diff --git a/DESCRIPTION b/DESCRIPTION
index 1f54d386..129c2df1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: AMR
-Version: 1.4.0.9033
-Date: 2020-12-08
+Version: 1.4.0.9034
+Date: 2020-12-09
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index d646153a..ca5d5331 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,5 @@
-# AMR 1.4.0.9033
-## Last updated: 8 December 2020
+# AMR 1.4.0.9034
+## Last updated: 9 December 2020
### New
* Function `is_new_episode()` to determine patient episodes which are not necessarily based on microorganisms. It also supports grouped variables with e.g. `mutate()`, `filter()` and `summarise()` of the `dplyr` package:
@@ -35,6 +35,7 @@
* Fixed a bug where `as.mo()` would not return results for known laboratory codes for microorganisms
* Fixed a bug where `as.ab()` would sometimes fail
* If using `as.rsi()` on MICs or disk diffusion while there is intrinsic antimicrobial resistance, a warning will be thrown to remind about this
+* Better tibble printing for MIC values
### Other
* All messages and warnings thrown by this package now break sentences on whole words
diff --git a/R/ab_from_text.R b/R/ab_from_text.R
index d12e4af9..c3149c98 100644
--- a/R/ab_from_text.R
+++ b/R/ab_from_text.R
@@ -63,7 +63,7 @@
#' ab_from_text("500 mg amoxi po and 400mg cipro iv", type = "admin")
#'
#' ab_from_text("500 mg amoxi po and 400mg cipro iv", collapse = ", ")
-#'
+#' \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]])
@@ -86,6 +86,7 @@
#' collapse = "|"))
#'
#' }
+#' }
ab_from_text <- function(text,
type = c("drug", "dose", "administration"),
collapse = NULL,
diff --git a/R/mic.R b/R/mic.R
index 7db9e0e7..8c8e8ba3 100755
--- a/R/mic.R
+++ b/R/mic.R
@@ -155,21 +155,21 @@ is.mic <- function(x) {
#' @export
#' @noRd
as.double.mic <- function(x, ...) {
- as.double(gsub("(<|=|>)+", "", as.character(x)))
+ as.double(gsub("[<=>]+", "", as.character(x)))
}
#' @method as.integer mic
#' @export
#' @noRd
as.integer.mic <- function(x, ...) {
- as.integer(gsub("(<|=|>)+", "", as.character(x)))
+ as.integer(gsub("[<=>]+", "", as.character(x)))
}
#' @method as.numeric mic
#' @export
#' @noRd
as.numeric.mic <- function(x, ...) {
- as.numeric(gsub("(<|=|>)+", "", as.character(x)))
+ as.numeric(gsub("[<=>]+", "", as.character(x)))
}
#' @method droplevels mic
@@ -183,9 +183,13 @@ droplevels.mic <- function(x, exclude = ifelse(anyNA(levels(x)), NULL, NA), ...)
