(v1.5.0.9017) unit testing

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.5.0.9016
+Version: 1.5.0.9017
 Date: 2021-02-08
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.5.0.9016
+# AMR 1.5.0.9017
 ## <small>Last updated:  8 February 2021</small>
 
 ### New
@@ -52,11 +52,11 @@
 * WHONET code `"PNV"` will now correctly be interpreted as `PHN`, the antibiotic code for phenoxymethylpenicillin ('peni V')
 * Fix for verbose output of `mdro(..., verbose = TRUE)` for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only *P. aeruginosa*)
 * `is.rsi.eligible()` now detects if the column name resembles an antibiotic name or code and now returns `TRUE` immediately if the input contains any of the values "R", "S" or "I". This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.
-* Functions  `get_episode()` and `is_new_episode()` now support less than a day as value for argument `episode_days` (e.g., to include one patient/test per hour)
+* Functions `get_episode()` and `is_new_episode()` now support less than a day as value for argument `episode_days` (e.g., to include one patient/test per hour)
 * Argument `ampc_cephalosporin_resistance` in `eucast_rules()` now also applies to value "I" (not only "S")
 * Updated colours of values R, S and I in tibble printing
 * Functions `print()` and `summary()` on a Principal Components Analysis object (`pca()`) now print additional group info if the original data was grouped using `dplyr::group_by()`
-* Improved speed of `guess_ab_col()`
+* Improved speed and reliability of `guess_ab_col()`. As this also internally improves the reliability of `first_isolate()` and `mdro()`, this might have a slight impact on the results of those functions.
 
 ### Other
 * Big documentation updates

R/aa_helper_functions.R

@@ -734,7 +734,7 @@ get_current_column <- function() {
 
 is_null_or_grouped_tbl <- function(x) {
   # attribute "grouped_df" might change at one point, so only set in one place; here.
-  is.null(x) || inherits(x, "grouped_tbl")
+  is.null(x) || inherits(x, "grouped_df")
 }
 
 unique_call_id <- function(entire_session = FALSE) {

R/filter_ab_class.R

@@ -147,9 +147,6 @@ filter_ab_class <- function(x,
   } else {
     scope_txt <- " and "
     scope_fn <- all
-    if (length(agents) > 1) {
-      operator <- gsub("is", "are", operator)
-    }
   }
   if (length(agents) > 1) {
     operator <- " are"

R/first_isolate.R

@@ -187,7 +187,8 @@ first_isolate <- function(x = NULL,
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
-    x <- get_current_data(arg_name = "x", call = -2)
+    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
+    meet_criteria(x, allow_class = "data.frame")
   }
   # remove data.table, grouping from tibbles, etc.
   x <- as.data.frame(x, stringsAsFactors = FALSE)
@@ -518,7 +519,8 @@ filter_first_isolate <- function(x = NULL,
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
-    x <- get_current_data(arg_name = "x", call = -2)
+    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
+    meet_criteria(x, allow_class = "data.frame")
   }
   subset(x, first_isolate(x = x,
                           col_date = col_date,
@@ -543,7 +545,8 @@ filter_first_weighted_isolate <- function(x = NULL,
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
-    x <- get_current_data(arg_name = "x", call = -2)
+    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
+    meet_criteria(x, allow_class = "data.frame")
   }
   y <- x
   if (is.null(col_keyantibiotics)) {

R/key_antibiotics.R

@@ -155,7 +155,8 @@ key_antibiotics <- function(x = NULL,
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
-    x <- get_current_data(arg_name = "x", call = -2)
+    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
+    meet_criteria(x, allow_class = "data.frame")
   }
   # force regular data.frame, not a tibble or data.table
   x <- as.data.frame(x, stringsAsFactors = FALSE)

R/mdro.R

@@ -218,7 +218,8 @@ mdro <- function(x = NULL,
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
-    x <- get_current_data(arg_name = "x", call = -2)
+    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
+    meet_criteria(x, allow_class = "data.frame")
   }
   
   # force regular data.frame, not a tibble or data.table

docs/404.html

@@ -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">1.5.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9017</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -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">1.5.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9017</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -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">1.5.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9017</span>
       </span>
     </div>
 

docs/authors.html

@@ -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">1.5.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9017</span>
       </span>
     </div>
 

docs/index.html

@@ -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">1.5.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9017</span>
       </span>
     </div>
 

docs/pkgdown.yml

@@ -12,7 +12,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-02-08T12:50Z
+last_built: 2021-02-08T19:58Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

docs/reference/index.html

@@ -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">1.5.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9017</span>
       </span>
     </div>
 

docs/survey.html

@@ -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">1.5.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9017</span>
       </span>
     </div>
 

