Note: the rules of ‘EUCAST Clinical Breakpoints v11.0 (2021)’ will be added in the next release, to be expected in February/March 2021.
+Note: the rules of ‘EUCAST Clinical Breakpoints v11.0 (2021)’ are implemented in the latest beta version, awaiting the next stable release (expected end of February)
PLEASE TAKE PART IN OUR SURVEY!
@@ -230,9 +230,9 @@ Since you are one of our users, we would like to know how you use the package an #> NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant() #> NOTE: Determining intrinsic resistance based on 'EUCAST Expert Rules' and #> 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 (2020). -#> Selecting aminoglycosides: 'AMK' (amikacin), 'GEN' (gentamicin), -#> 'KAN' (kanamycin), 'TOB' (tobramycin) -#> Selecting carbapenems: 'IPM' (imipenem), 'MEM' (meropenem) +#> Selecting aminoglycosides: columns 'AMK' (amikacin), 'GEN' (gentamicin), +#> 'KAN' (kanamycin) and 'TOB' (tobramycin) +#> Selecting carbapenems: columns 'IPM' (imipenem) and 'MEM' (meropenem)
Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. If you have a minute, please anonymously fill in this short questionnaire. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance!
Take me to the 5-min survey!With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (
mo_is_gram_negative()andmo_is_intrinsic_resistant()) and a column selection on two antibiotic groups (aminoglycosides()andcarbapenems()), the reference data about all microorganisms and all antibiotics in theAMRpackage make sure you get what you meant:
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 50d65fa8..4dd7b6e4 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -12,7 +12,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2021-02-04T15:47Z +last_built: 2021-02-08T12:50Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/AMR-deprecated.html b/docs/reference/AMR-deprecated.html index 380ea177..374f569e 100644 --- a/docs/reference/AMR-deprecated.html +++ b/docs/reference/AMR-deprecated.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/AMR.html b/docs/reference/AMR.html index fefb20cc..ecc5ff9a 100644 --- a/docs/reference/AMR.html +++ b/docs/reference/AMR.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/WHOCC.html b/docs/reference/WHOCC.html index a9fd6797..4720c377 100644 --- a/docs/reference/WHOCC.html +++ b/docs/reference/WHOCC.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/WHONET.html b/docs/reference/WHONET.html index 3c1f6f7e..308eb038 100644 --- a/docs/reference/WHONET.html +++ b/docs/reference/WHONET.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/ab_from_text.html b/docs/reference/ab_from_text.html index 17066236..ec9af198 100644 --- a/docs/reference/ab_from_text.html +++ b/docs/reference/ab_from_text.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html index 8acbae63..1aafb788 100644 --- a/docs/reference/ab_property.html +++ b/docs/reference/ab_property.html @@ -82,7 +82,7 @@ @@ -317,7 +317,7 @@ Details
-All output will be translated where possible.
+All output will be translated where possible.
The function
ab_url()will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.Stable Lifecycle
diff --git a/docs/reference/age.html b/docs/reference/age.html index a0fab4fc..78601d41 100644 --- a/docs/reference/age.html +++ b/docs/reference/age.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html index 2735e357..63b2104b 100644 --- a/docs/reference/age_groups.html +++ b/docs/reference/age_groups.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/antibiotic_class_selectors.html b/docs/reference/antibiotic_class_selectors.html index c63ae60e..187ba8de 100644 --- a/docs/reference/antibiotic_class_selectors.html +++ b/docs/reference/antibiotic_class_selectors.html @@ -83,7 +83,7 @@ @@ -244,33 +244,35 @@ -ab_class(ab_class, only_rsi_columns = NULL) +ab_class(ab_class, only_rsi_columns = FALSE) -aminoglycosides(only_rsi_columns = NULL) +aminoglycosides(only_rsi_columns = FALSE) -carbapenems(only_rsi_columns = NULL) +carbapenems(only_rsi_columns = FALSE) -cephalosporins(only_rsi_columns = NULL) +cephalosporins(only_rsi_columns = FALSE) -cephalosporins_1st(only_rsi_columns = NULL) +cephalosporins_1st(only_rsi_columns = FALSE) -cephalosporins_2nd(only_rsi_columns = NULL) +cephalosporins_2nd(only_rsi_columns = FALSE) -cephalosporins_3rd(only_rsi_columns = NULL) +cephalosporins_3rd(only_rsi_columns = FALSE) -cephalosporins_4th(only_rsi_columns = NULL) +cephalosporins_4th(only_rsi_columns = FALSE) -cephalosporins_5th(only_rsi_columns = NULL) +cephalosporins_5th(only_rsi_columns = FALSE) -fluoroquinolones(only_rsi_columns = NULL) +fluoroquinolones(only_rsi_columns = FALSE) -glycopeptides(only_rsi_columns = NULL) +glycopeptides(only_rsi_columns = FALSE) -macrolides(only_rsi_columns = NULL) +macrolides(only_rsi_columns = FALSE) -penicillins(only_rsi_columns = NULL) +oxazolidinones(only_rsi_columns = FALSE) -tetracyclines(only_rsi_columns = NULL)+penicillins(only_rsi_columns = FALSE) + +tetracyclines(only_rsi_columns = FALSE)Arguments
@@ -281,7 +283,7 @@
diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html index 65c4d12e..0e97a4ee 100644 --- a/docs/reference/antibiotics.html +++ b/docs/reference/antibiotics.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/as.ab.html b/docs/reference/as.ab.html index 09f5fd45..ecd7947a 100644 --- a/docs/reference/as.ab.html +++ b/docs/reference/as.ab.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html index 2db88276..14d40449 100644 --- a/docs/reference/as.disk.html +++ b/docs/reference/as.disk.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html index b76622be..3fd49dd1 100644 --- a/docs/reference/as.mic.html +++ b/docs/reference/as.mic.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html index 5d0e34b8..01cb0fed 100644 --- a/docs/reference/as.mo.html +++ b/docs/reference/as.mo.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html index 15b8497d..11a37fa6 100644 --- a/docs/reference/as.rsi.html +++ b/docs/reference/as.rsi.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html index fd999c68..7c4b9bab 100644 --- a/docs/reference/atc_online.html +++ b/docs/reference/atc_online.