definition of `compute_prevalence()` (needed later on);
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- `taxonomy <- readRDS("data-raw/<latest checkpoint>.rds")`;
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- the remainder of the script after that checkpoint's `saveRDS()` line.
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Number the logs (`build_2.log`, etc.).
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3. If the same section fails three times for different reasons, or the cause lies outside the
|
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script (e.g. the format of a source file changed fundamentally), stop and report (see "When to
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stop").
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## Step 3: review as an expert
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"It ran" means nothing. Assess the result critically before committing anything. Use the review
|
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blocks in the log and your own checks in a separate R session that loads the new data
|
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(`devtools::load_all(".")`) next to `microorganisms_old.rda`.
|
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Write down every check, what you found and what you decided as you go: these become the findings
|
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report and the checklist in step 5. Save the output of your own checks (sentinels, comparisons) as
|
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CSV files in `<review dir>` as well, e.g. `sentinel_organisms.csv` and `comparison_per_domain.csv`.
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|
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### 3a. The review blocks in the log
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For each `>>> REVIEW:` block (and its CSV file), decide whether the content is plausible, and act:
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- **"Homonyms of relevant genera"**: for every clinically relevant genus, is `best_domain` the
|
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organism a clinician means? For example, *Necator* and *Capillaria* are nematodes, *Trichophyton*
|
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and *Graphium* are fungi, *Trypanosoma* and *Giardia* are protists. A wrong winner means adding
|
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the genus to `genus_domain_override` and running again from `taxonomy_*.rds`.
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- **"Records removed as homonyms"**: the removed group must be other organisms with the same genus
|
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name, not the same organisms classified differently. If the same organisms were removed, extend
|
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the "move" rule in the script.
|
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- **"Not validly published ... kept as clinically relevant"** and **"Synonym genera with accepted
|
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species"**: plausible?
|
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- **"Removed taxa that were clinically relevant"**: every removal of a taxon with prevalence < 2 needs
|
||||
an explanation (renamed, merged, truly invalid). Unexplained removals are errors.
|
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- **"Genera that moved to another domain"**: each move changes MO codes. Accept only moves that are
|
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taxonomically correct.
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||||
- **"Relevant genera with a new or empty family"**: check every row. A new family is fine if it
|
||||
reflects a real reclassification; an empty family for a relevant genus is an error.
|
||||
- **Duplicate names or codes, codes with repeated elements, records without a valid code**: must
|
||||
all be 0 rows. If not, find the cause.
|
||||
|
||||
### 3b. Sentinel organisms
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||||
|
||||
Write a small R check in `<scratch>` and verify that each of these is present with the expected
|
||||
properties (current name, `status`, `domain`, `family`, prefix of `mo`). Each deviation must be
|
||||
explained or fixed:
|
||||
|
||||
| Name | Expected |
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||||
|---|---|
|
||||
| *Escherichia coli*, *Klebsiella pneumoniae* | Bacteria, Enterobacteriaceae, accepted, `B_` |
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||||
| *Staphylococcus aureus* | Bacteria, Staphylococcaceae, accepted |
|
||||
| *Pseudomonas aeruginosa* | Bacteria, Pseudomonadaceae |
|
||||
| *Acinetobacter baumannii* | Bacteria, Moraxellaceae |
|
||||
