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make rsi work in more cases, documentation update

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dr. M.S. (Matthijs) Berends
2023-02-22 14:38:57 +01:00
parent 380cbec0e8
commit dad25302f2
87 changed files with 401 additions and 327 deletions
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8
data-raw/_pre_commit_hook.R
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@ -148,11 +148,12 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
}
MO_CONS <- create_species_cons_cops("CoNS")
MO_COPS <- create_species_cons_cops("CoPS")
MO_STREP_ABCG <- AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$genus == "Streptococcus" &
AMR_env$MO_lookup$species %in% c(
MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms$genus == "Streptococcus" &
tolower(AMR::microorganisms$species) %in% c(
"pyogenes", "agalactiae", "dysgalactiae", "equi", "canis",
"group A", "group B", "group C", "group G"
"group a", "group b", "group c", "group g"
))]
MO_LANCEFIELD <- AMR::microorganisms$mo[which(AMR::microorganisms$mo %like% "^(B_STRPT_PYGN(_|$)|B_STRPT_AGLC(_|$)|B_STRPT_(DYSG|EQUI)(_|$)|B_STRPT_ANGN(_|$)|B_STRPT_(DYSG|CANS)(_|$)|B_STRPT_SNGN(_|$)|B_STRPT_SLVR(_|$))")]
MO_PREVALENT_GENERA <- c(
"Absidia", "Acanthamoeba", "Acremonium", "Aedes", "Alternaria", "Amoeba", "Ancylostoma", "Angiostrongylus",
"Anisakis", "Anopheles", "Apophysomyces", "Aspergillus", "Aureobasidium", "Basidiobolus", "Beauveria",
@ -285,6 +286,7 @@ suppressMessages(usethis::use_data(EUCAST_RULES_DF,
MO_CONS,
MO_COPS,
MO_STREP_ABCG,
MO_LANCEFIELD,
MO_PREVALENT_GENERA,
AB_LOOKUP,
AV_LOOKUP,

2
data-raw/ab.md5
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@ -1 +1 @@
43220347c34d06a5c57f2014a8ecaa82
8bf97fd5f1d8d82486902d05916ebca0

74
data-raw/antibiograms.html
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@ -11,7 +11,7 @@
<meta name="author" content="AMR package developers" />
<meta name="date" content="2023-02-08" />
<meta name="date" content="2023-02-18" />
<title>Generating antibiograms with the AMR package</title>
@ -353,7 +353,7 @@ display: none;
<h1 class="title toc-ignore">Generating antibiograms with the AMR
package</h1>
<h4 class="author">AMR package developers</h4>
<h4 class="date">2023-02-08</h4>
<h4 class="date">2023-02-18</h4>
</div>
@ -412,7 +412,7 @@ looks like:</p>
<td align="right">22</td>
</tr>
<tr class="even">
<td align="left">E. coli (0-462)</td>
<td align="left"><em>E. coli</em> (0-462)</td>
<td align="right">100</td>
<td align="right">98</td>
<td align="right">100</td>
@ -421,7 +421,7 @@ looks like:</p>
<td align="right">97</td>
</tr>
<tr class="odd">
<td align="left">E. faecalis (0-39)</td>
<td align="left"><em>E. faecalis</em> (0-39)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">100</td>
@ -430,7 +430,7 @@ looks like:</p>
<td align="right">0</td>
</tr>
<tr class="even">
<td align="left">K. pneumoniae (0-58)</td>
<td align="left"><em>K. pneumoniae</em> (0-58)</td>
<td align="right">NA</td>
<td align="right">90</td>
<td align="right">100</td>
@ -439,7 +439,7 @@ looks like:</p>
<td align="right">90</td>
</tr>
<tr class="odd">
<td align="left">P. aeruginosa (17-30)</td>
<td align="left"><em>P. aeruginosa</em> (17-30)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">NA</td>
@ -448,7 +448,7 @@ looks like:</p>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left">P. mirabilis (0-34)</td>
<td align="left"><em>P. mirabilis</em> (0-34)</td>
