new g.test() and edited freq()

tests/testthat/test-freq.R

@@ -10,43 +10,40 @@ test_that("frequency table works", {
                length(unique(septic_patients$date)))
 
   # int
-  expect_output(freq(septic_patients$age))
+  expect_output(print(freq(septic_patients$age)))
   # date
-  expect_output(freq(septic_patients$date))
+  expect_output(print(freq(septic_patients$date)))
   # factor
-  expect_output(freq(septic_patients$hospital_id))
+  expect_output(print(freq(septic_patients$hospital_id)))
 
   library(dplyr)
-  expect_output(septic_patients %>% select(1:2) %>% freq())
-  expect_output(septic_patients %>% select(1:3) %>% freq())
-  expect_output(septic_patients %>% select(1:4) %>% freq())
-  expect_output(septic_patients %>% select(1:5) %>% freq())
-  expect_output(septic_patients %>% select(1:6) %>% freq())
-  expect_output(septic_patients %>% select(1:7) %>% freq())
-  expect_output(septic_patients %>% select(1:8) %>% freq())
-  expect_output(septic_patients %>% select(1:9) %>% freq())
+  expect_output(septic_patients %>% select(1:2) %>% freq() %>% print())
+  expect_output(septic_patients %>% select(1:3) %>% freq() %>% print())
+  expect_output(septic_patients %>% select(1:4) %>% freq() %>% print())
+  expect_output(septic_patients %>% select(1:5) %>% freq() %>% print())
+  expect_output(septic_patients %>% select(1:6) %>% freq() %>% print())
+  expect_output(septic_patients %>% select(1:7) %>% freq() %>% print())
+  expect_output(septic_patients %>% select(1:8) %>% freq() %>% print())
+  expect_output(septic_patients %>% select(1:9) %>% freq() %>% print())
 
   # top 5
   expect_equal(
     septic_patients %>%
-      select(bactid) %>%
-      freq(as.data.frame = TRUE) %>%
+      freq(bactid) %>%
       top_freq(5) %>%
       length(),
     5)
   # there're more than 5 lowest values
   expect_gt(
     septic_patients %>%
-      select(bactid) %>%
-      freq(as.data.frame = TRUE) %>%
+      freq(bactid) %>%
       top_freq(-5) %>%
       length(),
     5)
   # n has length > 1
   expect_error(
     septic_patients %>%
-      select(bactid) %>%
-      freq(as.data.frame = TRUE) %>%
+      freq(bactid) %>%
       top_freq(n = c(1, 2))
   )
   # input must be freq tbl

tests/testthat/test-g.test.R

@@ -0,0 +1,19 @@
+context("g.test.R")
+
+test_that("G-test works", {
+
+  # example 1: clearfield rice vs. red rice
+  x <- c(772, 1611, 737)
+  x.expected <- vector2ratio(x, ratio = "1:2:1")
+  expect_equal(g.test(x, x.expected),
+               expected = 0.12574,
+               tolerance = 0.00001)
+
+  # example 2: red crossbills
+  x <- c(1752, 1895)
+  x.expected <- vector2ratio(x, ratio = c(1, 1))
+  expect_equal(g.test(x, x.expected),
+               expected = 0.01787343,
+               tolerance = 0.00000001)
+
+})

tests/testthat/test-mdro.R

@@ -13,7 +13,7 @@ test_that("MDRO works", {
   expect_equal(outcome %>% class(), c('ordered', 'factor'))
 
   # septic_patients should have these finding using Dutch guidelines
-  expect_equal(outcome %>% freq(as.data.frame = TRUE) %>% pull(count), c(3, 21))
+  expect_equal(outcome %>% freq() %>% pull(count), c(3, 21))
 
   expect_equal(BRMO(septic_patients, info = FALSE), MDRO(septic_patients, "nl", info = FALSE))