So only 91% is suitable for resistance analysis! We can now filter on
it with the filter() function, also from the
dplyr package:
-
+
our_data_1st <- our_data %>%
filter(first == TRUE)
For future use, the above two syntaxes can be shortened:
-
+
So we end up with 2 724 isolates for analysis. Now our data looks
like:
-
+
our_data_1st
#> # A tibble: 2,724 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first
@@ -441,7 +438,7 @@ like:
The base R summary() function gives a good first
impression, as it comes with support for the new mo and
sir classes that we now have in our data set:
-
+
summary(our_data_1st)
#> patient_id hospital date
#> Length:2724 Length:2724 Min. :2011-01-01
@@ -490,7 +487,7 @@ impression, as it comes with support for the new mo and
To just get an idea how the species are distributed, create a
frequency table with count() based on the name of the
microorganisms:
-
+
our_data %>%
count(mo_name(bacteria), sort = TRUE)
#> # A tibble: 4 × 2
@@ -517,7 +514,7 @@ microorganisms:
Using so-called antibiotic class selectors, you can select or filter
columns based on the antibiotic class that your antibiotic results are
in:
-
+
our_data_1st %>%
select(date, aminoglycosides())
#> ℹ For aminoglycosides() using column 'GEN' (gentamicin)
@@ -662,7 +659,7 @@ failure
function to create any of the above antibiogram types. For starters,
this is what the included example_isolates data set looks
like:
-
+
example_isolates
#> # A tibble: 2,000 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
@@ -691,7 +688,7 @@ like:
should be used. The antibiotics argument in the
antibiogram() function supports any (combination) of the
previously mentioned antibiotic class selectors:
-
+
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))
#> ℹ The function aminoglycosides() should be used inside a dplyr verb or
@@ -835,7 +832,7 @@ Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian,
Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish,
Swedish, Turkish, or Ukrainian. In this next example, we force the
language to be Spanish using the language argument:
-
+
antibiogram(example_isolates,
mo_transform = "gramstain",
antibiotics = aminoglycosides(),
@@ -889,7 +886,7 @@ language to be Spanish using the language argument:
To create a combined antibiogram, use antibiotic codes or names with
a plus + character like this:
-
+
antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
@@ -969,7 +966,7 @@ a plus + character like this:
To create a syndromic antibiogram, the syndromic_group
argument must be used. This can be any column in the data, or e.g. an
ifelse() with calculations based on certain columns:
-
+
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward")
@@ -1169,7 +1166,7 @@ Antibiogram) in which cases are predefined based on clinical or
demographic characteristics (e.g., endocarditis in 75+ females). This
next example is a simplification without clinical characteristics, but
just gives an idea of how a WISCA can be created:
-
+
wisca <- antibiogram(example_isolates,
antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain",
@@ -1237,7 +1234,7 @@ just gives an idea of how a WISCA can be created:
Antibiograms can be plotted using autoplot() from the
ggplot2 packages, since this AMR package
provides an extension to that function:
-
+
To calculate antimicrobial resistance in a more sensible way, also by
@@ -1266,12 +1263,12 @@ proportion of R (proportion_R()
I (proportion_SI(), equal to
susceptibility()). These functions can be used on their
own:
-
+
Or can be used in conjunction with group_by() and
summarise(), both from the dplyr package:
-
+
our_data_1st %>%
group_by(hospital) %>%
summarise(amoxicillin = resistance(AMX))
diff --git a/articles/AMR_for_Python.html b/articles/AMR_for_Python.html
index b05025450..00152bb4c 100644
--- a/articles/AMR_for_Python.html
+++ b/articles/AMR_for_Python.html
@@ -29,7 +29,7 @@
AMR (for R)
- 2.1.1.9122
+ 2.1.1.9123
Value
-
When used inside selecting or filtering, this returns a character vector of column names, with additional class "ab_selector". When used individually, this returns an 'ab' vector with all possible antimicrobial that the function would be able to select or filter.
+
When used inside selecting or filtering, this returns a character vector of column names, with additional class "ab_selector". When used individually, this returns an 'ab' vector with all possible antimicrobials that the function would be able to select or filter.
Details
@@ -199,6 +201,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
nitrofurans() can select:
furazidin (FUR), furazolidone (FRZ), nifurtoinol (NFR), nitrofurantoin (NIT), and nitrofurazone (NIZ)
oxazolidinones() can select:
cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD), and thiacetazone (THA)
penicillins() can select:
amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), cefepime/nacubactam (FNC), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)
+
phenicols() can select:
chloramphenicol (CHL), florfenicol (FLR), and thiamphenicol (THI)
polymyxins() can select:
colistin (COL), polymyxin B (PLB), and polymyxin B/polysorbate 80 (POP)
quinolones() can select:
besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
rifamycins() can select:
rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), and rifapentine (RFP)
diff --git a/reference/antibiotics.html b/reference/antibiotics.html
index bb20e211f..89e90bc0e 100644
--- a/reference/antibiotics.html
+++ b/reference/antibiotics.html
@@ -1,5 +1,5 @@
-
Data Sets with 605 Antimicrobial Drugs — antibiotics • AMR (for R)
+
Data Sets with 606 Antimicrobial Drugs — antibiotics • AMR (for R)
Skip to contents
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9122
+
2.1.1.9123