Introduction
@@ -144,21 +144,21 @@ make the structure of your data generally look like this:
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+2025-01-16
abcd
Escherichia coli
S
S
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+2025-01-16
abcd
Escherichia coli
S
R
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+2025-01-16
efgh
Escherichia coli
R
diff --git a/articles/AMR_with_tidymodels.html b/articles/AMR_with_tidymodels.html
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--- a/articles/AMR_with_tidymodels.html
+++ b/articles/AMR_with_tidymodels.html
@@ -140,7 +140,7 @@ package.
#> ✖ dplyr ::filter() masks stats ::filter() #> ✖ dplyr ::lag() masks stats ::lag() #> ✖ recipes ::step() masks stats ::step() #> • Dig deeper into tidy modeling with R at https://www.tmwr.org #> • Learn how to get started at https://www.tidymodels.org/start/ library ( AMR ) # For AMR data analysis # Load the example_isolates dataset
On this page
diff --git a/reference/as.sir.html b/reference/as.sir.html
index 27996fb28..76b3f6dec 100644
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@@ -786,16 +786,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
#> # A tibble: 57 × 16 #> datetime index ab_given mo_given host_given ab mo #> * <dttm> <int> <chr> <chr> <chr> <ab> <mo> #> 1 2025-01-15 15:22:23 4 AMX B_STRPT… human AMX B_STRPT_PNMN #> 2 2025-01-15 15:22:31 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR#> 3 2025-01-15 15:22:31 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR#> 4 2025-01-15 15:22:32 4 genta Escheri… cattle GEN B_ESCHR_COLI #> 5 2025-01-15 15:22:32 4 genta Escheri… cattle GEN B_ESCHR_COLI #> 6 2025-01-15 15:22:23 3 AMX B_STRPT… human AMX B_STRPT_PNMN #> 7 2025-01-15 15:22:31 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR#> 8 2025-01-15 15:22:31 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR#> 9 2025-01-15 15:22:32 3 tobra Escheri… horses TOB B_ESCHR_COLI #> 10 2025-01-15 15:22:32 3 tobra Escheri… horses TOB B_ESCHR_COLI #> 1 2025-01-16 11:00:46 4 AMX B_STRPT… human AMX B_STRPT_PNMN #> 2 2025-01-16 11:00:53 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR#> 3 2025-01-16 11:00:53 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR#> 4 2025-01-16 11:00:54 4 genta Escheri… cattle GEN B_ESCHR_COLI #> 5 2025-01-16 11:00:54 4 genta Escheri… cattle GEN B_ESCHR_COLI #> 6 2025-01-16 11:00:46 3 AMX B_STRPT… human AMX B_STRPT_PNMN #> 7 2025-01-16 11:00:53 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR#> 8 2025-01-16 11:00:53 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR#> 9 2025-01-16 11:00:54 3 tobra Escheri… horses TOB B_ESCHR_COLI #> 10 2025-01-16 11:00:54 3 tobra Escheri… horses TOB B_ESCHR_COLI #> # ℹ 47 more rows #> # ℹ 9 more variables: host <chr>, method <chr>, input <dbl>, outcome <sir>, #> # notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>, #> 1 J3 A 2012-11-21 E. coli R I S S #> 2 R7 A 2018-04-03 K. pneumoniae R I S S #> 3 P3 A 2014-09-19 E. coli R S S S #> 4 P10 A 2015-12-10 E. coli S I S S #> 5 B7 A 2015-03-02 E. coli S S S S #> 6 W3 A 2018-03-31 S. aureus R S R S #> 7 J8 A 2016-06-14 E. coli R S S S #> 8 M3 A 2015-10-25 E. coli R S S S #> 9 J3 A 2019-06-19 E. coli S S S S #> 10 G6 A 2015-04-27 S. aureus S S S S #> # ℹ 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"How to conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 24 Jun 2024. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLEPNE\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLPN\") #> Class 'mo' #> [1] B_KLBSL_PNMN mo_family(\"K. pneumoniae\") #> [1] \"Enterobacteriaceae\" mo_genus(\"K. pneumoniae\") #> [1] \"Klebsiella\" mo_species(\"K. pneumoniae\") #> [1] \"pneumoniae\" mo_gramstain(\"Klebsiella pneumoniae\") #> [1] \"Gram-negative\" mo_ref(\"K. pneumoniae\") #> [1] \"Trevisan, 1887\" mo_snomed(\"K. pneumoniae\") #> [[1]] #> [1] \"1098101000112102\" \"446870005\" \"1098201000112108\" \"409801009\" #> [5] \"56415008\" \"714315002\" \"713926009\" our_data$bacteria <- as.mo(our_data$bacteria, info = TRUE) #> ℹ Microorganism translation was uncertain for four microorganisms. Run #> mo_uncertainties() to review these uncertainties, or use #> add_custom_microorganisms() to add custom entries. mo_uncertainties() #> Matching scores are based on the resemblance between the input and the full #> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score. #> #> -------------------------------------------------------------------------------- #> \"E. coli\" -> Escherichia coli (B_ESCHR_COLI, 0.688) #> Also matched: Enterococcus crotali (0.650), Escherichia coli coli #> (0.643), Escherichia coli expressing (0.611), Enterobacter cowanii #> (0.600), Enterococcus columbae (0.595), Enterococcus camelliae (0.591), #> Enterococcus casseliflavus (0.577), Enterobacter cloacae cloacae #> (0.571), Enterobacter cloacae complex (0.571), and Enterobacter cloacae #> dissolvens (0.565) #> -------------------------------------------------------------------------------- #> \"K. pneumoniae\" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786) #> Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella #> pneumoniae pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis #> (0.658), Klebsiella pasteurii (0.500), Klebsiella planticola (0.500), #> Kingella potus (0.400), Kluyveromyces pseudotropicale (0.386), #> Kluyveromyces pseudotropicalis (0.363), Kosakonia pseudosacchari #> (0.361), and Kluyveromyces pseudotropicalis pseudotropicalis (0.361) #> -------------------------------------------------------------------------------- #> \"S. aureus\" -> Staphylococcus aureus (B_STPHY_AURS, 0.690) #> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus #> argenteus (0.625), Staphylococcus aureus anaerobius (0.625), #> Staphylococcus auricularis (0.615), Salmonella Aurelianis (0.595), #> Salmonella Aarhus (0.588), Salmonella Amounderness (0.587), #> Staphylococcus argensis (0.587), Streptococcus australis (0.587), and #> Salmonella choleraesuis arizonae (0.562) #> -------------------------------------------------------------------------------- #> \"S. pneumoniae\" -> Streptococcus pneumoniae (B_STRPT_PNMN, 0.750) #> Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus #> phocae salmonis (0.552), Serratia proteamaculans quinovora (0.545), #> Streptococcus pseudoporcinus (0.536), Staphylococcus piscifermentans #> (0.533), Staphylococcus pseudintermedius (0.532), Serratia #> proteamaculans proteamaculans (0.526), Streptococcus gallolyticus #> pasteurianus (0.526), Salmonella Portanigra (0.524), and Streptococcus #> periodonticum (0.519) #> #> Only the first 10 other matches of each record are shown. Run #> print(mo_uncertainties(), n = ...) to view more entries, or save #> mo_uncertainties() to an object."},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"antibiotic-results","dir":"Articles","previous_headings":"Preparation","what":"Antibiotic results","title":"How to conduct AMR data analysis","text":"column antibiotic test results must also cleaned. AMR package comes three new data types work test results: mic minimal inhibitory concentrations (MIC), disk disk diffusion diameters, sir SIR data interpreted already. package can also determine SIR values based MIC disk diffusion values, read .sir() page. now, just clean SIR columns data using dplyr: basically cleaning, time start data inclusion.","code":"# method 1, be explicit about the columns: our_data <- our_data %>% mutate_at(vars(AMX:GEN), as.sir) # method 2, let the AMR package determine the eligible columns our_data <- our_data %>% mutate_if(is_sir_eligible, as.sir) # result: our_data #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> #> 1 J3 A 2012-11-21 B_ESCHR_COLI R I S S #> 2 R7 A 2018-04-03 B_KLBSL_PNMN R I S S #> 3 P3 A 2014-09-19 B_ESCHR_COLI R S S S #> 4 P10 A 2015-12-10 B_ESCHR_COLI S I S S #> 5 B7 A 2015-03-02 B_ESCHR_COLI S S S S #> 6 W3 A 2018-03-31 B_STPHY_AURS R S R S #> 7 J8 A 2016-06-14 B_ESCHR_COLI R S S S #> 8 M3 A 2015-10-25 B_ESCHR_COLI R S S S #> 9 J3 A 2019-06-19 B_ESCHR_COLI S S S S #> 10 G6 A 2015-04-27 B_STPHY_AURS S S S S #> # ℹ 2,990 more rows"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"first-isolates","dir":"Articles","previous_headings":"Preparation","what":"First isolates","title":"How to conduct AMR data analysis","text":"need know isolates can actually use analysis without repetition bias. conduct analysis antimicrobial resistance, must include first isolate every patient per episode (Hindler et al., Clin Infect Dis. 2007). , easily get overestimate underestimate resistance antibiotic. Imagine patient admitted MRSA found 5 different blood cultures following weeks (yes, countries like Netherlands blood drawing policies). resistance percentage oxacillin isolates overestimated, included MRSA . clearly selection bias. Clinical Laboratory Standards Institute (CLSI) appoints follows: (…) preparing cumulative antibiogram guide clinical decisions empirical antimicrobial therapy initial infections, first isolate given species per patient, per analysis period (eg, one year) included, irrespective body site, antimicrobial susceptibility profile, phenotypical characteristics (eg, biotype). first isolate easily identified, cumulative antimicrobial susceptibility test data prepared using first isolate generally comparable cumulative antimicrobial susceptibility test data calculated methods, providing duplicate isolates excluded. M39-A4 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 4th Edition. CLSI, 2014. Chapter 6.4 AMR package includes methodology first_isolate() function able apply four different methods defined Hindler et al. 2007: phenotype-based, episode-based, patient-based, isolate-based. right method depends goals analysis, default phenotype-based method case method properly correct duplicate isolates. Read methods first_isolate() page. outcome function can easily added data: 91% suitable resistance analysis! can now filter filter() function, also dplyr package: future use, two syntaxes can shortened: end 2 724 isolates analysis. Now data looks like: Time analysis.","code":"our_data <- our_data %>% mutate(first = first_isolate(info = TRUE)) #> ℹ Determining first isolates using an episode length of 365 days #> ℹ Using column 'bacteria' as input for col_mo. #> ℹ Using column 'date' as input for col_date. #> ℹ Using column 'patient_id' as input for col_patient_id. #> ℹ Basing inclusion on all antimicrobial results, using a points threshold #> of 2 #> => Found 2,724 'phenotype-based' first isolates (90.8% of total where a #> microbial ID was available) our_data_1st <- our_data %>% filter(first == TRUE) our_data_1st <- our_data %>% filter_first_isolate() our_data_1st #> # A tibble: 2,724 × 9 #> patient_id hospital date bacteria AMX AMC CIP GEN first #> #> 1 J3 A 2012-11-21 B_ESCHR_COLI R I S S TRUE #> 2 R7 A 2018-04-03 B_KLBSL_PNMN R I S S TRUE #> 3 P3 A 2014-09-19 B_ESCHR_COLI R S S S TRUE #> 4 P10 A 2015-12-10 B_ESCHR_COLI S I S S TRUE #> 5 B7 A 2015-03-02 B_ESCHR_COLI S S S S TRUE #> 6 W3 A 2018-03-31 B_STPHY_AURS R S R S TRUE #> 7 M3 A 2015-10-25 B_ESCHR_COLI R S S S TRUE #> 8 J3 A 2019-06-19 B_ESCHR_COLI S S S S TRUE #> 9 G6 A 2015-04-27 B_STPHY_AURS S S S S TRUE #> 10 P4 A 2011-06-21 B_ESCHR_COLI S S S S TRUE #> # ℹ 2,714 more rows"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"analysing-the-data","dir":"Articles","previous_headings":"","what":"Analysing the data","title":"How to conduct AMR data analysis","text":"base R summary() function gives good first impression, comes support new mo sir classes now data set:","code":"summary(our_data_1st) #> patient_id hospital date #> Length:2724 Length:2724 Min. :2011-01-01 #> Class :character Class :character 1st Qu.:2013-04-07 #> Mode :character Mode :character Median :2015-06-03 #> Mean :2015-06-09 #> 3rd Qu.:2017-08-11 #> Max. :2019-12-27 #> bacteria AMX AMC #> Class :mo Class:sir Class:sir #> :0 %S :41.6% (n=1133) %S :52.6% (n=1432) #> Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) #> #1 :B_ESCHR_COLI %I :16.4% (n=446) %I :12.2% (n=333) #> #2 :B_STPHY_AURS %R :42.0% (n=1145) %R :35.2% (n=959) #> #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0) #> CIP GEN first #> Class:sir Class:sir Mode:logical #> %S :52.5% (n=1431) %S :61.0% (n=1661) TRUE:2724 #> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) #> %I : 6.5% (n=176) %I : 3.0% (n=82) #> %R :41.0% (n=1117) %R :36.0% (n=981) #> %NI : 0.0% (n=0) %NI : 0.0% (n=0) glimpse(our_data_1st) #> Rows: 2,724 #> Columns: 9 #> $ patient_id \"J3\", \"R7\", \"P3\", \"P10\", \"B7\", \"W3\", \"M3\", \"J3\", \"G6\", \"P4\"… #> $ hospital \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\",… #> $ date 2012-11-21, 2018-04-03, 2014-09-19, 2015-12-10, 2015-03-02… #> $ bacteria \"B_ESCHR_COLI\", \"B_KLBSL_PNMN\", \"B_ESCHR_COLI\", \"B_ESCHR_COL… #> $ AMX R, R, R, S, S, R, R, S, S, S, S, R, S, S, R, R, R, R, S, R,… #> $ AMC I, I, S, I, S, S, S, S, S, S, S, S, S, S, S, S, S, R, S, S,… #> $ CIP S, S, S, S, S, R, S, S, S, S, S, S, S, S, S, S, S, S, S, S,… #> $ GEN S, S, S, S, S, S, S, S, S, S, S, R, S, S, S, S, S, S, S, S,… #> $ first TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,… # number