# will be exported using s3_register() in R/zzz.R
pillar_shaft.mic <- function(x, ...) {
- out <- trimws(format(x))
+ crude_numbers <- as.double(x)
+ operators <- gsub("[^<=>]+", "", as.character(x))
+ pasted <- trimws(paste0(operators, trimws(format(crude_numbers))))
+ out <- pasted
out[is.na(x)] <- font_na(NA)
- create_pillar_column(out, align = "right", min_width = 4)
+ out <- gsub("(<|=|>)", font_silver("\\1"), out)
+ create_pillar_column(out, align = "right", width = max(nchar(pasted)))
}
# will be exported using s3_register() in R/zzz.R
diff --git a/docs/404.html b/docs/404.html
index 003d67d6..e7be93b2 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index 99243f25..2872e249 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/docs/articles/EUCAST.html b/docs/articles/EUCAST.html
index 204ae865..2942e1b7 100644
--- a/docs/articles/EUCAST.html
+++ b/docs/articles/EUCAST.html
@@ -39,7 +39,7 @@
AMR (for R)
- 1.4.0.9032
+ 1.4.0.9034
diff --git a/docs/articles/MDR.html b/docs/articles/MDR.html
index 1b563f33..403d2f89 100644
--- a/docs/articles/MDR.html
+++ b/docs/articles/MDR.html
@@ -39,7 +39,7 @@
AMR (for R)
- 1.4.0.9032
+ 1.4.0.9034
@@ -318,19 +318,19 @@ Unique: 2
head(my_TB_data)
# rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin
-# 1 S S R R R R
-# 2 R S S R S S
-# 3 S R R R S S
-# 4 S S S S S S
-# 5 R S R S R S
-# 6 S S R S S S
+# 1 R I R S S S
+# 2 S R I R R S
+# 3 R S R R R R
+# 4 R S I R I S
+# 5 S R S R S R
+# 6 R R S R S S
# kanamycin
# 1 R
-# 2 R
-# 3 R
+# 2 S
+# 3 S
# 4 S
-# 5 S
-# 6 S
+# 5 R
+# 6 R
We can now add the interpretation of MDR-TB to our data set. You can use:
mdro(my_TB_data, guideline = "TB")
@@ -361,40 +361,40 @@ Unique: 5
1 |
Mono-resistant |
-3327 |
-66.54% |
-3327 |
-66.54% |
+3244 |
+64.88% |
+3244 |
+64.88% |
2 |
Negative |
-632 |
-12.64% |
-3959 |
-79.18% |
+644 |
+12.88% |
+3888 |
+77.76% |
3 |
Multi-drug-resistant |
-536 |
-10.72% |
-4495 |
-89.90% |
+613 |
+12.26% |
+4501 |
+90.02% |
4 |
Poly-resistant |
-277 |
-5.54% |
-4772 |
-95.44% |
+304 |
+6.08% |
+4805 |
+96.10% |
5 |
Extensively drug-resistant |
-228 |
-4.56% |
+195 |
+3.90% |
5000 |
100.00% |
diff --git a/docs/articles/index.html b/docs/articles/index.html
index c23a520e..be09514a 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/docs/authors.html b/docs/authors.html
index 9f81bf1f..b0dd7268 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/docs/index.html b/docs/index.html
index 11fa6196..e6e1c6fe 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -43,7 +43,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
@@ -214,109 +214,103 @@ Since you are one of our users, we would like to know how you use the package an
-
+
-With AMR
(for R), you’ll always have a knowledgeable microbiologist at your side!
-
-# AMR works great with dplyr, but it's not required or neccesary
-library(AMR)
-library(dplyr)
-
-example_isolates %>%
- mutate(mo = mo_fullname(mo)) %>%
- filter(mo_is_gram_positive()) %>%
- select(mo, carbapenems(), glycopeptides())
-#> NOTE: Using column 'mo' as input for mo_is_gram_positive()
-#> Selecting cephalosporins: 'CAZ' (ceftazidime), 'CRO' (ceftriaxone),
-#> 'CTX' (cefotaxime), 'CXM' (cefuroxime),
-#> 'CZO' (cefazolin), 'FEP' (cefepime),
-#> 'FOX' (cefoxitin)
-#> Selecting glycopeptides: 'TEC' (teicoplanin), 'VAN' (vancomycin)
-
With only having defined a filter on Gram-positive micro-organisms (mo_is_gram_positive()
) and a selection of two antibiotic groups (carbapenems()
and glycopeptides()
), the reference data about all bugs and drugs in the AMR
package make sure you get what you meant:
+
With
AMR
(for R), there’s always a knowledgeable microbiologist by your side!