tests/testthat/test-ab_class_selectors.R

@@ -39,6 +39,7 @@ test_that("Antibiotic class selectors work", {
   expect_lt(example_isolates %>% dplyr::select(fluoroquinolones()) %>% ncol(), ncol(example_isolates))
   expect_lt(example_isolates %>% dplyr::select(glycopeptides()) %>% ncol(), ncol(example_isolates))
   expect_lt(example_isolates %>% dplyr::select(macrolides()) %>% ncol(), ncol(example_isolates))
+  expect_lt(example_isolates %>% dplyr::select(oxazolidinones()) %>% ncol(), ncol(example_isolates))
   expect_lt(example_isolates %>% dplyr::select(penicillins()) %>% ncol(), ncol(example_isolates))
   expect_lt(example_isolates %>% dplyr::select(tetracyclines()) %>% ncol(), ncol(example_isolates))
   

tests/testthat/test-filter_ab_class.R

@@ -30,17 +30,20 @@ test_that("ATC-group filtering works", {
   
   library(dplyr)
   expect_gt(example_isolates %>% filter_ab_class("carbapenem") %>% nrow(), 0)
-  expect_gt(example_isolates %>% filter_aminoglycosides() %>% nrow(), 0)
+  expect_gt(example_isolates %>% filter_aminoglycosides() %>% ncol(), 0)
-  expect_gt(example_isolates %>% filter_carbapenems() %>% nrow(), 0)
+  expect_gt(example_isolates %>% filter_carbapenems() %>% ncol(), 0)
-  expect_gt(example_isolates %>% filter_cephalosporins() %>% nrow(), 0)
+  expect_gt(example_isolates %>% filter_cephalosporins() %>% ncol(), 0)
-  expect_gt(example_isolates %>% filter_1st_cephalosporins() %>% nrow(), 0)
+  expect_gt(example_isolates %>% filter_1st_cephalosporins() %>% ncol(), 0)
-  expect_gt(example_isolates %>% filter_2nd_cephalosporins() %>% nrow(), 0)
+  expect_gt(example_isolates %>% filter_2nd_cephalosporins() %>% ncol(), 0)
-  expect_gt(example_isolates %>% filter_3rd_cephalosporins() %>% nrow(), 0)
+  expect_gt(example_isolates %>% filter_3rd_cephalosporins() %>% ncol(), 0)
-  expect_gt(example_isolates %>% filter_4th_cephalosporins() %>% nrow(), 0)
+  expect_gt(example_isolates %>% filter_4th_cephalosporins() %>% ncol(), 0)
-  expect_gt(example_isolates %>% filter_fluoroquinolones() %>% nrow(), 0)
+  expect_gt(example_isolates %>% filter_5th_cephalosporins() %>% ncol(), 0)
-  expect_gt(example_isolates %>% filter_glycopeptides() %>% nrow(), 0)
+  expect_gt(example_isolates %>% filter_fluoroquinolones() %>% ncol(), 0)
-  expect_gt(example_isolates %>% filter_macrolides() %>% nrow(), 0)
+  expect_gt(example_isolates %>% filter_glycopeptides() %>% ncol(), 0)
-  expect_gt(example_isolates %>% filter_tetracyclines() %>% nrow(), 0)
+  expect_gt(example_isolates %>% filter_macrolides() %>% ncol(), 0)
+  expect_gt(example_isolates %>% filter_oxazolidinones() %>% ncol(), 0)
+  expect_gt(example_isolates %>% filter_penicillins() %>% ncol(), 0)
+  expect_gt(example_isolates %>% filter_tetracyclines() %>% ncol(), 0)
 
   expect_gt(example_isolates %>% filter_carbapenems("R", "all") %>% nrow(), 0)
 

tests/testthat/test-first_isolate.R

@@ -50,7 +50,7 @@ test_that("first isolates work", {
                       type = "keyantibiotics",
                       info = TRUE),
         na.rm = TRUE)),
-    1396)
+    1395)
 
   # when not ignoring I
   expect_equal(
@@ -65,7 +65,7 @@ test_that("first isolates work", {
                       type = "keyantibiotics",
                       info = TRUE),
         na.rm = TRUE)),
-    1419)
+    1418)
   # when using points
   expect_equal(
     suppressWarnings(
@@ -78,7 +78,7 @@ test_that("first isolates work", {
                       type = "points",
                       info = TRUE),
         na.rm = TRUE)),
-    1399)
+    1398)
 
   # first non-ICU isolates
   expect_equal(

tests/testthat/test-mdro.R

@@ -47,7 +47,7 @@ test_that("mdro works", {
   library(dplyr)
   # example_isolates should have these finding using Dutch guidelines
   expect_equal(as.double(table(outcome)),
-               c(1969, 25, 6)) # 1969 neg, 25 unconfirmed, 6 pos
+               c(1970, 24, 6)) # 1970 neg, 24 unconfirmed, 6 pos
 
   expect_equal(brmo(example_isolates, info = FALSE),
                mdro(example_isolates, guideline = "BRMO", info = FALSE))
@@ -241,4 +241,9 @@ test_that("mdro works", {
                       guideline = custom_mdro_guideline(test ~ "A"), 
                       info = FALSE))
   
+  # print groups
+  library(dplyr)
+  expect_output(x <- mdro(example_isolates %>% group_by(hospital_id), info = TRUE))
+  expect_output(x <- mdro(example_isolates %>% group_by(hospital_id), guideline = custom, info = TRUE))
+  
 })