(v1.5.0.9003) verbose output of mdro()

2021-01-15 22:44:52 +01:00 · 2021-01-15 22:44:52 +01:00 · 7ebc534ccd
parent 6745f3fb17
commit 7ebc534ccd
35 changed files with 112 additions and 95 deletions
--- a/4
+++ b/4
@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.5.0.9002
-Date: 2021-01-14
+Version: 1.5.0.9003
+Date: 2021-01-15
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
    person(role = c("aut", "cre"), 
--- a/NEWS.md
+++ b/NEWS.md
@ -1,5 +1,5 @@
-# AMR 1.5.0.9002
-## <small>Last updated: 14 January 2021</small>
+# AMR 1.5.0.9003
+## <small>Last updated: 15 January 2021</small>

 ### New
 * Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
@ -31,6 +31,7 @@
 * Updated the data set `microorganisms.codes` (which contains popular LIS and WHONET codes for microorganisms) for some species of *Mycobacterium* that previously incorrectly returned *M. africanum*
 * Added Pretomanid (PMD, J04AK08) to the `antibiotics` data set
 * WHONET code `"PNV"` will now correctly be interpreted as `PHN`, the antibiotic code for phenoxymethylpenicillin ('peni V')
+* Fix for verbose output of `mdro(..., verbose = TRUE)` for German guideline (3MGRN and 4MGRN) and *P. aeruginosa* in Dutch guideline (BRMO)


 # AMR 1.5.0
--- a/R/bug_drug_combinations.R
+++ b/R/bug_drug_combinations.R
@ -69,8 +69,10 @@ bug_drug_combinations <- function(x,
  # -- mo
  if (is.null(col_mo)) {
    col_mo <- search_type_in_df(x = x, type = "mo")
+    stop_if(is.null(col_mo), "`col_mo` must be set")
+  } else {
+    stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
  }
-  stop_if(is.null(col_mo), "`col_mo` must be set")
  
  x_class <- class(x)
  x <- as.data.frame(x, stringsAsFactors = FALSE)
--- a/R/eucast_rules.R
+++ b/R/eucast_rules.R
@ -205,8 +205,10 @@ eucast_rules <- function(x,
  # -- mo
  if (is.null(col_mo)) {
    col_mo <- search_type_in_df(x = x, type = "mo", info = info)
+    stop_if(is.null(col_mo), "`col_mo` must be set")
+  } else {
+    stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
  }
-  stop_if(is.null(col_mo), "`col_mo` must be set")
  
  decimal.mark <- getOption("OutDec")
  big.mark <- ifelse(decimal.mark != ",", ",", ".")
--- a/R/first_isolate.R
+++ b/R/first_isolate.R
@ -202,7 +202,6 @@ first_isolate <- function(x,
  if (is.null(col_mo)) {
    col_mo <- search_type_in_df(x = x, type = "mo")
    stop_if(is.null(col_mo), "`col_mo` must be set")
-    stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
  }
  
  # -- date
--- a/R/guess_ab_col.R
+++ b/R/guess_ab_col.R
@ -122,7 +122,7 @@ get_column_abx <- function(x,
  meet_criteria(info, allow_class = "logical", has_length = 1)
  
  if (info == TRUE) {
-    message_("Auto-guessing columns suitable for analysis", appendLF = FALSE)
+    message_("Auto-guessing columns suitable for analysis", appendLF = FALSE, as_note = FALSE)
  }
  
  x <- as.data.frame(x, stringsAsFactors = FALSE)
--- a/R/key_antibiotics.R
+++ b/R/key_antibiotics.R
@ -168,8 +168,10 @@ key_antibiotics <- function(x,
  # -- mo
  if (is.null(col_mo)) {
    col_mo <- search_type_in_df(x = x, type = "mo")
+    stop_if(is.null(col_mo), "`col_mo` must be set")
+  } else {
+    stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
  }
-  stop_if(is.null(col_mo), "`col_mo` must be set")
  
  # check columns
  col.list <- c(universal_1, universal_2, universal_3, universal_4, universal_5, universal_6,
--- a/R/mdro.R
+++ b/R/mdro.R
@ -138,9 +138,6 @@ mdro <- function(x,
    }
  }
  
-  stop_ifnot(is.data.frame(x), "`x` must be a data.frame")
-  stop_if(any(dim(x) == 0), "`x` must contain rows and columns")
-  
  # force regular data.frame, not a tibble or data.table
  x <- as.data.frame(x, stringsAsFactors = FALSE)
  
