few extra tests

NEWS.md

@@ -26,6 +26,7 @@
     ```r
     my_list = list(age = septic_patients$age, sex = septic_patients$sex)
     my_list %>% freq(age)
+    my_list %>% freq(sex)
     ```
     
 #### Other
@@ -53,8 +54,8 @@
   * New Lancefield classification for *Streptococcus* to categorise them into Lancefield groups
 * For convience, new descriptive statistical functions `kurtosis` and `skewness` that are lacking in base R - they are generic functions and have support for vectors, data.frames and matrices
 * Function `g.test` to perform the Χ<sup>2</sup> distributed [*G*-test](https://en.wikipedia.org/wiki/G-test), which use is the same as `chisq.test`
-* Function `ratio` to transform a vector of values to a preset ratio
-  * For example: `ratio(c(10, 500, 10), ratio = "1:2:1")` would return `130, 260, 130`
+* ~~Function `ratio` to transform a vector of values to a preset ratio~~
+  * ~~For example: `ratio(c(10, 500, 10), ratio = "1:2:1")` would return `130, 260, 130`~~
 * Support for Addins menu in RStudio to quickly insert `%in%` or `%like%` (and give them keyboard shortcuts), or to view the datasets that come with this package
 * Function `p.symbol` to transform p values to their related symbols: `0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1`
 * Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS. These functions use the `clipr` package, but are a little altered to also support headless Linux servers (so you can use it in RStudio Server)

R/freq.R

@@ -413,11 +413,9 @@ frequency_tbl <- function(x,
   df <- df %>% summarise(count = n())
 
   if (df$item %>% paste(collapse = ',') %like% '\033') {
-    df <- df %>%
-      mutate(item = item %>%
     # remove escape char
     # see https://en.wikipedia.org/wiki/Escape_character#ASCII_escape_character
-               gsub('\033', ' ', ., fixed = TRUE))
+    df <- df %>% mutate(item = item %>% gsub('\033', ' ', ., fixed = TRUE))
   }
 
   # sort according to setting

tests/testthat/test-freq.R

@@ -51,6 +51,7 @@ test_that("frequency table works", {
   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())
+  expect_output(print(freq(septic_patients$age), nmax = 20))
 
   # top 5
   expect_equal(

tests/testthat/test-join_microorganisms.R

@@ -23,9 +23,18 @@ test_that("joins work", {
   expect_true(nrow(unjoined) < nrow(right))
   expect_true(nrow(unjoined) < nrow(full))
 
+
   expect_equal(nrow(inner_join_microorganisms("ESCCOL")), 1)
+  expect_equal(nrow(inner_join_microorganisms("ESCCOL", by = c("bactid" = "bactid"))), 1)
+  expect_warning(inner_join_microorganisms("Escherichia", by = c("bactid" = "genus")))
+
   expect_equal(nrow(left_join_microorganisms("ESCCOL")), 1)
+  expect_warning(left_join_microorganisms("Escherichia", by = c("bactid" = "genus")))
+
   expect_equal(nrow(semi_join_microorganisms("ESCCOL")), 1)
   expect_equal(nrow(anti_join_microorganisms("ESCCOL")), 0)
 
+  eexpect_warning(right_join_microorganisms("ESCCOL"))
+  eexpect_warning(full_join_microorganisms("ESCCOL"))
+
 })