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Conduct AMR analysis
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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Get properties of a microorganism
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Get properties of an antibiotic
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Other: benchmarks
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< h1 > Deprecated Functions< / h1 >
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< small class = "dont-index" > Source: < a href = 'https://github.com/msberends/AMR/blob/master/R/deprecated.R' > < code > R/deprecated.R< / code > < / a > < / small >
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< p > These functions are so-called '< a href = 'https://rdrr.io/r/base/Deprecated.html' > Deprecated< / a > '. < strong > They will be removed in a future release.< / strong > Using the functions will give a warning with the name of the function it has been replaced by (if there is one).< / p >
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< pre class = "usage" > < span class = 'fu' > p_symbol< / span > < span class = 'op' > (< / span > < span class = 'va' > p< / span > , emptychar < span class = 'op' > =< / span > < span class = 'st' > " "< / span > < span class = 'op' > )< / span >
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< span class = 'fu' > filter_first_weighted_isolate< / span > < span class = 'op' > (< / span >
x < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
col_date < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
col_patient_id < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
col_mo < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
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< span class = 'fu' > key_antibiotics< / span > < span class = 'op' > (< / span >
x < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
col_mo < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
universal_1 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "amoxicillin"< / span > < span class = 'op' > )< / span > ,
universal_2 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "amoxicillin/clavulanic acid"< / span > < span class = 'op' > )< / span > ,
universal_3 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "cefuroxime"< / span > < span class = 'op' > )< / span > ,
universal_4 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "piperacillin/tazobactam"< / span > < span class = 'op' > )< / span > ,
universal_5 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "ciprofloxacin"< / span > < span class = 'op' > )< / span > ,
universal_6 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "trimethoprim/sulfamethoxazole"< / span > < span class = 'op' > )< / span > ,
GramPos_1 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "vancomycin"< / span > < span class = 'op' > )< / span > ,
GramPos_2 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "teicoplanin"< / span > < span class = 'op' > )< / span > ,
GramPos_3 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "tetracycline"< / span > < span class = 'op' > )< / span > ,
GramPos_4 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "erythromycin"< / span > < span class = 'op' > )< / span > ,
GramPos_5 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "oxacillin"< / span > < span class = 'op' > )< / span > ,
GramPos_6 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "rifampin"< / span > < span class = 'op' > )< / span > ,
GramNeg_1 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "gentamicin"< / span > < span class = 'op' > )< / span > ,
GramNeg_2 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "tobramycin"< / span > < span class = 'op' > )< / span > ,
GramNeg_3 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "colistin"< / span > < span class = 'op' > )< / span > ,
GramNeg_4 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "cefotaxime"< / span > < span class = 'op' > )< / span > ,
GramNeg_5 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "ceftazidime"< / span > < span class = 'op' > )< / span > ,
GramNeg_6 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "meropenem"< / span > < span class = 'op' > )< / span > ,
warnings < span class = 'op' > =< / span > < span class = 'cn' > TRUE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > key_antibiotics_equal< / span > < span class = 'op' > (< / span >
< span class = 'va' > y< / span > ,
< span class = 'va' > z< / span > ,
type < span class = 'op' > =< / span > < span class = 'st' > "keyantimicrobials"< / span > ,
ignore_I < span class = 'op' > =< / span > < span class = 'cn' > TRUE< / span > ,
points_threshold < span class = 'op' > =< / span > < span class = 'fl' > 2< / span > ,
info < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
na.rm < span class = 'op' > =< / span > < span class = 'cn' > TRUE< / span > ,
< span class = 'va' > ...< / span >
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< span class = 'op' > )< / span >
< span class = 'fu' > filter_ab_class< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
< span class = 'va' > ab_class< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_aminoglycosides< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_betalactams< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_carbapenems< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_cephalosporins< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_1st_cephalosporins< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_2nd_cephalosporins< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_3rd_cephalosporins< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_4th_cephalosporins< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_5th_cephalosporins< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_fluoroquinolones< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_glycopeptides< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_macrolides< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_oxazolidinones< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_penicillins< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > filter_tetracyclines< / span > < span class = 'op' > (< / span >
< span class = 'va' > x< / span > ,
result < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
scope < span class = 'op' > =< / span > < span class = 'st' > "any"< / span > ,
only_rsi_columns < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > ,
< span class = 'va' > ...< / span >
2021-04-26 23:57:37 +02:00
< span class = 'op' > )< / span > < / pre >
2019-10-13 09:31:58 +02:00
2021-05-19 22:55:42 +02:00
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
< p > All antibiotic class selectors (such as < code > < a href = 'antibiotic_class_selectors.html' > carbapenems()< / a > < / code > , < code > < a href = 'antibiotic_class_selectors.html' > aminoglycosides()< / a > < / code > ) can now be used for filtering as well, making all their accompanying < code > filter_*()< / code > functions redundant (such as < code > filter_carbapenems()< / code > , < code > filter_aminoglycosides()< / code > ).< / p >
2021-01-18 16:57:56 +01:00
< h2 class = "hasAnchor" id = "retired-lifecycle" > < a class = "anchor" href = "#retired-lifecycle" > < / a > Retired Lifecycle< / h2 >
2020-01-05 17:22:09 +01:00
< p > < img src = 'figures/lifecycle_retired.svg' style = margin-bottom:5px / > < br / >
2020-05-22 20:15:19 +02:00
The < a href = 'lifecycle.html' > lifecycle< / a > of this function is < strong > retired< / strong > . A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.< / p >
2021-01-18 16:57:56 +01:00
< h2 class = "hasAnchor" id = "read-more-on-our-website-" > < a class = "anchor" href = "#read-more-on-our-website-" > < / a > Read more on Our Website!< / h2 >
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< p > On our website < a href = 'https://msberends.github.io/AMR/' > https://msberends.github.io/AMR/< / a > you can find < a href = 'https://msberends.github.io/AMR/articles/AMR.html' > a comprehensive tutorial< / a > about how to conduct AMR data analysis, the < a href = 'https://msberends.github.io/AMR/reference/' > complete documentation of all functions< / a > and < a href = 'https://msberends.github.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > . As we would like to better understand the backgrounds and needs of our users, please < a href = 'https://msberends.github.io/AMR/survey.html' > participate in our survey< / a > !< / p >
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< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.6.1.< / p >
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