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(v1.2.0.9004) rsi_df() fix for groups

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dr. M.S. (Matthijs) Berends 2020-06-09 16:18:03 +02:00
parent 40221e5244
commit 8b692ecfcf
17 changed files with 68 additions and 32 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.2.0.9003 Version: 1.2.0.9004
Date: 2020-06-05 Date: 2020-06-09
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

6
NEWS.md
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@ -1,12 +1,14 @@
# AMR 1.2.0.9003 # AMR 1.2.0.9004
## <small>Last updated: 05-Jun-2020</small> ## <small>Last updated: 09-Jun-2020</small>
### Changed ### Changed
* Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded * Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded
* All `*_join_microorganisms()` functions now return the original data class (e.g. tibbles and data.tables) * All `*_join_microorganisms()` functions now return the original data class (e.g. tibbles and data.tables)
* Fixed a bug where `as.ab()` would return an error on invalid input values * Fixed a bug where `as.ab()` would return an error on invalid input values
* Fixed a bug for using grouped versions of `rsi_df()`, `proportion_df()` and `count_df()`
* Added function `filter_penicillins()` to filter isolates on a specific result in any column with a name in the antimicrobial 'penicillins' class (more specific: ATC subgroup *Beta-lactam antibacterials, penicillins*) * Added function `filter_penicillins()` to filter isolates on a specific result in any column with a name in the antimicrobial 'penicillins' class (more specific: ATC subgroup *Beta-lactam antibacterials, penicillins*)
* Added official antimicrobial names to all `filter_ab_class()` functions, such as `filter_aminoglycosides()` * Added official antimicrobial names to all `filter_ab_class()` functions, such as `filter_aminoglycosides()`
* Added antibiotics code "FOX1" for cefoxitin screening (abbreviation "cfsc") to the `antibiotics` data set
# AMR 1.2.0 # AMR 1.2.0

9
R/guess_ab_col.R
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@ -114,9 +114,16 @@ get_column_abx <- function(x,
verbose = FALSE, verbose = FALSE,
...) { ...) {
message(font_blue("NOTE: Auto-guessing columns suitable for analysis..."), appendLF = FALSE) message(font_blue("NOTE: Auto-guessing columns suitable for analysis"), appendLF = FALSE)
x <- as.data.frame(x, stringsAsFactors = FALSE) x <- as.data.frame(x, stringsAsFactors = FALSE)
if (NROW(x) > 10000) {
# only test maximum of 10,000 values per column
message(font_blue(paste0(" (using only ", font_bold("the first 10,000 rows"), ")...")), appendLF = FALSE)
x <- x[1:10000, , drop = FALSE]
} else {
message(font_blue("..."), appendLF = FALSE)
}
x_bak <- x x_bak <- x
# only check columns that are a valid AB code, ATC code, name, abbreviation or synonym, # only check columns that are a valid AB code, ATC code, name, abbreviation or synonym,
# or already have the rsi class (as.rsi) # or already have the rsi class (as.rsi)

