(v3.0.1.9068) todo tracker update

.github/workflows/todo-tracker.yml

@@ -29,7 +29,6 @@
 
 on:
   push:
-    # only on main
     branches: "main"
 
 name: Update TODO Tracker
@@ -40,40 +39,228 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # full history required for git blame
 
-      - name: Generate TODO list from R/
+      - name: Generate TODO report
+        env:
+          GH_TOKEN: ${{ secrets.GH_REPO_SCOPE }}
         run: |
+          set -euo pipefail
           export TZ=Europe/Amsterdam
-          last_updated=$(date +"%e %B %Y %H:%M:%S %Z" | sed 's/^ *//')
-          echo "## \`TODO\` Report" > todo.md
-          echo "" >> todo.md
-          echo "**Last Updated: ${last_updated}**" >> todo.md
-          echo "" >> todo.md
-          echo "_This overview is automatically updated on each push to \`main\`. It provides an automated overview of all mentions of the text \`TODO\`._" >> todo.md
-          echo "" >> todo.md
-          todos=$(grep -rn --include=\*.{R,Rmd,yaml,yml,md,css,js}  --exclude={todo-tracker.yml,todo.md} "TODO" . || true)
-          if [ -z "$todos" ]; then
-            echo "✅ No TODOs found." >> todo.md
-          else
-            echo "$todos" | awk -F: -v repo="https://github.com/msberends/AMR/blob/main/" '
-              {
-                file = $1
-                gsub("^\\./", "", file)  # remove leading ./ if present
-                line = $2
-                text = substr($0, index($0,$3))
-                if (file != last_file) {
-                  if (last_file != "") print "```"
-                  print ""
-                  print "### [`" file "`](" repo file ")"
-                  print "```r"
-                  last_file = file
-                }
-                printf "L%s: %s\n", line, text
-              }
-            ' >> todo.md
-            echo "\`\`\`" >> todo.md
+
+          REPO="msberends/AMR"
+          REPO_URL="https://github.com/$REPO/blob/main"
+          NOW=$(date +%s)
+          LAST_UPDATED=$(date +"%e %B %Y %H:%M:%S %Z" | sed 's/^ *//')
+          STALE_DAYS=180
+
+          # ── helper: human-readable age ──────────────────────────────
+          format_age() {
+            local d=$1
+            if [ "$d" -lt 0 ] 2>/dev/null; then echo "unknown"; return; fi
+            local y=$((d / 365)) m=$(( (d % 365) / 30 ))
+            if [ "$y" -gt 0 ] && [ "$m" -gt 0 ]; then echo "${y}y ${m}m"
+            elif [ "$y" -gt 0 ]; then echo "${y}y"
+            elif [ "$m" -gt 0 ]; then echo "${m}m"
+            else echo "${d}d"
+            fi
+          }
+
+          export -f format_age
+
+          # ── step 1: find all markers ────────────────────────────────
+          grep -rn \
+            --include='*.R' --include='*.Rmd' --include='*.yaml' \
+            --include='*.yml' --include='*.md' --include='*.css' \
+            --include='*.js' \
+            --exclude='todo-tracker.yml' --exclude='todo.md' \
+            -E '\b(TODO|FIXME|HACK|XXX)\b' . > /tmp/raw.txt || true
+
+          if [ ! -s /tmp/raw.txt ]; then
+            echo -e "## \`TODO\` Report\n\n**Last Updated: ${LAST_UPDATED}**\n\nNo markers found." > todo.md
+            exit 0
           fi
 