of unique values per column: sapply(our_data_1st, n_distinct) #> patient_id hospital date bacteria AMX AMC CIP #> 260 3 1854 4 3 3 3 #> GEN first #> 3 1"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"availability-of-species","dir":"Articles","previous_headings":"Analysing the data","what":"Availability of species","title":"How to conduct AMR data analysis","text":"just get idea species distributed, create frequency table count() based name microorganisms:","code":"our_data %>% count(mo_name(bacteria), sort = TRUE) #> # A tibble: 4 × 2 #> `mo_name(bacteria)` n #> #> 1 Escherichia coli 1518 #> 2 Staphylococcus aureus 730 #> 3 Streptococcus pneumoniae 426 #> 4 Klebsiella pneumoniae 326 our_data_1st %>% count(mo_name(bacteria), sort = TRUE) #> # A tibble: 4 × 2 #> `mo_name(bacteria)` n #> #> 1 Escherichia coli 1321 #> 2 Staphylococcus aureus 682 #> 3 Streptococcus pneumoniae 402 #> 4 Klebsiella pneumoniae 319"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"select-and-filter-with-antibiotic-selectors","dir":"Articles","previous_headings":"Analysing the data","what":"Select and filter with antibiotic selectors","title":"How to conduct AMR data analysis","text":"Using -called antibiotic class selectors, can select filter columns based antibiotic class antibiotic results :","code":"our_data_1st %>% select(date, aminoglycosides()) #> ℹ For aminoglycosides() using column 'GEN' (gentamicin) #> # A tibble: 2,724 × 2 #> date GEN #> #> 1 2012-11-21 S #> 2 2018-04-03 S #> 3 2014-09-19 S #> 4 2015-12-10 S #> 5 2015-03-02 S #> 6 2018-03-31 S #> 7 2015-10-25 S #> 8 2019-06-19 S #> 9 2015-04-27 S #> 10 2011-06-21 S #> # ℹ 2,714 more rows our_data_1st %>% select(bacteria, betalactams()) #> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC' #> (amoxicillin/clavulanic acid) #> # A tibble: 2,724 × 3 #> bacteria AMX AMC #> #> 1 B_ESCHR_COLI R I #> 2 B_KLBSL_PNMN R I #> 3 B_ESCHR_COLI R S #> 4 B_ESCHR_COLI S I #> 5 B_ESCHR_COLI S S #> 6 B_STPHY_AURS R S #> 7 B_ESCHR_COLI R S #> 8 B_ESCHR_COLI S S #> 9 B_STPHY_AURS S S #> 10 B_ESCHR_COLI S S #> # ℹ 2,714 more rows our_data_1st %>% select(bacteria, where(is.sir)) #> # A tibble: 2,724 × 5 #> bacteria AMX AMC CIP GEN #> #> 1 B_ESCHR_COLI R I S S #> 2 B_KLBSL_PNMN R I S S #> 3 B_ESCHR_COLI R S S S #> 4 B_ESCHR_COLI S I S S #> 5 B_ESCHR_COLI S S S S #> 6 B_STPHY_AURS R S R S #> 7 B_ESCHR_COLI R S S S #> 8 B_ESCHR_COLI S S S S #> 9 B_STPHY_AURS S S S S #> 10 B_ESCHR_COLI S S S S #> # ℹ 2,714 more rows # filtering using AB selectors is also possible: our_data_1st %>% filter(any(aminoglycosides() == \"R\")) #> ℹ For aminoglycosides() using column 'GEN' (gentamicin) #> # A tibble: 981 × 9 #> patient_id hospital date bacteria AMX AMC CIP GEN first #> #> 1 J5 A 2017-12-25 B_STRPT_PNMN R S S R TRUE #> 2 X1 A 2017-07-04 B_STPHY_AURS R S S R TRUE #> 3 B3 A 2016-07-24 B_ESCHR_COLI S S S R TRUE #> 4 V7 A 2012-04-03 B_ESCHR_COLI S S S R TRUE #> 5 C9 A 2017-03-23 B_ESCHR_COLI S S S R TRUE #> 6 R1 A 2018-06-10 B_STPHY_AURS S S S R TRUE #> 7 S2 A 2013-07-19 B_STRPT_PNMN S S S R TRUE #> 8 P5 A 2019-03-09 B_STPHY_AURS S S S R TRUE #> 9 Q8 A 2019-08-10 B_STPHY_AURS S S S R TRUE #> 10 K5 A 2013-03-15 B_STRPT_PNMN S S S R TRUE #> # ℹ 971 more rows our_data_1st %>% filter(all(betalactams() == \"R\")) #> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC' #> (amoxicillin/clavulanic acid) #> # A tibble: 462 × 9 #> patient_id hospital date bacteria AMX AMC CIP GEN first #> #> 1 M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE #> 2 R10 A 2013-12-20 B_STPHY_AURS R R S S TRUE #> 3 R7 A 2015-10-25 B_STPHY_AURS R R S S TRUE #> 4 R8 A 2019-10-25 B_STPHY_AURS R R S S TRUE #> 5 B6 A 2016-11-20 B_ESCHR_COLI R R R R TRUE #> 6 I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE #> 7 N3 A 2014-12-29 B_STRPT_PNMN R R R S TRUE #> 8 Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE #> 9 X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE #> 10 V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE #> # ℹ 452 more rows # even works in base R (since R 3.0): our_data_1st[all(betalactams() == \"R\"), ] #> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC' #> (amoxicillin/clavulanic acid) #> # A tibble: 462 × 9 #> patient_id hospital date bacteria AMX AMC CIP GEN first #> #> 1 M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE #> 2 R10 A 2013-12-20 B_STPHY_AURS R R S S TRUE #> 3 R7 A 2015-10-25 B_STPHY_AURS R R S S TRUE #> 4 R8 A 2019-10-25 B_STPHY_AURS R R S S TRUE #> 5 B6 A 2016-11-20 B_ESCHR_COLI R R R R TRUE #> 6 I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE #> 7 N3 A 2014-12-29 B_STRPT_PNMN R R R S TRUE #> 8 Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE #> 9 X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE #> 10 V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE #> # ℹ 452 more rows"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"generate-antibiograms","dir":"Articles","previous_headings":"Analysing the data","what":"Generate antibiograms","title":"How to conduct AMR data analysis","text":"Since AMR v2.0 (March 2023), easy create different types antibiograms, support 20 different languages. four antibiogram types, proposed Klinker et al. (2021, DOI 10.1177/20499361211011373), supported new antibiogram() function: Traditional Antibiogram (TA) e.g, susceptibility Pseudomonas aeruginosa piperacillin/tazobactam (TZP) Combination Antibiogram (CA) e.g, sdditional susceptibility Pseudomonas aeruginosa TZP + tobramycin versus TZP alone Syndromic Antibiogram (SA) e.g, susceptibility Pseudomonas aeruginosa TZP among respiratory specimens (obtained among ICU patients ) Weighted-Incidence Syndromic Combination Antibiogram (WISCA) e.g, susceptibility Pseudomonas aeruginosa TZP among respiratory specimens (obtained among ICU patients ) male patients age >=65 years heart failure section, show use antibiogram() function create antibiogram types. starters, included example_isolates data set looks like:","code":"example_isolates #> # A tibble: 2,000 × 46 #> date patient age gender ward mo PEN OXA FLC AMX #> #> 1 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA #> 2 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA #> 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA #> 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA #> 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA #> 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA #> 7 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R #> 8 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R #> 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA #> 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC , AMP , TZP , CZO , FEP , #> # CXM , FOX , CTX , CAZ , CRO , GEN , #> # TOB , AMK , KAN , TMP , SXT , NIT , #> # FOS , LNZ , CIP , MFX , VAN , TEC , #> # TCY , TGC , DOX , ERY , CLI , AZM , #> # IPM , MEM , MTR , CHL , COL , MUP , …"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"traditional-antibiogram","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Traditional Antibiogram","title":"How to conduct AMR data analysis","text":"create traditional antibiogram, simply state antibiotics used. antibiotics argument antibiogram() function supports (combination) previously mentioned antibiotic class selectors: Notice antibiogram() function automatically prints right format using Quarto R Markdown (page), even applies italics taxonomic names (using italicise_taxonomy() internally). also uses language OS either English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, Ukrainian. next example, force language Spanish using language argument:","code":"antibiogram(example_isolates, antibiotics = c(aminoglycosides(), carbapenems())) #> ℹ The function aminoglycosides() should be used inside a dplyr verb or #> data.frame call, e.g.: #> • your_data %>% select(aminoglycosides()) #> • your_data %>% select(column_a, column_b, aminoglycosides()) #> • your_data %>% filter(any(aminoglycosides() == \"R\")) #> • your_data[, aminoglycosides()] #> • your_data[, c(\"column_a\", \"column_b\", aminoglycosides())] #> #> Now returning a vector of all possible antimicrobials that #> aminoglycosides() can select. #> ℹ The function carbapenems() should be used inside a dplyr verb or #> data.frame call, e.g.: #> • your_data %>% select(carbapenems()) #> • your_data %>% select(column_a, column_b, carbapenems()) #> • your_data %>% filter(any(carbapenems() == \"R\")) #> • your_data[, carbapenems()] #> • your_data[, c(\"column_a\", \"column_b\", carbapenems())] #> #> Now returning a vector of all possible antimicrobials that carbapenems() #> can select. antibiogram(example_isolates, mo_transform = \"gramstain\", antibiotics = aminoglycosides(), ab_transform = \"name\", language = \"es\") #> ℹ The function aminoglycosides() should be used inside a dplyr verb or #> data.frame call, e.g.: #> • your_data %>% select(aminoglycosides()) #> • your_data %>% select(column_a, column_b, aminoglycosides()) #> • your_data %>% filter(any(aminoglycosides() == \"R\")) #> • your_data[, aminoglycosides()] #> • your_data[, c(\"column_a\", \"column_b\", aminoglycosides())] #> #> Now returning a vector of all possible antimicrobials that #> aminoglycosides() can select."},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"combined-antibiogram","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Combined Antibiogram","title":"How to conduct AMR data analysis","text":"create combined antibiogram, use antibiotic codes names plus + character like :","code":"antibiogram(example_isolates, antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"syndromic-antibiogram","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Syndromic Antibiogram","title":"How to conduct AMR data analysis","text":"create syndromic antibiogram, syndromic_group argument must used. can column data, e.g. ifelse() calculations based certain columns:","code":"antibiogram(example_isolates, antibiotics = c(aminoglycosides(), carbapenems()), syndromic_group = \"ward\") #> ℹ The function aminoglycosides() should be used inside a dplyr verb or #> data.frame call, e.g.: #> • your_data %>% select(aminoglycosides()) #> • your_data %>% select(column_a, column_b, aminoglycosides()) #> • your_data %>% filter(any(aminoglycosides() == \"R\")) #> • your_data[, aminoglycosides()] #> • your_data[, c(\"column_a\", \"column_b\", aminoglycosides())] #> #> Now returning a vector of all possible antimicrobials that #> aminoglycosides() can select. #> ℹ The function carbapenems() should be used inside a dplyr verb or #> data.frame call, e.g.: #> • your_data %>% select(carbapenems()) #> • your_data %>% select(column_a, column_b, carbapenems()) #> • your_data %>% filter(any(carbapenems() == \"R\")) #> • your_data[, carbapenems()] #> • your_data[, c(\"column_a\", \"column_b\", carbapenems())] #> #> Now returning a vector of all possible antimicrobials that carbapenems() #> can select."},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"weighted-incidence-syndromic-combination-antibiogram-wisca","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Weighted-Incidence Syndromic Combination Antibiogram (WISCA)","title":"How to conduct AMR data analysis","text":"create WISCA, must state combination therapy antibiotics argument (similar Combination Antibiogram), define syndromic group syndromic_group argument (similar Syndromic Antibiogram) cases predefined based clinical demographic characteristics (e.g., endocarditis 75+ females). next example simplification without clinical characteristics, just gives idea WISCA can created:","code":"wisca <- antibiogram(example_isolates, antibiotics = c(\"AMC\", \"AMC+CIP\", \"TZP\", \"TZP+TOB\"), mo_transform = \"gramstain\", minimum = 10, # this should be >= 30, but now just as example syndromic_group = ifelse(example_isolates$age >= 65 & example_isolates$gender == \"M\", \"WISCA Group 1\", \"WISCA Group 2\")) wisca"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"plotting-antibiograms","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Plotting antibiograms","title":"How to conduct AMR data analysis","text":"Antibiograms can plotted using autoplot() ggplot2 packages, since AMR package provides extension function: calculate antimicrobial resistance sensible way, also correcting results, use resistance() susceptibility() functions.","code":"autoplot(wisca)"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"resistance-percentages","dir":"Articles","previous_headings":"Analysing the data","what":"Resistance percentages","title":"How to conduct AMR data analysis","text":"functions resistance() susceptibility() can used calculate antimicrobial resistance susceptibility. specific analyses, functions proportion_S(), proportion_SI(), proportion_I(), proportion_IR() proportion_R() can used determine proportion specific antimicrobial outcome. functions contain minimum argument, denoting minimum required number test results returning value. functions otherwise return NA. default minimum = 30, following CLSI M39-A4 guideline applying microbial epidemiology. per EUCAST guideline 2019, calculate resistance proportion R (proportion_R(), equal resistance()) susceptibility proportion S (proportion_SI(), equal susceptibility()). functions can used : can used conjunction group_by() summarise(), dplyr package: Author: Dr. Matthijs Berends, 26th Feb 2023","code":"our_data_1st %>% resistance(AMX) #> [1] 0.4203377 our_data_1st %>% group_by(hospital) %>% summarise(amoxicillin = resistance(AMX)) #> # A tibble: 3 × 2 #> hospital amoxicillin #> #> 1 A 0.340 #> 2 B 0.551 #> 3 C 0.370"},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"AMR for Python","text":"AMR package R powerful tool antimicrobial resistance (AMR) analysis. provides extensive features handling microbial antimicrobial data. However, work primarily Python, now intuitive option available: AMR Python Package Index. Python package wrapper round AMR R package. uses rpy2 package internally. Despite need R installed, Python users can now easily work AMR data directly Python code.