| *Enterococcus faecium* | Bacteria, Enterococcaceae |
|
||||
| *Streptococcus pneumoniae* | Bacteria, Streptococcaceae |
|
||||
| *Mycobacterium tuberculosis* | Bacteria, Mycobacteriaceae |
|
||||
| *Clostridioides difficile* | Bacteria, Peptostreptococcaceae |
|
||||
| *Tropheryma whipplei* | present (not validly published, but clinically essential) |
|
||||
| *Candida albicans* | Fungi, accepted |
|
||||
| *Candida auris* | synonym, with a current name in *Candidozyma* |
|
||||
| *Candidozyma auris*, *Nakaseomyces glabratus* | Fungi, accepted, prevalence < 2 |
|
||||
| *Aspergillus fumigatus* | Fungi, Aspergillaceae |
|
||||
| *Trichophyton rubrum* | Fungi, Arthrodermataceae, `F_` code (issue #309) |
|
||||
| *Mucor* (genus) | Fungi, Mucoraceae (not empty) |
|
||||
| *Blastomyces* (genus), *Blastomyces dermatitidis* | Fungi, both accepted |
|
||||
| *Cryptococcus neoformans*, *Pneumocystis jirovecii* | Fungi |
|
||||
| *Necator americanus* | Animalia (hookworm), not Fungi |
|
||||
| *Capillaria* (genus) | Animalia |
|
||||
| *Ascaris lumbricoides* | Animalia, Ascarididae |
|
||||
| *Echinococcus granulosus* | Animalia, Taeniidae |
|
||||
| *Plasmodium falciparum* | Protozoa, `P_` code |
|
||||
| *Toxoplasma gondii* | present, accepted |
|
||||
| *Leishmania donovani*, *Trypanosoma cruzi*, *Giardia* | Protozoa |
|
||||
| *Graphium* | only fungal species, no butterflies (e.g. no *Graphium sarpedon*) |
|
||||
| *Microsporidium* | still more than 100 species |
|
||||
|
||||
Also verify the most used organisms in the package's own data sets: every `mo` in
|
||||
`clinical_breakpoints`, `intrinsic_resistant`, `microorganisms.groups`, `microorganisms.codes` and
|
||||
`example_isolates` must exist in the new `microorganisms` (`anyNA()` checks at the end of the script).
|
||||
|
||||
### 3c. Comparison with the previous release
|
||||
|
||||
Make a table for the PR with, per domain: number of records old vs new, per rank and status. Every
|
||||
change of more than 5% in a domain needs an explanation. Also report:
|
||||
|
||||
- the number of MO codes of existing names (same full name and domain) that changed: this must be
|
||||
close to 0, every change must be explained;
|
||||
- that no new taxon received an MO code that was ever used for another taxon;
|
||||
- the distribution of `prevalence` by rank, old vs new;
|
||||
- the 30 most relevant (prevalence <= 1.25) new genera and species, and the 30 most relevant removed
|
||||
ones.
|
||||
|
||||
### 3d. Unit tests
|
||||
|
||||
After the data are saved and the package is reloaded, run the tests at the end of the script and then
|
||||
the full suite with `devtools::test()`. Analyse every failure: is the test outdated because of a
|
||||
real taxonomic change (then update the test, and explain why in the PR) or did the build break
|
||||
something (then fix the script)? Never weaken a test just to make it pass.
|
||||
|
||||
## Step 4: finish the package update
|
||||
|
||||
1. Update `TAXONOMY_VERSION` in `R/aa_globals.R` with the values from step 1.
|
||||
2. Run `devtools::document()`.
|
||||
3. `NEWS.md`: add one short bullet under `### Updates` (e.g. "Updated taxonomy of microorganisms to
|
||||
GBIF/COL <release>, LPSN and MycoBank of <month year>"), no full stop at the end. The version
|
||||
number in `DESCRIPTION` and on line 1 of `NEWS.md` is set by the git pre-commit hook; check after
|
||||
the first commit that it was bumped exactly once for this PR, following `CLAUDE.md`.
|
||||
|
||||
## Step 5: findings report for the human
|
||||
|
||||
Write `<review dir>/REPORT.md`. This is the permanent, git-tracked record of this update, so that the
|
||||
human can review it before merging and next year's run can learn from it. Structure:
|
||||
|
||||
1. **Sources**: name, release or accessed date and citation of each source.
|
||||
2. **Summary**: old vs new counts per domain, rank and status (the table from 3c), and the run time.
|
||||
3. **Script changes**: every change to the script, why, and which records it affected.
|
||||
4. **Checklist**: one checkbox per check, in this format:
|
||||
|
||||
```markdown
|
||||
- [ ] **Homonyms of relevant genera**: 98 genera in more than one domain; all winners plausible,
|
||||
except *Xus*: added to `genus_domain_override` as Animalia (nematode, 12 species), see
|
||||
[CSV](homonyms_of_relevant_genera_check_best_domain.csv)
|
||||
```
|
||||
|
||||
Every item states the check, the finding in numbers, your decision, and a link to the CSV file in
|
||||
`<review dir>` where relevant. There is one item for each review block of 3a, one for each sentinel
|
||||
organism of 3b that deviates (and one item for all sentinels that passed), one for each comparison
|
||||
of 3c, one for the unit tests (3d) and one for each changed test. Leave all boxes unticked: ticking
|
||||
them is the human's job, it means "reviewed and agreed".