+          # ── step 2: enrich with git blame & extract issue refs ──────
+          > /tmp/enriched.tsv
+          > /tmp/issues_seen.txt
+
+          while IFS= read -r match; do
+            clean=$(printf '%s\n' "$match" | sed 's|^\./||')
+            file=$(printf '%s\n' "$clean" | cut -d: -f1)
+            lineno=$(printf '%s\n' "$clean" | cut -d: -f2)
+            text=$(printf '%s\n' "$clean" | cut -d: -f3-)
+
+            # determine marker type (first match wins, TODO is default)
+            marker="TODO"
+            for m in FIXME HACK XXX; do
+              if printf '%s\n' "$text" | grep -qw "$m"; then marker="$m"; break; fi
+            done
+
+            # git blame timestamp
+            blame_ts=$(git blame -L "${lineno},${lineno}" --porcelain -- "$file" 2>/dev/null \
+              | awk '/^author-time/{print $2}' || echo "0")
+            blame_ts=${blame_ts:-0}
+
+            if [ "$blame_ts" -gt 0 ] 2>/dev/null; then
+              age_days=$(( (NOW - blame_ts) / 86400 ))
+            else
+              age_days=-1
+            fi
+
+            # extract issue references (#NNN)
+            issues=$(printf '%s\n' "$text" | grep -oE '#[0-9]+' | sed 's/#//' | tr '\n' ',' | sed 's/,$//' || true)
+            if [ -n "$issues" ]; then
+              for inum in $(echo "$issues" | tr ',' ' '); do
+                echo "$inum" >> /tmp/issues_seen.txt
+              done
+            fi
+
+            printf '%s\t%s\t%s\t%s\t%s\t%s\n' \
+              "$file" "$lineno" "$marker" "$age_days" "$issues" "$text" >> /tmp/enriched.tsv
+          done < /tmp/raw.txt
+
+          # ── step 3: query GitHub API for referenced issues ──────────
+          > /tmp/issue_info.tsv
+          if [ -s /tmp/issues_seen.txt ]; then
+            sort -un /tmp/issues_seen.txt | while read -r inum; do
+              info=$(gh api "/repos/$REPO/issues/$inum" \
+                --jq '"\(.state)\t\(.title)"' 2>/dev/null \
+                || echo "unknown	(could not fetch)")
+              printf '%s\t%s\n' "$inum" "$info" >> /tmp/issue_info.tsv
+            done
+          fi
+
+          # ── step 4: build the report ────────────────────────────────
+          {
+            # ── header ──
+            echo "## \`TODO\` Report"
+            echo ""
+            echo "**Last Updated: ${LAST_UPDATED}**"
+            echo ""
+            echo "_This overview is automatically updated on each push to \`main\`. It scans for \`TODO\`, \`FIXME\`, \`HACK\`, and \`XXX\` markers across the codebase._"
+            echo ""
+
+            # ── summary table ──
+            total=$(wc -l < /tmp/enriched.tsv | tr -d ' ')
+            files_affected=$(awk -F'\t' '{print $1}' /tmp/enriched.tsv | sort -u | wc -l | tr -d ' ')
+            todo_n=$(awk -F'\t' '$3=="TODO"' /tmp/enriched.tsv | wc -l | tr -d ' ')
+            fixme_n=$(awk -F'\t' '$3=="FIXME"' /tmp/enriched.tsv | wc -l | tr -d ' ')
+            hack_n=$(awk -F'\t' '$3=="HACK"' /tmp/enriched.tsv | wc -l | tr -d ' ')
+            xxx_n=$(awk -F'\t' '$3=="XXX"' /tmp/enriched.tsv | wc -l | tr -d ' ')
+            stale_n=$(awk -F'\t' -v s="$STALE_DAYS" '$4 > s' /tmp/enriched.tsv | wc -l | tr -d ' ')
+            linked_n=$(awk -F'\t' '$5 != ""' /tmp/enriched.tsv | wc -l | tr -d ' ')
+            unlinked_n=$(awk -F'\t' '$5 == ""' /tmp/enriched.tsv | wc -l | tr -d ' ')
+
+            # oldest marker
+            oldest_line=$(awk -F'\t' '$4 >= 0' /tmp/enriched.tsv | sort -t$'\t' -k4 -rn | head -1)
+            oldest_days=$(echo "$oldest_line" | cut -f4)
+            oldest_file=$(echo "$oldest_line" | cut -f1)
+            oldest_lineno=$(echo "$oldest_line" | cut -f2)
+            oldest_age=$(format_age "$oldest_days")
+
+            echo "### Summary"
+            echo ""
+            echo "| Metric | Value |"
+            echo "|:---|---:|"
+            echo "| Total markers | **${total}** |"
+            [ "$todo_n" -gt 0 ] && echo "| \`TODO\` | ${todo_n} |"