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"install","dir":"Articles","previous_headings":"","what":"Install","title":"AMR for Python","text":"Since Python package available official Python Package Index, can just run: Make sure R installed. need install AMR R package, installed automatically. Linux: macOS (using Homebrew): Windows, visit CRAN download page download install R.","code":"pip install AMR # Ubuntu / Debian sudo apt install r-base # Fedora: sudo dnf install R # CentOS/RHEL sudo yum install R brew install r"},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"cleaning-taxonomy","dir":"Articles","previous_headings":"Examples of Usage","what":"Cleaning Taxonomy","title":"AMR for Python","text":"’s example demonstrates clean microorganism drug names using AMR Python package:","code":"import pandas as pd import AMR # Sample data data = { \"MOs\": ['E. coli', 'ESCCOL', 'esco', 'Esche coli'], \"Drug\": ['Cipro', 'CIP', 'J01MA02', 'Ciproxin'] } df = pd.DataFrame(data) # Use AMR functions to clean microorganism and drug names df['MO_clean'] = AMR.mo_name(df['MOs']) df['Drug_clean'] = AMR.ab_name(df['Drug']) # Display the results print(df)"},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"explanation","dir":"Articles","previous_headings":"Examples of Usage > Cleaning Taxonomy","what":"Explanation","title":"AMR for Python","text":"mo_name: function standardises microorganism names. , different variations Escherichia coli (“E. coli”, “ESCCOL”, “esco”, “Esche coli”) converted correct, standardised form, “Escherichia coli”. ab_name: Similarly, function standardises antimicrobial names. different representations ciprofloxacin (e.g., “Cipro”, “CIP”, “J01MA02”, “Ciproxin”) converted standard name, “Ciprofloxacin”.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"taxonomic-data-sets-now-in-python","dir":"Articles","previous_headings":"Examples of Usage","what":"Taxonomic Data Sets Now in Python!","title":"AMR for Python","text":"Python user, might like important data sets AMR R package, microorganisms, antibiotics, clinical_breakpoints, example_isolates, now available regular Python data frames:","code":"AMR.microorganisms AMR.antibiotics"},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"calculating-amr","dir":"Articles","previous_headings":"Examples of Usage","what":"Calculating AMR","title":"AMR for Python","text":"","code":"import AMR import pandas as pd df = AMR.example_isolates result = AMR.resistance(df[\"AMX\"]) print(result) [0.59555556]"},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"generating-antibiograms","dir":"Articles","previous_headings":"Examples of Usage","what":"Generating Antibiograms","title":"AMR for Python","text":"One core functions AMR package generating antibiogram, table summarises antimicrobial susceptibility bacterial isolates. ’s can generate antibiogram Python: example, generate antibiogram selecting various antibiotics.","code":"result2a = AMR.antibiogram(df[[\"mo\", \"AMX\", \"CIP\", \"TZP\"]]) print(result2a) result2b = AMR.antibiogram(df[[\"mo\", \"AMX\", \"CIP\", \"TZP\"]], mo_transform = \"gramstain\") print(result2b)"},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"conclusion","dir":"Articles","previous_headings":"","what":"Conclusion","title":"AMR for Python","text":"AMR Python package, Python users can now effortlessly call R functions AMR R package. eliminates need complex rpy2 configurations provides clean, easy--use interface antimicrobial resistance analysis. examples provided demonstrate can applied typical workflows, standardising microorganism antimicrobial names calculating resistance. just running import AMR, users can seamlessly integrate robust features R AMR package Python workflows. Whether ’re cleaning data analysing resistance patterns, AMR Python package makes easy work AMR data Python.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"objective","dir":"Articles","previous_headings":"","what":"Objective","title":"AMR with tidymodels","text":"goal build predictive model using tidymodels framework determine Gramstain microorganism based microbial data. : Preprocess data using selector functions aminoglycosides() betalactams(). Define logistic regression model prediction. Use structured tidymodels workflow preprocess, train, evaluate model.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"data-preparation","dir":"Articles","previous_headings":"","what":"Data Preparation","title":"AMR with tidymodels","text":"begin loading required libraries preparing example_isolates dataset AMR package. Explanation: aminoglycosides() betalactams() dynamically select columns antibiotics classes. drop_na() ensures model receives complete cases training.","code":"# Load required libraries library(tidymodels) # For machine learning workflows, and data manipulation (dplyr, tidyr, ...) #> ── Attaching packages ────────────────────────────────────── tidymodels 1.2.0 ── #> ✔ broom 1.0.7 ✔ recipes 1.1.0 #> ✔ dials 1.3.0 ✔ rsample 1.2.1 #> ✔ dplyr 1.1.4 ✔ tibble 3.2.1 #> ✔ ggplot2 3.5.1 ✔ tidyr 1.3.1 #> ✔ infer 1.0.7 ✔ tune 1.2.1 #> ✔ modeldata 1.4.0 ✔ workflows 1.1.4 #> ✔ parsnip 1.2.1 ✔ workflowsets 1.1.0 #> ✔ purrr 1.0.2 ✔ yardstick 1.3.1 #> ── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ── #> ✖ purrr::discard() masks scales::discard() #> ✖ dplyr::filter() masks stats::filter() #> ✖ dplyr::lag() masks stats::lag() #> ✖ recipes::step() masks stats::step() #> • Dig deeper into tidy modeling with R at https://www.tmwr.org library(AMR) # For AMR data analysis # Load the example_isolates dataset data(\"example_isolates\") # Preloaded dataset with AMR results # Select relevant columns for prediction data <- example_isolates %>% # select AB results dynamically select(mo, aminoglycosides(), betalactams()) %>% # replace NAs with NI (not-interpretable) mutate(across(where(is.sir), ~replace_na(.x, \"NI\")), # make factors of SIR columns across(where(is.sir), as.integer), # get Gramstain of microorganisms mo = as.factor(mo_gramstain(mo))) %>% # drop NAs - the ones without a Gramstain (fungi, etc.) drop_na() #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For betalactams() using columns 'PEN' (benzylpenicillin), 'OXA' #> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP' #> (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM' #> (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime), #> 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)"},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"defining-the-workflow","dir":"Articles","previous_headings":"","what":"Defining the Workflow","title":"AMR with tidymodels","text":"now define tidymodels workflow, consists three steps: preprocessing, model specification, fitting.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"preprocessing-with-a-recipe","dir":"Articles","previous_headings":"Defining the Workflow","what":"1. Preprocessing with a Recipe","title":"AMR with tidymodels","text":"create recipe preprocess data modelling. Explanation: recipe(mo ~ ., data = data) take mo column outcome columns predictors. step_corr() removes predictors (.e., antibiotic columns) higher correlation 90%. Notice recipe contains just antibiotic selector functions - need define columns specifically.","code":"# Define the recipe for data preprocessing resistance_recipe <- recipe(mo ~ ., data = data) %>% step_corr(c(aminoglycosides(), betalactams()), threshold = 0.9) resistance_recipe #> #> ── Recipe ────────────────────────────────────────────────────────────────────── #> #> ── Inputs #> Number of variables by role #> outcome: 1 #> predictor: 20 #> #> ── Operations #> • Correlation filter on: c(aminoglycosides(), betalactams())"},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"specifying-the-model","dir":"Articles","previous_headings":"Defining the Workflow","what":"2. Specifying the Model","title":"AMR with tidymodels","text":"define logistic regression model since resistance prediction binary classification task. Explanation: logistic_reg() sets logistic regression model. set_engine(\"glm\") specifies use R’s built-GLM engine.","code":"# Specify a logistic regression model logistic_model <- logistic_reg() %>% set_engine(\"glm\") # Use the Generalized Linear Model engine logistic_model #> Logistic Regression Model Specification (classification) #> #> Computational engine: glm"},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"building-the-workflow","dir":"Articles","previous_headings":"Defining the Workflow","what":"3. Building the Workflow","title":"AMR with tidymodels","text":"bundle recipe model together workflow, organizes entire modeling process.","code":"# Combine the recipe and model into a workflow resistance_workflow <- workflow() %>% add_recipe(resistance_recipe) %>% # Add the preprocessing recipe add_model(logistic_model) # Add the logistic regression model"},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"training-and-evaluating-the-model","dir":"Articles","previous_headings":"","what":"Training and Evaluating the Model","title":"AMR with tidymodels","text":"train model, split data training testing sets. , fit workflow training set evaluate performance. Explanation: initial_split() splits data training testing sets. fit() trains workflow training set. Notice fit(), antibiotic selector functions internally called . training, functions called since stored recipe. Next, evaluate model testing data. Explanation: predict() generates predictions testing set. metrics() computes evaluation metrics like accuracy kappa. appears can predict Gram based AMR results 0.995 accuracy based AMR results aminoglycosides beta-lactam antibiotics. ROC curve looks like :","code":"# Split data into training and testing sets set.seed(123) # For reproducibility data_split <- initial_split(data, prop = 0.8) # 80% training, 20% testing training_data <- training(data_split) # Training set testing_data <- testing(data_split) # Testing set # Fit the workflow to the training data fitted_workflow <- resistance_workflow %>% fit(training_data) # Train the model #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For betalactams() using columns 'PEN' (benzylpenicillin), 'OXA' #> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP' #> (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM' #> (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime), #> 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem) # Make predictions on the testing set predictions <- fitted_workflow %>% predict(testing_data) # Generate predictions probabilities <- fitted_workflow %>% predict(testing_data, type = \"prob\") # Generate probabilities predictions <- predictions %>% bind_cols(probabilities) %>% bind_cols(testing_data) # Combine with true labels predictions #> # A tibble: 394 × 24 #> .pred_class `.pred_Gram-negative` `.pred_Gram-positive` mo GEN TOB #> #> 1 Gram-positive 1.07e- 1 8.93e- 1 Gram-p… 5 5 #> 2 Gram-positive 3.17e- 8 1.00e+ 0 Gram-p… 5 1 #> 3 Gram-negative 9.99e- 1 1.42e- 3 Gram-n… 5 5 #> 4 Gram-positive 2.22e-16 1 e+ 0 Gram-p… 5 5 #> 5 Gram-negative 9.46e- 1 5.42e- 2 Gram-n… 5 5 #> 6 Gram-positive 1.07e- 1 8.93e- 1 Gram-p… 5 5 #> 7 Gram-positive 2.22e-16 1 e+ 0 Gram-p… 1 5 #> 8 Gram-positive 2.22e-16 1 e+ 0 Gram-p… 4 4 #> 9 Gram-negative 1 e+ 0 2.22e-16 Gram-n… 1 1 #> 10 Gram-positive 6.05e-11 1.00e+ 0 Gram-p… 4 4 #> # ℹ 384 more rows #> # ℹ 18 more variables: AMK , KAN , PEN , OXA , FLC , #> # AMX , AMC , AMP , TZP , CZO , FEP , #> # CXM , FOX , CTX , CAZ , CRO , IPM , MEM # Evaluate model performance metrics <- predictions %>% metrics(truth = mo, estimate = .pred_class) # Calculate performance metrics metrics #> # A tibble: 2 × 3 #> .metric .estimator .estimate #> #> 1 accuracy binary 0.995 #> 2 kap binary 0.989 predictions %>% roc_curve(mo, `.pred_Gram-negative`) %>% autoplot()"},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"conclusion","dir":"Articles","previous_headings":"","what":"Conclusion","title":"AMR with tidymodels","text":"post, demonstrated build machine learning pipeline tidymodels framework AMR package. combining selector functions like aminoglycosides() betalactams() tidymodels, efficiently prepared data, trained model, evaluated performance. workflow extensible antibiotic classes resistance patterns, empowering users analyse AMR data systematically reproducibly.","code":""},{"path":"https://msberends.github.io/AMR/articles/EUCAST.