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/availability.html b/docs/reference/availability.html index 10d5be47..e05e8c7f 100644 --- a/docs/reference/availability.html +++ b/docs/reference/availability.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html index 65c3ba20..b62ad556 100644 --- a/docs/reference/bug_drug_combinations.html +++ b/docs/reference/bug_drug_combinations.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html index 2faa0041..87846951 100644 --- a/docs/reference/catalogue_of_life.html +++ b/docs/reference/catalogue_of_life.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html index d7391b4e..a1477fbd 100644 --- a/docs/reference/catalogue_of_life_version.html +++ b/docs/reference/catalogue_of_life_version.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/count.html b/docs/reference/count.html index 38b20baa..519aea1a 100644 --- a/docs/reference/count.html +++ b/docs/reference/count.html @@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible( diff --git a/docs/reference/dosage.html b/docs/reference/dosage.html index c4d9dd1b..73559e2f 100644 --- a/docs/reference/dosage.html +++ b/docs/reference/dosage.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html index 0a252aa0..042193fc 100644 --- a/docs/reference/eucast_rules.html +++ b/docs/reference/eucast_rules.html @@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied @@ -253,7 +253,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied version_breakpoints = 11, version_expertrules = 3.2, ampc_cephalosporin_resistance = NA, - only_rsi_columns = any(is.rsi(x)), + only_rsi_columns = FALSE, ... ) @@ -296,7 +296,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are appliedonly_rsi_columns -+ a logical to indicate whether only columns of class
<rsi>must be selected. If set toNULL(default), it will beTRUEif any column of the data was transformed to class<rsi>on beforehand, andFALSEotherwise.a logical to indicate whether only columns of class
<rsi>must be selected (defaults toFALSE)only_rsi_columns -+ a logical to indicate whether only antibiotic columns must be detected that were transformed to class
<rsi>on beforehand. Defaults toTRUEif any column ofxis of class<rsi>.a logical to indicate whether only antibiotic columns must be detected that were transformed to class
<rsi>on beforehand (defaults toFALSE)... diff --git a/docs/reference/example_isolates.html b/docs/reference/example_isolates.html index af3c64dc..3f28e745 100644 --- a/docs/reference/example_isolates.html +++ b/docs/reference/example_isolates.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/example_isolates_unclean.html b/docs/reference/example_isolates_unclean.html index 8a73aeae..312e4e9d 100644 --- a/docs/reference/example_isolates_unclean.html +++ b/docs/reference/example_isolates_unclean.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html index 2095cb91..b113c9b1 100644 --- a/docs/reference/filter_ab_class.html +++ b/docs/reference/filter_ab_class.html @@ -82,7 +82,7 @@ @@ -247,35 +247,121 @@ ab_class, result = NULL, scope = "any", - only_rsi_columns = any(is.rsi(x)), + only_rsi_columns = FALSE, ... ) -filter_aminoglycosides(x, result = NULL, scope = "any", ...) +filter_aminoglycosides( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_carbapenems(x, result = NULL, scope = "any", ...) +filter_carbapenems( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_cephalosporins(x, result = NULL, scope = "any", ...) +filter_cephalosporins( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_1st_cephalosporins(x, result = NULL, scope = "any", ...) +filter_1st_cephalosporins( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_2nd_cephalosporins(x, result = NULL, scope = "any", ...) +filter_2nd_cephalosporins( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_3rd_cephalosporins(x, result = NULL, scope = "any", ...) +filter_3rd_cephalosporins( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_4th_cephalosporins(x, result = NULL, scope = "any", ...) +filter_4th_cephalosporins( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_5th_cephalosporins(x, result = NULL, scope = "any", ...) +filter_5th_cephalosporins( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_fluoroquinolones(x, result = NULL, scope = "any", ...) +filter_fluoroquinolones( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_glycopeptides(x, result = NULL, scope = "any", ...) +filter_glycopeptides( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_macrolides(x, result = NULL, scope = "any", ...) +filter_macrolides( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_penicillins(x, result = NULL, scope = "any", ...) +filter_oxazolidinones( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_tetracyclines(x, result = NULL, scope = "any", ...) +filter_penicillins( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) + +filter_tetracyclines( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +)Arguments
@@ -298,7 +384,7 @@
diff --git a/docs/reference/index.html b/docs/reference/index.html index 59740f86..c08f1829 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ @@ -526,13 +526,13 @@only_rsi_columns -+ a logical to indicate whether only columns must be included that were transformed to class
<rsi>on beforehand. Defaults toTRUEif any column ofxis of class<rsi>.a logical to indicate whether only columns must be included that were transformed to class
<rsi>on beforehand (defaults toFALSE)... diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html index 813aaab0..b1bc7ee9 100644 --- a/docs/reference/first_isolate.html +++ b/docs/reference/first_isolate.html @@ -82,7 +82,7 @@ @@ -243,7 +243,7 @@first_isolate( - x, + x = NULL, col_date = NULL, col_patient_id = NULL, col_mo = NULL, @@ -264,7 +264,7 @@ ) filter_first_isolate( - x, + x = NULL, col_date = NULL, col_patient_id = NULL, col_mo = NULL, @@ -272,7 +272,7 @@ ) filter_first_weighted_isolate( - x, + x = NULL, col_date = NULL, col_patient_id = NULL, col_mo = NULL, @@ -285,7 +285,7 @@x -+ a data.frame containing isolates. Can be left blank for automatic determination.