+
# AMR works great with dplyr, but it's not required or neccesary
+library(AMR)
+library(dplyr)
+
+example_isolates %>%
+ mutate(mo = mo_fullname(mo)) %>%
+ filter(mo_is_gram_negative(), mo_is_intrinsic_resistant(ab = "cefotax")) %>%
+ select(mo, aminoglycosides(), carbapenems())
+#> NOTE: Using column 'mo' as input for mo_is_gram_negative()
+#> NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant()
+#> Selecting aminoglycosides: 'AMK' (amikacin), 'GEN' (gentamicin),
+ 'KAN' (kanamycin), 'TOB' (tobramycin)
+#> Selecting carbapenems: 'IPM' (imipenem), 'MEM' (meropenem)
+
With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (mo_is_gram_positive()
and mo_is_intrinsic_resistant()
) and a column selection on two antibiotic groups (aminoglycosides()
and carbapenems()
), the reference data about all microorganisms and all antibiotics in the AMR
package make sure you get what you meant:
-Enterococcus faecalis |
-R |
-R |
-R |
-R |
-R |
-R |
-R |
+Pseudomonas aeruginosa |
|
+I |
+R |
S |
+S |
+ |
-Enterococcus faecalis |
-R |
+Pseudomonas aeruginosa |
|
+I |
R |
-R |
-R |
-R |
-R |
- |
S |
+S |
+ |
-Enterococcus faecalis |
-R |
-R |
-R |
-R |
-R |
-R |
-R |
+Pseudomonas aeruginosa |
|
+I |
+R |
S |
+S |
+ |
-
-Streptococcus group B |
+Pseudomonas aeruginosa |
+S |
+S |
R |
S |
-S |
-S |
-S |
-S |
-S |
|
S |
-Staphylococcus epidermidis |
-R |
- |
- |
+Pseudomonas aeruginosa |
+S |
+S |
+R |
+S |
S |
- |
- |
- |
- |
S |
-Enterococcus faecium |
+Pseudomonas aeruginosa |
+S |
+S |
+R |
+S |
+S |
+S |
+
+
+Stenotrophomonas maltophilia |
R |
R |
R |
R |
R |
R |
+
+
+Pseudomonas aeruginosa |
+S |
+S |
R |
+S |
|
S |
@@ -462,7 +456,7 @@ Since you are one of our users, we would like to know how you use the package an
It analyses the data with convenient functions that use well-known methods.
-- Calculate the microbial susceptibility or resistance (and even co-resistance) with the
susceptibility()
and resistance()
functions, or be even more specific with the proportion_R()
, proportion_IR()
, proportion_I()
, proportion_SI()
and proportion_S()
functions. Similarly, the number of isolates can be determined with the count_resistant()
, count_susceptible()
and count_all()
functions. All these functions can be used with the dplyr
package (e.g. in conjunction with summarise()
)
+- Calculate the microbial susceptibility or resistance (and even co-resistance) with the
susceptibility()
and resistance()
functions, or be even more specific with the proportion_R()
, proportion_IR()
, proportion_I()
, proportion_SI()
and proportion_S()
functions. Similarly, the number of isolates can be determined with the count_resistant()
, count_susceptible()
and count_all()
functions. All these functions can be used with the dplyr
package (e.g. in conjunction with summarise()
)
- Plot AMR results with
geom_rsi()
, a function made for the ggplot2
package
- Predict antimicrobial resistance for the nextcoming years using logistic regression models with the
resistance_predict()
function
diff --git a/docs/news/index.html b/docs/news/index.html
index 9f63d7a8..6f134a7c 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
@@ -236,13 +236,13 @@
Source: NEWS.md
-
-
Header info is now available as a list, with the header
function
The parameter header
is now set to TRUE
at default, even for markdown
@@ -1442,20 +1443,20 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
Using portion_*
functions now throws a warning when total available isolate is below parameter minimum
Functions as.mo
, as.rsi
, as.mic
, as.atc
and freq
will not set package name as attribute anymore
-Frequency tables - freq()
:
+Frequency tables - freq()
:
Support for (un)selecting columns:
septic_patients %>%
- freq(hospital_id) %>%
+ freq(hospital_id) %>%
select(-count, -cum_count) # only get item, percent, cum_percent
Check for hms::is.hms
@@ -1473,7 +1474,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
Removed diacritics from all authors (columns microorganisms$ref
and microorganisms.old$ref
) to comply with CRAN policy to only allow ASCII characters
Fix for mo_property
not working properly
Fix for eucast_rules
where some Streptococci would become ceftazidime R in EUCAST rule 4.5
-Support for named vectors of class mo
, useful for top_freq()
+Support for named vectors of class mo
, useful for top_freq()
ggplot_rsi
and scale_y_percent
have breaks
parameter
AI improvements for as.mo
:
@@ -1634,12 +1635,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
Support for types (classes) list and matrix for freq
my_matrix = with(septic_patients, matrix(c(age, gender), ncol = 2))
-freq(my_matrix)