|
||||
5. **Needs a human**: also as checkboxes, everything you could not verify or decide, each with your
|
||||
recommendation. Be concrete, e.g. "COL lists *Enterobius vermicularis* as a synonym of ...;
|
||||
recommend to keep it accepted because ...". Keep this list honest: it is the most important part
|
||||
of the report.
|
||||
|
||||
## Step 6: commits and pull request
|
||||
|
||||
Commit in logical steps, so that the human can review them separately:
|
||||
|
||||
1. fixes to the script (if any), with the reason in the commit message;
|
||||
2. the source and intermediate files (`data-raw/taxonomy*.rds`);
|
||||
3. `data/microorganisms.rda` and the other updated data sets (`fix_old_mos()` section);
|
||||
4. `R/aa_globals.R`, documentation, `NEWS.md`, updated tests;
|
||||
5. `<review dir>`: `REPORT.md` and all CSV files.
|
||||
|
||||
Push the branch and open a PR to `main` with the title "Update taxonomy of microorganisms (YYYY-MM)".
|
||||
The PR description is the findings report: copy sections 1, 2 and 3 in short form, and copy the
|
||||
**Checklist** and **Needs a human** sections in full, with unticked checkboxes, so that the human can
|
||||
tick them one by one in the PR itself. Make the CSV links in the PR absolute links to the files on the
|
||||
branch. End with a line that the PR must not be merged before all boxes are ticked.
|
||||
|
||||
If the human comments on the PR or asks for changes later, update the script, run again from the
|
||||
appropriate checkpoint, and update both `REPORT.md` and the PR description, so that they stay identical.
|
||||
|
||||
## When to stop
|
||||
|
||||
Stop early, and report clearly what happened, only in these situations:
|
||||
|
||||
- source files are missing or clearly outdated (step 0);
|
||||
- insufficient memory or disk space;
|
||||
- the build keeps failing for reasons outside the script, or a source format changed so much that
|
||||
the parsing must be redesigned;
|
||||
- sentinel checks fail and you cannot find the cause after a thorough investigation.
|
||||
|
||||
In the last two situations, still write `REPORT.md` with everything you found so far and the exact
|
||||
point where you stopped, push the branch and open the PR **as a draft**, with the same checklist, so
|
||||
that the human can continue from there.
|
||||
In all other situations, finish completely and open a normal (non-draft) PR.
|
||||
+1
-1
@@ -206,7 +206,7 @@ Furthermore,
|
||||
\item Any genus present in the \strong{established} list also has \code{prevalence = 1.15} in the \link{microorganisms} data set;
|
||||
\item Any other genus present in the \strong{putative} list has \code{prevalence = 1.25} in the \link{microorganisms} data set;
|
||||
\item Any other species or subspecies of which the genus is present in the two aforementioned groups, has \code{prevalence = 1.5} in the \link{microorganisms} data set;
|
||||
\item Any \emph{non-bacterial} genus, species or subspecies of which the genus is present in the following list, has \code{prevalence = 1.25} in the \link{microorganisms} data set: \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acremonium}, \emph{Actinomucor}, \emph{Aedes}, \emph{Alternaria}, \emph{Amoeba}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arthroderma}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bipolaris}, \emph{Blastobotrys}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Candida}, \emph{Capillaria}, \emph{Chaetomium}, \emph{Chilomastix}, \emph{Chrysonilia}, \emph{Chrysosporium}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Clavispora}, \emph{Coccidioides}, \emph{Cokeromyces}, \emph{Conidiobolus}, \emph{Coniochaeta}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Cryptosporidium}, \emph{Cunninghamella}, \emph{Curvularia}, \emph{Cyberlindnera}, \emph{Debaryozyma}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Echinostoma}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Epidermophyton}, \emph{Exidia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Geotrichum}, \emph{Giardia}, \emph{Graphium}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hansenula}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hortaea}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