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(v1.7.1.9050) fix for as.mo

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dr. M.S. (Matthijs) Berends 2021-10-05 14:00:35 +02:00
parent 2bcf28281d
commit 8f5e5a3fc2
15 changed files with 50 additions and 41 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.7.1.9049 Version: 1.7.1.9050
Date: 2021-10-05 Date: 2021-10-05
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@ -1,4 +1,4 @@
# `AMR` 1.7.1.9049 # `AMR` 1.7.1.9050
## <small>Last updated: 5 October 2021</small> ## <small>Last updated: 5 October 2021</small>
### Breaking changes ### Breaking changes

38
R/atc_online.R
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@ -138,15 +138,21 @@ atc_online_property <- function(atc_code,
atc_url <- sub("%s", atc_code[i], atc_url, fixed = TRUE) atc_url <- sub("%s", atc_code[i], atc_url, fixed = TRUE)
if (property == "groups") { if (property == "groups") {
tbl <- read_html(atc_url) %pm>% out <- tryCatch(
read_html(atc_url) %pm>%
html_node("#content") %pm>% html_node("#content") %pm>%
html_children() %pm>% html_children() %pm>%
html_node("a") html_node("a"),
error = function(e) NULL)
if (is.null(out)) {
message_("Connection to ", atc_url, " failed.")
return(rep(NA, length(atc_code)))
}
# get URLS of items # get URLS of items
hrefs <- tbl %pm>% html_attr("href") hrefs <- out %pm>% html_attr("href")
# get text of items # get text of items
texts <- tbl %pm>% html_text() texts <- out %pm>% html_text()
# select only text items where URL like "code=" # select only text items where URL like "code="
texts <- texts[grepl("?code=", tolower(hrefs), fixed = TRUE)] texts <- texts[grepl("?code=", tolower(hrefs), fixed = TRUE)]
# last one is antibiotics, skip it # last one is antibiotics, skip it
@ -154,15 +160,21 @@ atc_online_property <- function(atc_code,
returnvalue <- c(list(texts), returnvalue) returnvalue <- c(list(texts), returnvalue)
} else { } else {
tbl <- read_html(atc_url) %pm>% out <- tryCatch(
read_html(atc_url) %pm>%
html_nodes("table") %pm>% html_nodes("table") %pm>%
html_table(header = TRUE) %pm>% html_table(header = TRUE) %pm>%
as.data.frame(stringsAsFactors = FALSE) as.data.frame(stringsAsFactors = FALSE),
error = function(e) NULL)
if (is.null(out)) {
message_("Connection to ", atc_url, " failed.")
return(rep(NA, length(atc_code)))
}
# case insensitive column names # case insensitive column names
colnames(tbl) <- gsub("^atc.*", "atc", tolower(colnames(tbl))) colnames(out) <- gsub("^atc.*", "atc", tolower(colnames(out)))
if (length(tbl) == 0) { if (length(out) == 0) {
warning_("ATC not found: ", atc_code[i], ". Please check ", atc_url, ".", call = FALSE) warning_("ATC not found: ", atc_code[i], ". Please check ", atc_url, ".", call = FALSE)
returnvalue[i] <- NA returnvalue[i] <- NA
next next
@ -170,15 +182,15 @@ atc_online_property <- function(atc_code,
if (property %in% c("atc", "name")) { if (property %in% c("atc", "name")) {
# ATC and name are only in first row # ATC and name are only in first row
returnvalue[i] <- tbl[1, property] returnvalue[i] <- out[1, property]
} else { } else {
if (!"adm.r" %in% colnames(tbl) | is.na(tbl[1, "adm.r"])) { if (!"adm.r" %in% colnames(out) | is.na(out[1, "adm.r"])) {
returnvalue[i] <- NA returnvalue[i] <- NA
next next
} else { } else {
for (j in seq_len(nrow(tbl))) { for (j in seq_len(nrow(out))) {
if (tbl[j, "adm.r"] == administration) { if (out[j, "adm.r"] == administration) {
returnvalue[i] <- tbl[j, property] returnvalue[i] <- out[j, property]
} }
} }
} }

2
R/mo.R
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@ -803,7 +803,7 @@ exec_as.mo <- function(x,
perl = TRUE)), uncertainty = -1) perl = TRUE)), uncertainty = -1)
next next
} }
if (x_backup_without_spp[i] %like_case% "haemoly.*strep") { if (x_backup_without_spp[i] %like_case% "ha?emoly.*strep") {
# Haemolytic streptococci in different languages # Haemolytic streptococci in different languages
x[i] <- lookup(mo == "B_STRPT_HAEM", uncertainty = -1) x[i] <- lookup(mo == "B_STRPT_HAEM", uncertainty = -1)
next next