a data.frame containing isolates. Can be left blank for automatic determination, see Examples.
col_date @@ -399,7 +399,7 @@Using
type = "keyantibiotics"and argumentignore_IAny difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With
ignore_I = FALSE, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in thekey_antibiotics()function.+ Using
-type = "points"and argumentpoints_thresholdA difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds
points_threshold, which default to2, an isolate will be (re)selected as a first weighted isolate.A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds
points_threshold, which defaults to2, an isolate will be (re)selected as a first weighted isolate.Stable Lifecycle
@@ -422,10 +422,12 @@ The lifecycle of this function is stable# `example_isolates` is a data set available in the AMR package. # See ?example_isolates. -# basic filtering on first isolates -example_isolates[first_isolate(), ] +example_isolates[first_isolate(example_isolates), ] # \donttest{ +# faster way, only works in R 3.2 and later: +example_isolates[first_isolate(), ] + # get all first Gram-negatives example_isolates[which(first_isolate() & mo_is_gram_negative()), ] diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html index aac8fd02..a4345ea9 100644 --- a/docs/reference/g.test.html +++ b/docs/reference/g.test.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/get_episode.html b/docs/reference/get_episode.html index 35e72b5a..15ccb343 100644 --- a/docs/reference/get_episode.html +++ b/docs/reference/get_episode.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html index 709ececb..c5319d89 100644 --- a/docs/reference/ggplot_rsi.html +++ b/docs/reference/ggplot_rsi.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html index 8bac0901..97b2edce 100644 --- a/docs/reference/guess_ab_col.html +++ b/docs/reference/guess_ab_col.html @@ -82,7 +82,7 @@ @@ -246,7 +246,7 @@ x = NULL, search_string = NULL, verbose = FALSE, - only_rsi_columns = any(is.rsi(x)) + only_rsi_columns = FALSE )Arguments
@@ -266,7 +266,7 @@only_rsi_columns -+ a logical to indicate whether only antibiotic columns must be detected that were transformed to class
<rsi>on beforehand. Defaults toTRUEif any column ofxis of class<rsi>.a logical to indicate whether only antibiotic columns must be detected that were transformed to class
<rsi>on beforehand (defaults toFALSE)- +
ab_class()aminoglycosides()carbapenems()cephalosporins()cephalosporins_1st()cephalosporins_2nd()cephalosporins_3rd()cephalosporins_4th()cephalosporins_5th()fluoroquinolones()glycopeptides()macrolides()penicillins()tetracyclines()
ab_class()aminoglycosides()carbapenems()cephalosporins()cephalosporins_1st()cephalosporins_2nd()cephalosporins_3rd()cephalosporins_4th()cephalosporins_5th()fluoroquinolones()glycopeptides()macrolides()oxazolidinones()penicillins()tetracyclines()Antibiotic Class Selectors
- +
filter_ab_class()filter_aminoglycosides()filter_carbapenems()filter_cephalosporins()filter_1st_cephalosporins()filter_2nd_cephalosporins()filter_3rd_cephalosporins()filter_4th_cephalosporins()filter_5th_cephalosporins()filter_fluoroquinolones()filter_glycopeptides()filter_macrolides()filter_penicillins()filter_tetracyclines()
filter_ab_class()filter_aminoglycosides()filter_carbapenems()filter_cephalosporins()filter_1st_cephalosporins()filter_2nd_cephalosporins()filter_3rd_cephalosporins()filter_4th_cephalosporins()filter_5th_cephalosporins()filter_fluoroquinolones()filter_glycopeptides()filter_macrolides()filter_oxazolidinones()filter_penicillins()filter_tetracyclines()Filter Isolates on Result in Antimicrobial Class
diff --git a/docs/reference/intrinsic_resistant.html b/docs/reference/intrinsic_resistant.html index e1b79c5b..c60cdb35 100644 --- a/docs/reference/intrinsic_resistant.html +++ b/docs/reference/intrinsic_resistant.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/isolate_identifier.html b/docs/reference/isolate_identifier.html index 0b0a9ff2..602a3dc5 100644 --- a/docs/reference/isolate_identifier.html +++ b/docs/reference/isolate_identifier.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/join.html b/docs/reference/join.html index c7fb67cc..9ff06ea1 100644 --- a/docs/reference/join.html +++ b/docs/reference/join.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/key_antibiotics.html b/docs/reference/key_antibiotics.html index a2e97fc0..d43042cc 100644 --- a/docs/reference/key_antibiotics.html +++ b/docs/reference/key_antibiotics.html @@ -82,7 +82,7 @@ @@ -243,7 +243,7 @@ key_antibiotics( - x, + x = NULL, col_mo = NULL, universal_1 = guess_ab_col(x, "amoxicillin"), universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"), @@ -380,7 +380,7 @@ The lifecycle of this function is stableUsing
type = "keyantibiotics"and argumentignore_IAny difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With
ignore_I = FALSE, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in thekey_antibiotics()function.+ Using
