new EUCAST rules: clinical breakpoints

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.4.0.9003
-Date: 2018-10-16
+Version: 0.4.0.9004
+Date: 2018-10-17
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(
@@ -47,6 +47,7 @@ Depends:
 Imports:
     backports,
     curl,
+    crayon (>= 1.3.0),
     data.table (>= 1.9.0),
     dplyr (>= 0.7.0),
     hms,

NAMESPACE

@@ -161,6 +161,13 @@ exportMethods(skewness.default)
 exportMethods(skewness.matrix)
 exportMethods(summary.mic)
 exportMethods(summary.rsi)
+importFrom(crayon,bgGreen)
+importFrom(crayon,bgRed)
+importFrom(crayon,bgYellow)
+importFrom(crayon,black)
+importFrom(crayon,blue)
+importFrom(crayon,bold)
+importFrom(crayon,green)
 importFrom(curl,nslookup)
 importFrom(data.table,as.data.table)
 importFrom(data.table,data.table)

NEWS.md

@@ -4,13 +4,21 @@
 * Function `count_all` to get all available isolates (that like all `portion_*` and `count_*` functions also supports `summarise` and `group_by`), the old `n_rsi` is now an alias of `count_all`
 
 #### Changed
+* Big changes to the `EUCAST_rules` function:
+  * It now also applies rules from the EUCAST 'Breakpoint tables for bacteria', version 8.1, 2018, http://www.eucast.org/clinical_breakpoints/ (see Source of the function)
+  * There's better error handling when rules cannot be applied (i.e. new values could not be inserted)
+  * A new `verbose` parameter can be set to `TRUE` to get very specific messages about which columns and rows were affected
+  * The amount of affected values will now only be measured once per row/column combination
+  * Data set `septic_patients` now reflects these changes
 * Added parameter `combine_IR` (TRUE/FALSE) to functions `portion_df` and `count_df`, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)
 * Fix for `portion_*(..., as_percent = TRUE)` when minimal amount of isolates would not be met
 * Using `portion_*` functions now throws a warning when total available isolate is below parameter `minimum`
-* `as.mo` will not set package name as attribute anymore
+* Functions `as.mo`, `as.rsi` and `as.mic` will not set package name as attribute anymore
+* Data set `septic_patients` is now a `data.frame`, not a tibble anymore
 * Check for `hms::is.hms` in frequency tables
 * 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 class `difftime` in frequency tables
 * Support for named vectors of class `mo`, useful for `top_freq()`
 * AI improvements for `as.mo`:
@@ -22,6 +30,7 @@
 * In `g.test`, when `sum(x)` is below 1000, suggest Fisher's Exact Test
 
 #### Other
+* New dependency on package `crayon`, to support formatted text in the console
 * Updated vignettes to comply with README
 
 

R/data.R

@@ -186,7 +186,7 @@
 #' Data set with 2000 blood culture isolates of septic patients
 #'
 #' An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This \code{data.frame} can be used to practice AMR analysis. For examples, press F1.
-#' @format A \code{\link{tibble}} with 2,000 observations and 49 variables:
+#' @format A \code{\link{data.frame}} with 2,000 observations and 49 variables:
 #' \describe{
 #'   \item{\code{date}}{date of receipt at the laboratory}
 #'   \item{\code{hospital_id}}{ID of the hospital, from A to D}
@@ -199,7 +199,6 @@
 #'   \item{\code{mo}}{ID of microorganism, see \code{\link{microorganisms}}}
 #'   \item{\code{peni:rifa}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{abname}}}
 #' }
-# source MOLIS (LIS of Certe) - \url{https://www.certe.nl}
 #' @examples
 #' # ----------- #
 #' # PREPARATION #