+            [ "$fixme_n" -gt 0 ] && echo "| \`FIXME\` | ${fixme_n} |"
+            [ "$hack_n" -gt 0 ] && echo "| \`HACK\` | ${hack_n} |"
+            [ "$xxx_n" -gt 0 ] && echo "| \`XXX\` | ${xxx_n} |"
+            echo "| Files affected | ${files_affected} |"
+            echo "| Stale (> 6 months) | ${stale_n} |"
+            echo "| Oldest marker | ${oldest_age}, \`${oldest_file}\` L${oldest_lineno} |"
+            echo "| Linked to issues | ${linked_n} |"
+            echo "| Unlinked (no issue ref) | ${unlinked_n} |"
+            echo ""
+
+            # ── by referenced issue ──
+            if [ -s /tmp/issue_info.tsv ]; then
+              echo "### By Referenced Issue"
+              echo ""
+
+              has_closed=false
+
+              while IFS=$'\t' read -r inum state title; do
+                count=$(awk -F'\t' -v n="$inum" '$5 ~ "(^|,)"n"(,|$)"' /tmp/enriched.tsv | wc -l | tr -d ' ')
+                [ "$state" = "closed" ] && has_closed=true
+
+                state_icon=""
+                [ "$state" = "closed" ] && state_icon=" :warning:"
+
+                echo "<details><summary><b>#${inum}</b> (${state}): <i>${title}</i> &mdash; ${count} marker(s)${state_icon}</summary>"
+                echo ""
+
+                awk -F'\t' -v n="$inum" '$5 ~ "(^|,)"n"(,|$)"' /tmp/enriched.tsv \
+                | while IFS=$'\t' read -r f l m d refs txt; do
+                  age_str=$(format_age "$d")
+                  flag=""
+                  [ "$d" -gt "$STALE_DAYS" ] 2>/dev/null && flag=" :warning:"
+                  # re-read the actual source line and trim leading/trailing whitespace
+                  src_text=$(sed -n "${l}p" "$f" 2>/dev/null | sed 's/^[[:space:]]*//;s/[[:space:]]*$//' || true)
+                  echo "- [\`${f}\` L${l}](${REPO_URL}/${f}#L${l}) (${age_str} ago)${flag}"
+                  [ -n "$src_text" ] && echo "  \`${src_text}\`"
+                done
+
+                echo ""
+                echo "</details>"
+                echo ""
+              done < /tmp/issue_info.tsv
+
+              if [ "$has_closed" = true ]; then
+                echo "> **Warning:** some markers reference closed issues and may be stale."
+                echo ""
+              fi
+            fi
+
+            # ── by file ──
+            echo "### By File"
+            echo ""
+
+            prev_file=""
+            prev_lineno=-99
+
+            while IFS=$'\t' read -r file lineno marker age_days issues text; do
+              if [ "$file" != "$prev_file" ]; then
+                # close previous code block
+                if [ -n "$prev_file" ]; then
+                  echo '```'
+                  echo ""
+                fi
+
+                file_count=$(awk -F'\t' -v f="$file" '$1==f' /tmp/enriched.tsv | wc -l | tr -d ' ')
+                echo "#### [\`${file}\`](${REPO_URL}/${file}) &mdash; ${file_count} marker(s)"
+                echo '```r'
+
+                prev_lineno=-99
+              fi
+
+              # blank line between non-sequential lines (visual grouping)
+              if [ "$file" = "$prev_file" ] && [ $((lineno - prev_lineno)) -gt 1 ]; then
+                echo ""
+              fi
+
+              age_str=$(format_age "$age_days")
+              flag=""
+              [ "$age_days" -gt "$STALE_DAYS" ] 2>/dev/null && flag=" !!"
+
+              # re-read the actual source line to avoid TSV round-trip corruption
+              src_line=$(sed -n "${lineno}p" "$file" 2>/dev/null | sed 's/[[:space:]]*$//' || true)
+              printf 'L%s: %s  ◁ %s ago%s\n' "$lineno" "$src_line" "$age_str" "$flag"
+
+              prev_file="$file"
+              prev_lineno="$lineno"
+            done < <(sort -t$'\t' -k1,1 -k2,2n /tmp/enriched.tsv)
+
+            # close final code block
+            if [ -n "$prev_file" ]; then
+              echo '```'
+            fi
+
+          } > todo.md
+
       - name: Update GitHub issue
         uses: peter-evans/create-or-update-comment@v4
         with:

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.0.1.9065
+Version: 3.0.1.9068
 Date: 2026-06-24
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9065
+# AMR 3.0.1.9068
 
 Planned as v3.1.0, end of June 2026.
 

R/data.R

@@ -143,11 +143,10 @@
 #' ### Manual additions
 #' For convenience, some entries were added manually:
 #'
+#' - All `r format_included_data_number(length(which(microorganisms$rank == "species group")))` groups and complexes of the [microorganisms.groups] data set, for cross-reference (examples include beta-haemolytic *Streptococcus* groups A to K, coagulase-negative *Staphylococcus* (CoNS), *Mycobacterium tuberculosis* complex, etc.)
 #' - `r format_included_data_number(microorganisms[which(microorganisms$source == "manually added" & microorganisms$genus == "Salmonella"), , drop = FALSE])` entries of *Salmonella*, such as the city-like serovars and groups A to H
-#' - `r format_included_data_number(length(which(microorganisms$rank == "species group")))` species groups (such as the beta-haemolytic *Streptococcus* groups A to K, coagulase-negative *Staphylococcus* (CoNS), *Mycobacterium tuberculosis* complex, etc.), of which the group compositions are stored in the [microorganisms.groups] data set
 #' - 1 entry of *Blastocystis* (*B.  hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993)
-#' - 1 entry of *Moraxella* (*M. catarrhalis*), which was formally named *Branhamella catarrhalis* (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
-#' - 8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)
+#' - `r sum(microorganisms$fullname %like% "unknown")` other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)
 #'
 #' The syntax used to transform the original data to a cleansed \R format, can be [found here](https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R).
 #' @inheritSection AMR Download Our Reference Data