20
R/rsi_calc.R
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@ -220,10 +220,18 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
.data <- .data[, which(!colnames(.data) %in% groups), drop = FALSE] .data <- .data[, which(!colnames(.data) %in% groups), drop = FALSE]
} }
for (i in seq_len(ncol(.data))) { for (i in seq_len(ncol(.data))) {
col_results <- as.data.frame(as.matrix(table(.data[, i, drop = TRUE]))) values <- .data[, i, drop = TRUE]
if (isTRUE(combine_SI)) {
values <- factor(values, levels = c("SI", "R"), ordered = TRUE)
} else if (isTRUE(combine_IR)) {
values <- factor(values, levels = c("S", "IR"), ordered = TRUE)
} else {
values <- factor(values, levels = c("S", "I", "R"), ordered = TRUE)
}
col_results <- as.data.frame(as.matrix(table(values)))
col_results$interpretation <- rownames(col_results) col_results$interpretation <- rownames(col_results)
col_results$isolates <- col_results[, 1, drop = TRUE] col_results$isolates <- col_results[, 1, drop = TRUE]
if (nrow(col_results) > 0) { if (NROW(col_results) > 0 && sum(col_results$isolates, na.rm = TRUE) > 0) {
if (sum(col_results$isolates, na.rm = TRUE) >= minimum) { if (sum(col_results$isolates, na.rm = TRUE) >= minimum) {
col_results$value <- col_results$isolates / sum(col_results$isolates, na.rm = TRUE) col_results$value <- col_results$isolates / sum(col_results$isolates, na.rm = TRUE)
} else { } else {
@ -237,6 +245,12 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
isolates = col_results$isolates, isolates = col_results$isolates,
stringsAsFactors = FALSE) stringsAsFactors = FALSE)
if (data_has_groups) { if (data_has_groups) {
if (nrow(group_values) < nrow(out_new)) {
# repeat group_values for the number of rows in out_new
repeated <- rep(seq_len(nrow(group_values)),
each = nrow(out_new) / nrow(group_values))
group_values <- group_values[repeated, , drop = FALSE]
}
out_new <- cbind(group_values, out_new) out_new <- cbind(group_values, out_new)
} }
out <- rbind(out, out_new) out <- rbind(out, out_new)
@ -273,7 +287,7 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
if (data_has_groups) { if (data_has_groups) {
# ordering by the groups and two more: "antibiotic" and "interpretation" # ordering by the groups and two more: "antibiotic" and "interpretation"
out <- out[do.call("order", out[, seq_len(length(groups) + 2)]), ] out <- ungroup(out[do.call("order", out[, seq_len(length(groups) + 2)]), ])
} else { } else {
out <- out[order(out$antibiotic, out$interpretation), ] out <- out[order(out$antibiotic, out$interpretation), ]
} }

3
data-raw/antibiotics.txt
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@ -89,7 +89,8 @@
"CTF" "J01DC07" 43708 "Cefotiam" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefotiam\", \"cefotiam?\", \"cefotiamum\", \"ceradolan\", \"ceradon\", \"haloapor\")" 1.2 "g" 4 "g" "CTF" "J01DC07" 43708 "Cefotiam" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefotiam\", \"cefotiam?\", \"cefotiamum\", \"ceradolan\", \"ceradon\", \"haloapor\")" 1.2 "g" 4 "g"
"CHE" 125846 "Cefotiam hexetil" "Cephalosporins (3rd gen.)" "" "c(\"cefotiam cilexetil\", \"pansporin t\")" "CHE" 125846 "Cefotiam hexetil" "Cephalosporins (3rd gen.)" "" "c(\"cefotiam cilexetil\", \"pansporin t\")"
"FOV" 9578573 "Cefovecin" "Cephalosporins (3rd gen.)" "" "" "FOV" 9578573 "Cefovecin" "Cephalosporins (3rd gen.)" "" ""
"FOX" "J01DC01" 441199 "Cefoxitin" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfox\", \"cfsc\", \"cfx\", \"cfxt\", \"cx\", \"fox\", \"fx\")" "c(\"cefoxitin\", \"cefoxitina\", \"cefoxitine\", \"cefoxitinum\", \"cefoxotin\", \"cephoxitin\", \"mefoxin\", \"mefoxitin\", \"rephoxitin\")" 6 "g" "c(\"25240-3\", \"3448-8\")" "FOX" "J01DC01" 441199 "Cefoxitin" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfox\", \"cfx\", \"cfxt\", \"cx\", \"fox\", \"fx\")" "c(\"cefoxitin\", \"cefoxitina\", \"cefoxitine\", \"cefoxitinum\", \"cefoxotin\", \"cephoxitin\", \"mefoxin\", \"mefoxitin\", \"rephoxitin\")" 6 "g" "c(\"25240-3\", \"3448-8\")"
"FOX1" "Cefoxitin screening" "Cephalosporins (2nd gen.)" "cfsc" "" "NA"
"ZOP" 9571080 "Cefozopran" "Cephalosporins (4th gen.)" "" "cefozopran" "ZOP" 9571080 "Cefozopran" "Cephalosporins (4th gen.)" "" "cefozopran"
"CFZ" 68597 "Cefpimizole" "Cephalosporins (3rd gen.)" "" "c(\"cefpimizol\", \"cefpimizole\", \"cefpimizole sodium\", \"cefpimizolum\")" "CFZ" 68597 "Cefpimizole" "Cephalosporins (3rd gen.)" "" "c(\"cefpimizol\", \"cefpimizole\", \"cefpimizole sodium\", \"cefpimizolum\")"
"CPM" "J01DD11" 636405 "Cefpiramide" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefpiramide\", \"cefpiramide acid\", \"cefpiramido\", \"cefpiramidum\")" 2 "g" "CPM" "J01DD11" 636405 "Cefpiramide" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefpiramide\", \"cefpiramide acid\", \"cefpiramido\", \"cefpiramidum\")" 2 "g"

