mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 19:26:13 +01:00
(v1.2.0.9004) rsi_df() fix for groups
This commit is contained in:
parent
40221e5244
commit
8b692ecfcf
@ -1,6 +1,6 @@
|
||||
Package: AMR
|
||||
Version: 1.2.0.9003
|
||||
Date: 2020-06-05
|
||||
Version: 1.2.0.9004
|
||||
Date: 2020-06-09
|
||||
Title: Antimicrobial Resistance Analysis
|
||||
Authors@R: c(
|
||||
person(role = c("aut", "cre"),
|
||||
|
||||
6
NEWS.md
6
NEWS.md
@ -1,12 +1,14 @@
|
||||
# AMR 1.2.0.9003
|
||||
## <small>Last updated: 05-Jun-2020</small>
|
||||
# AMR 1.2.0.9004
|
||||
## <small>Last updated: 09-Jun-2020</small>
|
||||
|
||||
### Changed
|
||||
* 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)
|
||||
* 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 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
|
||||
|
||||
|
||||
@ -114,9 +114,16 @@ get_column_abx <- function(x,
|
||||
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)
|
||||
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
|
||||
# only check columns that are a valid AB code, ATC code, name, abbreviation or synonym,
|
||||
# or already have the rsi class (as.rsi)
|
||||
|
||||
20
R/rsi_calc.R
20
R/rsi_calc.R
@ -220,10 +220,18 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
|
||||
.data <- .data[, which(!colnames(.data) %in% groups), drop = FALSE]
|
||||
}
|
||||
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$interpretation <- rownames(col_results)
|
||||
col_results$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) {
|
||||
col_results$value <- col_results$isolates / sum(col_results$isolates, na.rm = TRUE)
|
||||
} else {
|
||||
@ -237,6 +245,12 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
|
||||
isolates = col_results$isolates,
|
||||
stringsAsFactors = FALSE)
|
||||
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 <- rbind(out, out_new)
|
||||
@ -273,7 +287,7 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
|
||||
|
||||
if (data_has_groups) {
|
||||
# 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 {
|
||||
out <- out[order(out$antibiotic, out$interpretation), ]
|
||||
}
|
||||
|
||||
@ -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"
|
||||
"CHE" 125846 "Cefotiam hexetil" "Cephalosporins (3rd gen.)" "" "c(\"cefotiam cilexetil\", \"pansporin t\")"
|
||||
"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"
|
||||
"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"
|
||||
|
||||
@ -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("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("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
|
||||
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"))
|
||||
@ -579,7 +588,7 @@ antibiotics <- antibiotics %>%
|
||||
# set as data.frame again
|
||||
antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
|
||||
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 ----
|
||||
for (i in 1:nrow(antibiotics)) {
|
||||
|
||||
Binary file not shown.
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.2.0.9003</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.2.0.9003</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.2.0.9003</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.2.0.9003</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.2.0.9003</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -229,13 +229,13 @@
|
||||
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-1209003" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.2.0.9003">
|
||||
<a href="#amr-1209003" class="anchor"></a>AMR 1.2.0.9003<small> Unreleased </small>
|
||||
<div id="amr-1209004" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.2.0.9004">
|
||||
<a href="#amr-1209004" class="anchor"></a>AMR 1.2.0.9004<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-05-jun-2020" class="section level2">
|
||||
<div id="last-updated-09-jun-2020" class="section level2">
|
||||
<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>
|
||||
<div id="changed" class="section level3">
|
||||
<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>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 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 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>Added antibiotics code “FOX1” for cefoxitin screening (abbreviation “cfsc”) to the <code>antibiotics</code> data set</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@ -10,7 +10,7 @@ articles:
|
||||
WHONET: WHONET.html
|
||||
benchmarks: benchmarks.html
|
||||
resistance_predict: resistance_predict.html
|
||||
last_built: 2020-06-05T11:55Z
|
||||
last_built: 2020-06-09T14:15Z
|
||||
urls:
|
||||
reference: https://msberends.gitlab.io/AMR/reference
|
||||
article: https://msberends.gitlab.io/AMR/articles
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<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 -->
|
||||
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
@ -48,7 +48,7 @@
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<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:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
|
||||
|
||||
@ -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">1.2.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -226,7 +226,7 @@
|
||||
<div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<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>
|
||||
<div class="hidden name"><code>antibiotics.Rd</code></div>
|
||||
</div>
|
||||
@ -243,7 +243,7 @@
|
||||
<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>
|
||||
<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>
|
||||
|
||||
@ -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">1.2.0.9003</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -478,7 +478,7 @@
|
||||
<td>
|
||||
<p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data sets with 557 antimicrobials</p></td>
|
||||
<td><p>Data sets with 558 antimicrobials</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
|
||||
@ -4,9 +4,9 @@
|
||||
\name{antibiotics}
|
||||
\alias{antibiotics}
|
||||
\alias{antivirals}
|
||||
\title{Data sets with 557 antimicrobials}
|
||||
\title{Data sets with 558 antimicrobials}
|
||||
\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{
|
||||
\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}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user