+freq(my_matrix)
For lists, subsetting is possible:
my_list = list(age = septic_patients$age, gender = septic_patients$gender)
-my_list %>% freq(age)
-my_list %>% freq(gender)
+my_list %>% freq(age)
+my_list %>% freq(gender)
@@ -1713,13 +1714,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
- A vignette to explain its usage
- Support for
rsi
(antimicrobial resistance) to use as input
-- Support for
table
to use as input: freq(table(x, y))
+ - Support for
table
to use as input: freq(table(x, y))
- Support for existing functions
hist
and plot
to use a frequency table as input: hist(freq(df$age))
- Support for
as.vector
, as.data.frame
, as_tibble
and format
-- Support for quasiquotation:
freq(mydata, mycolumn)
is the same as mydata %>% freq(mycolumn)
+ - Support for quasiquotation:
freq(mydata, mycolumn)
is the same as mydata %>% freq(mycolumn)
- Function
top_freq
function to return the top/below n items as vector
- Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index c800554d..7d381094 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: 2020-12-08T11:37Z
+last_built: 2020-12-09T08:37Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles
diff --git a/docs/reference/ab_from_text.html b/docs/reference/ab_from_text.html
index a2c01c9f..9905f47b 100644
--- a/docs/reference/ab_from_text.html
+++ b/docs/reference/ab_from_text.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.4.0.9032
+ 1.4.0.9034
@@ -323,7 +323,7 @@ The lifecycle of this function is maturing<
ab_from_text("500 mg amoxi po and 400mg cipro iv", type = "admin")
ab_from_text("500 mg amoxi po and 400mg cipro iv", collapse = ", ")
-
+# \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]])
@@ -346,6 +346,7 @@ The lifecycle of this function is maturing<
collapse = "|"))
}
+# }
diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html
index 12ff9aac..2af30a61 100644
--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html
index 0cca5e08..ed298d2d 100644
--- a/docs/reference/catalogue_of_life.html
+++ b/docs/reference/catalogue_of_life.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html
index c03542ff..eb421a81 100644
--- a/docs/reference/catalogue_of_life_version.html
+++ b/docs/reference/catalogue_of_life_version.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html
index d48572e3..d0fd46cb 100644
--- a/docs/reference/first_isolate.html
+++ b/docs/reference/first_isolate.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.4.0.9032
+ 1.4.0.9034
diff --git a/docs/reference/index.html b/docs/reference/index.html
index cb67584b..3b1a04a5 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/docs/reference/is_new_episode.html b/docs/reference/is_new_episode.html
index 3a94cf1e..8f624d66 100644
--- a/docs/reference/is_new_episode.html
+++ b/docs/reference/is_new_episode.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.4.0.9032
+ 1.4.0.9034
diff --git a/docs/reference/key_antibiotics.html b/docs/reference/key_antibiotics.html
index af60ae2b..a618d050 100644
--- a/docs/reference/key_antibiotics.html
+++ b/docs/reference/key_antibiotics.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.4.0.9032
+ 1.4.0.9034
diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html
index e107d19f..88d0900b 100644
--- a/docs/reference/mdro.html
+++ b/docs/reference/mdro.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html
index 75e7064b..ee6c71af 100644
--- a/docs/reference/microorganisms.codes.html
+++ b/docs/reference/microorganisms.codes.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html
index c2da73b3..716ee8de 100644
--- a/docs/reference/microorganisms.html
+++ b/docs/reference/microorganisms.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html
index a2d90fb0..e7e8e4bf 100644
--- a/docs/reference/microorganisms.old.html
+++ b/docs/reference/microorganisms.old.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html
index 1c8fe6f5..4da3b42a 100644
--- a/docs/reference/mo_property.html
+++ b/docs/reference/mo_property.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html
index 5dc74f06..67f4df64 100644
--- a/docs/reference/resistance_predict.html
+++ b/docs/reference/resistance_predict.html
@@ -82,7 +82,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/docs/survey.html b/docs/survey.html
index 2e924c96..52dc6730 100644
--- a/docs/survey.html
+++ b/docs/survey.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9033
+ 1.4.0.9034
diff --git a/index.md b/index.md
index 7e8860dc..293cc20a 100644
--- a/index.md
+++ b/index.md
@@ -22,7 +22,7 @@ This package is [fully independent of any other R package](https://en.wikipedia.
