diff --git a/DESCRIPTION b/DESCRIPTION index c3d4dd0a..7ae540d2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 2.1.1.9084 -Date: 2024-09-30 +Version: 2.1.1.9086 +Date: 2024-10-02 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index fc0e0458..77bd9386 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9084 +# AMR 2.1.1.9086 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)* diff --git a/R/sysdata.rda b/R/sysdata.rda index aae784c9..9918dc4e 100755 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/data-raw/AMRforRGPT.pdf b/data-raw/AMRforRGPT.pdf new file mode 100644 index 00000000..68e3124e Binary files /dev/null and b/data-raw/AMRforRGPT.pdf differ diff --git a/data-raw/AMRforRGPT.pptx b/data-raw/AMRforRGPT.pptx new file mode 100644 index 00000000..07ca8aa3 Binary files /dev/null and b/data-raw/AMRforRGPT.pptx differ diff --git a/data-raw/AMRforRGPT.svg b/data-raw/AMRforRGPT.svg new file mode 100644 index 00000000..df39fe9b --- /dev/null +++ b/data-raw/AMRforRGPT.svg @@ -0,0 +1,2456 @@ + + + + diff --git a/data-raw/_pre_commit_checks.R b/data-raw/_pre_commit_checks.R index d87adb32..8bf82377 100644 --- a/data-raw/_pre_commit_checks.R +++ b/data-raw/_pre_commit_checks.R @@ -169,6 +169,7 @@ pre_commit_lst$MO_WHO_PRIORITY_GENERA <- c( "Coccidioides", "Cryptococcus", "Enterococcus", + "Escherichia", "Fusarium", "Haemophilus", "Helicobacter", diff --git a/data-raw/microorganisms.dta b/data-raw/microorganisms.dta index dd5b3a93..54cdc974 100644 Binary files a/data-raw/microorganisms.dta and b/data-raw/microorganisms.dta differ diff --git a/data-raw/microorganisms.feather b/data-raw/microorganisms.feather index 3cbb6da8..37becc61 100644 Binary files a/data-raw/microorganisms.feather and b/data-raw/microorganisms.feather differ diff --git a/data-raw/microorganisms.md5 b/data-raw/microorganisms.md5 index bfee2524..86f3d3f2 100644 --- a/data-raw/microorganisms.md5 +++ b/data-raw/microorganisms.md5 @@ -1 +1 @@ -5b5544d28deade33092925a6758277c4 +f38201f0751cfc3a0993dcf9141609a1 diff --git a/data-raw/microorganisms.parquet b/data-raw/microorganisms.parquet index bba8a34b..a41b866c 100644 Binary files a/data-raw/microorganisms.parquet and b/data-raw/microorganisms.parquet differ diff --git a/data-raw/microorganisms.rds b/data-raw/microorganisms.rds index ed5e1798..53dd25b9 100644 Binary files a/data-raw/microorganisms.rds and b/data-raw/microorganisms.rds differ diff --git a/data-raw/microorganisms.sav b/data-raw/microorganisms.sav index ee5f0ee4..3621fb7e 100644 Binary files a/data-raw/microorganisms.sav and b/data-raw/microorganisms.sav differ diff --git a/data-raw/microorganisms.txt b/data-raw/microorganisms.txt index 99934a87..ba36f6a6 100644 --- a/data-raw/microorganisms.txt +++ b/data-raw/microorganisms.txt @@ -23741,19 +23741,19 @@ "B_ECRBM_RMSM" "Erythromicrobium ramosum" "synonym" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Sphingomonadales" "Erythrobacteraceae" "Erythromicrobium" "ramosum" "" "species" "Yurkov et al., 1994" "LPSN" "776049" "515600" "12988" "3221406" 2 "434593006" "B_ERMNS" "Erythromonas" "synonym" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Erythromonas" "" "" "genus" "Yurkov et al., 1997" "LPSN" "515601" "1302" "515246" "8926" 2 "" "B_ERMNS_URSN" "Erythromonas ursincola" "synonym" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Erythromonas" "ursincola" "" "species" "Yurkov et al., 1997" "LPSN" "776051" "515601" "774092" 2 "" -"B_ESCHR" "Escherichia" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "" "" "genus" "Castellani et al., 1919" "facultative anaerobe" "LPSN" "515602" "482" "11158430" 1.15 "407310004,407251000,407281008,407284000,407283006,407160000,407285004,407159005,407287007,407290001,407291002,407289005,407293004,407222004,407295006,407294005,407297003,407260008,407299000,407300008,407301007,103429008,124994003,407303005,407306002,407305003,407308001,407253002,407254008,407262000,407263005,407265003,407264004,407267006,407269009,407256005,407271009,407199008,407273007,407275000,407258006,407278003,407279006,407277008,407231004,407235008,407234007,407233001,407237000,407239002,407241001,407243003,407245005,407246006,407227005,407229008,715877003,407203008,407161001,407204002,407158002,407207009,407206000,407209007,407211003,407214006,407213000,407219001,407217004,407218009,407216008,407220007,407221006,407224003,407225002,414103002,407197005,407198000,407196001,407202003,407201005,407182007,407184008,407163003,407186005,407190007,407189003,407188006,407192004,407194003,407165005,407169004,407168007,407173001,407172006,407171004,407175008,406629008,406628000,407177000,407179002,407180004,407156003,407157007,116398008,417207000,64735005,713416009" -"B_ESCHR_ADCR" "Escherichia adecarboxylata" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "adecarboxylata" "" "species" "Leclerc, 1962" "likely facultative anaerobe" "LPSN" "776052" "515602" "777447" 1.15 "" -"B_ESCHR_ALBR" "Escherichia albertii" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "albertii" "" "species" "Huys et al., 2003" "facultative anaerobe" "LPSN" "776053" "515602" "5427575" 1.15 "419388003" -"B_ESCHR_BLTT" "Escherichia blattae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "blattae" "" "species" "Burgess et al., 1973" "likely facultative anaerobe" "LPSN" "776056" "515602" "788468" 1.5 "" -"B_ESCHR_COLI" "Escherichia coli" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "coli" "" "species" "Castellani et al., 1919" "facultative anaerobe" "LPSN" "776057" "515602" "11286021" 1.15 "1095001000112106,715307006,737528008,416989002,116397003,414097009,414098004,414099007,414100004,116395006,735270003,116396007,83285000,116394005,112283007,710886005,710887001,710888006,710889003,414132004,721892009,416812001,416740004,417216001,457541006,710253004,416530004,417189006,409800005,713925008,444771000124108,838549008" -"B_ESCHR_COLI_COLI" "Escherichia coli coli" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "coli" "coli" "subspecies" "GBIF" "776057" "12233256" "11286021" 1.15 "" -"B_ESCHR_COLI_EXPR" "Escherichia coli expressing" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "coli" "expressing" "subspecies" "AmSOD" "GBIF" "776057" "12239548" "11286021" 1.15 "" -"B_ESCHR_DYSN" "Escherichia dysenteriae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "dysenteriae" "" "species" "likely facultative anaerobe" "GBIF" "515602" "10862979" 1.5 "" -"B_ESCHR_FRGS" "Escherichia fergusonii" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "fergusonii" "" "species" "Farmer et al., 1985" "facultative anaerobe" "LPSN" "776059" "515602" "5427571" 1.15 "72461005" -"B_ESCHR_HRMN" "Escherichia hermannii" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "hermannii" "" "species" "Brenner et al., 1983" "facultative anaerobe" "LPSN" "776060" "515602" "5427572" 1.5 "85786000" -"B_ESCHR_MRMT" "Escherichia marmotae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "marmotae" "" "species" "Liu et al., 2015" "likely facultative anaerobe" "LPSN" "792928" "515602" "8869052" 1.5 "14961000146107" -"B_ESCHR_RUYS" "Escherichia ruysiae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "ruysiae" "" "species" "Van der Putten et al., 2021" "likely facultative anaerobe" "LPSN" "17322" "515602" "11776954" 1.5 "" -"B_ESCHR_VLNR" "Escherichia vulneris" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "vulneris" "" "species" "Brenner et al., 1983" "likely facultative anaerobe" "LPSN" "776063" "515602" "796273" "5427573" 1.15 "" +"B_ESCHR" "Escherichia" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "" "" "genus" "Castellani et al., 