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to apply EUCAST rules","text":"EUCAST rules? European Committee Antimicrobial Susceptibility Testing (EUCAST) states website: EUCAST expert rules tabulated collection expert knowledge intrinsic resistances, exceptional resistance phenotypes interpretive rules may applied antimicrobial susceptibility testing order reduce errors make appropriate recommendations reporting particular resistances. Europe, lot medical microbiological laboratories already apply rules (Brown et al., 2015). package features latest insights intrinsic resistance unusual phenotypes (v3.1, 2016). Moreover, eucast_rules() function use purpose can also apply additional rules, like forcing ampicillin = R isolates amoxicillin/clavulanic acid = R.","code":""},{"path":"https://msberends.github.io/AMR/articles/EUCAST.html","id":"examples","dir":"Articles","previous_headings":"","what":"Examples","title":"How to apply EUCAST rules","text":"rules can used discard impossible bug-drug combinations data. example, Klebsiella produces beta-lactamase prevents ampicillin (amoxicillin) working . words, practically every strain Klebsiella resistant ampicillin. Sometimes, laboratory data can still contain strains ampicillin susceptible ampicillin. antibiogram available identification available, antibiogram re-interpreted based identification (namely, Klebsiella). EUCAST expert rules solve , can applied using eucast_rules(): convenient function mo_is_intrinsic_resistant() uses guideline, allows check one specific microorganisms antibiotics: EUCAST rules can used correction, can also used filling known resistance susceptibility based results antimicrobials drugs. process called interpretive reading, basically form imputation, part eucast_rules() function well:","code":"oops <- data.frame( mo = c( \"Klebsiella\", \"Escherichia\" ), ampicillin = \"S\" ) oops #> mo ampicillin #> 1 Klebsiella S #> 2 Escherichia S eucast_rules(oops, info = FALSE) #> mo ampicillin #> 1 Klebsiella R #> 2 Escherichia S mo_is_intrinsic_resistant( c(\"Klebsiella\", \"Escherichia\"), \"ampicillin\" ) #> [1] TRUE FALSE mo_is_intrinsic_resistant( \"Klebsiella\", c(\"ampicillin\", \"kanamycin\") ) #> [1] TRUE FALSE data <- data.frame( mo = c( \"Staphylococcus aureus\", \"Enterococcus faecalis\", \"Escherichia coli\", \"Klebsiella pneumoniae\", \"Pseudomonas aeruginosa\" ), VAN = \"-\", # Vancomycin AMX = \"-\", # Amoxicillin COL = \"-\", # Colistin CAZ = \"-\", # Ceftazidime CXM = \"-\", # Cefuroxime PEN = \"S\", # Benzylenicillin FOX = \"S\", # Cefoxitin stringsAsFactors = FALSE ) data eucast_rules(data)"},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"type-of-input","dir":"Articles","previous_headings":"","what":"Type of input","title":"How to determine multi-drug resistance (MDR)","text":"mdro() function takes data set input, regular data.frame. tries automatically determine right columns info isolates, name species columns results antimicrobial agents. See help page info set right settings data command ?mdro. WHONET data (data), settings automatically set correctly.","code":""},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"guidelines","dir":"Articles","previous_headings":"","what":"Guidelines","title":"How to determine multi-drug resistance (MDR)","text":"mdro() function support multiple guidelines. can select guideline guideline parameter. Currently supported guidelines (case-insensitive): guideline = \"CMI2012\" (default) Magiorakos AP, Srinivasan et al. “Multidrug-resistant, extensively drug-resistant pandrug-resistant bacteria: international expert proposal interim standard definitions acquired resistance.” Clinical Microbiology Infection (2012) (link) guideline = \"EUCAST3.2\" (simply guideline = \"EUCAST\") European international guideline - EUCAST Expert Rules Version 3.2 “Intrinsic Resistance Unusual Phenotypes” (link) guideline = \"EUCAST3.1\" European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance Exceptional Phenotypes Tables” (link) guideline = \"TB\" international guideline multi-drug resistant tuberculosis - World Health Organization “Companion handbook guidelines programmatic management drug-resistant tuberculosis” (link) guideline = \"MRGN\" German national guideline - Mueller et al. (2015) Antimicrobial Resistance Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6 guideline = \"BRMO\" Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)” (link) Please suggest (country-specific) guidelines letting us know: https://github.com/msberends/AMR/issues/new.","code":""},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"custom-guidelines","dir":"Articles","previous_headings":"Guidelines","what":"Custom Guidelines","title":"How to determine multi-drug resistance (MDR)","text":"can also use custom guideline. Custom guidelines can set custom_mdro_guideline() function. great importance custom rules determine MDROs hospital, e.g., rules dependent ward, state contact isolation variables data. familiar case_when() dplyr package, recognise input method set rules. Rules must set using R considers ‘formula notation’: row/isolate matches first rule, value first ~ (case ‘Elderly Type ’) set MDRO value. Otherwise, second rule tried . maximum number rules unlimited. can print rules set console overview. Colours help reading console supports colours. outcome function can used guideline argument mdro() function: rules set (custom object case) exported shared file location using saveRDS() collaborate multiple users. custom rules set imported using readRDS().","code":"custom <- custom_mdro_guideline( CIP == \"R\" & age > 60 ~ \"Elderly Type A\", ERY == \"R\" & age > 60 ~ \"Elderly Type B\" ) custom #> A set of custom MDRO rules: #> 1. If CIP is \"R\" and age is higher than 60 then: Elderly Type A #> 2. If ERY is \"R\" and age is higher than 60 then: Elderly Type B #> 3. Otherwise: Negative #> #> Unmatched rows will return NA. #> Results will be of class 'factor', with ordered levels: Negative < Elderly Type A < Elderly Type B x <- mdro(example_isolates, guideline = custom) table(x) #> x #> Negative Elderly Type A Elderly Type B #> 1070 198 732"},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"examples","dir":"Articles","previous_headings":"","what":"Examples","title":"How to determine multi-drug resistance (MDR)","text":"mdro() function always returns ordered factor predefined guidelines. example, output default guideline Magiorakos et al. returns factor levels ‘Negative’, ‘MDR’, ‘XDR’ ‘PDR’ order. next example uses example_isolates data set. data set included package contains full antibiograms 2,000 microbial isolates. reflects reality can used practise AMR data analysis. test MDR/XDR/PDR guideline data set, get: Frequency table Class: factor > ordered (numeric) Length: 2,000 Levels: 4: Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant … Available: 1,745 (87.25%, NA: 255 = 12.75%) Unique: 2 another example, create data set determine multi-drug resistant TB: column names automatically verified valid drug names codes, worked exactly way: data set now looks like : can now add interpretation MDR-TB data set. can use: shortcut mdr_tb(): Create frequency table results: Frequency table Class: factor > ordered (numeric) Length: 5,000 Levels: 5: Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant <… Available: 5,000 (100%, NA: 0 = 0%) Unique: 5","code":"library(dplyr) # to support pipes: %>% library(cleaner) # to create frequency tables example_isolates %>% mdro() %>% freq() # show frequency table of the result #> Warning: in mdro(): NA introduced for isolates where the available percentage of #> antimicrobial classes was below 50% (set with pct_required_classes) # random_sir() is a helper function to generate # a random vector with values S, I and R my_TB_data <- data.frame( rifampicin = random_sir(5000), isoniazid = random_sir(5000), gatifloxacin = random_sir(5000), ethambutol = random_sir(5000), pyrazinamide = random_sir(5000), moxifloxacin = random_sir(5000), kanamycin = random_sir(5000) ) my_TB_data <- data.frame( RIF = random_sir(5000), INH = random_sir(5000), GAT = random_sir(5000), ETH = random_sir(5000), PZA = random_sir(5000), MFX = random_sir(5000), KAN = random_sir(5000) ) head(my_TB_data) #> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin #> 1 I R S S S S #> 2 S S I R R S #> 3 R I I I R I #> 4 I S S S S S #> 5 I I I S I S #> 6 R S R S I I #> kanamycin #> 1 R #> 2 I #> 3 S #> 4 I #> 5 I #> 6 I mdro(my_TB_data, guideline = \"TB\") my_TB_data$mdr <- mdr_tb(my_TB_data) #> ℹ No column found as input for col_mo, assuming all rows contain #> Mycobacterium tuberculosis. freq(my_TB_data$mdr)"},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/PCA.html","id":"transforming","dir":"Articles","previous_headings":"","what":"Transforming","title":"How to conduct principal component analysis (PCA) for AMR","text":"PCA, need transform AMR data first. example_isolates data set package looks like: Now transform data set resistance percentages per taxonomic order genus:","code":"library(AMR) library(dplyr) glimpse(example_isolates) #> Rows: 2,000 #> Columns: 46 #> $ date 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-01-13, 2… #> $ patient \"A77334\", \"A77334\", \"067927\", \"067927\", \"067927\", \"067927\", \"4… #> $ age 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 71, 75, 50… #> $ gender \"F\", \"F\", \"F\", \"F\", \"F\", \"F\", \"M\", \"M\", \"F\", \"F\", \"M\", \"M\", \"M… #> $ ward \"Clinical\", \"Clinical\", \"ICU\", \"ICU\", \"ICU\", \"ICU\", \"Clinical\"… #> $ mo \"B_ESCHR_COLI\", \"B_ESCHR_COLI\", \"B_STPHY_EPDR\", \"B_STPHY_EPDR\",… #> $ PEN R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, S,… #> $ OXA NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ FLC NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, NA, R, R… #> $ AMX NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N… #> $ AMC I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, I, NA, N… #> $ AMP NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N… #> $ TZP NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ CZO NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,… #> $ FEP NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ CXM I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R, R, S, S… #> $ FOX NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,… #> $ CTX NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S… #> $ CAZ NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S, R, R, … #> $ CRO NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S… #> $ GEN NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ TOB NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA, NA, NA… #> $ AMK NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ KAN NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ TMP R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R, R, R, … #> $ SXT R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, S, NA, N… #> $ NIT NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R,… #> $ FOS NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ LNZ R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N… #> $ CIP NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, NA, S, S… #> $ MFX NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ VAN R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S, S, S, … #> $ TEC R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N… #> $ TCY R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S, I, R, … #> $ TGC NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA… #> $ DOX NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA… #> $ ERY R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,… #> $ CLI R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, R, R, NA… #> $ AZM R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,… #> $ IPM NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S… #> $ MEM NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ MTR NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ CHL NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ COL NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R, R, R, … #> $ MUP NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ RIF R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N… resistance_data <- example_isolates %>% group_by( order = mo_order(mo), # group on anything, like order genus = mo_genus(mo) ) %>% # and genus as we do here summarise_if(is.sir, resistance) %>% # then get resistance of all drugs select( order, genus, AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT ) # and select only relevant columns head(resistance_data) #> # A tibble: 6 × 10 #> # Groups: order [5] #> order genus AMC CXM CTX CAZ GEN TOB TMP SXT #> #> 1 (unknown order) (unknown ge… NA NA NA NA NA NA NA NA #> 2 Actinomycetales Schaalia NA NA NA NA NA NA NA NA #> 3 Bacteroidales Bacteroides NA NA NA NA NA NA NA NA #> 4 Campylobacterales Campylobact… NA NA NA NA NA NA NA NA #> 5 Caryophanales Gemella NA NA NA NA NA NA NA NA #> 6 Caryophanales Listeria NA NA NA NA NA NA NA NA"},{"path":"https://msberends.github.io/AMR/articles/PCA.html","id":"perform-principal-component-analysis","dir":"Articles","previous_headings":"","what":"Perform principal component analysis","title":"How to conduct principal component analysis (PCA) for AMR","text":"new pca() function automatically filter rows contain numeric values selected variables, now need : result can reviewed good old summary() function: Good news. first two components explain total 93.3% variance (see PC1 PC2 values Proportion Variance. can create -called biplot base R biplot() function, see antimicrobial resistance per drug explain difference per microorganism.","code":"pca_result <- pca(resistance_data) #> ℹ Columns selected for PCA: \"AMC\", \"CAZ\", \"CTX\", \"CXM\", \"GEN\", \"SXT\", #> \"TMP\", and \"TOB\". Total observations available: 7. summary(pca_result) #> Groups (n=4, named as 'order'): #> [1] \"Caryophanales\" \"Enterobacterales\" \"Lactobacillales\" \"Pseudomonadales\" #> Importance of components: #> PC1 PC2 PC3 PC4 PC5 PC6 PC7 #> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16 #> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00 #> Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00 #> Groups (n=4, named as 'order'): #> [1] \"Caryophanales\" \"Enterobacterales\" \"Lactobacillales\" \"Pseudomonadales\""},{"path":"https://msberends.github.io/AMR/articles/PCA.html","id":"plotting-the-results","dir":"Articles","previous_headings":"","what":"Plotting the results","title":"How to conduct principal component analysis (PCA) for AMR","text":"can’t see explanation points. Perhaps works better new ggplot_pca() function, automatically adds right labels even groups: can also print ellipse per group, edit appearance:","code":"biplot(pca_result) ggplot_pca(pca_result) ggplot_pca(pca_result, ellipse = TRUE) + ggplot2::labs(title = \"An AMR/PCA biplot!