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(v1.5.0.9003) verbose output of mdro()

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dr. M.S. (Matthijs) Berends 2021-01-15 22:44:52 +01:00
parent 6745f3fb17
commit 7ebc534ccd
35 changed files with 112 additions and 95 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.5.0.9002 Version: 1.5.0.9003
Date: 2021-01-14 Date: 2021-01-15
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

5
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.5.0.9002 # AMR 1.5.0.9003
## <small>Last updated: 14 January 2021</small> ## <small>Last updated: 15 January 2021</small>
### New ### 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. * 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* * 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 * 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') * 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 # AMR 1.5.0

4
R/bug_drug_combinations.R
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@ -69,8 +69,10 @@ bug_drug_combinations <- function(x,
# -- mo # -- mo
if (is.null(col_mo)) { if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "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_class <- class(x)
x <- as.data.frame(x, stringsAsFactors = FALSE) x <- as.data.frame(x, stringsAsFactors = FALSE)

4
R/eucast_rules.R
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@ -205,8 +205,10 @@ eucast_rules <- function(x,
# -- mo # -- mo
if (is.null(col_mo)) { if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo", info = info) 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") decimal.mark <- getOption("OutDec")
big.mark <- ifelse(decimal.mark != ",", ",", ".") big.mark <- ifelse(decimal.mark != ",", ",", ".")

1
R/first_isolate.R
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@ -202,7 +202,6 @@ first_isolate <- function(x,
if (is.null(col_mo)) { if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo") col_mo <- search_type_in_df(x = x, type = "mo")
stop_if(is.null(col_mo), "`col_mo` must be set") 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 # -- date

2
R/guess_ab_col.R
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@ -122,7 +122,7 @@ get_column_abx <- function(x,
meet_criteria(info, allow_class = "logical", has_length = 1) meet_criteria(info, allow_class = "logical", has_length = 1)
if (info == TRUE) { 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) x <- as.data.frame(x, stringsAsFactors = FALSE)

4
R/key_antibiotics.R
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@ -168,8 +168,10 @@ key_antibiotics <- function(x,
# -- mo # -- mo
if (is.null(col_mo)) { if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "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 # check columns
col.list <- c(universal_1, universal_2, universal_3, universal_4, universal_5, universal_6, col.list <- c(universal_1, universal_2, universal_3, universal_4, universal_5, universal_6,

