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AMR
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(v1.5.0.9007) updated unit tests

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dr. M.S. (Matthijs) Berends 2021-01-18 18:45:43 +01:00
parent 4eab095306
commit 27f084d819
17 changed files with 47 additions and 43 deletions
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8
.github/workflows/check.yaml vendored
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@ -64,8 +64,8 @@ jobs:
- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
# - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
# - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
@ -75,8 +75,8 @@ jobs:
- {os: ubuntu-16.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# - {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
env:

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.5.0.9006
Version: 1.5.0.9007
Date: 2021-01-18
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.5.0.9006
# AMR 1.5.0.9007
## <small>Last updated: 18 January 2021</small>
### New

4
R/mdro.R
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@ -805,6 +805,7 @@ mdro <- function(x,
x[which(x$genus == "Escherichia" & x$species == "hermannii"), ab_NA(c(TCC, TZP))] <- NA
x[which((x$genus == "Citrobacter" & x$species == "freundii")
| (x$genus == "Enterobacter" & x$species == "aerogenes")
| (x$genus == "Klebsiella" & x$species == "aerogenes") # new name (2017)
| (x$genus == "Enterobacter" & x$species == "cloacae")
| (x$genus == "Hafnia" & x$species == "alvei")
| (x$genus == "Morganella" & x$species == "morganii")
@ -824,6 +825,7 @@ mdro <- function(x,
x[which((x$genus == "Citrobacter" & x$species == "koseri")
| (x$genus == "Citrobacter" & x$species == "freundii")
| (x$genus == "Enterobacter" & x$species == "aerogenes")
| (x$genus == "Klebsiella" & x$species == "aerogenes") # new name (2017)
| (x$genus == "Enterobacter" & x$species == "cloacae")
| (x$genus == "Escherichia" & x$species == "hermannii")
| (x$genus == "Hafnia" & x$species == "alvei")
@ -836,6 +838,7 @@ mdro <- function(x,
| (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(AMP)] <- NA
x[which((x$genus == "Citrobacter" & x$species == "freundii")
| (x$genus == "Enterobacter" & x$species == "aerogenes")
| (x$genus == "Klebsiella" & x$species == "aerogenes") # new name (2017)
| (x$genus == "Enterobacter" & x$species == "cloacae")
| (x$genus == "Hafnia" & x$species == "alvei")
| (x$genus == "Morganella" & x$species == "morganii")
@ -845,6 +848,7 @@ mdro <- function(x,
x[which((x$genus == "Citrobacter" & x$species == "freundii")
| (x$genus == "Citrobacter" & x$species == "koseri")
| (x$genus == "Enterobacter" & x$species == "aerogenes")
| (x$genus == "Klebsiella" & x$species == "aerogenes") # new name (2017)
| (x$genus == "Enterobacter" & x$species == "cloacae")
| (x$genus == "Hafnia" & x$species == "alvei")
| (x$genus == "Providencia" & x$species == "rettgeri")

BIN
data-raw/AMR_1.5.0.9006.tar.gz → data-raw/AMR_1.5.0.9007.tar.gz
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2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9007</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -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">1.5.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9007</span>
</span>
</div>

2
docs/articles/index.html
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@ -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">1.5.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9007</span>
</span>
</div>

2
docs/authors.html
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@ -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">1.5.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9007</span>
</span>
</div>

2
docs/index.html
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@ -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">1.5.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9007</span>
</span>
</div>

8
docs/news/index.html
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@ -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">1.5.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9007</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1509006" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9006">
<a href="#amr-1509006" class="anchor"></a>AMR 1.5.0.9006<small> Unreleased </small>
<div id="amr-1509007" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9007">
<a href="#amr-1509007" class="anchor"></a>AMR 1.5.0.9007<small> Unreleased </small>
</h1>
<div id="last-updated-18-january-2021" class="section level2">
<h2 class="hasAnchor">

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-01-18T15:57Z
last_built: 2021-01-18T17:45Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

2
docs/reference/index.html
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@ -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">1.5.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9007</span>
</span>
</div>

2
docs/survey.html
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@ -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">1.5.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9007</span>
</span>
</div>