13
data-raw/reproduction_of_antibiotics.R
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@ -322,7 +322,16 @@ antibiotics[which(antibiotics$ab == as.ab("cefuroxim")), "abbreviations"][[1]] <
antibiotics[which(antibiotics$ab == as.ab("cefotaxim")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefotaxim")), "abbreviations"][[1]], "cftx")) antibiotics[which(antibiotics$ab == as.ab("cefotaxim")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefotaxim")), "abbreviations"][[1]], "cftx"))
antibiotics[which(antibiotics$ab == as.ab("ceftazidime")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("ceftazidime")), "abbreviations"][[1]], "cftz")) antibiotics[which(antibiotics$ab == as.ab("ceftazidime")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("ceftazidime")), "abbreviations"][[1]], "cftz"))
antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]], "cfpi")) antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]], "cfpi"))
antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]], "cfxt", "cfsc")) antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]], "cfxt"))
# Add cefoxitin screening
class(antibiotics$ab) <- "character"
antibiotics <- rbind(antibiotics,data.frame(ab = "FOX1", atc = NA, cid = NA,
name = "Cefoxitin screening",
group = "Cephalosporins (2nd gen.)", atc_group1 = NA, atc_group2 = NA,
abbreviations = "cfsc", synonyms = NA,
oral_ddd = NA, oral_units = NA, iv_ddd = NA, iv_units = NA,
loinc = NA,
stringsAsFactors = FALSE))
# More GLIMS codes # More GLIMS codes
antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "cftz")) antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "cftz"))
antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]], "cftr")) antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]], "cftr"))
@ -579,7 +588,7 @@ antibiotics <- antibiotics %>%
# set as data.frame again # set as data.frame again
antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE) antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
class(antibiotics$ab) <- c("ab", "character") class(antibiotics$ab) <- c("ab", "character")
antibiotics <- antibiotics %>% arrange(name) antibiotics <- antibiotics %>% dplyr::arrange(name)
# make all abbreviations and synonyms lower case, unique and alphabetically sorted ---- # make all abbreviations and synonyms lower case, unique and alphabetically sorted ----
for (i in 1:nrow(antibiotics)) { for (i in 1:nrow(antibiotics)) {

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data/antibiotics.rda
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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.gitlab.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</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">1.2.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</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">1.2.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</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">1.2.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</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">1.2.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
</span> </span>
</div> </div>

