mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 06:46:11 +01:00
(v0.8.0.9005) fix unit tests
This commit is contained in:
parent
d2e8249edd
commit
412077a6f2
@ -117,7 +117,7 @@ coverage:
|
||||
script:
|
||||
- apt-get install --yes git
|
||||
# codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd
|
||||
- Rscript -e "cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))"
|
||||
- Rscript -e "Sys.setenv(NOT_CRAN = 'true'); cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))"
|
||||
coverage: '/Code coverage: \d+\.\d+/'
|
||||
|
||||
pages:
|
||||
|
@ -1,5 +1,5 @@
|
||||
Package: AMR
|
||||
Version: 0.8.0.9004
|
||||
Version: 0.8.0.9005
|
||||
Date: 2019-10-26
|
||||
Title: Antimicrobial Resistance Analysis
|
||||
Authors@R: c(
|
||||
|
2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
|
||||
# AMR 0.8.0.9004
|
||||
# AMR 0.8.0.9005
|
||||
<small>Last updated: 26-Oct-2019</small>
|
||||
|
||||
### New
|
||||
|
@ -52,6 +52,7 @@ globalVariables(c(".",
|
||||
"Last name",
|
||||
"lookup",
|
||||
"mdr",
|
||||
"MDRO",
|
||||
"median",
|
||||
"microorganisms",
|
||||
"microorganisms.codes",
|
||||
|
2
R/mdro.R
2
R/mdro.R
@ -461,7 +461,7 @@ mdro <- function(x,
|
||||
left_join_microorganisms(by = col_mo) %>%
|
||||
# add unconfirmed to where genus is available
|
||||
mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_),
|
||||
row_number = 1:nrow(x)) %>%
|
||||
row_number = seq_len(nrow(x))) %>%
|
||||
# transform to data.frame so subsetting is possible with x[y, z] (might not be the case with tibble/data.table/...)
|
||||
as.data.frame(stringsAsFactors = FALSE)
|
||||
|
||||
|
2
R/mo.R
2
R/mo.R
@ -241,7 +241,6 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
|
||||
pull(mo)
|
||||
|
||||
# don't save valid fullnames to history (i.e. values that are in microorganisms$fullname)
|
||||
# set_mo_history(x, y, 0, force = isTRUE(list(...)$force_mo_history), disable = isTRUE(list(...)$disable_mo_history))
|
||||
|
||||
} else {
|
||||
# will be checked for mo class in validation and uses exec_as.mo internally if necessary
|
||||
@ -636,7 +635,6 @@ exec_as.mo <- function(x,
|
||||
x[i] <- found[1L]
|
||||
if (initial_search == TRUE) {
|
||||
# don't save valid fullnames to history (i.e. values that are in microorganisms$fullname)
|
||||
# set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
|
||||
}
|
||||
next
|
||||
}
|
||||
|
@ -19,4 +19,3 @@ ignore:
|
||||
- "R/atc_online.R"
|
||||
- "R/mo_source.R"
|
||||
- "R/resistance_predict.R"
|
||||
- "R/aa_test.R"
|
||||
|
@ -84,7 +84,7 @@
|
||||
</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">0.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -84,7 +84,7 @@
|
||||
</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">0.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -84,7 +84,7 @@
|
||||
</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">0.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -84,7 +84,7 @@
|
||||
</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">0.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -45,7 +45,7 @@
|
||||
</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">0.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -84,7 +84,7 @@
|
||||
</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">0.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -231,9 +231,9 @@
|
||||
|
||||
</div>
|
||||
|
||||
<div id="amr-0-8-0-9004" class="section level1">