@ -154,8 +151,8 @@ mdro <- function(x,
    warning_("Using `country` is deprecated, use `guideline` instead. Please see ?mdro.", call = FALSE)
    guideline <- list(...)$country
  }
-
-    guideline.bak <- guideline
+  
+  guideline.bak <- guideline
  guideline <- tolower(gsub("[^a-zA-Z0-9.]+", "", guideline))
  if (is.null(guideline)) {
    # default to the paper by Magiorakos et al. (2012)
@ -182,9 +179,9 @@ mdro <- function(x,
  }
  if (is.null(col_mo) & guideline$code == "tb") {
    message_("No column found as input for `col_mo`, ",
-             font_bold("assuming all records contain", font_italic("Mycobacterium tuberculosis.")))
-             x$mo <- as.mo("Mycobacterium tuberculosis")
-             col_mo <- "mo"
+             font_bold(paste0("assuming all records contain", font_italic("Mycobacterium tuberculosis"), ".")))
+    x$mo <- as.mo("Mycobacterium tuberculosis") # consider overkill at all times: MO_lookup[which(MO_lookup$fullname == "Mycobacterium tuberculosis"), "mo", drop = TRUE]
+    col_mo <- "mo"
  }
  stop_if(is.null(col_mo), "`col_mo` must be set")
  stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
@ -873,7 +870,9 @@ mdro <- function(x,
    # MDR (=2): >=3 classes affected
    x[which(x$classes_affected >= 3), "MDRO"] <- 2
    if (verbose == TRUE) {
-      x[which(x$classes_affected >= 3), "reason"] <- paste0("at least 3 classes contain R or I: ", x$classes_affected[which(x$classes_affected >= 3)],
+      x[which(x$classes_affected >= 3), "reason"] <- paste0("at least 3 classes contain R",
+                                                            ifelse(!isTRUE(combine_SI), " or I", ""), ": ",
+                                                            x$classes_affected[which(x$classes_affected >= 3)],
                                                            " out of ", x$classes_available[which(x$classes_affected >= 3)], " available classes")
    }
    
@ -1044,49 +1043,55 @@ mdro <- function(x,
    # Germany -----------------------------------------------------------------
    CTX_or_CAZ <- CTX %or% CAZ
    IPM_or_MEM <- IPM %or% MEM
-    x$missing <- NA_character_
-    if (is.na(PIP)) PIP <- "missing"
-    if (is.na(CTX_or_CAZ)) CTX_or_CAZ <- "missing"
-    if (is.na(IPM_or_MEM)) IPM_or_MEM <- "missing"
-    if (is.na(IPM)) IPM <- "missing"
-    if (is.na(MEM)) MEM <- "missing"
-    if (is.na(CIP)) CIP <- "missing"
    
    # Table 1
-    x[which((x$order == "Enterobacterales" |  # following in fact the old Enterobacteriaceae classification
-               (x$genus == "Acinetobacter" & x$species ==  "baumannii")) &
-              x[, PIP] == "R" &
-              x[, CTX_or_CAZ] == "R" &
-              x[, IPM_or_MEM] == "S" &
-              x[, CIP] == "R"),
-      "MDRO"] <- 2 # 2 = 3MRGN
+    trans_tbl(2, # 3MRGN
+              which((x$order == "Enterobacterales" |  # following in fact the old Enterobacteriaceae classification
+                       (x$genus == "Acinetobacter" & x$species ==  "baumannii")) &
+                      x[, PIP, drop = TRUE] == "R" &
+                      x[, CTX_or_CAZ, drop = TRUE] == "R" &
+                      x[, IPM_or_MEM, drop = TRUE] == "S" &
+                      x[, CIP, drop = TRUE] == "R"),
+              c(PIP, CTX, CAZ, IPM, MEM, CIP),
+              "any")
    
-    x[which((x$order == "Enterobacterales" |  # following in fact the old Enterobacteriaceae classification
-               (x$genus == "Acinetobacter" & x$species ==  "baumannii")) &
-              x[, PIP] == "R" &
-              x[, CTX_or_CAZ] == "R" &
-              x[, IPM_or_MEM] == "R" &
-              x[, CIP] == "R"),
-      "MDRO"] <- 3 # 3 = 4MRGN, overwrites 3MRGN if applicable
+    trans_tbl(3, # 4MRGN, overwrites 3MRGN if applicable
+              which((x$order == "Enterobacterales" |  # following in fact the old Enterobacteriaceae classification
+                       (x$genus == "Acinetobacter" & x$species ==  "baumannii")) &
+                      x[, PIP, drop = TRUE] == "R" &
+                      x[, CTX_or_CAZ, drop = TRUE] == "R" &
+                      x[, IPM_or_MEM, drop = TRUE] == "R" &
+                      x[, CIP, drop = TRUE] == "R"),
+              c(PIP, CTX, CAZ, IPM, MEM, CIP),
+              "any")
    