R/mic.R

@@ -22,7 +22,7 @@
 #' @rdname as.mic
 #' @param x vector
 #' @param na.rm a logical indicating whether missing values should be removed
-#' @return Ordered factor with new class \code{mic} and new attribute \code{package}
+#' @return Ordered factor with new class \code{mic}
 #' @keywords mic
 #' @export
 #' @importFrom dplyr %>%
@@ -148,11 +148,8 @@ as.mic <- function(x, na.rm = FALSE) {
               list_missing, call. = FALSE)
     }
 
-    x <- factor(x = x,
-                levels = lvls,
-                ordered = TRUE)
+    x <- factor(x, levels = lvls, ordered = TRUE)
     class(x) <- c('mic', 'ordered', 'factor')
-    attr(x, 'package') <- 'AMR'
     x
   }
 }

R/rsi.R

@@ -22,7 +22,7 @@
 #' @rdname as.rsi
 #' @param x vector
 #' @details The function \code{is.rsi.eligible} returns \code{TRUE} when a columns contains only valid antimicrobial interpretations (S and/or I and/or R), and \code{FALSE} otherwise.
-#' @return Ordered factor with new class \code{rsi} and new attribute \code{package}
+#' @return Ordered factor with new class \code{rsi}
 #' @keywords rsi
 #' @export
 #' @importFrom dplyr %>%
@@ -81,9 +81,8 @@ as.rsi <- function(x) {
               list_missing, call. = FALSE)
     }
 
-    x <- x %>% factor(levels = c("S", "I", "R"), ordered = TRUE)
+    x <- factor(x, levels = c("S", "I", "R"), ordered = TRUE)
     class(x) <- c('rsi', 'ordered', 'factor')
-    attr(x, 'package') <- 'AMR'
     x
   }
 }

README.md

@@ -202,7 +202,7 @@ Adjust it with any parameter you know from the `ggplot2` package:
 septic_patients %>%
   select(amox, nitr, fosf, trim, cipr) %>%
   ggplot_rsi(datalabels = FALSE, 
-             width = 0.5, colour = "black", size = 1, linetype = 2, alpha = 0.25)
+             width = 0.5, colour = "purple", size = 1, linetype = 2, alpha = 0.5)
 ```
 
 ![example_3_rsi](man/figures/rsi_example3.png)
@@ -225,6 +225,41 @@ septic_patients %>%
 
 You could use this to group on anything in your plots: Gram stain, age (group), genus, geographic location, et cetera.
 
+Is there a significant difference between hospital A and D when it comes to Fosfomycin?
+```r
+check_A_and_D <- septic_patients %>%
+  filter(hospital_id %in% c("A", "D")) %>% # filter on only hospitals A and D
+  select(hospital_id, fosf) %>%            # select the hospitals and fosfomycin
+  group_by(hospital_id) %>%
+  count_df(combine_IR = TRUE) %>%          # count all isolates per group (hospital_id)
+  tidyr::spread(hospital_id, Value) %>%    # transform output so A and D are columns
+  select(A, D) %>%                         # and select these only
+  as.matrix()                              # transform to good old matrix for fisher.test
+
+check_A_and_D
+#       A  D
+# [1,] 24 33
+# [2,] 25 77
+```
+
+Total sum is lower than 1,000 so we'd prefer a [Fisher's exact test](https://en.wikipedia.org/wiki/Fisher%27s_exact_test), not a [*G*-test](https://en.wikipedia.org/wiki/G-test) (or its formerly used equivalent, the famous [Chi<sup>2</sup> test](https://en.wikipedia.org/wiki/Chi-squared_test)):
+```
+fisher.test(check_A_and_D)
+# 
+# 	Fisher's Exact Test for Count Data
+# 
+# data:  .
+# p-value = 0.03104
+# alternative hypothesis: true odds ratio is not equal to 1
+# 95 percent confidence interval:
+#  1.054283 4.735995
+# sample estimates:
+# odds ratio 
+#   2.228006 
+```
+
+Well, there you go!
+
 #### MIC
 