R/mo_property.R

@@ -83,6 +83,7 @@
 #' @examples
 #' # taxonomic tree -----------------------------------------------------------
 #'
+#' mo_domain("Klebsiella pneumoniae")
 #' mo_kingdom("Klebsiella pneumoniae")
 #' mo_phylum("Klebsiella pneumoniae")
 #' mo_class("Klebsiella pneumoniae")
@@ -92,6 +93,8 @@
 #' mo_species("Klebsiella pneumoniae")
 #' mo_subspecies("Klebsiella pneumoniae")
 #'
+#' # all in one go
+#' mo_taxonomy("Klebsiella pneumoniae")
 #'
 #' # full names and short names -----------------------------------------------
 #'
@@ -112,6 +115,7 @@
 #' mo_url("Klebsiella pneumoniae")
 #' mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
 #'
+#' mo_group_members("Streptococcus group A")
 #' mo_group_members(c(
 #'   "Streptococcus group A",
 #'   "Streptococcus group C",
@@ -155,6 +159,7 @@
 #'
 #' mo_fullname("Staph epidermidis")
 #' mo_fullname("Staph epidermidis", Becker = TRUE)
+#'
 #' mo_shortname("Staph epidermidis")
 #' mo_shortname("Staph epidermidis", Becker = TRUE)
 #'
@@ -163,6 +168,7 @@
 #'
 #' mo_fullname("Strep agalactiae")
 #' mo_fullname("Strep agalactiae", Lancefield = TRUE)
+#'
 #' mo_shortname("Strep agalactiae")
 #' mo_shortname("Strep agalactiae", Lancefield = TRUE)
 #'
@@ -175,10 +181,10 @@
 #' mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
 #' mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
 #'
-#' # mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated
-#' mo_kingdom("Klebsiella pneumoniae")
+#' # mo_type is equal to mo_domain, but mo_domain will remain untranslated
+#' mo_domain("Klebsiella pneumoniae")
 #' mo_type("Klebsiella pneumoniae")
-#' mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
+#' mo_domain("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
 #' mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated
 #'
 #' mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de")
@@ -807,19 +813,19 @@ mo_taxonomy <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio
   language <- validate_language(language)
   meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
 
-  x <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
+  x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
   metadata <- get_mo_uncertainties()
 
   out <- list(
-    domain = mo_domain(x, language = language, keep_synonyms = keep_synonyms),
-    kingdom = mo_kingdom(x, language = language, keep_synonyms = keep_synonyms),
-    phylum = mo_phylum(x, language = language, keep_synonyms = keep_synonyms),
-    class = mo_class(x, language = language, keep_synonyms = keep_synonyms),
-    order = mo_order(x, language = language, keep_synonyms = keep_synonyms),
-    family = mo_family(x, language = language, keep_synonyms = keep_synonyms),
-    genus = mo_genus(x, language = language, keep_synonyms = keep_synonyms),
-    species = mo_species(x, language = language, keep_synonyms = keep_synonyms),
-    subspecies = mo_subspecies(x, language = language, keep_synonyms = keep_synonyms)
+    domain = mo_domain(x.mo, language = language, keep_synonyms = keep_synonyms),
+    kingdom = suppressMessages(mo_kingdom(x.mo, language = language, keep_synonyms = keep_synonyms)),
+    phylum = mo_phylum(x.mo, language = language, keep_synonyms = keep_synonyms),
+    class = mo_class(x.mo, language = language, keep_synonyms = keep_synonyms),
+    order = mo_order(x.mo, language = language, keep_synonyms = keep_synonyms),
+    family = mo_family(x.mo, language = language, keep_synonyms = keep_synonyms),
+    genus = mo_genus(x.mo, language = language, keep_synonyms = keep_synonyms),
+    species = mo_species(x.mo, language = language, keep_synonyms = keep_synonyms),
+    subspecies = mo_subspecies(x.mo, language = language, keep_synonyms = keep_synonyms)
   )
 
   load_mo_uncertainties(metadata)

index.md

@@ -230,7 +230,7 @@ wisca(example_isolates,
 
 | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
 |:---|:---|:---|
-| 70.1% (64.9-75.7%) | 93.6% (92.2-95%) | 89.8% (86.7-92.3%) |
+| 69.9% (64.7-75.2%) | 93.7% (92.2-95.1%) | 89.8% (86.8-92.3%) |
 
 WISCA supports stratification by any clinical variable, so you can
 generate syndrome-specific or ward-specific coverage estimates:
@@ -245,9 +245,9 @@ wisca(example_isolates,
 
 | Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
 |:---|:---|:---|:---|
-| Clinical | 74.5% (69.3-80.1%) | 93.7% (92-95.1%) | 90.5% (87.1-93.1%) |
-| ICU | 56.7% (48-65.5%) | 86.7% (83.4-89.8%) | 82.9% (78.2-87.3%) |
-| Outpatient | 57.8% (46.4-69.7%) | 76.5% (70.1-82.2%) | 67.9% (57.9-77.5%) |
+| Clinical | 74.6% (69-80.1%) | 93.6% (91.9-95.1%) | 90.5% (86.9-93%) |
+| ICU | 57% (48.7-65.8%) | 86.7% (83.7-89.7%) | 82.8% (77.9-87.2%) |
+| Outpatient | 57.5% (46.5-68.7%) | 76.7% (70.6-82.4%) | 67.5% (57.2-76.7%) |
 