118
R/mdro.R
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@ -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 # force regular data.frame, not a tibble or data.table
x <- as.data.frame(x, stringsAsFactors = FALSE) x <- as.data.frame(x, stringsAsFactors = FALSE)
@ -155,7 +152,7 @@ mdro <- function(x,
guideline <- list(...)$country guideline <- list(...)$country
} }
guideline.bak <- guideline guideline.bak <- guideline
guideline <- tolower(gsub("[^a-zA-Z0-9.]+", "", guideline)) guideline <- tolower(gsub("[^a-zA-Z0-9.]+", "", guideline))
if (is.null(guideline)) { if (is.null(guideline)) {
# default to the paper by Magiorakos et al. (2012) # default to the paper by Magiorakos et al. (2012)
@ -182,9 +179,9 @@ mdro <- function(x,
} }
if (is.null(col_mo) & guideline$code == "tb") { if (is.null(col_mo) & guideline$code == "tb") {
message_("No column found as input for `col_mo`, ", message_("No column found as input for `col_mo`, ",
font_bold("assuming all records contain", font_italic("Mycobacterium tuberculosis."))) font_bold(paste0("assuming all records contain", font_italic("Mycobacterium tuberculosis"), ".")))
x$mo <- as.mo("Mycobacterium tuberculosis") x$mo <- as.mo("Mycobacterium tuberculosis") # consider overkill at all times: MO_lookup[which(MO_lookup$fullname == "Mycobacterium tuberculosis"), "mo", drop = TRUE]
col_mo <- "mo" col_mo <- "mo"
} }
stop_if(is.null(col_mo), "`col_mo` must be set") stop_if(is.null(col_mo), "`col_mo` must be set")
stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found") stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
@ -873,7 +870,9 @@ mdro <- function(x,
# MDR (=2): >=3 classes affected # MDR (=2): >=3 classes affected
x[which(x$classes_affected >= 3), "MDRO"] <- 2 x[which(x$classes_affected >= 3), "MDRO"] <- 2
if (verbose == TRUE) { if (verbose == TRUE) {
x[which(x$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$classes_affected >= 3)], " available classes") " out of ", x$classes_available[which(x$classes_affected >= 3)], " available classes")
} }
@ -1044,49 +1043,55 @@ mdro <- function(x,
# Germany ----------------------------------------------------------------- # Germany -----------------------------------------------------------------
CTX_or_CAZ <- CTX %or% CAZ CTX_or_CAZ <- CTX %or% CAZ
IPM_or_MEM <- IPM %or% MEM IPM_or_MEM <- IPM %or% MEM
x$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 # Table 1
x[which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification trans_tbl(2, # 3MRGN
(x$genus == "Acinetobacter" & x$species == "baumannii")) & which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification
x[, PIP] == "R" & (x$genus == "Acinetobacter" & x$species == "baumannii")) &
x[, CTX_or_CAZ] == "R" & x[, PIP, drop = TRUE] == "R" &
x[, IPM_or_MEM] == "S" & x[, CTX_or_CAZ, drop = TRUE] == "R" &
x[, CIP] == "R"), x[, IPM_or_MEM, drop = TRUE] == "S" &
"MDRO"] <- 2 # 2 = 3MRGN x[, CIP, drop = TRUE] == "R"),
c(PIP, CTX, CAZ, IPM, MEM, CIP),
"any")
x[which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification trans_tbl(3, # 4MRGN, overwrites 3MRGN if applicable
(x$genus == "Acinetobacter" & x$species == "baumannii")) & which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification
x[, PIP] == "R" & (x$genus == "Acinetobacter" & x$species == "baumannii")) &
x[, CTX_or_CAZ] == "R" & x[, PIP, drop = TRUE] == "R" &
x[, IPM_or_MEM] == "R" & x[, CTX_or_CAZ, drop = TRUE] == "R" &
x[, CIP] == "R"), x[, IPM_or_MEM, drop = TRUE] == "R" &
"MDRO"] <- 3 # 3 = 4MRGN, overwrites 3MRGN if applicable x[, CIP, drop = TRUE] == "R"),
c(PIP, CTX, CAZ, IPM, MEM, CIP),
"any")
x[which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification trans_tbl(3, # 4MRGN, overwrites 3MRGN if applicable
(x$genus == "Acinetobacter" & x$species == "baumannii")) & which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification
x[, IPM] == "R" | x[, MEM] == "R"), (x$genus == "Acinetobacter" & x$species == "baumannii")) &
"MDRO"] <- 3 # 3 = 4MRGN, always when imipenem or meropenem is R (x[, IPM, drop = TRUE] == "R" | x[, MEM, drop = TRUE] == "R")),
c(IPM, MEM),
"any")
x[which(x$genus == "Pseudomonas" & x$species == "aeruginosa" & trans_tbl(2, # 3MRGN, if only 1 group is S
(x[, PIP] == "S") + which(x$genus == "Pseudomonas" & x$species == "aeruginosa" &
(x[, CTX_or_CAZ] == "S") + (x[, PIP, drop = TRUE] == "S") +
(x[, IPM_or_MEM] == "S") + (x[, CTX_or_CAZ, drop = TRUE] == "S") +
(x[, CIP] == "S") == 1), (x[, IPM_or_MEM, drop = TRUE] == "S") +
"MDRO"] <- 2 # 2 = 3MRGN, if only 1 group is S (x[, CIP, drop = TRUE] == "S") == 1),
c(PIP, CTX, CAZ, IPM, MEM, CIP),
"any")
x[which((x$genus == "Pseudomonas" & x$species == "aeruginosa") & trans_tbl(3, # 4MRGN otherwise
x[, PIP] == "R" & which((x$genus == "Pseudomonas" & x$species == "aeruginosa") &
x[, CTX_or_CAZ] == "R" & (x[, PIP, drop = TRUE] == "R" | x[, TZP, drop = TRUE] == "R") &
x[, IPM_or_MEM] == "R" & x[, CTX_or_CAZ, drop = TRUE] == "R" &
x[, CIP] == "R"), x[, IPM_or_MEM, drop = TRUE] == "R" &
"MDRO"] <- 3 # 3 = 4MRGN 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$code == "brmo") { if (guideline$code == "brmo") {
@ -1139,17 +1144,21 @@ mdro <- function(x,
& !ab_missing(CAZ) & !ab_missing(CAZ)
& !ab_missing(TZP)) { & !ab_missing(TZP)) {
x$psae <- 0 x$psae <- 0
x[which(x[, MEM] == "R" | x[, IPM] == "R"), "psae"] <- 1 + x[which(x[, MEM] == "R" | x[, IPM] == "R"), "psae"] x[which(x[, 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] == "R" & x[, TOB] == "R"), "psae"] <- 1 + x[which(x[, GEN] == "R" & x[, TOB] == "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] == "R"), "psae"] <- 1 + x[which(x[, CIP] == "R"), "psae"] x[which(x[, CIP, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, CIP, drop = TRUE] == "R"), "psae"]
x[which(x[, CAZ] == "R"), "psae"] <- 1 + x[which(x[, CAZ] == "R"), "psae"] x[which(x[, CAZ, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, CAZ, drop = TRUE] == "R"), "psae"]
x[which(x[, TZP] == "R"), "psae"] <- 1 + x[which(x[, TZP] == "R"), "psae"] x[which(x[, TZP, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, TZP, drop = TRUE] == "R"), "psae"]
} else { } else {
x$psae <- 0 x$psae <- 0
} }
trans_tbl(3,
which(x$genus == "Pseudomonas" & x$species == "aeruginosa" & x$psae >= 3),
c(CAZ, CIP, GEN, IPM, MEM, TOB, TZP),
"any")
x[which( x[which(
x$genus == "Pseudomonas" & x$species == "aeruginosa" x$genus == "Pseudomonas" & x$species == "aeruginosa"
& x$psae >= 3), "MDRO"] <- 3 & x$psae >= 3), "reason"] <- paste0("at least 3 classes contain R", ifelse(!isTRUE(combine_SI), " or I", ""))
# Table 3 # Table 3
trans_tbl(3, trans_tbl(3,
@ -1224,6 +1233,7 @@ mdro <- function(x,
1)))) 1))))
# keep all real TB, make other species NA # keep all real TB, make other species NA
x$MDRO <- ifelse(x$fullname == "Mycobacterium tuberculosis", x$MDRO, NA_real_) x$MDRO <- ifelse(x$fullname == "Mycobacterium tuberculosis", x$MDRO, NA_real_)
x$reason <- "PDR/MDR/XDR criteria were met"
} }
if (info == TRUE) { if (info == TRUE) {
@ -1248,7 +1258,7 @@ mdro <- function(x,
if (guideline$code == "cmi2012") { if (guideline$code == "cmi2012") {
if (any(x$MDRO == -1, na.rm = TRUE)) { if (any(x$MDRO == -1, na.rm = TRUE)) {
warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ", 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 # set these -1s to NA
x[which(x$MDRO == -1), "MDRO"] <- NA_integer_ x[which(x$MDRO == -1), "MDRO"] <- NA_integer_
} }
@ -1280,8 +1290,8 @@ mdro <- function(x,
col_mo, col_mo,
"MDRO", "MDRO",
"reason", "reason",
"columns_nonsusceptible")] "columns_nonsusceptible"),
#x drop = FALSE]
} else { } else {
x$MDRO x$MDRO
} }