\")"},{"path":"https://msberends.github.io/AMR/articles/WHONET.html","id":"import-of-data","dir":"Articles","previous_headings":"","what":"Import of data","title":"How to work with WHONET data","text":"tutorial assumes already imported WHONET data e.g. readxl package. RStudio, can done using menu button ‘Import Dataset’ tab ‘Environment’. Choose option ‘Excel’ select exported file. Make sure date fields imported correctly. example syntax look like : package comes example data set WHONET. use analysis.","code":"library(readxl) data <- read_excel(path = \"path/to/your/file.xlsx\")"},{"path":"https://msberends.github.io/AMR/articles/WHONET.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to work with WHONET data","text":"First, load relevant packages yet . use tidyverse analyses. . don’t know yet, suggest read website: https://www.tidyverse.org/. transform variables simplify automate analysis: Microorganisms transformed microorganism codes (called mo) using Catalogue Life reference data set, contains ~70,000 microorganisms taxonomic kingdoms Bacteria, Fungi Protozoa. tranformation .mo(). function also recognises almost WHONET abbreviations microorganisms. Antimicrobial results interpretations clean valid. words, contain values \"S\", \"\" \"R\". exactly .sir() function . errors warnings, values transformed succesfully. also created package dedicated data cleaning checking, called cleaner package. freq() function can used create frequency tables. let’s check data, couple frequency tables: Frequency table Class: character Length: 500 Available: 500 (100%, NA: 0 = 0%) Unique: 38 Shortest: 11 Longest: 40 (omitted 28 entries, n = 57 [11.4%]) Frequency table Class: factor > ordered > sir (numeric) Length: 500 Levels: 5: S < SDD < < R < NI Available: 481 (96.2%, NA: 19 = 3.8%) Unique: 3 Drug: Amoxicillin/clavulanic acid (AMC, J01CR02) Drug group: Beta-lactams/penicillins %SI: 78.59%","code":"library(dplyr) # part of tidyverse library(ggplot2) # part of tidyverse library(AMR) # this package library(cleaner) # to create frequency tables # transform variables data <- WHONET %>% # get microbial ID based on given organism mutate(mo = as.mo(Organism)) %>% # transform everything from \"AMP_ND10\" to \"CIP_EE\" to the new `sir` class mutate_at(vars(AMP_ND10:CIP_EE), as.sir) # our newly created `mo` variable, put in the mo_name() function data %>% freq(mo_name(mo), nmax = 10) # our transformed antibiotic columns # amoxicillin/clavulanic acid (J01CR02) as an example data %>% freq(AMC_ND2)"},{"path":"https://msberends.github.io/AMR/articles/WHONET.html","id":"a-first-glimpse-at-results","dir":"Articles","previous_headings":"","what":"A first glimpse at results","title":"How to work with WHONET data","text":"easy ggplot already give lot information, using included ggplot_sir() function:","code":"data %>% group_by(Country) %>% select(Country, AMP_ND2, AMC_ED20, CAZ_ED10, CIP_ED5) %>% ggplot_sir(translate_ab = \"ab\", facet = \"Country\", datalabels = FALSE)"},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"microorganisms-full-microbial-taxonomy","dir":"Articles","previous_headings":"","what":"microorganisms: Full Microbial Taxonomy","title":"Data sets for download / own use","text":"data set 78 678 rows 26 columns, containing following column names:mo, fullname, status, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, oxygen_tolerance, source, lpsn, lpsn_parent, lpsn_renamed_to, mycobank, mycobank_parent, mycobank_renamed_to, gbif, gbif_parent, gbif_renamed_to, prevalence, snomed. data set R available microorganisms, load AMR package. last updated 4 October 2024 13:28:44 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (1.8 MB) Download tab-separated text file (17.7 MB) Download Microsoft Excel workbook (8.7 MB) Download Apache Feather file (8.3 MB) Download Apache Parquet file (3.8 MB) Download IBM SPSS Statistics data file (29 MB) Download Stata DTA file (92.5 MB) NOTE: exported files SPSS Stata contain first 50 SNOMED codes per record, file size otherwise exceed 100 MB; file size limit GitHub. file structures compression techniques inefficient. Advice? Use R instead. ’s free much better many ways. tab-separated text file Microsoft Excel workbook contain SNOMED codes comma separated values.","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source","dir":"Articles","previous_headings":"microorganisms: Full Microbial Taxonomy","what":"Source","title":"Data sets for download / own use","text":"data set contains full microbial taxonomy six kingdoms List Prokaryotic names Standing Nomenclature (LPSN), MycoBank, Global Biodiversity Information Facility (GBIF): Parte, AC et al. (2020). List Prokaryotic names Standing Nomenclature (LPSN) moves DSMZ. International Journal Systematic Evolutionary Microbiology, 70, 5607-5612; . Accessed https://lpsn.dsmz.de June 24th, 2024. Vincent, R et al (2013). MycoBank gearing new horizons. IMA Fungus, 4(2), 371-9; . Accessed https://www.mycobank.org June 24th, 2024. GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset . Accessed https://www.gbif.org June 24th, 2024. Reimer, LC et al. (2022). BacDive 2022: knowledge base standardized bacterial archaeal data. Nucleic Acids Res., 50(D1):D741-D74; . Accessed https://bacdive.dsmz.de July 16th, 2024. Public Health Information Network Vocabulary Access Distribution System (PHIN VADS). US Edition SNOMED CT 1 September 2020. Value Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: https://phinvads.cdc.gov","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example-content","dir":"Articles","previous_headings":"microorganisms: Full Microbial Taxonomy","what":"Example content","title":"Data sets for download / own use","text":"Included (sub)species per taxonomic kingdom: Example rows filtering genus Escherichia:","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"antibiotics-antibiotic-antifungal-drugs","dir":"Articles","previous_headings":"","what":"antibiotics: Antibiotic (+Antifungal) Drugs","title":"Data sets for download / own use","text":"data set 486 rows 14 columns, containing following column names:ab, cid, name, group, atc, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, loinc. data set R available antibiotics, load AMR package. last updated 15 January 2025 15:14:09 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (42 kB) Download tab-separated text file (0.1 MB) Download Microsoft Excel workbook (74 kB) Download Apache Feather file (0.1 MB) Download Apache Parquet file (0.1 MB) Download IBM SPSS Statistics data file (0.4 MB) Download Stata DTA file (0.4 MB) tab-separated text, Microsoft Excel, SPSS, Stata files contain ATC codes, common abbreviations, trade names LOINC codes comma separated values.","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-1","dir":"Articles","previous_headings":"antibiotics: Antibiotic (+Antifungal) Drugs","what":"Source","title":"Data sets for download / own use","text":"data set contains EARS-Net ATC codes gathered WHONET, compound IDs PubChem. also contains brand names (synonyms) found PubChem Defined Daily Doses (DDDs) oral parenteral administration. ATC/DDD index Collaborating Centre Drug Statistics Methodology (note: may used commercial purposes, freely available CC website personal use) PubChem US National Library Medicine WHONET software 2019 LOINC (Logical Observation Identifiers Names Codes)","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"antivirals-antiviral-drugs","dir":"Articles","previous_headings":"","what":"antivirals: Antiviral Drugs","title":"Data sets for download / own use","text":"data set 120 rows 11 columns, containing following column names:av, name, atc, cid, atc_group, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, loinc. data set R available antivirals, load AMR package. last updated 20 October 2023 12:51:48 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (6 kB) Download tab-separated text file (17 kB) Download Microsoft Excel workbook (16 kB) Download Apache Feather file (16 kB) Download Apache Parquet file (13 kB) Download IBM SPSS Statistics data file (32 kB) Download Stata DTA file (78 kB) tab-separated text, Microsoft Excel, SPSS, Stata files contain trade names LOINC codes comma separated values.","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-2","dir":"Articles","previous_headings":"antivirals: Antiviral Drugs","what":"Source","title":"Data sets for download / own use","text":"data set contains ATC codes gathered compound IDs PubChem. also contains brand names (synonyms) found PubChem Defined Daily Doses (DDDs) oral parenteral administration. ATC/DDD index Collaborating Centre Drug Statistics Methodology (note: may used commercial purposes, freely available CC website personal use) PubChem US National Library Medicine LOINC (Logical Observation Identifiers Names Codes)","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir","dir":"Articles","previous_headings":"","what":"clinical_breakpoints: Interpretation from MIC values & disk diameters to SIR","title":"Data sets for download / own use","text":"data set 34 063 rows 14 columns, containing following column names:guideline, type, host, method, site, mo, rank_index, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R, uti, is_SDD. data set R available clinical_breakpoints, load AMR package. last updated 29 September 2024 20:17:56 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (70 kB) Download tab-separated text file (3.1 MB) Download Microsoft Excel workbook (2 MB) Download Apache Feather file (1.5 MB) Download Apache Parquet file (0.1 MB) Download IBM SPSS Statistics data file (5.6 MB) Download Stata DTA file (9.3 MB)","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-3","dir":"Articles","previous_headings":"clinical_breakpoints: Interpretation from MIC values & disk diameters to SIR","what":"Source","title":"Data sets for download / own use","text":"data set contains interpretation rules MIC values disk diffusion diameters. Included guidelines CLSI (2011-2024) EUCAST (2011-2024). Clinical breakpoints package validated imported WHONET, free desktop Windows application developed supported Collaborating Centre Surveillance Antimicrobial Resistance. can read website. developers WHONET AMR package contact sharing work. highly appreciate development WHONET software. CEO CLSI chairman EUCAST endorsed work public use AMR package (consequently use breakpoints) June 2023, future development distributing clinical breakpoints discussed meeting CLSI, EUCAST, , developers WHONET AMR package. NOTE: AMR package (WHONET software well) contains internal methods apply guidelines, rather complex. example, breakpoints must applied certain species groups (case package available microorganisms.groups data set). important considered using breakpoints use.