 ```r

man/EUCAST.Rd

@@ -3,14 +3,23 @@
 \name{EUCAST_rules}
 \alias{EUCAST_rules}
 \alias{interpretive_reading}
-\title{EUCAST expert rules}
+\title{EUCAST rules}
 \source{
-EUCAST Expert Rules Version 2.0: \cr
-  Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60. \cr
-  \url{https://doi.org/10.1111/j.1469-0691.2011.03703.x} \cr
-  \cr
-  EUCAST Expert Rules Version 3.1 (Intrinsic Resistance and Exceptional Phenotypes Tables): \cr
-  \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
+\itemize{
+    \item{
+      EUCAST Expert Rules. Version 2.0, 2012. \cr
+      Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60. \cr
+      \url{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
+    }
+    \item{
+      EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016.  \cr
+      \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
+    }
+    \item{
+      EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 8.1, 2018. \cr
+      \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx}
+    }
+  }
 }
 \usage{
 EUCAST_rules(tbl, col_mo = "mo", info = TRUE, amcl = "amcl",
@@ -25,11 +34,11 @@ EUCAST_rules(tbl, col_mo = "mo", info = TRUE, amcl = "amcl",
   line = "line", mero = "mero", mezl = "mezl", mino = "mino",
   moxi = "moxi", nali = "nali", neom = "neom", neti = "neti",
   nitr = "nitr", norf = "norf", novo = "novo", oflo = "oflo",
-  peni = "peni", pita = "pita", poly = "poly", pris = "pris",
-  qida = "qida", rifa = "rifa", roxi = "roxi", siso = "siso",
-  teic = "teic", tetr = "tetr", tica = "tica", tige = "tige",
-  tobr = "tobr", trim = "trim", trsu = "trsu", vanc = "vanc",
-  col_bactid = "bactid")
+  oxac = "oxac", peni = "peni", pita = "pita", poly = "poly",
+  pris = "pris", qida = "qida", rifa = "rifa", roxi = "roxi",
+  siso = "siso", teic = "teic", tetr = "tetr", tica = "tica",
+  tige = "tige", tobr = "tobr", trim = "trim", trsu = "trsu",
+  vanc = "vanc", col_bactid = "bactid", verbose = FALSE)
 
 interpretive_reading(...)
 }
@@ -40,23 +49,25 @@ interpretive_reading(...)
 
 \item{info}{print progress}
 
-\item{amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, peni, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
+\item{amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
 
 \item{col_bactid}{Deprecated. Use \code{col_mo} instead.}
 
+\item{verbose}{a logical to indicate whether extensive info should be printed to the console about which rows and columns are effected with their old and new values}
+
 \item{...}{parameters that are passed on to \code{EUCAST_rules}}
 }
 \value{
 table with edited variables of antibiotics.
 }
 \description{
-Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
+Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
 }
 \section{Antibiotics}{
 
 Abbrevations of the column containing antibiotics:
 
- \strong{amcl}: amoxicillin and beta-lactamase inhibitor (\emph{J01CR02}),
+ \strong{amcl}: amoxicillin+clavulanic acid (\emph{J01CR02}),
  \strong{amik}: amikacin (\emph{J01GB06}),
  \strong{amox}: amoxicillin (\emph{J01CA04}),
  \strong{ampi}: ampicillin (\emph{J01CA01}),
@@ -85,7 +96,7 @@ Abbrevations of the column containing antibiotics:
  \strong{fosf}: fosfomycin (\emph{J01XX01}),
  \strong{fusi}: fusidic acid (\emph{J01XC01}),
  \strong{gent}: gentamicin (\emph{J01GB03}),
- \strong{imip}: imipenem and cilastatin (\emph{J01DH51}),
+ \strong{imip}: imipenem (\emph{J01DH51}),
  \strong{kana}: kanamycin (\emph{J01GB04}),
  \strong{levo}: levofloxacin (\emph{J01MA12}),
  \strong{linc}: lincomycin (\emph{J01FF02}),
@@ -101,8 +112,8 @@ Abbrevations of the column containing antibiotics:
  \strong{norf}: norfloxacin (\emph{J01MA06}),
  \strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
  \strong{oflo}: ofloxacin (\emph{J01MA01}),
- \strong{peni}: penicillins, combinations with other antibacterials (\emph{J01RA01}),
- \strong{pita}: piperacillin and beta-lactamase inhibitor (\emph{J01CR05}),
+ \strong{peni}: penicillin (\emph{J01RA01}),
+ \strong{pita}: piperacillin+tazobactam (\emph{J01CR05}),
  \strong{poly}: polymyxin B (\emph{J01XB02}),
  \strong{pris}: pristinamycin (\emph{J01FG01}),
  \strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}),