 **For AMR surveillance**, traditional antibiograms remain the right tool
 for tracking resistance per species over time:

man/microorganisms.Rd

@@ -59,11 +59,10 @@ Included taxonomic data from \href{https://lpsn.dsmz.de}{LPSN}, \href{https://ww
 
 For convenience, some entries were added manually:
 \itemize{
+\item All 37 groups and complexes of the \link{microorganisms.groups} data set, for cross-reference (examples include beta-haemolytic \emph{Streptococcus} groups A to K, coagulase-negative \emph{Staphylococcus} (CoNS), \emph{Mycobacterium tuberculosis} complex, etc.)
 \item ~1 500 entries of \emph{Salmonella}, such as the city-like serovars and groups A to H
-\item 37 species groups (such as the beta-haemolytic \emph{Streptococcus} groups A to K, coagulase-negative \emph{Staphylococcus} (CoNS), \emph{Mycobacterium tuberculosis} complex, etc.), of which the group compositions are stored in the \link{microorganisms.groups} data set
 \item 1 entry of \emph{Blastocystis} (\emph{B.  hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
-\item 1 entry of \emph{Moraxella} (\emph{M. catarrhalis}), which was formally named \emph{Branhamella catarrhalis} (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
-\item 8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)
+\item 9 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)
 }
 
 The syntax used to transform the original data to a cleansed \R format, can be \href{https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R}{found here}.

man/mo_property.Rd

@@ -401,6 +401,7 @@ Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct
 \examples{
 # taxonomic tree -----------------------------------------------------------
 
+mo_domain("Klebsiella pneumoniae")
 mo_kingdom("Klebsiella pneumoniae")
 mo_phylum("Klebsiella pneumoniae")
 mo_class("Klebsiella pneumoniae")
@@ -410,6 +411,8 @@ mo_genus("Klebsiella pneumoniae")
 mo_species("Klebsiella pneumoniae")
 mo_subspecies("Klebsiella pneumoniae")
 
+# all in one go
+mo_taxonomy("Klebsiella pneumoniae")
 
 # full names and short names -----------------------------------------------
 
@@ -430,6 +433,7 @@ mo_rank("Klebsiella pneumoniae")
 mo_url("Klebsiella pneumoniae")
 mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
 
+mo_group_members("Streptococcus group A")
 mo_group_members(c(
   "Streptococcus group A",
   "Streptococcus group C",
@@ -473,6 +477,7 @@ mo_shortname("K. pneu rh")
 
 mo_fullname("Staph epidermidis")
 mo_fullname("Staph epidermidis", Becker = TRUE)
+
 mo_shortname("Staph epidermidis")
 mo_shortname("Staph epidermidis", Becker = TRUE)
 
@@ -481,6 +486,7 @@ mo_shortname("Staph epidermidis", Becker = TRUE)
 
 mo_fullname("Strep agalactiae")
 mo_fullname("Strep agalactiae", Lancefield = TRUE)
+
 mo_shortname("Strep agalactiae")
 mo_shortname("Strep agalactiae", Lancefield = TRUE)
 
@@ -493,10 +499,10 @@ mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish
 mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
 mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
 
-# mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated
-mo_kingdom("Klebsiella pneumoniae")
+# mo_type is equal to mo_domain, but mo_domain will remain untranslated
+mo_domain("Klebsiella pneumoniae")
 mo_type("Klebsiella pneumoniae")
-mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
+mo_domain("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
 mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated
 
 mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de")