1919" "facultative anaerobe" "LPSN" "515602" "482" "11158430" 1 "407310004,407251000,407281008,407284000,407283006,407160000,407285004,407159005,407287007,407290001,407291002,407289005,407293004,407222004,407295006,407294005,407297003,407260008,407299000,407300008,407301007,103429008,124994003,407303005,407306002,407305003,407308001,407253002,407254008,407262000,407263005,407265003,407264004,407267006,407269009,407256005,407271009,407199008,407273007,407275000,407258006,407278003,407279006,407277008,407231004,407235008,407234007,407233001,407237000,407239002,407241001,407243003,407245005,407246006,407227005,407229008,715877003,407203008,407161001,407204002,407158002,407207009,407206000,407209007,407211003,407214006,407213000,407219001,407217004,407218009,407216008,407220007,407221006,407224003,407225002,414103002,407197005,407198000,407196001,407202003,407201005,407182007,407184008,407163003,407186005,407190007,407189003,407188006,407192004,407194003,407165005,407169004,407168007,407173001,407172006,407171004,407175008,406629008,406628000,407177000,407179002,407180004,407156003,407157007,116398008,417207000,64735005,713416009" +"B_ESCHR_ADCR" "Escherichia adecarboxylata" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "adecarboxylata" "" "species" "Leclerc, 1962" "likely facultative anaerobe" "LPSN" "776052" "515602" "777447" 1 "" +"B_ESCHR_ALBR" "Escherichia albertii" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "albertii" "" "species" "Huys et al., 2003" "facultative anaerobe" "LPSN" "776053" "515602" "5427575" 1 "419388003" +"B_ESCHR_BLTT" "Escherichia blattae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "blattae" "" "species" "Burgess et al., 1973" "likely facultative anaerobe" "LPSN" "776056" "515602" "788468" 1 "" +"B_ESCHR_COLI" "Escherichia coli" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "coli" "" "species" "Castellani et al., 1919" "facultative anaerobe" "LPSN" "776057" "515602" "11286021" 1 "1095001000112106,715307006,737528008,416989002,116397003,414097009,414098004,414099007,414100004,116395006,735270003,116396007,83285000,116394005,112283007,710886005,710887001,710888006,710889003,414132004,721892009,416812001,416740004,417216001,457541006,710253004,416530004,417189006,409800005,713925008,444771000124108,838549008" +"B_ESCHR_COLI_COLI" "Escherichia coli coli" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "coli" "coli" "subspecies" "GBIF" "776057" "12233256" "11286021" 1 "" +"B_ESCHR_COLI_EXPR" "Escherichia coli expressing" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "coli" "expressing" "subspecies" "AmSOD" "GBIF" "776057" "12239548" "11286021" 1 "" +"B_ESCHR_DYSN" "Escherichia dysenteriae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "dysenteriae" "" "species" "likely facultative anaerobe" "GBIF" "515602" "10862979" 1 "" +"B_ESCHR_FRGS" "Escherichia fergusonii" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "fergusonii" "" "species" "Farmer et al., 1985" "facultative anaerobe" "LPSN" "776059" "515602" "5427571" 1 "72461005" +"B_ESCHR_HRMN" "Escherichia hermannii" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "hermannii" "" "species" "Brenner et al., 1983" "facultative anaerobe" "LPSN" "776060" "515602" "5427572" 1 "85786000" +"B_ESCHR_MRMT" "Escherichia marmotae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "marmotae" "" "species" "Liu et al., 2015" "likely facultative anaerobe" "LPSN" "792928" "515602" "8869052" 1 "14961000146107" +"B_ESCHR_RUYS" "Escherichia ruysiae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "ruysiae" "" "species" "Van der Putten et al., 2021" "likely facultative anaerobe" "LPSN" "17322" "515602" "11776954" 1 "" +"B_ESCHR_VLNR" "Escherichia vulneris" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Escherichia" "vulneris" "" "species" "Brenner