man/MDRO.Rd

@@ -175,7 +175,7 @@ When \code{country} will be left blank, guidelines will be taken from EUCAST Exp
 
 Abbrevations of the column containing antibiotics:
 
- \strong{amcl}: amoxicillin and beta-lactamase inhibitor (\emph{J01CR02}),
+ \strong{amcl}: amoxicillin+clavulanic acid (\emph{J01CR02}),
  \strong{amik}: amikacin (\emph{J01GB06}),
  \strong{amox}: amoxicillin (\emph{J01CA04}),
  \strong{ampi}: ampicillin (\emph{J01CA01}),
@@ -204,7 +204,7 @@ Abbrevations of the column containing antibiotics:
  \strong{fosf}: fosfomycin (\emph{J01XX01}),
  \strong{fusi}: fusidic acid (\emph{J01XC01}),
  \strong{gent}: gentamicin (\emph{J01GB03}),
- \strong{imip}: imipenem and cilastatin (\emph{J01DH51}),
+ \strong{imip}: imipenem (\emph{J01DH51}),
  \strong{kana}: kanamycin (\emph{J01GB04}),
  \strong{levo}: levofloxacin (\emph{J01MA12}),
  \strong{linc}: lincomycin (\emph{J01FF02}),
@@ -220,8 +220,8 @@ Abbrevations of the column containing antibiotics:
  \strong{norf}: norfloxacin (\emph{J01MA06}),
  \strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
  \strong{oflo}: ofloxacin (\emph{J01MA01}),
- \strong{peni}: penicillins, combinations with other antibacterials (\emph{J01RA01}),
- \strong{pita}: piperacillin and beta-lactamase inhibitor (\emph{J01CR05}),
+ \strong{peni}: penicillin (\emph{J01RA01}),
+ \strong{pita}: piperacillin+tazobactam (\emph{J01CR05}),
  \strong{poly}: polymyxin B (\emph{J01XB02}),
  \strong{pris}: pristinamycin (\emph{J01FG01}),
  \strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}),

man/as.mic.Rd

@@ -15,7 +15,7 @@ is.mic(x)
 \item{na.rm}{a logical indicating whether missing values should be removed}
 }
 \value{
-Ordered factor with new class \code{mic} and new attribute \code{package}
+Ordered factor with new class \code{mic}
 }
 \description{
 This transforms a vector to a new class \code{mic}, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as \code{NA} with a warning.

man/as.rsi.Rd

@@ -16,7 +16,7 @@ is.rsi.eligible(x)
 \item{x}{vector}
 }
 \value{
-Ordered factor with new class \code{rsi} and new attribute \code{package}
+Ordered factor with new class \code{rsi}
 }
 \description{
 This transforms a vector to a new class \code{rsi}, which is an ordered factor with levels \code{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning.