<td align="right">NA</td>
<td align="right">94</td>
<td align="right">94</td>
@ -457,7 +457,7 @@ looks like:</p>
<td align="right">94</td>
</tr>
<tr class="odd">
<td align="left">S. aureus (2-233)</td>
<td align="left"><em>S. aureus</em> (2-233)</td>
<td align="right">NA</td>
<td align="right">99</td>
<td align="right">NA</td>
@ -466,7 +466,7 @@ looks like:</p>
<td align="right">98</td>
</tr>
<tr class="even">
<td align="left">S. epidermidis (8-163)</td>
<td align="left"><em>S. epidermidis</em> (8-163)</td>
<td align="right">0</td>
<td align="right">79</td>
<td align="right">NA</td>
@ -475,7 +475,7 @@ looks like:</p>
<td align="right">51</td>
</tr>
<tr class="odd">
<td align="left">S. hominis (3-80)</td>
<td align="left"><em>S. hominis</em> (3-80)</td>
<td align="right">NA</td>
<td align="right">92</td>
<td align="right">NA</td>
@ -484,7 +484,7 @@ looks like:</p>
<td align="right">85</td>
</tr>
<tr class="even">
<td align="left">S. pneumoniae (11-117)</td>
<td align="left"><em>S. pneumoniae</em> (11-117)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">NA</td>
@ -518,49 +518,49 @@ looks like:</p>
<td align="right">NA</td>
</tr>
<tr class="even">
<td align="left">E. coli (416-461)</td>
<td align="left"><em>E. coli</em> (416-461)</td>
<td align="right">94</td>
<td align="right">100</td>
<td align="right">99</td>
</tr>
<tr class="odd">
<td align="left">K. pneumoniae (53-58)</td>
<td align="left"><em>K. pneumoniae</em> (53-58)</td>
<td align="right">89</td>
<td align="right">93</td>
<td align="right">93</td>
</tr>
<tr class="even">
<td align="left">P. aeruginosa (27-30)</td>
<td align="left"><em>P. aeruginosa</em> (27-30)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="odd">
<td align="left">P. mirabilis (27-34)</td>
<td align="left"><em>P. mirabilis</em> (27-34)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left">S. aureus (7-231)</td>
<td align="left"><em>S. aureus</em> (7-231)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="odd">
<td align="left">S. epidermidis (5-128)</td>
<td align="left"><em>S. epidermidis</em> (5-128)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left">S. hominis (0-74)</td>
<td align="left"><em>S. hominis</em> (0-74)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="odd">
<td align="left">S. pneumoniae (112-112)</td>
<td align="left"><em>S. pneumoniae</em> (112-112)</td>
<td align="right">100</td>
<td align="right">100</td>
<td align="right">100</td>
@ -576,6 +576,16 @@ looks like:</p>
syndromic_group = &quot;ward&quot;)
)</code></pre>
<table>
<colgroup>
<col width="29%" />
<col width="33%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
</colgroup>
<thead>
<tr class="header">
<th align="left">Syndromic Group</th>
@ -621,7 +631,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">E. coli (0-299)</td>
<td align="left">E. <em>coli</em> (0-299)</td>
<td align="right">100</td>
<td align="right">98</td>
<td align="right">100</td>
@ -631,7 +641,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">E. coli (0-137)</td>
<td align="left">E. <em>coli</em> (0-137)</td>
<td align="right">100</td>
<td align="right">99</td>
<td align="right">100</td>
@ -641,7 +651,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">K. pneumoniae (0-51)</td>
<td align="left">K. <em>pneumoniae</em> (0-51)</td>
<td align="right">NA</td>
<td align="right">92</td>
<td align="right">100</td>
@ -651,7 +661,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left">P. mirabilis (0-30)</td>