BIN
data-raw/AMR_1.5.0.9002.tar.gz → data-raw/AMR_1.5.0.9003.tar.gz
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2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

13
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>
@ -236,13 +236,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1509002" class="section level1"> <div id="amr-1509003" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9002"> <h1 class="page-header" data-toc-text="1.5.0.9003">
<a href="#amr-1509002" class="anchor"></a>AMR 1.5.0.9002<small> Unreleased </small> <a href="#amr-1509003" class="anchor"></a>AMR 1.5.0.9003<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-14-january-2021" class="section level2"> <div id="last-updated-15-january-2021" class="section level2">
<h2 class="hasAnchor"> <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> </h2>
<div id="new" class="section level3"> <div id="new" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -284,6 +284,7 @@
</li> </li>
<li>Added Pretomanid (PMD, J04AK08) to the <code>antibiotics</code> data set</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>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> </ul>
</div> </div>
</div> </div>

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-01-14T14:48Z last_built: 2021-01-15T21:44Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

2
docs/reference/antibiotics.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/as.ab.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/as.mo.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/as.rsi.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/dosage.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/eucast_rules.html
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@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/filter_ab_class.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/first_isolate.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/intrinsic_resistant.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/isolate_identifier.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/mdro.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/microorganisms.codes.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/microorganisms.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/mo_matching_score.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/mo_property.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/resistance_predict.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/reference/rsi_translation.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/survey.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>