et al., 1983" "likely facultative anaerobe" "LPSN" "776063" "515602" "796273" "5427573" 1 "" "P_ESTST" "Estiastra" "accepted" "Protozoa" "" "" "" "" "Estiastra" "" "" "genus" "Eisenack, 1959" "GBIF" "3208159" "7" 2 "" "P_ESTST_MAGN" "Estiastra magna" "accepted" "Protozoa" "" "" "" "" "Estiastra" "magna" "" "species" "Eisenack, 1959" "GBIF" "4918097" "3208159" 2 "" "P_ESTST_MINM" "Estiastra minima" "accepted" "Protozoa" "" "" "" "" "Estiastra" "minima" "" "species" "Volkova, 1969" "GBIF" "4918094" "3208159" 2 "" diff --git a/data-raw/microorganisms.xlsx b/data-raw/microorganisms.xlsx index 55bc8e45..6e9b9c19 100644 Binary files a/data-raw/microorganisms.xlsx and b/data-raw/microorganisms.xlsx differ diff --git a/data/microorganisms.rda b/data/microorganisms.rda index 4ebf915b..3d8ac4ce 100644 Binary files a/data/microorganisms.rda and b/data/microorganisms.rda differ diff --git a/index.md b/index.md index f0665b93..d1336891 100644 --- a/index.md +++ b/index.md @@ -9,6 +9,8 @@ * Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC**, **SNOMED CT**, and **NCBI** * 100% free of costs and dependencies, highly suitable for places with **limited resources** + +
https://msberends.github.io/AMR
https://doi.org/10.18637/jss.v104.i03
diff --git a/man/as.mo.Rd b/man/as.mo.Rd index 300c7fa3..bfa5de0e 100644 --- a/man/as.mo.Rd +++ b/man/as.mo.Rd @@ -207,7 +207,7 @@ Furthermore, When calculating the matching score, all characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses. -All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.598}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.381}, a less prevalent microorganism in humans), although the latter would alphabetically come first. +All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.381}, a less prevalent microorganism in humans), although the latter would alphabetically come first. } \section{Reference Data Publicly Available}{ diff --git a/man/mo_matching_score.Rd b/man/mo_matching_score.Rd index ecc589f7..b6d0f0bd 100644 --- a/man/mo_matching_score.Rd +++ b/man/mo_matching_score.Rd @@ -55,7 +55,7 @@ Furthermore, When calculating the matching score, all characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses. -All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.598}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.381}, a less prevalent microorganism in humans), although the latter would alphabetically come first. +All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.381}, a less prevalent microorganism in humans), although the latter would alphabetically come first. } \section{Reference Data Publicly Available}{ diff --git a/pkgdown/assets/AMRforRGPT.svg b/pkgdown/assets/AMRforRGPT.svg new file mode 100644 index 00000000..df39fe9b --- /dev/null +++ b/pkgdown/assets/AMRforRGPT.svg @@ -0,0 +1,2456 @@ + + + + diff --git a/pkgdown/assets/logo.svg b/pkgdown/assets/logo.svg index 40c6633c..964c0eca 100644 --- a/pkgdown/assets/logo.svg +++ b/pkgdown/assets/logo.svg @@ -6,7 +6,7 @@ xml:space="preserve" id="svg2" version="1.1" - sodipodi:docname="AMR-new-logo-shape.svg" + sodipodi:docname="logo.svg" inkscape:version="1.3.2 (091e20e, 2023-11-25)" xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" @@ -26,14 +26,14 @@ inkscape:pagecheckerboard="0" inkscape:deskcolor="#d1d1d1" showguides="true" - inkscape:zoom="1.1061075" - inkscape:cx="344.90318" - inkscape:cy="321.84936" - inkscape:window-width="1920" - inkscape:window-height="1103" - inkscape:window-x="0" + inkscape:zoom="0.93102768" + inkscape:cx="239.52027" + inkscape:cy="341.02101" + inkscape:window-width="1632" + inkscape:window-height="1044" + inkscape:window-x="83" inkscape:window-y="43" - inkscape:window-maximized="1" + inkscape:window-maximized="0" inkscape:current-layer="svg2" />