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(v0.7.1.9084) CI fix

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dr. M.S. (Matthijs) Berends 2019-09-23 20:55:54 +02:00
parent 8ce252fbc5
commit 76dc948067
12 changed files with 61 additions and 64 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.7.1.9083 Version: 0.7.1.9084
Date: 2019-09-23 Date: 2019-09-23
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9083 # AMR 0.7.1.9084
<small>Last updated: 23-Sep-2019</small> <small>Last updated: 23-Sep-2019</small>
### Breaking ### Breaking

1
R/globals.R
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@ -53,6 +53,7 @@ globalVariables(c(".",
"mdr", "mdr",
"median", "median",
"microorganisms", "microorganisms",
"microorganisms.codes",
"missing_names", "missing_names",
"mo", "mo",
"mono_count", "mono_count",

9
R/mo.R
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@ -652,9 +652,9 @@ exec_as.mo <- function(x,
if (!is.null(reference_df)) { if (!is.null(reference_df)) {
# self-defined reference # self-defined reference
if (x_backup[i] %in% reference_df[, 1]) { if (x_backup[i] %in% reference_df[, 1]) {
ref_mo <- reference_df[reference_df[, 1] == x_backup[i], "mo"] ref_mo <- reference_df[reference_df[, 1] == x_backup[i], "mo"][[1L]]
if (ref_mo %in% data_to_check[, mo]) { if (ref_mo %in% microorganismsDT[, mo]) {
x[i] <- data_to_check[mo == ref_mo, ..property][[1]][1L] x[i] <- microorganismsDT[mo == ref_mo, ..property][[1]][1L]
next next
} else { } else {
warning("Value '", x_backup[i], "' was found in reference_df, but '", ref_mo, "' is not a valid MO code.", call. = FALSE) warning("Value '", x_backup[i], "' was found in reference_df, but '", ref_mo, "' is not a valid MO code.", call. = FALSE)
@ -769,8 +769,7 @@ exec_as.mo <- function(x,
} }
next next
} }
if (toupper(x_backup_without_spp[i]) == 'CRS' if (toupper(x_backup_without_spp[i]) == 'CRSM') {
| toupper(x_backup_without_spp[i]) == 'CRSM') {
# co-trim resistant S. maltophilia # co-trim resistant S. maltophilia
x[i] <- microorganismsDT[mo == 'B_STNTR_MLTP', ..property][[1]][1L] x[i] <- microorganismsDT[mo == 'B_STNTR_MLTP', ..property][[1]][1L]
if (initial_search == TRUE) { if (initial_search == TRUE) {

2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</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">0.7.1.9083</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9084</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9083</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9084</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</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">0.7.1.9083</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9084</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -42,7 +42,7 @@
</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">0.7.1.9083</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9084</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9083</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9084</span>
</span> </span>
</div> </div>
@ -225,9 +225,9 @@
</div> </div>
<div id="amr-0-7-1-9083" class="section level1"> <div id="amr-0-7-1-9084" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9083" class="anchor"></a>AMR 0.7.1.9083<small> Unreleased </small> <a href="#amr-0-7-1-9084" class="anchor"></a>AMR 0.7.1.9084<small> Unreleased </small>
</h1> </h1>
<p><small>Last updated: 23-Sep-2019</small></p> <p><small>Last updated: 23-Sep-2019</small></p>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
@ -1280,7 +1280,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9083">0.7.1.9083</a></li> <li><a href="#amr-0-7-1-9084">0.7.1.9084</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li> <li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li> <li><a href="#amr-0-6-1">0.6.1</a></li>

2
docs/reference/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9083</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9084</span>
</span> </span>
</div> </div>

11
tests/testthat/test-mo.R
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@ -110,7 +110,7 @@ test_that("as.mo works", {
# too few characters # too few characters
expect_warning(as.mo("ab")) expect_warning(as.mo("ab"))
expect_equal(suppressWarnings(as.character(as.mo(c("Qq species", "", "CRS", "K. pneu rhino", "esco")))), expect_equal(suppressWarnings(as.character(as.mo(c("Qq species", "", "CRSM", "K. pneu rhino", "esco")))),
c("UNKNOWN", NA_character_, "B_STNTR_MLTP", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI")) c("UNKNOWN", NA_character_, "B_STNTR_MLTP", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI"))
# check for Becker classification # check for Becker classification
@ -221,14 +221,9 @@ test_that("as.mo works", {
expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID"))) expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID")))
# combination of existing mo and other code # combination of existing mo and other code
expect_identical(suppressWarnings(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL")))), expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
c("B_ESCHR_COLI", "B_ESCHR_COLI")) c("B_ESCHR_COLI", "B_ESCHR_COLI"))
# expect_equal(mo_fullname(c("E. spp.",
# "E. spp",
# "E. species")),
# rep("Escherichia species", 3))
# from different sources # from different sources
expect_equal(as.character(as.mo( expect_equal(as.character(as.mo(
c("PRTMIR", "bclcer", "B_ESCHR_COLI"))), c("PRTMIR", "bclcer", "B_ESCHR_COLI"))),
@ -259,7 +254,7 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("con")), "UNKNOWN") expect_equal(as.character(as.mo("con")), "UNKNOWN")
expect_equal(as.character(as.mo("xxx")), NA_character_) expect_equal(as.character(as.mo("xxx")), NA_character_)
expect_equal(as.character(as.mo(c("xxx", "con", "eco"))), c(NA_character_, "UNKNOWN", "B_ESCHR_COLI")) expect_equal(as.character(as.mo(c("xxx", "con", "eco"))), c(NA_character_, "UNKNOWN", "B_ESCHR_COLI"))
expect_equal(as.character(as.mo(c("other", "none", "unknown"))), expect_equal(as.character(as.mo(c("other", "none", "unknown"))),
rep("UNKNOWN", 3)) rep("UNKNOWN", 3))
expect_null(mo_failures()) expect_null(mo_failures())

2
tests/testthat/test-mo_property.R
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@ -90,6 +90,8 @@ test_that("mo_property works", {
expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968") expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999") expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
# old codes must throw a warning in mo_* family
expect_warning(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))
# outcome of mo_fullname must always return the fullname from the data set # outcome of mo_fullname must always return the fullname from the data set
library(dplyr) library(dplyr)