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data-raw/AMR_latest.tar.gz
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2
data-raw/whonet_bugfixes.R
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@ -7,5 +7,5 @@ microorganisms.codes[which(microorganisms.codes$code == "ENT"), "mo"] <- as.mo("
microorganisms.codes[which(microorganisms.codes$code == "STR"), "mo"] <- as.mo("streptococcus") microorganisms.codes[which(microorganisms.codes$code == "STR"), "mo"] <- as.mo("streptococcus")
microorganisms.codes[which(microorganisms.codes$code == "CDF"), "mo"] <- as.mo("clostridium difficile") microorganisms.codes[which(microorganisms.codes$code == "CDF"), "mo"] <- as.mo("clostridium difficile")
microorganisms.codes[which(microorganisms.codes$code == "HA-"), "mo"] <- as.mo("haemophilus influenzae") microorganisms.codes[which(microorganisms.codes$code == "HA-"), "mo"] <- as.mo("haemophilus influenzae")
usethis::use_data(microorganisms.codes, overwrite = TRUE) usethis::use_data(microorganisms.codes, overwrite = TRUE, version = 2)
rm(microorganisms.codes) rm(microorganisms.codes)

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data/microorganisms.codes.rda
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2
docs/articles/datasets.html
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@ -44,7 +44,7 @@
</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">1.7.1.9049</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9050</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -92,7 +92,7 @@
</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">1.7.1.9049</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9050</span>
</span> </span>
</div> </div>
@ -240,9 +240,9 @@
<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-1719049" class="section level1"> <div id="amr-1719050" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9049"> <h1 class="page-header" data-toc-text="1.7.1.9050">
<a href="#amr-1719049" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9049</h1> <a href="#amr-1719050" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9050</h1>
<div id="last-updated-5-october-2021" class="section level2"> <div id="last-updated-5-october-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-5-october-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 5 October 2021</small> <a href="#last-updated-5-october-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 5 October 2021</small>

2
docs/reference/ab_property.html
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@ -93,7 +93,7 @@
</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">1.7.1.9040</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9050</span>
</span> </span>
</div> </div>

4
docs/reference/index.html
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@ -92,7 +92,7 @@
</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">1.7.1.9040</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9050</span>
</span> </span>
</div> </div>
@ -478,7 +478,7 @@
<td> <td>
<p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p> <p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
</td> </td>
<td><p>Data Set with 5,605 Common Microorganism Codes</p></td> <td><p>Data Set with 5,604 Common Microorganism Codes</p></td>
</tr><tr> </tr><tr>
<td> <td>

12
docs/reference/microorganisms.codes.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 Set with 5,605 Common Microorganism Codes — microorganisms.codes • AMR (for R)</title> <title>Data Set with 5,604 Common Microorganism Codes — microorganisms.codes • 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 Set with 5,605 Common Microorganism Codes — microorganisms.codes" /> <meta property="og:title" content="Data Set with 5,604 Common Microorganism Codes — microorganisms.codes" />
<meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions." /> <meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" /> <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
<meta name="twitter:card" content="summary_large_image" /> <meta name="twitter:card" content="summary_large_image" />
@ -93,7 +93,7 @@
</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">1.7.1.9030</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9050</span>
</span> </span>
</div> </div>
@ -237,7 +237,7 @@
<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 Set with 5,605 Common Microorganism Codes</h1> <h1>Data Set with 5,604 Common Microorganism Codes</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small> <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>microorganisms.codes.Rd</code></div> <div class="hidden name"><code>microorganisms.codes.Rd</code></div>
</div> </div>
@ -251,7 +251,7 @@
<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>
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 5,605 observations and 2 variables:</p><ul> <p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 5,604 observations and 2 variables:</p><ul>
<li><p><code>code</code><br /> Commonly used code of a microorganism</p></li> <li><p><code>code</code><br /> Commonly used code of a microorganism</p></li>
<li><p><code>mo</code><br /> ID of the microorganism in the <a href='microorganisms.html'>microorganisms</a> data set</p></li> <li><p><code>mo</code><br /> ID of the microorganism in the <a href='microorganisms.html'>microorganisms</a> data set</p></li>
</ul> </ul>
@ -288,7 +288,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p> <p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

2
docs/reference/translate.html
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@ -93,7 +93,7 @@
</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">1.7.1.9040</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9050</span>
</span> </span>
</div> </div>

4
man/microorganisms.codes.Rd
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@ -3,9 +3,9 @@
\docType{data} \docType{data}
\name{microorganisms.codes} \name{microorganisms.codes}
\alias{microorganisms.codes} \alias{microorganisms.codes}
\title{Data Set with 5,605 Common Microorganism Codes} \title{Data Set with 5,604 Common Microorganism Codes}
\format{ \format{
A \link{data.frame} with 5,605 observations and 2 variables: A \link{data.frame} with 5,604 observations and 2 variables:
\itemize{ \itemize{
\item \code{code}\cr Commonly used code of a microorganism \item \code{code}\cr Commonly used code of a microorganism
\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set \item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set

3
tests/tinytest.R
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@ -37,8 +37,5 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
color = FALSE) color = FALSE)
cat("SUMMARY:\n") cat("SUMMARY:\n")
print(summary(out)) print(summary(out))
cat("WARNINGS:\n")
print(warnings())
cat(attributes(out)$duration, "\n")
} }
} }