Kloeckera}, \emph{Kluyveromyces}, \emph{Kodamaea}, \emph{Lacazia}, \emph{Leishmania}, \emph{Lichtheimia}, \emph{Lodderomyces}, \emph{Lomentospora}, \emph{Madurella}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microascus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Millerozyma}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Nannizzia}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Paecilomyces}, \emph{Paracoccidioides}, \emph{Pediculus}, \emph{Penicillium}, \emph{Phaeoacremonium}, \emph{Phaeomoniella}, \emph{Phialophora}, \emph{Phlebotomus}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Plasmodium}, \emph{Pneumocystis}, \emph{Pseudallescheria}, \emph{Pseudoscopulariopsis}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Purpureocillium}, \emph{Quambalaria}, \emph{Rhinocladiella}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Saccharomyces}, \emph{Saksenaea}, \emph{Saprochaete}, \emph{Sarcoptes}, \emph{Scedosporium}, \emph{Schistosoma}, \emph{Schizophyllum}, \emph{Schizosaccharomyces}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Spirometra}, \emph{Sporobolomyces}, \emph{Sporopachydermia}, \emph{Sporothrix}, \emph{Sporotrichum}, \emph{Stachybotrys}, \emph{Strongyloides}, \emph{Syncephalastrum}, \emph{Syngamus}, \emph{Taenia}, \emph{Talaromyces}, \emph{Teleomorph}, \emph{Toxocara}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ulocladium}, \emph{Ustilago}, \emph{Verticillium}, \emph{Wallemia}, \emph{Wangiella}, \emph{Wickerhamomyces}, \emph{Wuchereria}, \emph{Yarrowia}, or \emph{Zygosaccharomyces};
|
||||
\item Any \emph{non-bacterial} genus, species or subspecies of which the genus is present in the following list, has \code{prevalence = 1.25} in the \link{microorganisms} data set: \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acremonium}, \emph{Actinomucor}, \emph{Aedes}, \emph{Alternaria}, \emph{Amoeba}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apiotrichum}, \emph{Apophysomyces}, \emph{Arthroderma}, \emph{Ascaris}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Babesia}, \emph{Balamuthia}, \emph{Balantioides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bipolaris}, \emph{Blastobotrys}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Brugia}, \emph{Candida}, \emph{Candidozyma}, \emph{Capillaria}, \emph{Chaetomium}, \emph{Chilomastix}, \emph{Chrysonilia}, \emph{Chrysosporium}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Clavispora}, \emph{Clonorchis}, \emph{Coccidioides}, \emph{Cokeromyces}, \emph{Conidiobolus}, \emph{Coniochaeta}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Cryptosporidium}, \emph{Cunninghamella}, \emph{Curvularia}, \emph{Cutaneotrichosporon}, \emph{Cyberlindnera}, \emph{Cyclospora}, \emph{Cystoisospora}, \emph{Debaryozyma}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Diutina}, \emph{Echinococcus}, \emph{Echinostoma}, \emph{Emergomyces}, \emph{Emmonsia}, \emph{Encephalitozoon}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Enterocytozoon}, \emph{Epidermophyton}, \emph{Exidia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Fasciolopsis}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Geotrichum}, \emph{Giardia}, \emph{Graphium}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hansenula}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hortaea}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Kazachstania}, \emph{Kloeckera}, \emph{Kluyveromyces}, \emph{Kodamaea}, \emph{Lacazia}, \emph{Leishmania}, \emph{Lichtheimia}, \emph{Loa}, \emph{Lodderomyces}, \emph{Lomentospora}, \emph{Madurella}, \emph{Magnusiomyces}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Mansonella}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microascus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Millerozyma}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Naegleria}, \emph{Nakaseomyces}, \emph{Nannizzia}, \emph{Necator}, \emph{Nectria}, \emph{Neocosmospora}, \emph{Ochroconis}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Onchocerca}, \emph{Opisthorchis}, \emph{Paecilomyces}, \emph{Paracoccidioides}, \emph{Paragonimus}, \emph{Pediculus}, \emph{Penicillium}, \emph{Phaeoacremonium}, \emph{Phaeomoniella}, \emph{Phialophora}, \emph{