-    x[which((x$order == "Enterobacterales" |  # following in fact the old Enterobacteriaceae classification
-               (x$genus == "Acinetobacter" & x$species ==  "baumannii")) &
-              x[, IPM] == "R" | x[, MEM] == "R"),
-      "MDRO"] <- 3 # 3 = 4MRGN, always when imipenem or meropenem is R
+    trans_tbl(3, # 4MRGN, overwrites 3MRGN if applicable
+              which((x$order == "Enterobacterales" |  # following in fact the old Enterobacteriaceae classification
+                       (x$genus == "Acinetobacter" & x$species ==  "baumannii")) &
+                      (x[, IPM, drop = TRUE] == "R" | x[, MEM, drop = TRUE] == "R")),
+              c(IPM, MEM),
+              "any")
    
-    x[which(x$genus == "Pseudomonas" & x$species == "aeruginosa" &
-              (x[, PIP] == "S") +
-              (x[, CTX_or_CAZ] == "S") +
-              (x[, IPM_or_MEM] == "S") +
-              (x[, CIP] == "S") == 1),
-      "MDRO"] <- 2 # 2 = 3MRGN, if only 1 group is S
+    trans_tbl(2, # 3MRGN, if only 1 group is S
+              which(x$genus == "Pseudomonas" & x$species == "aeruginosa" &
+                      (x[, PIP, drop = TRUE] == "S") +
+                      (x[, CTX_or_CAZ, drop = TRUE] == "S") +
+                      (x[, IPM_or_MEM, drop = TRUE] == "S") +
+                      (x[, CIP, drop = TRUE] == "S") == 1),
+              c(PIP, CTX, CAZ, IPM, MEM, CIP),
+              "any")
    
-    x[which((x$genus == "Pseudomonas" & x$species == "aeruginosa") &
-              x[, PIP] == "R" &
-              x[, CTX_or_CAZ] == "R" &
-              x[, IPM_or_MEM] == "R" &
-              x[, CIP] == "R"),
-      "MDRO"] <- 3 # 3 = 4MRGN
+    trans_tbl(3, # 4MRGN otherwise
+              which((x$genus == "Pseudomonas" & x$species == "aeruginosa") &
+                      (x[, PIP, drop = TRUE] == "R" | x[, TZP, drop = TRUE] == "R") &
+                      x[, CTX_or_CAZ, drop = TRUE] == "R" &
+                      x[, IPM_or_MEM, drop = TRUE] == "R" &
+                      x[, CIP, drop = TRUE] == "R"),
+              c(PIP, CTX, CAZ, IPM, MEM, CIP),
+              "any")
+    
+    x[which(x$MDRO == 2), "reason"] <- "3MRGN"
+    x[which(x$MDRO == 3), "reason"] <- "4MRGN"
  }
  
  if (guideline$code == "brmo") {
@ -1139,17 +1144,21 @@ mdro <- function(x,
        & !ab_missing(CAZ)
        & !ab_missing(TZP)) {
      x$psae <- 0
-      x[which(x[, MEM] == "R" | x[, IPM] == "R"), "psae"] <- 1 + x[which(x[, MEM] == "R" | x[, IPM] == "R"), "psae"]
-      x[which(x[, GEN] == "R" & x[, TOB] == "R"), "psae"] <- 1 + x[which(x[, GEN] == "R" & x[, TOB] == "R"), "psae"]
-      x[which(x[, CIP] == "R"), "psae"] <- 1 + x[which(x[, CIP] == "R"), "psae"]
-      x[which(x[, CAZ] == "R"), "psae"] <- 1 + x[which(x[, CAZ] == "R"), "psae"]
-      x[which(x[, TZP] == "R"), "psae"] <- 1 + x[which(x[, TZP] == "R"), "psae"]
+      x[which(x[, MEM, drop = TRUE] == "R" | x[, IPM, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, MEM, drop = TRUE] == "R" | x[, IPM, drop = TRUE] == "R"), "psae"]
+      x[which(x[, GEN, drop = TRUE] == "R" & x[, TOB, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, GEN, drop = TRUE] == "R" & x[, TOB, drop = TRUE] == "R"), "psae"]
+      x[which(x[, CIP, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, CIP, drop = TRUE] == "R"), "psae"]
+      x[which(x[, CAZ, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, CAZ, drop = TRUE] == "R"), "psae"]
+      x[which(x[, TZP, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, TZP, drop = TRUE] == "R"), "psae"]
    } else {
      x$psae <- 0
    }
+    trans_tbl(3,
+              which(x$genus == "Pseudomonas" & x$species == "aeruginosa" & x$psae >= 3),
+              c(CAZ, CIP, GEN, IPM, MEM, TOB, TZP),
+              "any")
    x[which(
      x$genus == "Pseudomonas" & x$species == "aeruginosa"
-      & x$psae >= 3), "MDRO"] <- 3
+      & x$psae >= 3), "reason"] <- paste0("at least 3 classes contain R", ifelse(!isTRUE(combine_SI), " or I", ""))
    