13
tests/testthat/test-eucast_rules.R
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@ -50,20 +50,21 @@ test_that("EUCAST rules work", {
expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S", stringsAsFactors = TRUE)))
expect_identical(colnames(example_isolates),
colnames(suppressWarnings(eucast_rules(example_isolates))))
colnames(suppressWarnings(eucast_rules(example_isolates, info = FALSE))))
expect_output(suppressMessages(eucast_rules(example_isolates, info = TRUE)))
a <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
"Enterobacter aerogenes"),
"Enterobacter cloacae"),
amox = "-", # Amoxicillin
stringsAsFactors = FALSE)
b <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
"Enterobacter aerogenes"),
"Enterobacter cloacae"),
amox = "R", # Amoxicillin
stringsAsFactors = FALSE)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
expect_output(suppressMessages(suppressWarnings(eucast_rules(a, "mo", info = TRUE))))
a <- data.frame(mo = c("Staphylococcus aureus",
"Streptococcus group A"),
@ -81,8 +82,8 @@ test_that("EUCAST rules work", {
example_isolates %>%
mutate(TIC = as.rsi("R"),
PIP = as.rsi("S")) %>%
eucast_rules(col_mo = "mo", version_expertrules = 3.1) %>%
left_join_microorganisms() %>%
eucast_rules(col_mo = "mo", version_expertrules = 3.1, info = FALSE) %>%
left_join_microorganisms(by = "mo") %>%
filter(family == "Enterobacteriaceae") %>%
pull(PIP) %>%
unique() %>%

13
tests/testthat/test-mdro.R
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@ -34,13 +34,13 @@ test_that("mdro works", {
expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE))
expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))
outcome <- suppressWarnings(mdro(example_isolates))
outcome <- mdro(example_isolates, "eucast3.1", info = TRUE)
outcome <- eucast_exceptional_phenotypes(example_isolates, info = TRUE)
expect_output(suppressMessages(suppressWarnings(mdro(example_isolates, info = TRUE))))
expect_output(suppressMessages(suppressWarnings(mdro(example_isolates, "eucast3.1", info = TRUE))))
expect_output(outcome <- suppressMessages(suppressWarnings(eucast_exceptional_phenotypes(example_isolates, info = TRUE))))
# check class
expect_equal(class(outcome), c("ordered", "factor"))
outcome <- mdro(example_isolates, "nl", info = TRUE)
expect_output(outcome <- mdro(example_isolates, "nl", info = TRUE))
# check class
expect_equal(class(outcome), c("ordered", "factor"))
@ -228,15 +228,14 @@ test_that("mdro works", {
"ERY == 'R' & age > 60" ~ "Elderly Type B",
as_factor = TRUE)
expect_output(print(custom))
x <- mdro(example_isolates, guideline = custom, info = TRUE)
expect_equal(as.double(table(x)), c(43, 891, 1066))
expect_output(x <- mdro(example_isolates, guideline = custom, info = TRUE))
expect_equal(as.double(table(x)), c(1066, 43, 891))
expect_output(print(custom_mdro_guideline(AMX == "R" ~ "test", as_factor = FALSE)))
expect_error(custom_mdro_guideline())
expect_error(custom_mdro_guideline("test"))
expect_error(custom_mdro_guideline("test" ~ c(1:3)))
expect_error(custom_mdro_guideline("test" ~ A))
expect_error(custom_mdro_guideline(test ~ "A"))
expect_warning(mdro(example_isolates,
# since `test` gives an error, it will be ignored with a warning
guideline = custom_mdro_guideline(test ~ "A"),

24
tests/testthat/test-resistance_predict.R
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@ -27,25 +27,25 @@ context("resistance_predict.R")
test_that("prediction of rsi works", {
skip_on_cran()
AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COLI") %>%
rsi_predict(col_ab = "AMX",
col_date = "date",
model = "binomial",
minimum = 10,
info = TRUE) %>%
pull("value")
library(dplyr)
expect_output(AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COLI") %>%
rsi_predict(col_ab = "AMX",
col_date = "date",
model = "binomial",
minimum = 10,
info = TRUE) %>%
pull("value"))
# AMX resistance will increase according to data set `example_isolates`
expect_true(AMX_R[3] < AMX_R[20])
x <- resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial")
expect_output(x <- suppressMessages(resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial", info = TRUE)))
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(plot(x))
expect_silent(ggplot_rsi_predict(x))
expect_error(ggplot_rsi_predict(example_isolates))
library(dplyr, warn.conflicts = FALSE)
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",