Phlebotomus}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Plasmodium}, \emph{Pneumocystis}, \emph{Pseudallescheria}, \emph{Pseudoscopulariopsis}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Purpureocillium}, \emph{Quambalaria}, \emph{Rasamsonia}, \emph{Rhinocladiella}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Saccharomyces}, \emph{Saksenaea}, \emph{Saprochaete}, \emph{Sarcocystis}, \emph{Sarcoptes}, \emph{Scedosporium}, \emph{Schistosoma}, \emph{Schizophyllum}, \emph{Schizosaccharomyces}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Spirometra}, \emph{Sporobolomyces}, \emph{Sporopachydermia}, \emph{Sporothrix}, \emph{Sporotrichum}, \emph{Stachybotrys}, \emph{Strongyloides}, \emph{Syncephalastrum}, \emph{Syngamus}, \emph{Taenia}, \emph{Talaromyces}, \emph{Teleomorph}, \emph{Toxocara}, \emph{Toxoplasma}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ulocladium}, \emph{Ustilago}, \emph{Verticillium}, \emph{Wallemia}, \emph{Wangiella}, \emph{Wickerhamomyces}, \emph{Wuchereria}, \emph{Yarrowia}, or \emph{Zygosaccharomyces};
|
||||
\item All other records have \code{prevalence = 2.0} in the \link{microorganisms} data set.
|
||||
}
|
||||
|
||||
|
||||
@@ -47,7 +47,7 @@ Furthermore,
|
||||
\item Any genus present in the \strong{established} list also has \code{prevalence = 1.15} in the \link{microorganisms} data set;
|
||||
\item Any other genus present in the \strong{putative} list has \code{prevalence = 1.25} in the \link{microorganisms} data set;
|
||||
\item Any other species or subspecies of which the genus is present in the two aforementioned groups, has \code{prevalence = 1.5} in the \link{microorganisms} data set;
|
||||
\item Any \emph{non-bacterial} genus, species or subspecies of which the genus is present in the following list, has \code{prevalence = 1.25} in the \link{microorganisms} data set: \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acremonium}, \emph{Actinomucor}, \emph{Aedes}, \emph{Alternaria}, \emph{Amoeba}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arthroderma}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bipolaris}, \emph{Blastobotrys}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Candida}, \emph{Capillaria}, \emph{Chaetomium}, \emph{Chilomastix}, \emph{Chrysonilia}, \emph{Chrysosporium}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Clavispora}, \emph{Coccidioides}, \emph{Cokeromyces}, \emph{Conidiobolus}, \emph{Coniochaeta}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Cryptosporidium}, \emph{Cunninghamella}, \emph{Curvularia}, \emph{Cyberlindnera}, \emph{Debaryozyma}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Echinostoma}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Epidermophyton}, \emph{Exidia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Geotrichum}, \emph{Giardia}, \emph{Graphium}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hansenula}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hortaea}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Kloeckera}, \emph{Kluyveromyces}, \emph{Kodamaea}, \emph{Lacazia}, \emph{Leishmania}, \emph{Lichtheimia}, \emph{Lodderomyces}, \emph{Lomentospora}, \emph{Madurella}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microascus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Millerozyma}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Nannizzia}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Paecilomyces}, \emph{Paracoccidioides}, \emph{Pediculus}, \emph{Penicillium}, \emph{Phaeoacremonium}, \emph{Phaeomoniella}, \emph{Phialophora}, \emph{Phlebotomus}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Plasmodium}, \emph{Pneumocystis}, \emph{Pseudallescheria}, \emph{Pseudoscopulariopsis}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Purpureocillium}, \emph{Quambalaria}, \emph{Rhinocladiella}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Saccharomyces}, \emph{Saksenaea}, \emph{Saprochaete}, \emph{Sarcoptes}, \emph{Scedosporium}, \emph{Schistosoma}, \emph{Schizophyllum}, \emph{Schizosaccharomyces}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Spirometra}, \emph{Sporobolomyces}, \emph{Sporopachydermia}, \emph{Sporothrix}, \emph{Sporotrichum}, \emph{Stachybotrys}, \emph{Strongyloides}, \emph{Syncephalastrum}, \emph{Syngamus}, \emph{Taenia}, \emph{Talaromyces}, \emph{Teleomorph}, \emph{Toxocara}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ulocladium}, \emph{Ustilago}, \emph{Verticillium}, \emph{Wallemia}, \emph{Wangiella}, \emph{Wickerhamomyces}, \emph{Wuchereria}, \emph{Yarrowia}, or \emph{Zygosaccharomyces};
