(v1.3.0.9030) matching score update

tests/testthat/test-count.R

@@ -37,7 +37,7 @@ test_that("counts work", {
   expect_equal(suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
                count_SI(example_isolates$AMX))
   
-  library(dplyr)
+  library(dplyr, warn.conflicts = FALSE)
   expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
   expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687)
   expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764)

tests/testthat/test-disk.R

@@ -37,7 +37,7 @@ test_that("disk works", {
   expect_warning(as.disk("INVALID VALUE"))
   
   expect_output(print(as.disk(12)))
-  library(dplyr)
+  library(dplyr, warn.conflicts = FALSE)
   expect_output(print(tibble(d = as.disk(12))))
 
 })

tests/testthat/test-eucast_rules.R

@@ -72,7 +72,7 @@ test_that("EUCAST rules work", {
   expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
   
   # piperacillin must be R in Enterobacteriaceae when tica is R
-  library(dplyr)
+  library(dplyr, warn.conflicts = FALSE)
   expect_equal(suppressWarnings(
     example_isolates %>%
       mutate(TIC = as.rsi("R"),
@@ -85,7 +85,7 @@ test_that("EUCAST rules work", {
       as.character()),
     "R")
   
-  # Azithromicin and Clarythromycin must be equal to Erythromycin
+  # Azithromycin and Clarythromycin must be equal to Erythromycin
   a <- eucast_rules(data.frame(mo = example_isolates$mo,
                                ERY = example_isolates$ERY,
                                AZM = as.rsi("R"),

tests/testthat/test-ggplot_rsi.R

@@ -27,7 +27,7 @@ test_that("ggplot_rsi works", {
   
   skip_if_not_installed("ggplot2")
 
-  library(dplyr)
+  library(dplyr, warn.conflicts = FALSE)
   library(ggplot2)
   
   pdf(NULL) # prevent Rplots.pdf being created

tests/testthat/test-join_microorganisms.R

@@ -57,7 +57,7 @@ test_that("joins work", {
   expect_warning(right_join_microorganisms("B_ESCHR_COLI"))
   expect_warning(full_join_microorganisms("B_ESCHR_COLI"))
   
-  library(dplyr)
+  library(dplyr, warn.conflicts = FALSE)
   x <- tibble(bact = as.mo("E.coli"))
   expect_warning(left_join_microorganisms(x %>% group_by(bact), "bact"))
 

tests/testthat/test-key_antibiotics.R

@@ -32,6 +32,6 @@ test_that("keyantibiotics work", {
   expect_true(key_antibiotics_equal(".SS", "SI.", ignore_I = TRUE))
   expect_false(key_antibiotics_equal(".SS", "SI.", ignore_I = FALSE))
   
-  library(dplyr)
+  library(dplyr, warn.conflicts = FALSE)
   expect_warning(key_antibiotics(example_isolates %>% slice(rep(1, 10))))
 })

tests/testthat/test-mo.R

@@ -25,7 +25,7 @@ test_that("as.mo works", {
   
   skip_on_cran()
   
-  library(dplyr)
+  library(dplyr, warn.conflicts = FALSE)
  
   MOs <- microorganisms %>% filter(!is.na(mo), nchar(mo) > 3)
   expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))

tests/testthat/test-resistance_predict.R

@@ -40,7 +40,7 @@ test_that("prediction of rsi works", {
   expect_silent(ggplot_rsi_predict(x))
   expect_error(ggplot_rsi_predict(example_isolates))
 
-  library(dplyr)
+  library(dplyr, warn.conflicts = FALSE)
 
   expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
                             model = "binomial",

tests/testthat/test-rsi.R

@@ -54,7 +54,7 @@ test_that("rsi works", {
   expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)),
                    rep(FALSE, length(example_isolates)))
   
-  library(dplyr)
+  library(dplyr, warn.conflicts = FALSE)
   # 40 rsi columns
   expect_equal(example_isolates %>%
                  mutate_at(vars(PEN:RIF), as.character) %>%