man/septic_patients.Rd

@@ -4,7 +4,7 @@
 \name{septic_patients}
 \alias{septic_patients}
 \title{Data set with 2000 blood culture isolates of septic patients}
-\format{A \code{\link{tibble}} with 2,000 observations and 49 variables:
+\format{A \code{\link{data.frame}} with 2,000 observations and 49 variables:
 \describe{
   \item{\code{date}}{date of receipt at the laboratory}
   \item{\code{hospital_id}}{ID of the hospital, from A to D}

tests/testthat/test-count.R

@@ -2,18 +2,18 @@ context("count.R")
 
 test_that("counts work", {
   # amox resistance in `septic_patients`
-  expect_equal(count_R(septic_patients$amox), 662)
+  expect_equal(count_R(septic_patients$amox), 683)
   expect_equal(count_I(septic_patients$amox), 3)
-  expect_equal(count_S(septic_patients$amox), 335)
+  expect_equal(count_S(septic_patients$amox), 486)
   expect_equal(count_R(septic_patients$amox) + count_I(septic_patients$amox),
                count_IR(septic_patients$amox))
   expect_equal(count_S(septic_patients$amox) + count_I(septic_patients$amox),
                count_SI(septic_patients$amox))
 
   library(dplyr)
-  expect_equal(septic_patients %>% count_S(amcl), 1057)
-  expect_equal(septic_patients %>% count_S(amcl, gent), 1396)
-  expect_equal(septic_patients %>% count_all(amcl, gent), 1517)
+  expect_equal(septic_patients %>% count_S(amcl), 1291)
+  expect_equal(septic_patients %>% count_S(amcl, gent), 1609)
+  expect_equal(septic_patients %>% count_all(amcl, gent), 1747)
   expect_identical(septic_patients %>% count_all(amcl, gent),
                    septic_patients %>% count_S(amcl, gent) +
                      septic_patients %>% count_IR(amcl, gent))

tests/testthat/test-eucast.R

@@ -8,30 +8,26 @@ test_that("EUCAST rules work", {
   expect_identical(colnames(septic_patients),
                    colnames(suppressWarnings(EUCAST_rules(septic_patients))))
 
-  a <- data.frame(mo =
-                    c("KLEPNE",  # Klebsiella pneumoniae
-                      "PSEAER",  # Pseudomonas aeruginosa
-                      "ENTAER"), # Enterobacter aerogenes
+  a <- data.frame(mo = c("KLEPNE",  # Klebsiella pneumoniae
+                         "PSEAER",  # Pseudomonas aeruginosa
+                         "ENTAER"), # Enterobacter aerogenes
                   amox = "-",           # Amoxicillin
                   stringsAsFactors = FALSE)
-  b <- data.frame(mo =
-                    c("KLEPNE",  # Klebsiella pneumoniae
-                      "PSEAER",  # Pseudomonas aeruginosa
-                      "ENTAER"), # Enterobacter aerogenes
-                  amox = "R",           # Amoxicillin
+  b <- data.frame(mo = c("KLEPNE",  # Klebsiella pneumoniae
+                         "PSEAER",  # Pseudomonas aeruginosa
+                         "ENTAER"), # Enterobacter aerogenes
+                  amox = "R",       # Amoxicillin
                   stringsAsFactors = FALSE)
   expect_identical(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
   expect_identical(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
 
-  a <- data.frame(mo =
-                    c("STAAUR",  # Staphylococcus aureus
-                      "STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
-                  coli = "-",           # Colistin
+  a <- data.frame(mo = c("STAAUR",  # Staphylococcus aureus
+                         "STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
+                  coli = "-",       # Colistin
                   stringsAsFactors = FALSE)
-  b <- data.frame(mo =
-                    c("STAAUR",  # Staphylococcus aureus
-                      "STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
-                  coli = "R",           # Colistin
+  b <- data.frame(mo = c("STAAUR",  # Staphylococcus aureus
+                         "STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
+                  coli = "R",       # Colistin
                   stringsAsFactors = FALSE)
   expect_equal(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
 