    # Table 3
    trans_tbl(3,
@ -1224,6 +1233,7 @@ mdro <- function(x,
                                          1))))
    # keep all real TB, make other species NA
    x$MDRO <- ifelse(x$fullname == "Mycobacterium tuberculosis", x$MDRO, NA_real_)
+    x$reason <- "PDR/MDR/XDR criteria were met"
  }
  
  if (info == TRUE) {
@ -1248,7 +1258,7 @@ mdro <- function(x,
  if (guideline$code == "cmi2012") {
    if (any(x$MDRO == -1, na.rm = TRUE)) {
      warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
-              percentage(pct_required_classes), " (set with `pct_required_classes`)", call = FALSE)
+               percentage(pct_required_classes), " (set with `pct_required_classes`)", call = FALSE)
      # set these -1s to NA
      x[which(x$MDRO == -1), "MDRO"] <- NA_integer_
    }
@ -1280,8 +1290,8 @@ mdro <- function(x,
          col_mo,
          "MDRO",
          "reason",
-          "columns_nonsusceptible")]
-    #x
+          "columns_nonsusceptible"), 
+      drop = FALSE]
  } else {
    x$MDRO
  }
--- a/data-raw/AMR_1.5.0.9003.tar.gz
+++ b/data-raw/AMR_1.5.0.9003.tar.gz
--- a/docs/404.html
+++ b/docs/404.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/authors.html
+++ b/docs/authors.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/index.html
+++ b/docs/index.html
@ -43,7 +43,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/news/index.html
+++ b/docs/news/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

@ -236,13 +236,13 @@
      <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
    </div>

-    <div id="amr-1509002" class="section level1">
-<h1 class="page-header" data-toc-text="1.5.0.9002">
-<a href="#amr-1509002" class="anchor"></a>AMR 1.5.0.9002<small> Unreleased </small>
+    <div id="amr-1509003" class="section level1">
+<h1 class="page-header" data-toc-text="1.5.0.9003">
+<a href="#amr-1509003" class="anchor"></a>AMR 1.5.0.9003<small> Unreleased </small>
 </h1>
-<div id="last-updated-14-january-2021" class="section level2">
+<div id="last-updated-15-january-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-14-january-2021" class="anchor"></a><small>Last updated: 14 January 2021</small>
+<a href="#last-updated-15-january-2021" class="anchor"></a><small>Last updated: 15 January 2021</small>
 </h2>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
@ -284,6 +284,7 @@
 </li>
 <li>Added Pretomanid (PMD, J04AK08) to the <code>antibiotics</code> data set</li>
 <li>WHONET code <code>"PNV"</code> will now correctly be interpreted as <code>PHN</code>, the antibiotic code for phenoxymethylpenicillin (‘peni V’)</li>
+<li>Fix for verbose output of <code><a href="../reference/mdro.html">mdro(..., verbose = TRUE)</a></code> for German guideline (3MGRN and 4MGRN) and <em>P. aeruginosa</em> in Dutch guideline (BRMO)</li>
 </ul>
 </div>
 </div>
--- 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: 2021-01-14T14:48Z
+last_built: 2021-01-15T21:44Z
 urls:
  reference: https://msberends.github.io/AMR//reference
  article: https://msberends.github.io/AMR//articles
--- a/docs/reference/antibiotics.html
+++ b/docs/reference/antibiotics.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/as.ab.html
+++ b/docs/reference/as.ab.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/as.rsi.html
+++ b/docs/reference/as.rsi.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/dosage.html
+++ b/docs/reference/dosage.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- 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
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/filter_ab_class.html
+++ b/docs/reference/filter_ab_class.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/first_isolate.html
+++ b/docs/reference/first_isolate.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/intrinsic_resistant.html
+++ b/docs/reference/intrinsic_resistant.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/isolate_identifier.html
+++ b/docs/reference/isolate_identifier.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/mdro.html
+++ b/docs/reference/mdro.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/microorganisms.codes.html
+++ b/docs/reference/microorganisms.codes.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/microorganisms.html
+++ b/docs/reference/microorganisms.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/mo_matching_score.html
+++ b/docs/reference/mo_matching_score.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/mo_property.html
+++ b/docs/reference/mo_property.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/resistance_predict.html
+++ b/docs/reference/resistance_predict.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/reference/rsi_translation.html
+++ b/docs/reference/rsi_translation.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>

--- a/docs/survey.html
+++ b/docs/survey.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
      </span>
    </div>