(v1.4.0.9039) more unit tests

tests/testthat/test-count.R

@@ -92,4 +92,11 @@ test_that("counts work", {
   expect_error(count_df(c("A", "B", "C")))
   expect_error(count_df(example_isolates[, "date"]))
   
+  # grouping in rsi_calc_df() (= backbone of rsi_df())
+  expect_true("hospital_id" %in% (example_isolates %>% 
+                group_by(hospital_id) %>% 
+                select(hospital_id, AMX, CIP, gender) %>%
+                rsi_df() %>% 
+                colnames()))
+  
 })

tests/testthat/test-disk.R

@@ -39,7 +39,12 @@ test_that("disk works", {
   expect_s3_class(c(x[1], x[9]), "disk")
   expect_s3_class(unique(x[1], x[9]), "disk")
   expect_warning(as.disk("INVALID VALUE"))
+  x[2] <- 32
+  expect_s3_class(x, "disk")
   
+  pdf(NULL) # prevent Rplots.pdf being created
+  expect_silent(plot(as.disk(c(10, 20, 40))))
+
   expect_output(print(as.disk(12)))
   library(dplyr, warn.conflicts = FALSE)
   expect_output(print(tibble(d = as.disk(12))))

tests/testthat/test-first_isolate.R

@@ -150,6 +150,8 @@ test_that("first isolates work", {
                              col_date = "non-existing col",
                              col_mo = "mo"))
 
+  require("dplyr")
+  
   # look for columns itself
   expect_message(first_isolate(example_isolates))
   expect_message(first_isolate(example_isolates %>%
@@ -166,6 +168,14 @@ test_that("first isolates work", {
                      first_isolate(col_date = "date",
                                    col_mo = "mo",
                                    col_patient_id = "patient_id"))
+  
+  # support for WHONET
+  expect_message(example_isolates %>%
+                   select(-patient_id) %>%
+                   mutate(`First name` = "test",
+                          `Last name` = "test", 
+                          Sex = "Female") %>% 
+                   first_isolate(info = TRUE))
 
   # missing dates should be no problem
   df <- example_isolates
@@ -203,6 +213,9 @@ test_that("first isolates work", {
   # notice that all mo's are distinct, so all are TRUE
   expect_true(all(example_isolates %pm>%
                     pm_distinct(mo, .keep_all = TRUE) %pm>%
-                    first_isolate() == TRUE))
+                    first_isolate(info = TRUE) == TRUE))
+  
+  # only one isolate, so return fast
+  expect_true(first_isolate(data.frame(mo = "Escherichia coli", date = Sys.Date(), patient = "patient"), info = TRUE))
 
 })

tests/testthat/test-like.R

@@ -31,8 +31,15 @@ test_that("`like` works", {
   
   expect_true("test" %like% "test")
   expect_false("test" %like_case% "TEST")
+  expect_true(factor("test") %like% factor("t"))
+  expect_true(factor("test") %like% "t")
+  expect_true("test" %like% factor("t"))
 
   expect_true(as.factor("test") %like% "TEST")
   expect_identical(factor(c("Test case", "Something different", "Yet another thing")) %like% c("case", "diff", "yet"),
                    c(TRUE, TRUE, TRUE))
+  expect_identical("test" %like% c("t", "e", "s", "t"),
+                   c(TRUE, TRUE, TRUE, TRUE))
+  expect_identical(factor("test") %like% factor(c("t", "e", "s", "t")),
+                   c(TRUE, TRUE, TRUE, TRUE))
 })

tests/testthat/test-mic.R

@@ -43,9 +43,11 @@ test_that("mic works", {
   expect_s3_class(x[[1]], "mic")
   expect_s3_class(c(x[1], x[9]), "mic")
   expect_s3_class(unique(x[1], x[9]), "mic")
+  expect_s3_class(droplevels(c(x[1], x[9])), "mic")
+  x[2] <- 32
+  expect_s3_class(x, "mic")
   expect_warning(as.mic("INVALID VALUE"))
   
-
   pdf(NULL) # prevent Rplots.pdf being created
   expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
   expect_silent(plot(as.mic(c(1, 2, 4, 8))))
@@ -56,4 +58,7 @@ test_that("mic works", {
                            "<NA>" = "0",
                            "Min." = "2",
                            "Max." = "8"), class = c("summaryDefault", "table")))
+  
+  library(dplyr, warn.conflicts = FALSE)
+  expect_output(print(tibble(m = as.mic(2:4))))
 })

tests/testthat/test-pca.R

@@ -49,7 +49,18 @@ test_that("PCA works", {
   expect_s3_class(pca_model, "pca")
   
   pdf(NULL) # prevent Rplots.pdf being created
-  
   ggplot_pca(pca_model, ellipse = TRUE)
   ggplot_pca(pca_model, arrows_textangled = FALSE)
+  
+  if (require("dplyr")) {
+    resistance_data <- example_isolates %>% 
+      group_by(order = mo_order(mo),
+               genus = mo_genus(mo)) %>%
+      summarise_if(is.rsi, resistance, minimum = 0)
+    pca_result <- resistance_data %>%         
+      pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, "SXT") 
+    expect_s3_class(pca_result, "prcomp")
+    ggplot_pca(pca_result, ellipse = TRUE)
+    ggplot_pca(pca_result, ellipse = FALSE, arrows_textangled = FALSE, scale = FALSE)
+  }
 })