<td align="left">P. <em>mirabilis</em> (0-30)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">NA</td>
@ -661,7 +671,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. aureus (2-150)</td>
<td align="left">S. <em>aureus</em> (2-150)</td>
<td align="right">NA</td>
<td align="right">99</td>
<td align="right">NA</td>
@ -671,7 +681,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">S. aureus (0-66)</td>
<td align="left">S. <em>aureus</em> (0-66)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">NA</td>
@ -681,7 +691,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. epidermidis (4-79)</td>
<td align="left">S. <em>epidermidis</em> (4-79)</td>
<td align="right">NA</td>
<td align="right">82</td>
<td align="right">NA</td>
@ -691,7 +701,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">S. epidermidis (4-75)</td>
<td align="left">S. <em>epidermidis</em> (4-75)</td>
<td align="right">NA</td>
<td align="right">72</td>
<td align="right">NA</td>
@ -701,7 +711,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. hominis (1-45)</td>
<td align="left">S. <em>hominis</em> (1-45)</td>
<td align="right">NA</td>
<td align="right">96</td>
<td align="right">NA</td>
@ -711,7 +721,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left">S. pneumoniae (5-78)</td>
<td align="left">S. <em>pneumoniae</em> (5-78)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">NA</td>
@ -721,7 +731,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="left">S. pneumoniae (5-30)</td>
<td align="left">S. <em>pneumoniae</em> (5-30)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">NA</td>
@ -745,8 +755,8 @@ looks like:</p>
)</code></pre>
<table>
<colgroup>
<col width="23%" />
<col width="35%" />
<col width="24%" />
<col width="34%" />
<col width="5%" />
<col width="14%" />
<col width="5%" />

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data-raw/antibiotics.txt
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@ -410,7 +410,7 @@
"SLT3" "Sulfamerazine/trimethoprim" "Trimethoprims" "J01EE07" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "" "" ""
"SUM" 5327 "Sulfamethazine" "Other antibacterials" "NA" "" "azolmetazin,benzene sulfonamide,calfspan,calfspan tablets,cremomethazine,diazil,diazilsulfadine,dimezathine,intradine,kelametazine,mermeth,metazin,neasina,neazina,nsulfanilamide,panazin,pirmazin,primazin,sa iii,solfadimidina,spanbolet,sulfadimerazine,sulfadimesin,sulfadimesine,sulfadimethyldiazine,sulfadimezin,sulfadimezine,sulfadimezinum,sulfadimidin,sulfadimidina,sulfadimidine,sulfadimidinum,sulfadine,sulfametazina,sulfametazyny,sulfamethazine,sulfamethiazine,sulfamezathine,sulfamidine,sulfasure sr bolus,sulfodimesin,sulfodimezine,sulka k boluses,sulka s boluses,sulmet,sulphadimidine,sulphamethasine,sulphamethazine,sulphamezathine,sulphamidine,sulphodimezine,superseptil,superseptyl,vertolan" "87592-2"
"SLF4" 5328 "Sulfamethizole" "Trimethoprims" "B05CA04,D06BA04,J01EB02,S01AB01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sfmz" "ayerlucil,lucosil,methazol,microsul,nsulfanilamide,proklar,renasul,salimol,solfametizolo,sulamethizole,sulfa gram,sulfamethizol,sulfamethizole,sulfamethizolum,sulfametizol,sulfapyelon,sulfstat,sulfurine,sulphamethizole,tetracid,thidicur,thiosulfil,thiosulfil forte,ultrasul,urocydal,urodiaton,urolucosil,urosulfin" 4 "g" "60175-7,60176-5,60177-3"