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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">1.2.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
</span> </span>
</div> </div>
@ -229,13 +229,13 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1209003" class="section level1"> <div id="amr-1209004" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9003"> <h1 class="page-header" data-toc-text="1.2.0.9004">
<a href="#amr-1209003" class="anchor"></a>AMR 1.2.0.9003<small> Unreleased </small> <a href="#amr-1209004" class="anchor"></a>AMR 1.2.0.9004<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-05-jun-2020" class="section level2"> <div id="last-updated-09-jun-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-05-jun-2020" class="anchor"></a><small>Last updated: 05-Jun-2020</small> <a href="#last-updated-09-jun-2020" class="anchor"></a><small>Last updated: 09-Jun-2020</small>
</h2> </h2>
<div id="changed" class="section level3"> <div id="changed" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -244,9 +244,12 @@
<li>Fixed a bug where <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> would not work on a tibble when the <code>tibble</code> or <code>dplyr</code> package was loaded</li> <li>Fixed a bug where <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> would not work on a tibble when the <code>tibble</code> or <code>dplyr</code> package was loaded</li>
<li>All <code>*_join_microorganisms()</code> functions now return the original data class (e.g. tibbles and data.tables)</li> <li>All <code>*_join_microorganisms()</code> functions now return the original data class (e.g. tibbles and data.tables)</li>
<li>Fixed a bug where <code><a href="../reference/as.ab.html">as.ab()</a></code> would return an error on invalid input values</li> <li>Fixed a bug where <code><a href="../reference/as.ab.html">as.ab()</a></code> would return an error on invalid input values</li>
<li>Fixed a bug for using grouped versions of <code><a href="../reference/proportion.html">rsi_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code>
</li>
<li>Added function <code><a href="../reference/filter_ab_class.html">filter_penicillins()</a></code> to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup <em>Beta-lactam antibacterials, penicillins</em>)</li> <li>Added function <code><a href="../reference/filter_ab_class.html">filter_penicillins()</a></code> to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup <em>Beta-lactam antibacterials, penicillins</em>)</li>
<li>Added official antimicrobial names to all <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> functions, such as <code><a href="../reference/filter_ab_class.html">filter_aminoglycosides()</a></code> <li>Added official antimicrobial names to all <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> functions, such as <code><a href="../reference/filter_ab_class.html">filter_aminoglycosides()</a></code>
</li> </li>
<li>Added antibiotics code “FOX1” for cefoxitin screening (abbreviation “cfsc”) to the <code>antibiotics</code> data set</li>
</ul> </ul>
</div> </div>
</div> </div>

2
docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html WHONET: WHONET.html
benchmarks: benchmarks.html benchmarks: benchmarks.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
last_built: 2020-06-05T11:55Z last_built: 2020-06-09T14:15Z
urls: urls:
reference: https://msberends.gitlab.io/AMR/reference reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles article: https://msberends.gitlab.io/AMR/articles

10
docs/reference/antibiotics.html
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@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Data sets with 557 antimicrobials — antibiotics • AMR (for R)</title> <title>Data sets with 558 antimicrobials — antibiotics • AMR (for R)</title>
<!-- favicons --> <!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"> <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet"> <link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script> <script src="../extra.js"></script>
<meta property="og:title" content="Data sets with 557 antimicrobials — antibiotics" /> <meta property="og:title" content="Data sets with 558 antimicrobials — antibiotics" />
<meta property="og:description" content="Two data sets containing all antibiotics/antimycotics and antivirals. Use as.ab() or one of the ab_property() functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes." /> <meta property="og:description" content="Two data sets containing all antibiotics/antimycotics and antivirals. Use as.ab() or one of the ab_property() functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" /> <meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -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">1.2.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
</span> </span>
</div> </div>
@ -226,7 +226,7 @@
<div class="row"> <div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header"> <div class="page-header">
<h1>Data sets with 557 antimicrobials</h1> <h1>Data sets with 558 antimicrobials</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small> <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>antibiotics.Rd</code></div> <div class="hidden name"><code>antibiotics.Rd</code></div>
</div> </div>
@ -243,7 +243,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<h3>For the antibiotics data set: a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 455 observations and 14 variables:</h3> <h3>For the antibiotics data set: a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 456 observations and 14 variables:</h3>
<ul> <ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (like <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li> <li><p><code>ab</code><br /> Antibiotic ID as used in this package (like <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>

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</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">1.2.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
</span> </span>
</div> </div>
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<td> <td>
<p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p> <p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p>
</td> </td>
<td><p>Data sets with 557 antimicrobials</p></td> <td><p>Data sets with 558 antimicrobials</p></td>
</tr><tr> </tr><tr>
<td> <td>

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\name{antibiotics} \name{antibiotics}
\alias{antibiotics} \alias{antibiotics}
\alias{antivirals} \alias{antivirals}
\title{Data sets with 557 antimicrobials} \title{Data sets with 558 antimicrobials}
\format{ \format{
\subsection{For the \link{antibiotics} data set: a \code{\link{data.frame}} with 455 observations and 14 variables:}{ \subsection{For the \link{antibiotics} data set: a \code{\link{data.frame}} with 456 observations and 14 variables:}{
\itemize{ \itemize{
\item \code{ab}\cr Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available \item \code{ab}\cr Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
\item \code{atc}\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02} \item \code{atc}\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}