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"intrinsic_resistant-intrinsic-bacterial-resistance","dir":"Articles","previous_headings":"","what":"intrinsic_resistant: Intrinsic Bacterial Resistance","title":"Data sets for download / own use","text":"data set 301 583 rows 2 columns, containing following column names:mo ab. data set R available intrinsic_resistant, load AMR package. last updated 29 September 2024 20:17:56 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (0.1 MB) Download tab-separated text file (10.9 MB) Download Microsoft Excel workbook (3 MB) Download Apache Feather file (2.5 MB) Download Apache Parquet file (0.3 MB) Download IBM SPSS Statistics data file (16.2 MB) Download Stata DTA file (25 MB)","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-4","dir":"Articles","previous_headings":"intrinsic_resistant: Intrinsic Bacterial Resistance","what":"Source","title":"Data sets for download / own use","text":"data set contains defined intrinsic resistance EUCAST bug-drug combinations, based ‘EUCAST Expert Rules’ ‘EUCAST Intrinsic Resistance Unusual Phenotypes’ v3.3 (2021).","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example-content-4","dir":"Articles","previous_headings":"intrinsic_resistant: Intrinsic Bacterial Resistance","what":"Example content","title":"Data sets for download / own use","text":"Example rows filtering Enterobacter cloacae:","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"dosage-dosage-guidelines-from-eucast","dir":"Articles","previous_headings":"","what":"dosage: Dosage Guidelines from EUCAST","title":"Data sets for download / own use","text":"data set 503 rows 9 columns, containing following column names:ab, name, type, dose, dose_times, administration, notes, original_txt, eucast_version. data set R available dosage, load AMR package. last updated 22 June 2023 13:10:59 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (3 kB) Download tab-separated text file (43 kB) Download Microsoft Excel workbook (25 kB) Download Apache Feather file (21 kB) Download Apache Parquet file (9 kB) Download IBM SPSS Statistics data file (64 kB) Download Stata DTA file (0.1 MB)","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-5","dir":"Articles","previous_headings":"dosage: Dosage Guidelines from EUCAST","what":"Source","title":"Data sets for download / own use","text":"EUCAST breakpoints used package based dosages data set. Currently included dosages data set meant : (), ‘EUCAST Clinical Breakpoint Tables’ v11.0 (2021), ‘EUCAST Clinical Breakpoint Tables’ v12.0 (2022).","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example_isolates-example-data-for-practice","dir":"Articles","previous_headings":"","what":"example_isolates: Example Data for Practice","title":"Data sets for download / own use","text":"data set 2 000 rows 46 columns, containing following column names:date, patient, age, gender, ward, mo, PEN, OXA, FLC, AMX, AMC, AMP, TZP, CZO, FEP, CXM, FOX, CTX, CAZ, CRO, GEN, TOB, AMK, KAN, TMP, SXT, NIT, FOS, LNZ, CIP, MFX, VAN, TEC, TCY, TGC, DOX, ERY, CLI, AZM, IPM, MEM, MTR, CHL, COL, MUP, RIF. data set R available example_isolates, load AMR package. last updated 15 June 2024 13:33:49 UTC. Find info structure data set .","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-6","dir":"Articles","previous_headings":"example_isolates: Example Data for Practice","what":"Source","title":"Data sets for download / own use","text":"data set contains randomised fictitious data, reflects reality can used practise AMR data analysis.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example_isolates_unclean-example-data-for-practice","dir":"Articles","previous_headings":"","what":"example_isolates_unclean: Example Data for Practice","title":"Data sets for download / own use","text":"data set 3 000 rows 8 columns, containing following column names:patient_id, hospital, date, bacteria, AMX, AMC, CIP, GEN. data set R available example_isolates_unclean, load AMR package. last updated 27 August 2022 18:49:37 UTC. Find info structure data set .","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-7","dir":"Articles","previous_headings":"example_isolates_unclean: Example Data for Practice","what":"Source","title":"Data sets for download / own use","text":"data set contains randomised fictitious data, reflects reality can used practise AMR data analysis.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"microorganisms-groups-species-groups-and-microbiological-complexes","dir":"Articles","previous_headings":"","what":"microorganisms.groups: Species Groups and Microbiological Complexes","title":"Data sets for download / own use","text":"data set 521 rows 4 columns, containing following column names:mo_group, mo, mo_group_name, mo_name. data set R available microorganisms.groups, load AMR package. last updated 29 September 2024 20:17:56 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (5 kB) Download tab-separated text file (49 kB) Download Microsoft Excel workbook (19 kB) Download Apache Feather file (19 kB) Download Apache Parquet file (13 kB) Download IBM SPSS Statistics data file (63 kB) Download Stata DTA file (81 kB)","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-8","dir":"Articles","previous_headings":"microorganisms.groups: Species Groups and Microbiological Complexes","what":"Source","title":"Data sets for download / own use","text":"data set contains species groups microbiological complexes, used clinical_breakpoints data set.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"microorganisms-codes-common-laboratory-codes","dir":"Articles","previous_headings":"","what":"microorganisms.codes: Common Laboratory Codes","title":"Data sets for download / own use","text":"data set 4 971 rows 2 columns, containing following column names:code mo. data set R available microorganisms.codes, load AMR package. last updated 29 September 2024 20:17:56 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (22 kB) Download tab-separated text file (0.1 MB) Download Microsoft Excel workbook (82 kB) Download Apache Feather file (85 kB) Download Apache Parquet file (56 kB) Download IBM SPSS Statistics data file (0.1 MB) Download Stata DTA file (0.1 MB)","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-9","dir":"Articles","previous_headings":"microorganisms.codes: Common Laboratory Codes","what":"Source","title":"Data sets for download / own use","text":"data set contains commonly used codes microorganisms, laboratory systems WHONET.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/resistance_predict.html","id":"needed-r-packages","dir":"Articles","previous_headings":"","what":"Needed R packages","title":"How to predict antimicrobial resistance","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. AMR package depends packages even extends use functions.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"tidyverse\", \"AMR\"))"},{"path":"https://msberends.github.io/AMR/articles/resistance_predict.html","id":"prediction-analysis","dir":"Articles","previous_headings":"","what":"Prediction analysis","title":"How to predict antimicrobial resistance","text":"package contains function resistance_predict(), takes input functions AMR data analysis. Based date column, calculates cases per year uses regression model predict antimicrobial resistance. basically easy : function look date column col_date set. running commands, summary regression model printed unless using resistance_predict(..., info = FALSE). text printed summary - actual result (output) function data.frame containing year: number observations, actual observed resistance, estimated resistance standard error estimation: function plot available base R, can extended packages depend output based type input. extended function cope resistance predictions: fastest way plot result. automatically adds right axes, error bars, titles, number available observations type model. also support ggplot2 package custom function ggplot_sir_predict() create appealing plots:","code":"# resistance prediction of piperacillin/tazobactam (TZP): resistance_predict(tbl = example_isolates, col_date = \"date\", col_ab = \"TZP\", model = \"binomial\") # or: example_isolates %>% resistance_predict( col_ab = \"TZP\", model = \"binomial\" ) # to bind it to object 'predict_TZP' for example: predict_TZP <- example_isolates %>% resistance_predict( col_ab = \"TZP\", model = \"binomial\" ) predict_TZP #> # A tibble: 34 × 7 #> year value se_min se_max observations observed estimated #> * #> 1 2002 0.2 NA NA 15 0.2 0.0562 #> 2 2003 0.0625 NA NA 32 0.0625 0.0616 #> 3 2004 0.0854 NA NA 82 0.0854 0.0676 #> 4 2005 0.05 NA NA 60 0.05 0.0741 #> 5 2006 0.0508 NA NA 59 0.0508 0.0812 #> 6 2007 0.121 NA NA 66 0.121 0.0889 #> 7 2008 0.0417 NA NA 72 0.0417 0.0972 #> 8 2009 0.0164 NA NA 61 0.0164 0.106 #> 9 2010 0.0566 NA NA 53 0.0566 0.116 #> 10 2011 0.183 NA NA 93 0.183 0.127 #> # ℹ 24 more rows plot(predict_TZP) ggplot_sir_predict(predict_TZP) # choose for error bars instead of a ribbon ggplot_sir_predict(predict_TZP, ribbon = FALSE)"},{"path":"https://msberends.github.io/AMR/articles/resistance_predict.html","id":"choosing-the-right-model","dir":"Articles","previous_headings":"Prediction analysis","what":"Choosing the right model","title":"How to predict antimicrobial resistance","text":"Resistance easily predicted; look vancomycin resistance Gram-positive bacteria, spread (.e. standard error) enormous: Vancomycin resistance 100% ten years, might remain low. can define model model parameter. model chosen generalised linear regression model using binomial distribution, assuming period zero resistance followed period increasing resistance leading slowly resistance. Valid values : vancomycin resistance Gram-positive bacteria, linear model might appropriate: model also available object, attribute:","code":"example_isolates %>% filter(mo_gramstain(mo, language = NULL) == \"Gram-positive\") %>% resistance_predict(col_ab = \"VAN\", year_min = 2010, info = FALSE, model = \"binomial\") %>% ggplot_sir_predict() example_isolates %>% filter(mo_gramstain(mo, language = NULL) == \"Gram-positive\") %>% resistance_predict(col_ab = \"VAN\", year_min = 2010, info = FALSE, model = \"linear\") %>% ggplot_sir_predict() model <- attributes(predict_TZP)$model summary(model)$family #> #> Family: binomial #> Link function: logit summary(model)$coefficients #> Estimate Std. Error z value Pr(>|z|) #> (Intercept) -200.67944891 46.17315349 -4.346237 1.384932e-05 #> year 0.09883005 0.02295317 4.305725 1.664395e-05"},{"path":"https://msberends.github.io/AMR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Matthijs S. Berends. Author, maintainer. Dennis Souverein. Author, contributor. Erwin E. . Hassing. Author, contributor. Andrew P. Norgan. Contributor. Anita Williams. Contributor. Annick Lenglet. Contributor. Anthony Underwood. Contributor. Anton Mymrikov. Contributor. Bart C. Meijer. Contributor. Christian F. Luz. Contributor. Dmytro Mykhailenko. Contributor. Eric H. L. C. M. Hazenberg. Contributor. Gwen Knight. Contributor. Jason Stull. Contributor. Javier Sanchez. Contributor. Jonas Salm. Contributor. Judith M. Fonville. Contributor. Larisse Bolton. Contributor. Matthew Saab. Contributor. Peter Dutey-Magni. Contributor. Rogier P. Schade. Contributor. Sofia Ny. Contributor. Alex W. Friedrich. Thesis advisor. Bhanu N. M. Sinha. Thesis advisor. Casper J. Albers. Thesis advisor. Corinna Glasner. Thesis advisor.","code":""},{"path":"https://msberends.github.io/AMR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022). “AMR: R Package Working Antimicrobial Resistance Data.” Journal Statistical Software, 104(3), 1–31. doi:10.18637/jss.v104.i03.","code":"@Article{, title = {{AMR}: An {R} Package for Working with Antimicrobial Resistance Data}, author = {Matthijs S. Berends and Christian F. Luz and Alexander W. Friedrich and Bhanu N. M. Sinha and Casper J. Albers and Corinna Glasner}, journal = {Journal of Statistical Software}, year = {2022}, volume = {104}, number = {3}, pages = {1--31}, doi = {10.18637/jss.v104.i03}, }"},{"path":"https://msberends.github.io/AMR/index.html","id":"the-amr-package-for-r-","dir":"","previous_headings":"","what":"Antimicrobial Resistance Data Analysis","title":"Antimicrobial Resistance Data Analysis","text":"Provides --one solution antimicrobial resistance (AMR) data analysis One Health approach Used 175 countries, available 20 languages Generates antibiograms - traditional, combined, syndromic, even WISCA Provides full microbiological taxonomy extensive info antimicrobial drugs Applies recent CLSI EUCAST clinical veterinary breakpoints MICs, disk zones ECOFFs Corrects duplicate isolates, calculates predicts AMR per antibiotic class Integrates WHONET, ATC, EARS-Net, PubChem, LOINC, SNOMED CT, NCBI 100% free costs dependencies, highly suitable places limited resources Now available Python ! Click read . https://msberends.github.io/AMR https://doi.org/10.18637/jss.v104.i03","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"introduction","dir":"","previous_headings":"","what":"Introduction","title":"Antimicrobial Resistance Data Analysis","text":"AMR package free open-source R package zero dependencies simplify analysis prediction Antimicrobial Resistance (AMR) work microbial antimicrobial data properties, using evidence-based methods. aim provide standard clean reproducible AMR data analysis, can therefore empower epidemiological analyses continuously enable surveillance treatment evaluation setting. Many different researchers around globe continually helping us make successful durable project! work published Journal Statistical Software (Volume 104(3); DOI 10.18637/jss.v104.i03) formed basis two PhD theses (DOI 10.33612/diss.177417131 DOI 10.33612/diss.192486375). installing package, R knows ~52,000 distinct microbial species (updated December 2022) ~600 antibiotic, antimycotic antiviral drugs name code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC SNOMED CT), knows valid SIR MIC values. integral clinical breakpoint guidelines CLSI EUCAST included, even epidemiological cut-(ECOFF) values. supports can read data format, including WHONET data. package works Windows, macOS Linux versions R since R-3.0 (April 2013). designed work setting, including limited resources. created routine data analysis academic research Faculty Medical Sciences University Groningen, collaboration non-profit organisations Certe Medical Diagnostics Advice Foundation University Medical Center Groningen.","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"used-in-over-175-countries-available-in-20-languages","dir":"","previous_headings":"Introduction","what":"Used in over 175 countries, available in 20 languages","title":"Antimicrobial Resistance Data Analysis","text":"Since first public release early 2018, R package used almost countries world. Click map enlarge see country names. help contributors corners world, AMR package available English, Czech, Chinese, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, Ukrainian. Antimicrobial drug (group) names colloquial microorganism names provided languages.