Since its first public release in early 2018, this package has been downloaded from 135 countries. Click the map to enlarge.
-##### With `AMR` (for R), you'll always have a knowledgeable microbiologist at your side!
+##### With `AMR` (for R), there's always a knowledgeable microbiologist by your side!
```r
# AMR works great with dplyr, but it's not required or neccesary
@@ -31,26 +31,27 @@ library(dplyr)
example_isolates %>%
mutate(mo = mo_fullname(mo)) %>%
- filter(mo_is_gram_positive()) %>%
- select(mo, carbapenems(), glycopeptides())
-#> NOTE: Using column 'mo' as input for mo_is_gram_positive()
-#> Selecting cephalosporins: 'CAZ' (ceftazidime), 'CRO' (ceftriaxone),
-#> 'CTX' (cefotaxime), 'CXM' (cefuroxime),
-#> 'CZO' (cefazolin), 'FEP' (cefepime),
-#> 'FOX' (cefoxitin)
-#> Selecting glycopeptides: 'TEC' (teicoplanin), 'VAN' (vancomycin)
+ filter(mo_is_gram_negative(), mo_is_intrinsic_resistant(ab = "cefotax")) %>%
+ select(mo, aminoglycosides(), carbapenems())
+#> NOTE: Using column 'mo' as input for mo_is_gram_negative()
+#> NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant()
+#> Selecting aminoglycosides: 'AMK' (amikacin), 'GEN' (gentamicin),
+ 'KAN' (kanamycin), 'TOB' (tobramycin)
+#> Selecting carbapenems: 'IPM' (imipenem), 'MEM' (meropenem)
```
-With only having defined a filter on Gram-positive micro-organisms (`mo_is_gram_positive()`) and a selection of two antibiotic groups (`carbapenems()` and `glycopeptides()`), the reference data about [all bugs](./reference/microorganisms.html) and [drugs](./reference/antibiotics.html) in the `AMR` package make sure you get what you meant:
+With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (`mo_is_gram_positive()` 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:
-| mo | CAZ | CRO | CTX | CXM | CZO | FEP | FOX | TEC | VAN |
-|:-----------------------------|:---:|:---:|:---:|:---:|:---:|:---:|:---:|:---:|:---:|
-| *Enterococcus faecalis* | R | R | R | R | R | R | R | | S |
-| *Enterococcus faecalis* | R | | R | R | R | R | R | | S |
-| *Enterococcus faecalis* | R | R | R | R | R | R | R | | S |
-| *Streptococcus* group B | R | S | S | S | S | S | S | | S |
-| *Staphylococcus epidermidis* | R | | | S | | | | | S |
-| *Enterococcus faecium* | R | R | R | R | R | R | R | | S |
+| mo | AMK | GEN | KAN | TOB | IPM | MEM |
+|:------------------------------|:---------:|:---------:|:---------:|:---------:|:---------:|:---------:|
+|*Pseudomonas aeruginosa* | | I | R | S | S | |
+|*Pseudomonas aeruginosa* | | I | R | S | S | |
+|*Pseudomonas aeruginosa* | | I | R | S | S | |
+|*Pseudomonas aeruginosa* | S | S | R | S | | S |
+|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
+|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
+|*Stenotrophomonas maltophilia* | R | R | R | R | R | R |
+|*Pseudomonas aeruginosa* | S | S | R | S | | S |