-type = "points"and argumentpoints_thresholdA difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds
points_threshold, which default to2, an isolate will be (re)selected as a first weighted isolate.A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds
points_threshold, which defaults to2, an isolate will be (re)selected as a first weighted isolate.Read more on Our Website!
diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html index d74ca3c1..1d2e6c7a 100644 --- a/docs/reference/kurtosis.html +++ b/docs/reference/kurtosis.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/like.html b/docs/reference/like.html index 17097aec..66999fd5 100644 --- a/docs/reference/like.html +++ b/docs/reference/like.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html index c838960e..c5e2c9b2 100644 --- a/docs/reference/mdro.html +++ b/docs/reference/mdro.html @@ -82,7 +82,7 @@ @@ -243,33 +243,28 @@mdro( - x, + x = NULL, guideline = "CMI2012", col_mo = NULL, info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE, verbose = FALSE, - only_rsi_columns = any(is.rsi(x)), + only_rsi_columns = FALSE, ... ) custom_mdro_guideline(..., as_factor = TRUE) -brmo(x, guideline = "BRMO", only_rsi_columns = any(is.rsi(x)), ...) +brmo(x = NULL, only_rsi_columns = FALSE, ...) -mrgn(x, guideline = "MRGN", only_rsi_columns = any(is.rsi(x)), ...) +mrgn(x = NULL, only_rsi_columns = FALSE, ...) -mdr_tb(x, guideline = "TB", only_rsi_columns = any(is.rsi(x)), ...) +mdr_tb(x = NULL, only_rsi_columns = FALSE, ...) -mdr_cmi2012(x, guideline = "CMI2012", only_rsi_columns = any(is.rsi(x)), ...) +mdr_cmi2012(x = NULL, only_rsi_columns = FALSE, ...) -eucast_exceptional_phenotypes( - x, - guideline = "EUCAST", - only_rsi_columns = any(is.rsi(x)), - ... -)+eucast_exceptional_phenotypes(x = NULL, only_rsi_columns = FALSE, ...)Arguments
@@ -304,7 +299,7 @@
only_rsi_columns -+ a logical to indicate whether only antibiotic columns must be detected that were transformed to class
<rsi>on beforehand. Defaults toTRUEif any column ofxis of class<rsi>.a logical to indicate whether only antibiotic columns must be detected that were transformed to class
<rsi>on beforehand (defaults toFALSE)... diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html index 5407ecad..7287e7d5 100644 --- a/docs/reference/microorganisms.codes.html +++ b/docs/reference/microorganisms.codes.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html index 8b5ac3fc..dae989b1 100644 --- a/docs/reference/microorganisms.html +++ b/docs/reference/microorganisms.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html index 00c10218..53fed7f3 100644 --- a/docs/reference/microorganisms.old.html +++ b/docs/reference/microorganisms.old.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/mo_matching_score.html b/docs/reference/mo_matching_score.html index 329388e4..c49afc36 100644 --- a/docs/reference/mo_matching_score.html +++ b/docs/reference/mo_matching_score.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index 46c08ec6..42278533 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -82,7 +82,7 @@ @@ -349,9 +349,9 @@The short name -
mo_shortname()- almost always returns the first character of the genus and the full species, like"E. coli". Exceptions are abbreviations of staphylococci (such as "CoNS", Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as "GBS", Group B Streptococci). Please bear in mind that e.g. E. coli could mean Escherichia coli (kingdom of Bacteria) as well as Entamoeba coli (kingdom of Protozoa). Returning to the full name will be done usingas.mo()internally, giving priority to bacteria and human pathogens, i.e."E. coli"will be considered Escherichia coli. In other words,mo_fullname(mo_shortname("Entamoeba coli"))returns"Escherichia coli".Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions
mo_kingdom()andmo_domain()return the exact same results.The Gram stain -
-mo_gramstain()- will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, PMID 11837318), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a valueNA. Functionsmo_is_gram_negative()andmo_is_gram_positive()always returnTRUEorFALSE(except when the input isNAor the MO code isUNKNOWN), thus always returnFALSEfor species outside the taxonomic kingdom of Bacteria.Determination of yeasts -
-mo_is_yeast()- will be based on the taxonomic phylum, class and order. Budding yeasts are true fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). The true yeasts are separated into one main order Saccharomycetales. For all microorganisms that are in one of those two groups, the function will returnTRUE. It returnsFALSEfor all other taxonomic entries.Intrinsic resistance -
-mo_is_intrinsic_resistant()- will be determined based on the intrinsic_resistant data set, which is based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 (2020). Themo_is_intrinsic_resistant()can be vectorised over argumentsx(input for microorganisms) and overab(input for antibiotics).All output will be translated where possible.