@@ -48,17 +44,35 @@ test_that("EUCAST rules work", {
       unique() %>%
       as.character()),
     "R")
+
   # azit and clar must be equal to eryt
-  expect_equal(suppressWarnings(
+  a <- suppressWarnings(
     septic_patients %>%
-      mutate(azit = as.rsi("R"),
-             clar = as.rsi("R")) %>%
+      transmute(mo,
+                eryt,
+                azit = as.rsi("R"),
+                clar = as.rsi("R")) %>%
       EUCAST_rules(col_mo = "mo") %>%
-      pull(clar)),
-    suppressWarnings(
-      septic_patients %>%
-        EUCAST_rules(col_mo = "mo") %>%
-        left_join_microorganisms() %>%
-        pull(eryt)))
+      pull(clar))
+  b <-   suppressWarnings(
+    septic_patients %>%
+      select(mo, eryt) %>%
+      EUCAST_rules(col_mo = "mo") %>%
+      pull(eryt))
+
+  expect_identical(a[!is.na(b)],
+                   b[!is.na(b)])
+
+  # amox is inferred by benzylpenicillin in Kingella kingae
+  expect_equal(
+    as.list(EUCAST_rules(
+      data.frame(mo = as.mo("Kingella kingae"),
+                 peni = "S",
+                 amox = "-",
+                 stringsAsFactors = FALSE)
+      , info = FALSE))$amox,
+    "S")
+
+  expect_message(suppressWarnings(EUCAST_rules(septic_patients, verbose = TRUE)))
 
 })

tests/testthat/test-portion.R

@@ -2,8 +2,8 @@ context("portion.R")
 
 test_that("portions works", {
   # amox resistance in `septic_patients`
-  expect_equal(portion_R(septic_patients$amox), 0.662, tolerance = 0.0001)
-  expect_equal(portion_I(septic_patients$amox), 0.003, tolerance = 0.0001)
+  expect_equal(portion_R(septic_patients$amox), 0.5827645, tolerance = 0.0001)
+  expect_equal(portion_I(septic_patients$amox), 0.0025597, tolerance = 0.0001)
   expect_equal(1 - portion_R(septic_patients$amox) - portion_I(septic_patients$amox),
                portion_S(septic_patients$amox))
   expect_equal(portion_R(septic_patients$amox) + portion_I(septic_patients$amox),
@@ -12,17 +12,17 @@ test_that("portions works", {
                portion_SI(septic_patients$amox))
 
   expect_equal(septic_patients %>% portion_S(amcl),
-               0.6706853,
+               0.7062363,
                tolerance = 0.001)
   expect_equal(septic_patients %>% portion_S(amcl, gent),
-               0.9202373,
+               0.9210074,
                tolerance = 0.001)
 
   # amcl+genta susceptibility around 92.1%
   expect_equal(suppressWarnings(rsi(septic_patients$amcl,
                                     septic_patients$gent,
                                     interpretation = "S")),
-               0.9202373,
+               0.9210074,
                tolerance = 0.000001)
 
   # percentages
@@ -57,7 +57,7 @@ test_that("portions works", {
                                     septic_patients$gent)))
   expect_equal(suppressWarnings(n_rsi(as.character(septic_patients$amcl,
                                                    septic_patients$gent))),
-               1576)
+               1828)
 
   # check for errors
   expect_error(portion_IR("test", minimum = "test"))
@@ -83,16 +83,16 @@ test_that("portions works", {
 })
 
 test_that("old rsi works", {
-  # amox resistance in `septic_patients` should be around 66.33%
-  expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.665, tolerance = 0.0001)
-  expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.665, tolerance = 0.0001)
+  # amox resistance in `septic_patients` should be around 58.53%
+  expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.5853, tolerance = 0.0001)
+  expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.5853, tolerance = 0.0001)
 
   # pita+genta susceptibility around 98.09%
   expect_equal(suppressWarnings(rsi(septic_patients$pita,
                                     septic_patients$gent,
                                     interpretation = "S",
                                     info = TRUE)),
-               0.9540412,
+               0.9498886,
                tolerance = 0.0001)
 
   # count of cases