"SMX" 5329 "Sulfamethoxazole" "Trimethoprims" "J01EC01" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "sfmx,sulf" "azo gantanol,bactrim,bactrimel,cotrimoxazole,eusaprim,gamazole,gantanol,gantanol ds,metoxal,nsulfanilamide,nsulphanilamide,radonil,septran,septrin,simsinomin,sinomin,solfametossazolo,sulfamethalazole,sulfamethoxazol,sulfamethoxazole,sulfamethoxazolum,sulfamethoxizole,sulfamethylisoxazole,sulfametoxazol,sulfisomezole,sulmeprim,sulphamethalazole,sulphamethoxazol,sulphamethoxazole,sulphisomezole,urobak" 2 "g" "10342-4,25271-8,39772-9,59971-2,59972-0,60333-2,72674-5,80549-9,80974-9"
"SMX" 5329 "Sulfamethoxazole" "Trimethoprims" "J01EC01" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "sfmx,sulf" "azo gantanol,gamazole,gantanol,gantanol ds,metoxal,nsulfanilamide,nsulphanilamide,radonil,septran,simsinomin,sinomin,solfametossazolo,sulfamethalazole,sulfamethoxazol,sulfamethoxazole,sulfamethoxazolum,sulfamethoxizole,sulfamethylisoxazole,sulfametoxazol,sulfisomezole,sulmeprim,sulphamethalazole,sulphamethoxazol,sulphamethoxazole,sulphisomezole,urobak" 2 "g" "10342-4,25271-8,39772-9,59971-2,59972-0,60333-2,72674-5,80549-9,80974-9"
"SLF5" 5330 "Sulfamethoxypyridazine" "Trimethoprims" "J01ED05" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "altezol,davosin,depovernil,kineks,lederkyn,lentac,lisulfen,longin,medicel,midicel,midikel,myasul,nsulfanilamide,opinsul,paramid,paramid supra,petrisul,piridolo,quinoseptyl,retamid,retasulfin,retasulphine,slosul,spofadazine,sulfalex,sulfapyridazine,sulfdurazin,sulfozona,sultirene,vinces" 0.5 "g" ""
"SLF6" 19596 "Sulfametomidine" "Trimethoprims" "J01ED03" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "duroprocin,methofadin,methofazine,nsulfanilamide,solfametomidina,sulfamethomidine,sulfametomidin,sulfametomidina,sulfametomidine,sulfametomidinum" ""
"SLF7" 5326 "Sulfametoxydiazine" "Trimethoprims" "J01ED04" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "bayrena,berlicid,dairena,durenat,juvoxin,kinecid,kirocid,longasulf,methoxypyrimal,nsulfanilamide,solfametossidiazina,sulfameter,sulfamethorine,sulfamethoxine,sulfamethoxydiazin,sulfamethoxydiazine,sulfamethoxydin,sulfamethoxydine,sulfametin,sulfametinum,sulfametorin,sulfametorine,sulfametorinum,sulfametoxidiazina,sulfametoxidine,sulfametoxydiazine,sulfametoxydiazinum,sulphameter,sulphamethoxydiazine,supramid,ultrax" 0.5 "g" ""

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data-raw/reproduction_of_antibiotics.R
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@ -188,7 +188,7 @@ abx2 <- abx2 %>%
abx2$abbr <- lapply(as.list(abx2$abbr), function(x) unlist(strsplit(x, "|", fixed = TRUE)))
# Update Compound IDs and Trade Names ----
# Update Compound IDs and Synonyms ----
# vector with official names, returns vector with CIDs
get_CID <- function(ab) {
@ -307,6 +307,7 @@ get_synonyms <- function(CID, clean = TRUE) {
# get brand names from PubChem (3-4 min)
synonyms <- get_synonyms(CIDs)
synonyms.bak <- synonyms
# add existing ones (will be cleaned later)
for (i in seq_len(length(synonyms))) {
old <- antibiotics$synonyms[[i]]
@ -318,6 +319,13 @@ for (i in seq_len(length(synonyms))) {
antibiotics$synonyms <- synonyms
stop("remember to remove co-trimoxazole as synonyms from SXT (Sulfamethoxazole), so it only exists in SXT!")
sulfa <- antibiotics[which(antibiotics$ab == "SMX"), "synonyms", drop = TRUE][[1]]
cotrim <- antibiotics[which(antibiotics$ab == "SXT"), "synonyms", drop = TRUE][[1]]
sulfa <- sulfa[!sulfa %in% cotrim]
antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]][[1]] <- sulfa
# now go to end of this file