+Determination of yeasts -
+mo_is_yeast()- will be based on the taxonomic kingdom and class. Budding yeasts are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). True yeasts are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will returnTRUE. It returnsFALSEotherwise (except when the input isNAor the MO code isUNKNOWN).Intrinsic resistance -
+mo_is_intrinsic_resistant()- will be determined based on the intrinsic_resistant data set, which is based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 (2020). Themo_is_intrinsic_resistant()functions can be vectorised over argumentsx(input for microorganisms) and overab(input for antibiotics).All output will be translated where possible.
The function
mo_url()will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.Stable Lifecycle
diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html index 90eaae79..2030f513 100644 --- a/docs/reference/mo_source.html +++ b/docs/reference/mo_source.html @@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p diff --git a/docs/reference/pca.html b/docs/reference/pca.html index 1b5fced1..06ac67fc 100644 --- a/docs/reference/pca.html +++ b/docs/reference/pca.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/plot.html b/docs/reference/plot.html index 1857ffd6..b71efe64 100644 --- a/docs/reference/plot.html +++ b/docs/reference/plot.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html index 62590c08..3424c0dd 100644 --- a/docs/reference/proportion.html +++ b/docs/reference/proportion.html @@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be diff --git a/docs/reference/random.html b/docs/reference/random.html index 6bfa9f6d..f9c48cdd 100644 --- a/docs/reference/random.html +++ b/docs/reference/random.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html index 3f1e5b43..9728ccb0 100644 --- a/docs/reference/resistance_predict.html +++ b/docs/reference/resistance_predict.html @@ -82,7 +82,7 @@ @@ -287,7 +287,7 @@x -+ a data.frame containing isolates. Can be left blank for automatic determination.
a data.frame containing isolates. Can be left blank for automatic determination, see Examples.
col_ab diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html index a37725c4..713dcef4 100644 --- a/docs/reference/rsi_translation.html +++ b/docs/reference/rsi_translation.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/skewness.html b/docs/reference/skewness.html index d84086dd..65d21c0d 100644 --- a/docs/reference/skewness.html +++ b/docs/reference/skewness.html @@ -83,7 +83,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu diff --git a/docs/reference/translate.html b/docs/reference/translate.html index 16209a9b..372f3cc4 100644 --- a/docs/reference/translate.html +++ b/docs/reference/translate.html @@ -82,7 +82,7 @@ diff --git a/docs/survey.html b/docs/survey.html index 0ba3b116..90349031 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ diff --git a/index.md b/index.md index 852bfefe..52e24b55 100644 --- a/index.md +++ b/index.md @@ -1,6 +1,6 @@ # `AMR` (for R)-*Note: the rules of 'EUCAST Clinical Breakpoints v11.0 (2021)' will be added in the next release, to be expected in February/March 2021.* +*Note: the rules of 'EUCAST Clinical Breakpoints v11.0 (2021)' are implemented in [the latest beta version](./#latest-development-version), awaiting the next stable release (expected end of February)* > **PLEASE TAKE PART IN OUR SURVEY!** > Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. **If you have a minute, please [anonymously fill in this short questionnaire](./survey.html)**. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance! @@ -39,9 +39,9 @@ example_isolates %>% #> NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant() #> NOTE: Determining intrinsic resistance based on 'EUCAST Expert Rules' and #> 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 (2020). -#> Selecting aminoglycosides: 'AMK' (amikacin), 'GEN' (gentamicin), -#> 'KAN' (kanamycin), 'TOB' (tobramycin) -#> Selecting carbapenems: 'IPM' (imipenem), 'MEM' (meropenem) +#> Selecting aminoglycosides: columns 'AMK' (amikacin), 'GEN' (gentamicin), +#> 'KAN' (kanamycin) and 'TOB' (tobramycin) +#> Selecting carbapenems: columns 'IPM' (imipenem) and 'MEM' (meropenem) ``` With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (`mo_is_gram_negative()` and `mo_is_intrinsic_resistant()`) and a column selection on two antibiotic groups (`aminoglycosides()` and `carbapenems()`), the reference data about [all microorganisms](./reference/microorganisms.html) and [all antibiotics](./reference/antibiotics.html) in the `AMR` package make sure you get what you meant: diff --git a/man/ab_property.Rd b/man/ab_property.Rd index fa3a9855..23c68f3b 100644 --- a/man/ab_property.Rd +++ b/man/ab_property.Rd @@ -72,7 +72,7 @@ ab_property(x, property = "name", language = get_locale(), ...) Use these functions to return a specific property of an antibiotic from the \link{antibiotics} data set. All input values will be evaluated internally with \code{\link[=as.ab]{as.ab()}}. } \details{ -All output will be \link{translate}d where possible. +All output \link[=translate]{will be translated} where possible. The function \code{\link[=ab_url]{ab_url()}} will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available. } diff --git a/man/antibiotic_class_selectors.Rd b/man/antibiotic_class_selectors.Rd index f220e5fb..8c3097eb 100644 --- a/man/antibiotic_class_selectors.Rd +++ b/man/antibiotic_class_selectors.Rd @@ -14,42 +14,45 @@ \alias{fluoroquinolones} \alias{glycopeptides} \alias{macrolides} +\alias{oxazolidinones} \alias{penicillins} \alias{tetracyclines} \title{Antibiotic Class Selectors} \usage{ -ab_class(ab_class, only_rsi_columns = NULL) +ab_class(ab_class, only_rsi_columns = FALSE) -aminoglycosides(only_rsi_columns = NULL) +aminoglycosides(only_rsi_columns = FALSE) -carbapenems(only_rsi_columns = NULL) +carbapenems(only_rsi_columns = FALSE) -cephalosporins(only_rsi_columns = NULL) +cephalosporins(only_rsi_columns = FALSE) -cephalosporins_1st(only_rsi_columns = NULL) +cephalosporins_1st(only_rsi_columns = FALSE) -cephalosporins_2nd(only_rsi_columns = NULL) +cephalosporins_2nd(only_rsi_columns = FALSE) -cephalosporins_3rd(only_rsi_columns = NULL) +cephalosporins_3rd(only_rsi_columns = FALSE) -cephalosporins_4th(only_rsi_columns = NULL) +cephalosporins_4th(only_rsi_columns = FALSE) -cephalosporins_5th(only_rsi_columns = NULL) +cephalosporins_5th(only_rsi_columns = FALSE) -fluoroquinolones(only_rsi_columns = NULL) +fluoroquinolones(only_rsi_columns = FALSE) -glycopeptides(only_rsi_columns = NULL) +glycopeptides(only_rsi_columns = FALSE) -macrolides(only_rsi_columns = NULL) +macrolides(only_rsi_columns = FALSE) -penicillins(only_rsi_columns = NULL) +oxazolidinones(only_rsi_columns = FALSE) -tetracyclines(only_rsi_columns = NULL) +penicillins(only_rsi_columns = FALSE) + +tetracyclines(only_rsi_columns = FALSE) } \arguments{ \item{ab_class}{an antimicrobial class, like \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.} -\item{only_rsi_columns}{a logical to indicate whether only columns of class \href{[rsi]}{\verb{
}} must be selected. If set to \code{NULL} (default), it will be \code{TRUE} if any column of the data was \href{[rsi]}{transformed to class \verb{ }} on beforehand, and \code{FALSE} otherwise.} +\item{only_rsi_columns}{a logical to indicate whether only columns of class \href{[rsi]}{\verb{ }} must be selected (defaults to \code{FALSE})} } \description{ These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}} diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd index 138d4345..a0dc008f 100644 --- a/man/eucast_rules.Rd +++ b/man/eucast_rules.Rd @@ -26,7 +26,7 @@ eucast_rules( version_breakpoints = 11, version_expertrules = 3.2, ampc_cephalosporin_resistance = NA, - only_rsi_columns = any(is.rsi(x)), + only_rsi_columns = FALSE, ... ) @@ -49,7 +49,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11) \item{ampc_cephalosporin_resistance}{a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2}; '\emph{EUCAST Expert Rules v3.2 on Enterobacterales}' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of \code{NA} for this argument will remove results for these agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia} and \emph{Serratia}.} -\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{ }} on beforehand. Defaults to \code{TRUE} if any column of \code{x} is of class \verb{ }.} +\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{ }} on beforehand (defaults to \code{FALSE})} \item{...}{column name of an antibiotic, see section \emph{Antibiotics} below} diff --git a/man/filter_ab_class.Rd b/man/filter_ab_class.Rd index 80d2a381..2d5240df 100644 --- a/man/filter_ab_class.Rd +++ b/man/filter_ab_class.Rd @@ -13,6 +13,7 @@ \alias{filter_fluoroquinolones} \alias{filter_glycopeptides} \alias{filter_macrolides} +\alias{filter_oxazolidinones} \alias{filter_penicillins} \alias{filter_tetracyclines} \title{Filter Isolates on Result in Antimicrobial Class} @@ -22,35 +23,121 @@ filter_ab_class( ab_class, result = NULL, scope = "any", - only_rsi_columns = any(is.rsi(x)), + only_rsi_columns = FALSE, ... ) -filter_aminoglycosides(x, result = NULL, scope = "any", ...) +filter_aminoglycosides( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_carbapenems(x, result = NULL, scope = "any", ...) +filter_carbapenems( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_cephalosporins(x, result = NULL, scope = "any", ...) +filter_cephalosporins( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_1st_cephalosporins(x, result = NULL, scope = "any", ...) +filter_1st_cephalosporins( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_2nd_cephalosporins(x, result = NULL, scope = "any", ...) +filter_2nd_cephalosporins( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_3rd_cephalosporins(x, result = NULL, scope = "any", ...) +filter_3rd_cephalosporins( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_4th_cephalosporins(x, result = NULL, scope = "any", ...) +filter_4th_cephalosporins( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_5th_cephalosporins(x, result = NULL, scope = "any", ...) +filter_5th_cephalosporins( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_fluoroquinolones(x, result = NULL, scope = "any", ...) +filter_fluoroquinolones( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_glycopeptides(x, result = NULL, scope = "any", ...) +filter_glycopeptides( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_macrolides(x, result = NULL, scope = "any", ...) +filter_macrolides( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_penicillins(x, result = NULL, scope = "any", ...) +filter_oxazolidinones( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) -filter_tetracyclines(x, result = NULL, scope = "any", ...) +filter_penicillins( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) + +filter_tetracyclines( + x, + result = NULL, + scope = "any", + only_rsi_columns = FALSE, + ... +) } \arguments{ \item{x}{a data set} @@ -61,7 +148,7 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...) \item{scope}{the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}} -\item{only_rsi_columns}{a logical to indicate whether only columns must be included that were \href{[rsi]}{transformed to class \verb{ }} on beforehand. Defaults to \code{TRUE} if any column of \code{x} is of class \verb{ }.} +\item{only_rsi_columns}{a logical to indicate whether only columns must be included that were \href{[rsi]}{transformed to class \verb{ }} on beforehand (defaults to \code{FALSE})} \item{...}{arguments passed on to \code{\link[=filter_ab_class]{filter_ab_class()}}} } diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd index 5fb0a309..53c572cb 100755 --- a/man/first_isolate.Rd +++ b/man/first_isolate.Rd @@ -12,7 +12,7 @@ Methodology of this function is strictly based on: } \usage{ first_isolate( - x, + x = NULL, col_date = NULL, col_patient_id = NULL, col_mo = NULL, @@ -33,7 +33,7 @@ first_isolate( ) filter_first_isolate( - x, + x = NULL, col_date = NULL, col_patient_id = NULL, col_mo = NULL, @@ -41,7 +41,7 @@ filter_first_isolate( ) filter_first_weighted_isolate( - x, + x = NULL, col_date = NULL, col_patient_id = NULL, col_mo = NULL, @@ -50,7 +50,7 @@ filter_first_weighted_isolate( ) } \arguments{ -\item{x}{a \link{data.frame} containing isolates. Can be left blank for automatic determination.} +\item{x}{a \link{data.frame} containing isolates. Can be left blank for automatic determination, see \emph{Examples}.} \item{col_date}{column name of the result date (or date that is was received on the lab), defaults to the first column with a date class} @@ -130,7 +130,7 @@ There are two ways to determine whether isolates can be included as first weight Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With \code{ignore_I = FALSE}, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the \code{\link[=key_antibiotics]{key_antibiotics()}} function. \item Using \code{type = "points"} and argument \code{points_threshold} -A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, which default to \code{2}, an isolate will be (re)selected as a first weighted isolate. +A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, which defaults to \code{2}, an isolate will be (re)selected as a first weighted isolate. } } @@ -151,10 +151,12 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/ # `example_isolates` is a data set available in the AMR package. # See ?example_isolates. -# basic filtering on first isolates -example_isolates[first_isolate(), ] +example_isolates[first_isolate(example_isolates), ] \donttest{ +# faster way, only works in R 3.2 and later: +example_isolates[first_isolate(), ] + # get all first Gram-negatives example_isolates[which(first_isolate() & mo_is_gram_negative()), ] diff --git a/man/guess_ab_col.Rd b/man/guess_ab_col.Rd index ef2a14ab..a566673e 100644 --- a/man/guess_ab_col.Rd +++ b/man/guess_ab_col.Rd @@ -8,7 +8,7 @@ guess_ab_col( x = NULL, search_string = NULL, verbose = FALSE, - only_rsi_columns = any(is.rsi(x)) + only_rsi_columns = FALSE ) } \arguments{ @@ -18,7 +18,7 @@ guess_ab_col( \item{verbose}{a logical to indicate whether additional info should be printed} -\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{ }} on beforehand. Defaults to \code{TRUE} if any column of \code{x} is of class \verb{ }.} +\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{ }} on beforehand (defaults to \code{FALSE})} } \value{ A column name of \code{x}, or \code{NULL} when no result is found. diff --git a/man/key_antibiotics.Rd b/man/key_antibiotics.Rd index 79bac695..c48da92b 100755 --- a/man/key_antibiotics.Rd +++ b/man/key_antibiotics.Rd @@ -6,7 +6,7 @@ \title{Key Antibiotics for First (Weighted) Isolates} \usage{ key_antibiotics( - x, + x = NULL, col_mo = NULL, universal_1 = guess_ab_col(x, "amoxicillin"), universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"), @@ -125,7 +125,7 @@ There are two ways to determine whether isolates can be included as first weight Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With \code{ignore_I = FALSE}, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the \code{\link[=key_antibiotics]{key_antibiotics()}} function. \item Using \code{type = "points"} and argument \code{points_threshold} -A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, which default to \code{2}, an isolate will be (re)selected as a first weighted isolate. +A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, which defaults to \code{2}, an isolate will be (re)selected as a first weighted isolate. } } diff --git a/man/mdro.Rd b/man/mdro.Rd index d846ff56..3cb9c258 100644 --- a/man/mdro.Rd +++ b/man/mdro.Rd @@ -20,33 +20,28 @@ See the supported guidelines above for the list of publications used for this fu } \usage{ mdro( - x, + x = NULL, guideline = "CMI2012", col_mo = NULL, info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE, verbose = FALSE, - only_rsi_columns = any(is.rsi(x)), + only_rsi_columns = FALSE, ... ) custom_mdro_guideline(..., as_factor = TRUE) -brmo(x, guideline = "BRMO", only_rsi_columns = any(is.rsi(x)), ...) +brmo(x = NULL, only_rsi_columns = FALSE, ...) -mrgn(x, guideline = "MRGN", only_rsi_columns = any(is.rsi(x)), ...) +mrgn(x = NULL, only_rsi_columns = FALSE, ...) -mdr_tb(x, guideline = "TB", only_rsi_columns = any(is.rsi(x)), ...) +mdr_tb(x = NULL, only_rsi_columns = FALSE, ...) -mdr_cmi2012(x, guideline = "CMI2012", only_rsi_columns = any(is.rsi(x)), ...) +mdr_cmi2012(x = NULL, only_rsi_columns = FALSE, ...) -eucast_exceptional_phenotypes( - x, - guideline = "EUCAST", - only_rsi_columns = any(is.rsi(x)), - ... -) +eucast_exceptional_phenotypes(x = NULL, only_rsi_columns = FALSE, ...) } \arguments{ \item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.} @@ -63,7 +58,7 @@ eucast_exceptional_phenotypes( \item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.} -\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{ }} on beforehand. Defaults to \code{TRUE} if any column of \code{x} is of class \verb{ }.} +\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{ }} on beforehand (defaults to \code{FALSE})} \item{...}{in case of \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}}: a set of rules, see section \emph{Using Custom Guidelines} below. Otherwise: column name of an antibiotic, see section \emph{Antibiotics} below.} diff --git a/man/mo_property.Rd b/man/mo_property.Rd index c683ad8f..7f90e656 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -126,11 +126,11 @@ Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and so The Gram stain - \code{\link[=mo_gramstain]{mo_gramstain()}} - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, \href{https://pubmed.ncbi.nlm.nih.gov/11837318}{PMID 11837318}), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value \code{NA}. Functions \code{\link[=mo_is_gram_negative]{mo_is_gram_negative()}} and \code{\link[=mo_is_gram_positive]{mo_is_gram_positive()}} always return \code{TRUE} or \code{FALSE} (except when the input is \code{NA} or the MO code is \code{UNKNOWN}), thus always return \code{FALSE} for species outside the taxonomic kingdom of Bacteria. -Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be based on the taxonomic phylum, class and order. Budding yeasts are true fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). The true yeasts are separated into one main order Saccharomycetales. For all microorganisms that are in one of those two groups, the function will return \code{TRUE}. It returns \code{FALSE} for all other taxonomic entries. +Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). \emph{True yeasts} are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (except when the input is \code{NA} or the MO code is \code{UNKNOWN}). -Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2} (2020). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics). +Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2} (2020). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} functions can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics). -All output will be \link{translate}d where possible. +All output \link[=translate]{will be translated} where possible. The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. } diff --git a/man/resistance_predict.Rd b/man/resistance_predict.Rd index 36ee1dcb..d90029a6 100644 --- a/man/resistance_predict.Rd +++ b/man/resistance_predict.Rd @@ -47,7 +47,7 @@ ggplot_rsi_predict( ) } \arguments{ -\item{x}{a \link{data.frame} containing isolates. Can be left blank for automatic determination.} +\item{x}{a \link{data.frame} containing isolates. Can be left blank for automatic determination, see \emph{Examples}.} \item{col_ab}{column name of \code{x} containing antimicrobial interpretations (\code{"R"}, \code{"I"} and \code{"S"})} diff --git a/tests/testthat/test-_misc.R b/tests/testthat/test-_misc.R index 3a89e5f9..8827ece3 100755 --- a/tests/testthat/test-_misc.R +++ b/tests/testthat/test-_misc.R @@ -54,3 +54,12 @@ test_that("looking up ab columns works", { expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE)) expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE)) }) + +test_that("looking up ab columns works", { + skip_on_cran() + library(dplyr) + + # we rely on "grouped_tbl" being a class of grouped tibbles, so: + expect_true(is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id))) + +})