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(v0.8.0.9036) complete documentation rewrite

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-11-28 22:32:17 +01:00
parent 7c28b392b1
commit c5f00f4a9f
138 changed files with 2797 additions and 2484 deletions
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24
data-raw/eucast_rules.tsv
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@ -1,6 +1,6 @@
# -------------------------------------------------------------------------------------------------------------------------------
# For editing this EUCAST reference file, these values can all be used for target antibiotics:
# 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_without_CAZ',
# 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_except_CAZ',
# 'fluoroquinolones', 'glycopeptides', 'macrolides', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins'
# and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'.
# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
@ -29,9 +29,9 @@ genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoin
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints
genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints
genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints
genus is Staphylococcus FOX S carbapenems, cephalosporins_without_CAZ S Staphylococcus Breakpoints
genus is Staphylococcus FOX I carbapenems, cephalosporins_without_CAZ I Staphylococcus Breakpoints
genus is Staphylococcus FOX R carbapenems, cephalosporins_without_CAZ R Staphylococcus Breakpoints
genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints
genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints
genus is Staphylococcus FOX R carbapenems, cephalosporins_except_CAZ R Staphylococcus Breakpoints
genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Staphylococcus Breakpoints
genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints
genus is Staphylococcus ERY I AZM, CLR, RXT I Staphylococcus Breakpoints
@ -44,9 +44,9 @@ genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints
genus is Enterococcus NOR S CIP, LVX S Enterococcus Breakpoints
genus is Enterococcus NOR I CIP, LVX I Enterococcus Breakpoints
genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN S aminopenicillins, ureidopenicillins, cephalosporins_without_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN I aminopenicillins, ureidopenicillins, cephalosporins_without_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN R aminopenicillins, ureidopenicillins, cephalosporins_without_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ NOR S LVX, MFX S Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints
@ -171,17 +171,17 @@ genus_species is Staphylococcus haemolyticus CAZ R Table 04: Intrinsic resista
genus_species is Staphylococcus intermedius CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Staphylococcus pseudintermedius CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus is Streptococcus FUS, CAZ, aminoglycosides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_without_CAZ, aminoglycosides, macrolides, CLI, QDA, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Enterococcus gallinarum FUS, CAZ, cephalosporins_without_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Enterococcus casseliflavus FUS, CAZ, cephalosporins_without_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_without_CAZ, aminoglycosides, macrolides, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Enterococcus gallinarum FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Enterococcus casseliflavus FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus is Corynebacterium FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Listeria monocytogenes cephalosporins R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus one_of Leuconostoc, Pediococcus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus is Lactobacillus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Clostridium ramosum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Clostridium innocuum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G) PEN S aminopenicillins, cephalosporins_without_CAZ, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G) PEN S aminopenicillins, cephalosporins_except_CAZ, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules
genus is Enterococcus AMP R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules
genus is Enterococcus AMX R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules
family is Enterobacteriaceae TIC, PIP R, S PIP R Table 09: Interpretive rules for B-lactam agents and Gram-negative rods Expert Rules

Can't render this file because it contains an unexpected character in line 6 and column 96.

2
data-raw/internals.R
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@ -16,7 +16,7 @@ eucast_rules_file$reference.rule_group <- factor(eucast_rules_file$reference.rul
eucast_rules_file <- dplyr::arrange(eucast_rules_file,
reference.rule_group,
reference.rule)
eucast_rules_file$reference.rule_group <- as.character(eucast_rules_file$reference.rule_group)
# Translations ----
translations_file <- utils::read.delim(file = "data-raw/translations.tsv",