|
||||
<div id="amr-0-8-0-9005" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-0-8-0-9004" class="anchor"></a>AMR 0.8.0.9004<small> Unreleased </small>
|
||||
<a href="#amr-0-8-0-9005" class="anchor"></a>AMR 0.8.0.9005<small> Unreleased </small>
|
||||
</h1>
|
||||
<p><small>Last updated: 26-Oct-2019</small></p>
|
||||
<div id="new" class="section level3">
|
||||
@ -1321,7 +1321,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<div id="tocnav">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#amr-0-8-0-9004">0.8.0.9004</a></li>
|
||||
<li><a href="#amr-0-8-0-9005">0.8.0.9005</a></li>
|
||||
<li><a href="#amr-0-8-0">0.8.0</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>
|
||||
|
@ -84,7 +84,7 @@
|
||||
</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">0.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -125,7 +125,7 @@ test_that("mdro works", {
|
||||
2)
|
||||
|
||||
# check the guideline by Magiorakos et al. (2012), the default guideline
|
||||
stau <- tibble::tribble(
|
||||
stau <- tribble(
|
||||
~mo, ~GEN, ~RIF, ~CPT, ~OXA, ~CIP, ~MFX, ~SXT, ~FUS, ~VAN, ~TEC, ~TLV, ~TGC, ~CLI, ~DAP, ~ERY, ~LNZ, ~CHL, ~FOS, ~QDA, ~TCY, ~DOX, ~MNO,
|
||||
"S. aureus", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
|
||||
"S. aureus", "R", "R", "R", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
|
||||
@ -134,7 +134,7 @@ test_that("mdro works", {
|
||||
)
|
||||
expect_equal(as.integer(mdro(stau)), c(1:4))
|
||||
|
||||
ente <- tibble::tribble(
|
||||
ente <- tribble(
|
||||
~mo, ~GEH, ~STH, ~IPM, ~MEM, ~DOR, ~CIP, ~LVX, ~MFX, ~VAN, ~TEC, ~TGC, ~DAP, ~LNZ, ~AMP, ~QDA, ~DOX, ~MNO,
|
||||
"Enterococcus", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
|
||||
"Enterococcus", "R", "R", "R", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
|
||||
@ -143,7 +143,7 @@ test_that("mdro works", {
|
||||
)
|
||||
expect_equal(as.integer(mdro(ente)), c(1:4))
|
||||
|
||||
entero <- tibble::tribble(
|
||||
entero <- tribble(
|
||||
~mo, ~GEN, ~TOB, ~AMK, ~NET, ~CPT, ~TCC, ~TZP, ~ETP, ~IPM, ~MEM, ~DOR, ~CZO, ~CXM, ~CTX, ~CAZ, ~FEP, ~FOX, ~CTT, ~CIP, ~SXT, ~TGC, ~ATM, ~AMP, ~AMC, ~SAM, ~CHL, ~FOS, ~COL, ~TCY, ~DOX, ~MNO,
|
||||
"E. coli", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
|
||||
"E. coli", "R", "R", "R", "R", "R", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
|
||||
@ -152,7 +152,7 @@ test_that("mdro works", {
|
||||
)
|
||||
expect_equal(as.integer(mdro(entero)), c(1:4))
|
||||
|
||||
pseud <- tibble::tribble(
|
||||
pseud <- tribble(
|
||||
~mo, ~GEN, ~TOB, ~AMK, ~NET, ~IPM, ~MEM, ~DOR, ~CAZ, ~FEP, ~CIP, ~LVX, ~TCC, ~TZP, ~ATM, ~FOS, ~COL, ~PLB,
|
||||
"P. aeruginosa", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
|
||||
"P. aeruginosa", "R", "S", "S", "S", "R", "S", "S", "S", "R", "S", "S", "S", "S", "S", "S", "S", "S",
|
||||
@ -161,7 +161,7 @@ test_that("mdro works", {
|
||||
)
|
||||
expect_equal(as.integer(mdro(pseud)), c(1:4))
|
||||
|
||||
acin <- tibble::tribble(
|
||||
acin <- tribble(
|
||||
~mo, ~GEN, ~TOB, ~AMK, ~NET, ~IPM, ~MEM, ~DOR, ~CIP, ~LVX, ~TZP, ~TCC, ~CTX, ~CRO, ~CAZ, ~FEP, ~SXT, ~SAM, ~COL, ~PLB, ~TCY, ~DOX, ~MNO,
|
||||
"A. baumannii", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
|
||||
"A. baumannii", "R", "R", "R", "R", "S", "R", "S", "S", "S", "S", "S", "S", "S", "S", "R", "S", "S", "S", "S", "S", "S", "S",
|
||||
|
Loading…
Reference in New Issue
Block a user