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/index.html","id":"filtering-and-selecting-data","dir":"","previous_headings":"Practical examples","what":"Filtering and selecting data","title":"Antimicrobial Resistance Data Analysis","text":"One powerful functions package, aside calculating plotting AMR, selecting filtering based antibiotic columns. can done using -called antibiotic class selectors work base R, dplyr data.table: defined row filter Gram-negative bacteria intrinsic resistance cefotaxime (mo_is_gram_negative() mo_is_intrinsic_resistant()) column selection two antibiotic groups (aminoglycosides() carbapenems()), reference data microorganisms antibiotics AMR package make sure get meant: base R equivalent : base R code work version R since April 2013 (R-3.0). Moreover, code works identically data.table package, starting :","code":"# AMR works great with dplyr, but it's not required or neccesary library(AMR) library(dplyr) example_isolates %>% mutate(bacteria = mo_fullname()) %>% # filtering functions for microorganisms: filter(mo_is_gram_negative(), mo_is_intrinsic_resistant(ab = \"cefotax\")) %>% # antibiotic selectors: select(bacteria, aminoglycosides(), carbapenems()) library(AMR) example_isolates$bacteria <- mo_fullname(example_isolates$mo) example_isolates[which(mo_is_gram_negative() & mo_is_intrinsic_resistant(ab = \"cefotax\")), c(\"bacteria\", aminoglycosides(), carbapenems())] example_isolates <- data.table::as.data.table(example_isolates)"},{"path":"https://msberends.github.io/AMR/index.html","id":"generating-antibiograms","dir":"","previous_headings":"Practical examples","what":"Generating antibiograms","title":"Antimicrobial Resistance Data Analysis","text":"AMR package supports generating traditional, combined, syndromic, even weighted-incidence syndromic combination antibiograms (WISCA). used inside R Markdown Quarto, table printed right output format automatically (markdown, LaTeX, HTML, etc.). combination antibiograms, clear combined antibiotics yield higher empiric coverage: Like many functions package, antibiogram() comes support 20 languages often detected automatically based system language:","code":"antibiogram(example_isolates, antibiotics = c(aminoglycosides(), carbapenems())) antibiogram(example_isolates, antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"), mo_transform = \"gramstain\") antibiogram(example_isolates, antibiotics = c(\"cipro\", \"tobra\", \"genta\"), # any arbitrary name or code will work mo_transform = \"gramstain\", ab_transform = \"name\", language = \"uk\") # Ukrainian"},{"path":"https://msberends.github.io/AMR/index.html","id":"calculating-resistance-per-group","dir":"","previous_headings":"Practical examples","what":"Calculating resistance per group","title":"Antimicrobial Resistance Data Analysis","text":"manual approach, can use resistance susceptibility() function: use antibiotic class selectors select series antibiotic columns:","code":"example_isolates %>% # group by ward: group_by(ward) %>% # calculate AMR using resistance() for gentamicin and tobramycin # and get their 95% confidence intervals using sir_confidence_interval(): summarise(across(c(GEN, TOB), list(total_R = resistance, conf_int = function(x) sir_confidence_interval(x, collapse = \"-\")))) library(AMR) library(dplyr) out <- example_isolates %>% # group by ward: group_by(ward) %>% # calculate AMR using resistance(), over all aminoglycosides and polymyxins: summarise(across(c(aminoglycosides(), polymyxins()), resistance)) out # transform the antibiotic columns to names: out %>% set_ab_names() # transform the antibiotic column to ATC codes: out %>% set_ab_names(property = \"atc\")"},{"path":"https://msberends.github.io/AMR/index.html","id":"what-else-can-you-do-with-this-package","dir":"","previous_headings":"","what":"What else can you do with this package?","title":"Antimicrobial Resistance Data Analysis","text":"package intended comprehensive toolbox integrated AMR data analysis. package can used : Reference taxonomy microorganisms, since package contains microbial (sub)species List Prokaryotic names Standing Nomenclature (LPSN) Global Biodiversity Information Facility (GBIF) (manual) Interpreting raw MIC disk diffusion values, based CLSI EUCAST guideline (manual) Retrieving antimicrobial drug names, doses forms administration clinical health care records (manual) Determining first isolates used AMR data analysis (manual) Calculating antimicrobial resistance (tutorial) Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (tutorial) Calculating (empirical) susceptibility mono therapy combination therapies (tutorial) Predicting future antimicrobial resistance using regression models (tutorial) Getting properties microorganism (like Gram stain, species, genus family) (manual) Getting properties antibiotic (like name, code EARS-Net/ATC/LOINC/PubChem, defined daily dose trade name) (manual) Plotting antimicrobial resistance (tutorial) Applying EUCAST expert rules (manual) Getting SNOMED codes microorganism, getting properties microorganism based SNOMED code (manual) Getting LOINC codes antibiotic, getting properties antibiotic based LOINC code (manual) Machine reading EUCAST CLSI guidelines 2011-2021 translate MIC values disk diffusion diameters SIR (link) Principal component analysis AMR (tutorial)","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/index.html","id":"latest-official-version","dir":"","previous_headings":"Get this package","what":"Latest official version","title":"Antimicrobial Resistance Data Analysis","text":"package available official R network (CRAN). Install package R CRAN using command: downloaded installed automatically. RStudio, click menu Tools > Install Packages… type “AMR” press Install. Note: functions website may available latest release. use functions data sets mentioned website, install latest development version.","code":"install.packages(\"AMR\")"},{"path":"https://msberends.github.io/AMR/index.html","id":"latest-development-version","dir":"","previous_headings":"Get this package","what":"Latest development version","title":"Antimicrobial Resistance Data Analysis","text":"Please read Developer Guideline . latest unpublished development version can installed GitHub two ways: Manually, using: Automatically, using rOpenSci R-universe platform, adding R-universe address list repositories (‘repos’): , can install update AMR package like official release (e.g., using install.packages(\"AMR\") RStudio via Tools > Check Package Updates…).","code":"install.packages(\"remotes\") # if you haven't already remotes::install_github(\"msberends/AMR\") options(repos = c(getOption(\"repos\"), msberends = \"https://msberends.r-universe.dev\"))"},{"path":"https://msberends.github.io/AMR/index.html","id":"get-started","dir":"","previous_headings":"","what":"Get started","title":"Antimicrobial Resistance Data Analysis","text":"find conduct AMR data analysis, please continue reading get started click link ‘’ menu.","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"partners","dir":"","previous_headings":"","what":"Partners","title":"Antimicrobial Resistance Data Analysis","text":"development package part , related , made possible following non-profit organisations initiatives:","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"copyright","dir":"","previous_headings":"","what":"Copyright","title":"Antimicrobial Resistance Data Analysis","text":"R package free, open-source software licensed GNU General Public License v2.0 (GPL-2). nutshell, means package: May used commercial purposes May used private purposes May used patent purposes May modified, although: Modifications must released license distributing package Changes made code must documented May distributed, although: Source code must made available package distributed copy license copyright notice must included package. Comes LIMITATION liability Comes warranty","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":null,"dir":"Reference","previous_headings":"","what":"Options for the AMR package — AMR-options","title":"Options for the AMR package — AMR-options","text":"overview package-specific options() can set AMR package.","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":"options","dir":"Reference","previous_headings":"","what":"Options","title":"Options for the AMR package — AMR-options","text":"AMR_antibiogram_formatting_type numeric (1-12) use antibiogram(), indicate formatting type use. AMR_breakpoint_type character use .sir(), indicate breakpoint type use. must either \"ECOFF\", \"animal\", \"human\". AMR_cleaning_regex regular expression (case-insensitive) use .mo() mo_* functions, clean user input. default outcome mo_cleaning_regex(), removes texts brackets texts \"species\" \"serovar\". AMR_custom_ab file location RDS file, use custom antimicrobial drugs package. explained add_custom_antimicrobials(). AMR_custom_mo file location RDS file, use custom microorganisms package. explained add_custom_microorganisms(). AMR_eucastrules character set default types rules eucast_rules() function, must one : \"breakpoints\", \"expert\", \"\", \"custom\", \"\", defaults c(\"breakpoints\", \"expert\"). AMR_guideline character set default guideline interpreting MIC values disk diffusion diameters .sir(). Can guideline name (e.g., \"CLSI\") name year (e.g. \"CLSI 2019\"). default latest implemented EUCAST guideline, currently \"EUCAST 2024\". Supported guideline currently EUCAST (2011-2024) CLSI (2011-2024). AMR_ignore_pattern regular expression ignore (.e., make NA) match given .mo() mo_* functions. AMR_include_PKPD logical use .sir(), indicate PK/PD clinical breakpoints must applied last resort - default TRUE. AMR_include_screening logical use .sir(), indicate clinical breakpoints screening allowed - default FALSE. AMR_keep_synonyms logical use .mo() mo_* functions, indicate old, previously valid taxonomic names must preserved corrected currently accepted names. default FALSE. AMR_locale character set language AMR package, can one supported language names ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (), Japanese (ja), Norwegian (), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), Ukrainian (uk). default current system language (supported, English otherwise). AMR_mo_source file location manual code list used .mo() mo_* functions. explained set_mo_source().","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":"saving-settings-between-sessions","dir":"Reference","previous_headings":"","what":"Saving Settings Between Sessions","title":"Options for the AMR package — AMR-options","text":"Settings R saved globally thus lost R exited. can save options .Rprofile file, user-specific file. can edit using: file, can set options ... ...add Portuguese language support antibiotics, allow PK/PD rules interpreting MIC values .sir().","code":"utils::file.edit(\"~/.Rprofile\") options(AMR_locale = \"pt\") options(AMR_include_PKPD = TRUE)"},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":"share-options-within-team","dir":"Reference","previous_headings":"","what":"Share Options Within Team","title":"Options for the AMR package — AMR-options","text":"global approach, e.g. within (data) team, save options file remote file location, shared network drive, user read file automatically start-. work way: Save plain text file e.g. \"X:/team_folder/R_options.R\" fill preferred settings. user, open .Rprofile file using utils::file.edit(\"~/.Rprofile\") put : Reload R/RStudio check settings getOption(), e.g. getOption(\"AMR_locale\") set value. Now team settings configured one place, can maintained .","code":"source(\"X:/team_folder/R_options.R\")"},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":null,"dir":"Reference","previous_headings":"","what":"The AMR Package — AMR","title":"The AMR Package — AMR","text":"Welcome AMR package. AMR package free open-source R package zero dependencies simplify analysis prediction Antimicrobial Resistance (AMR) work microbial antimicrobial data properties, using evidence-based methods. aim provide standard clean reproducible AMR data analysis, can therefore empower epidemiological analyses continuously enable surveillance treatment evaluation setting. Many different researchers around globe continually helping us make successful durable project! work published Journal Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03 ) formed basis two PhD theses (doi:10.33612/diss.177417131 doi:10.33612/diss.192486375 ). installing package, R knows ~79 000 microorganisms (updated June 2024) ~610 antibiotic, antimycotic antiviral drugs name code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC SNOMED CT), knows valid SIR MIC values. integral clinical breakpoint guidelines CLSI EUCAST included, even epidemiological cut-(ECOFF) values. supports can read data format, including WHONET data. package works Windows, macOS Linux versions R since R-3.0 (April 2013). designed work setting, including limited resources. created routine data analysis academic research Faculty Medical Sciences public University Groningen, collaboration non-profit organisations Certe Medical Diagnostics Advice Foundation University Medical Center Groningen. AMR package available English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, Ukrainian. Antimicrobial drug (group) names colloquial microorganism names provided languages.","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"The AMR Package — AMR","text":"cite AMR publications use: Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022). \"AMR: R Package Working Antimicrobial Resistance Data.\" Journal Statistical Software, 104(3), 1-31. doi:10.18637/jss.v104.i03 BibTeX entry LaTeX users :","code":"@Article{, title = {{AMR}: An {R} Package for Working with Antimicrobial Resistance Data}, author = {Matthijs S. Berends and Christian F. Luz and Alexander W. Friedrich and Bhanu N. M. Sinha and Casper J. Albers and Corinna Glasner}, journal = {Journal of Statistical Software}, year = {2022}, volume = {104}, number = {3}, pages = {1--31}, doi = {10.18637/jss.v104.i03}, }"},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"The AMR Package — AMR","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"The AMR Package — AMR","text":"Maintainer: Matthijs S. Berends m.s.berends@umcg.nl (ORCID) Authors: Dennis Souverein (ORCID) [contributor] Erwin E. . Hassing [contributor] contributors: Andrew P. Norgan (ORCID) [contributor] Anita Williams (ORCID) [contributor] Annick Lenglet (ORCID) [contributor] Anthony Underwood (ORCID) [contributor] Anton Mymrikov [contributor] Bart C. Meijer [contributor] Christian F. Luz (ORCID) [contributor] Dmytro Mykhailenko [contributor] Eric H. L. C. M. Hazenberg [contributor] Gwen Knight (ORCID) [contributor] Jason Stull (ORCID) [contributor] Javier Sanchez (ORCID) [contributor] Jonas Salm [contributor] Judith M. Fonville [contributor] Larisse Bolton (ORCID) [contributor] Matthew Saab [contributor] Peter Dutey-Magni (ORCID) [contributor] Rogier P. Schade [contributor] Sofia Ny (ORCID) [contributor] Alex W. Friedrich (ORCID) [thesis advisor] Bhanu N. M. Sinha (ORCID) [thesis advisor] Casper J. Albers (ORCID) [thesis advisor] Corinna Glasner (ORCID) [thesis advisor]","code":""},{"path":"https://msberends.github.io/AMR/reference/WHOCC.html","id":null,"dir":"Reference","previous_headings":"","what":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","title":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","text":"antimicrobial drugs official names, ATC codes, ATC groups defined daily dose (DDD) included package, using Collaborating Centre Drug Statistics Methodology.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHOCC.html","id":"whocc","dir":"Reference","previous_headings":"","what":"WHOCC","title":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","text":"package contains ~550 antibiotic, antimycotic antiviral drugs Anatomical Therapeutic Chemical (ATC) codes, ATC groups Defined Daily Dose (DDD) World Health Organization Collaborating Centre Drug Statistics Methodology (WHOCC, https://atcddd.fhi.) Pharmaceuticals Community Register European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). become gold standard international drug utilisation monitoring research. WHOCC located Oslo Norwegian Institute Public Health funded Norwegian government. European Commission executive European Union promotes general interest. NOTE: WHOCC copyright allow use commercial purposes, unlike info package. See https://atcddd.fhi./copyright_disclaimer/.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHOCC.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","text":"","code":"as.ab(\"meropenem\") #> Class 'ab' #> [1] MEM ab_name(\"J01DH02\") #> [1] \"Meropenem\" ab_tradenames(\"flucloxacillin\") #> [1] \"culpen\" \"floxacillin\" \"floxacillinsodium\" #> [4] \"floxapen\" \"floxapensodiumsalt\" \"fluclox\" #> [7] \"flucloxacilina\" \"flucloxacilline\" \"flucloxacillinum\" #> [10] \"fluorochloroxacillin\" \"staphylex\""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with 500 Isolates - WHONET Example — WHONET","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"example data set exact structure export file WHONET. files can used package, example data set shows. antibiotic results example_isolates data set. patient names created using online surname generators place practice purposes.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"","code":"WHONET"},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"tibble 500 observations 53 variables: Identification number ID sample Specimen number ID specimen Organism Name microorganism. analysis, transform valid microbial class, using .mo(). Country Country origin Laboratory Name laboratory Last name Fictitious last name patient First name Fictitious initial patient Sex Fictitious gender patient Age Fictitious age patient Age category Age group, can also looked using age_groups() Date admissionDate hospital admission Specimen dateDate specimen received laboratory Specimen type Specimen type group Specimen type (Numeric) Translation \"Specimen type\" Reason Reason request Differential Diagnosis Isolate number ID isolate Organism type Type microorganism, can also looked using mo_type() Serotype Serotype microorganism Beta-lactamase Microorganism produces beta-lactamase? ESBL Microorganism produces extended spectrum beta-lactamase? Carbapenemase Microorganism produces carbapenemase? MRSA screening test Microorganism possible MRSA? Inducible clindamycin resistance Clindamycin can induced? Comment comments Date data entryDate data entered WHONET AMP_ND10:CIP_EE 28 different antibiotics. can lookup abbreviations antibiotics data set, use e.g. ab_name(\"AMP\") get official name immediately. analysis, transform valid antibiotic class, using .sir().","code":""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"","code":"WHONET #> # A tibble: 500 × 53 #> `Identification number` `Specimen number` Organism Country Laboratory #> #> 1 fe41d7bafa 1748 SPN Belgium National … #> 2 91f175ec37 1767 eco The Netherlands National … #> 3 cc4015056e 1343 eco The Netherlands National … #> 4 e864b692f5 1894 MAP Denmark National … #> 5 3d051fe345 1739 PVU Belgium National … #> 6 c80762a08d 1846 103 The Netherlands National … #> 7 8022d3727c 1628 103 Denmark National … #> 8 f3dc5f553d 1493 eco The Netherlands National … #> 9 15add38f6c 1847 eco France National … #> 10 fd41248def 1458 eco Germany National … #> # ℹ 490 more rows #> # ℹ 48 more variables: `Last name` , `First name` , Sex , #> # Age , `Age category` , `Date of admission` , #> # `Specimen date` , `Specimen type` , #> # `Specimen type (Numeric)` , Reason , `Isolate number` , #> # `Organism type` , Serotype , `Beta-lactamase` , ESBL , #> # Carbapenemase , `MRSA screening test` , …"},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"Use function e.g. clinical texts health care records. returns list antimicrobial drugs, doses forms administration found texts.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"","code":"ab_from_text( text, type = c(\"drug\", \"dose\", \"administration\"), collapse = NULL, translate_ab = FALSE, thorough_search = NULL, info = interactive(), ... )"},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"text text analyse type type property search , either \"drug\", \"dose\" \"administration\", see Examples collapse character pass paste(, collapse = ...) return one character per element text, see Examples translate_ab type = \"drug\": column name antibiotics data set translate antibiotic abbreviations , using ab_property(). default FALSE. Using TRUE equal using \"name\". thorough_search logical indicate whether input must extensively searched misspelling faulty input values. Setting TRUE take considerably time using FALSE. default, turn TRUE input elements contain maximum three words. info logical indicate whether progress bar printed - default TRUE interactive mode ... arguments passed .ab()","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"list, character collapse NULL","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"function also internally used .ab(), although searches first drug name throw note drug names returned. Note: .ab() function may use long regular expression match brand names antimicrobial drugs. may fail systems.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"argument-type","dir":"Reference","previous_headings":"","what":"Argument type","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"default, function search antimicrobial drug names. text elements searched official names, ATC codes brand names. uses .ab() internally, correct misspelling. type = \"dose\" (similar, like \"dosing\", \"doses\"), text elements searched numeric values higher 100 resemble years. output numeric. supports unit (g, mg, IE, etc.) multiple values one clinical text, see Examples. type = \"administration\" (abbreviations, like \"admin\", \"adm\"), text elements searched form drug administration. supports following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal vaginal. Abbreviations oral ('po', 'per os') become \"oral\", values intravenous ('iv', 'intraven') become \"iv\". supports multiple values one clinical text, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"argument-collapse","dir":"Reference","previous_headings":"","what":"Argument collapse","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"Without using collapse, function return list. can convenient use e.g. inside mutate()):df %>% mutate(abx = ab_from_text(clinical_text)) returned AB codes can transformed official names, groups, etc. ab_* functions ab_name() ab_group(), using translate_ab argument. using collapse, function return character:df %>% mutate(abx = ab_from_text(clinical_text, collapse = \"|\"))","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"","code":"# mind the bad spelling of amoxicillin in this line, # straight from a true health care record: ab_from_text(\"28/03/2020 regular amoxicilliin 500mg po tid\") #> [[1]] #> Class 'ab' #> [1] AMX #> ab_from_text(\"500 mg amoxi po and 400mg cipro iv\") #> [[1]] #> Class 'ab' #> [1] AMX CIP #> ab_from_text(\"500 mg amoxi po and 400mg cipro iv\", type = \"dose\") #> [[1]] #> [1] 500 400 #> ab_from_text(\"500 mg amoxi po and 400mg cipro iv\", type = \"admin\") #> [[1]] #> [1] \"oral\" \"iv\" #> ab_from_text(\"500 mg amoxi po and 400mg cipro iv\", collapse = \", \") #> [1] \"AMX, CIP\" # \\donttest{ # if you want to know which antibiotic groups were administered, do e.g.: abx <- ab_from_text(\"500 mg amoxi po and 400mg cipro iv\") ab_group(abx[[1]]) #> [1] \"Beta-lactams/penicillins\" \"Quinolones\" if (require(\"dplyr\")) { tibble(clinical_text = c( \"given 400mg cipro and 500 mg amox\", \"started on doxy iv today\" )) %>% mutate( abx_codes = ab_from_text(clinical_text), abx_doses = ab_from_text(clinical_text, type = \"doses\"), abx_admin = ab_from_text(clinical_text, type = \"admin\"), abx_coll = ab_from_text(clinical_text, collapse = \"|\"), abx_coll_names = ab_from_text(clinical_text, collapse = \"|\", translate_ab = \"name\" ), abx_coll_doses = ab_from_text(clinical_text, type = \"doses\", collapse = \"|\" ), abx_coll_admin = ab_from_text(clinical_text, type = \"admin\", collapse = \"|\" ) ) } #> Loading required package: dplyr #> #> Attaching package: ‘dplyr’ #> The following objects are masked from ‘package:stats’: #> #> filter, lag #> The following objects are masked from ‘package:base’: #> #> intersect, setdiff, setequal, union #> # A tibble: 2 × 8 #> clinical_text abx_codes abx_doses abx_admin abx_coll abx_coll_names #> #> 1 given 400mg cipro and 5… CIP|AMX Ciprofloxacin… #> 2 started on doxy iv today DOX Doxycycline #> # ℹ 2 more variables: abx_coll_doses , abx_coll_admin