|
||||
\item Any \emph{non-bacterial} genus, species or subspecies of which the genus is present in the following list, has \code{prevalence = 1.25} in the \link{microorganisms} data set: \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acremonium}, \emph{Actinomucor}, \emph{Aedes}, \emph{Alternaria}, \emph{Amoeba}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apiotrichum}, \emph{Apophysomyces}, \emph{Arthroderma}, \emph{Ascaris}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Babesia}, \emph{Balamuthia}, \emph{Balantioides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bipolaris}, \emph{Blastobotrys}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Brugia}, \emph{Candida}, \emph{Candidozyma}, \emph{Capillaria}, \emph{Chaetomium}, \emph{Chilomastix}, \emph{Chrysonilia}, \emph{Chrysosporium}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Clavispora}, \emph{Clonorchis}, \emph{Coccidioides}, \emph{Cokeromyces}, \emph{Conidiobolus}, \emph{Coniochaeta}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Cryptosporidium}, \emph{Cunninghamella}, \emph{Curvularia}, \emph{Cutaneotrichosporon}, \emph{Cyberlindnera}, \emph{Cyclospora}, \emph{Cystoisospora}, \emph{Debaryozyma}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Diutina}, \emph{Echinococcus}, \emph{Echinostoma}, \emph{Emergomyces}, \emph{Emmonsia}, \emph{Encephalitozoon}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Enterocytozoon}, \emph{Epidermophyton}, \emph{Exidia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Fasciolopsis}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Geotrichum}, \emph{Giardia}, \emph{Graphium}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hansenula}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hortaea}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Kazachstania}, \emph{Kloeckera}, \emph{Kluyveromyces}, \emph{Kodamaea}, \emph{Lacazia}, \emph{Leishmania}, \emph{Lichtheimia}, \emph{Loa}, \emph{Lodderomyces}, \emph{Lomentospora}, \emph{Madurella}, \emph{Magnusiomyces}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Mansonella}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microascus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Millerozyma}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Naegleria}, \emph{Nakaseomyces}, \emph{Nannizzia}, \emph{Necator}, \emph{Nectria}, \emph{Neocosmospora}, \emph{Ochroconis}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Onchocerca}, \emph{Opisthorchis}, \emph{Paecilomyces}, \emph{Paracoccidioides}, \emph{Paragonimus}, \emph{Pediculus}, \emph{Penicillium}, \emph{Phaeoacremonium}, \emph{Phaeomoniella}, \emph{Phialophora}, \emph{Phlebotomus}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Plasmodium}, \emph{Pneumocystis}, \emph{Pseudallescheria}, \emph{Pseudoscopulariopsis}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Purpureocillium}, \emph{Quambalaria}, \emph{Rasamsonia}, \emph{Rhinocladiella}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Saccharomyces}, \emph{Saksenaea}, \emph{Saprochaete}, \emph{Sarcocystis}, \emph{Sarcoptes}, \emph{Scedosporium}, \emph{Schistosoma}, \emph{Schizophyllum}, \emph{Schizosaccharomyces}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Spirometra}, \emph{Sporobolomyces}, \emph{Sporopachydermia}, \emph{Sporothrix}, \emph{Sporotrichum}, \emph{Stachybotrys}, \emph{Strongyloides}, \emph{Syncephalastrum}, \emph{Syngamus}, \emph{Taenia}, \emph{Talaromyces}, \emph{Teleomorph}, \emph{Toxocara}, \emph{Toxoplasma}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ulocladium}, \emph{Ustilago}, \emph{Verticillium}, \emph{Wallemia}, \emph{Wangiella}, \emph{Wickerhamomyces}, \emph{Wuchereria}, \emph{Yarrowia}, or \emph{Zygosaccharomyces};
|
||||
\item All other records have \code{prevalence = 2.0} in the \link{microorganisms} data set.
|
||||
}
|
||||
|
||||
|
||||
Reference in new issue
Block a user