more unit tests

NEWS.md

@@ -1,6 +1,7 @@
 # 0.2.0
 #### New
 * Full support for Windows, Linux and macOS
+* Full support for old R versions, only R-3.0.0 (April 2013) or later is needed
 * Function `guess_bactid` to determine the ID of a microorganism based on genus/species or known abbreviations like MRSA
 * Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
 * Function `MDRO` to determine Multi Drug Resistant Organisms (MDRO) with support for country-specific guidelines. Suggest your own via [this link](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E). Functions `BRMO` and `MRGN` are wrappers for Dutch and German guidelines, respectively
@@ -9,7 +10,6 @@
 * New print format for tibbles and data.tables
 
 #### Changed
-* Support for old R versions, only R-3.0.0 (April 2013) or later is needed
 * Renamed dataset `ablist` to `antibiotics`
 * Renamed dataset `bactlist` to `microorganisms`
 * Added more microorganisms to `bactlist`

R/first_isolates.R

@@ -50,6 +50,7 @@
 #' @export
 #' @importFrom dplyr arrange_at lag between row_number filter mutate arrange
 #' @return A vector to add to table, see Examples.
+#' @source Methodology of this function is based on: "M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition", 2014, Clinical and Laboratory Standards Institute. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
 #' @examples
 #' # septic_patients is a dataset available in the AMR package
 #' ?septic_patients

README.md

@@ -8,12 +8,15 @@ This R package was created for academic research by PhD students of the Faculty
 ## Why this package?
 This R package contains functions to make microbiological, epidemiological data analysis easier. It allows the use of some new classes to work with MIC values and antimicrobial interpretations (i.e. values S, I and R).
 
-With AMR you can also apply EUCAST rules to isolates, identify first isolates of every patient, translate antibiotic codes from the lab (like `"AMOX"`) or the [WHO](https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no) (like `"J01CA04"`) to trivial names (like `"amoxicillin"`), or predict antimicrobial resistance for the nextcoming years with the `rsi_predict` function.
+With `AMR` you can also:
+* Conduct AMR analysis with the `rsi()` function, that can also be used with the `dplyr` package (e.g. in conjunction with `summarise`) to calculate the resistance percentages of different antibiotic columns of a table.
+* Predict antimicrobial resistance for the nextcoming years with the `rsi_predict()` function
+* Apply [EUCAST rules to isolates](http://www.eucast.org/expert_rules_and_intrinsic_resistance/) with the `EUCAST_rules()` function
+* Identify first isolates of every patient [using guidelines from the CLSI](https://clsi.org/standards/products/microbiology/documents/m39/) (Clinical and Laboratory Standards Institute) with the `first_isolate()` function
+* Translate antibiotic codes from the lab (like `"AMOX"`) or the [WHO](https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no) (like `"J01CA04"`) to trivial names (like `"amoxicillin"`) with the `abname()` function
 
 With the `MDRO` function (abbreviation of mutli-drug resistant organisms), you can check your isolates for exceptional resistance with country-specific guidelines. Currently guidelines for Germany and the Netherlands are supported. Please suggest addition of your own country here: [https://github.com/msberends/AMR/issues](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E).
 
-For regular AMR analysis, the `rsi` function can be used. This function als works with the `dplyr` package (e.g. in conjunction with `summarise`) to calculate the resistance percentages of different antibiotic columns of a table.
-
 This package contains an example data set `septic_patients`, consisting of 2000 isolates from anonymised septic patients between 2001 and 2017.
 
 ## How to get it?
@@ -32,7 +35,7 @@ This package is available on CRAN and also here on GitHub.
   - `install.packages("AMR")`
 
 - <img src="https://exploratory.io/favicon.ico" alt="Exploratory favicon" height="20px"> In [Exploratory.io](https://exploratory.io):
-  - (Exploratory.io costs $40/month, but is free for students and teachers; if you have an `@umcg.nl` or `@rug.nl` email address, [click here to enroll](https://exploratory.io/plan?plan=Community))
+  - (Exploratory.io costs $40/month but the somewhat limited Community Plan is free for students and teachers, [click here to enroll](https://exploratory.io/plan?plan=Community))
   - Start the software and log in
   - Click on your username at the right hand side top
   - Click on `R Packages`
@@ -276,7 +279,7 @@ bactlist      # A tibble: 2,507 x 10
   
 <sup>1</sup> Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
 
-<sup>2</sup> Department of Medical, Market and Innovation (MMI), Certe Medische diagnostiek & advies, Groningen, the Netherlands
+<sup>2</sup> Certe Medical Diagnostics & Advice, Groningen, the Netherlands
 
 ## Copyright
 [![License](https://img.shields.io/github/license/msberends/AMR.svg?colorB=3679BC)](https://github.com/msberends/AMR/blob/master/LICENSE)
@@ -287,6 +290,8 @@ This R package is licensed under the [GNU General Public License (GPL) v2.0](htt
 
 - May be used for private purposes
 
+- May **not** be used for patent purposes
+
 - May be modified, although:
 
   - Modifications **must** be released under the same license when distributing the package

man/first_isolate.Rd

@@ -3,6 +3,9 @@
 \name{first_isolate}
 \alias{first_isolate}
 \title{Determine first (weighted) isolates}
+\source{
+Methodology of this function is based on: "M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition", 2014, Clinical and Laboratory Standards Institute. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
+}
 \usage{
 first_isolate(tbl, col_date, col_patient_id, col_bactid = NA,
   col_testcode = NA, col_specimen = NA, col_icu = NA,

tests/testthat/test-first_isolates.R

@@ -17,7 +17,6 @@ test_that("first isolates work", {
                                  info = FALSE)), 1960)
 
   # septic_patients contains 1962 out of 2000 first *weighted* isolates
-  #septic_ptns$keyab <- suppressWarnings(key_antibiotics(septic_ptns))
   expect_equal(
     suppressWarnings(sum(
       first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
@@ -29,6 +28,13 @@ test_that("first isolates work", {
                     info = TRUE))),
     1962)
 
+  # septic_patients contains 1733 out of 2000 first non-ICU isolates
+  expect_equal(
+    sum(
+      first_isolate(septic_patients, col_bactid = "bactid", col_date = "date", col_patient_id = "patient_id", col_icu = "ward_icu", info = TRUE, icu_exclude = TRUE)),
+    1733
+  )
+
   # set 1500 random observations to be of specimen type 'Urine'
   random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
   expect_lt(sum(

tests/testthat/test-misc.R

@@ -1,7 +1,7 @@
 context("misc.R")
 
 test_that("`like` works", {
-  expect_true("test" %like% "^t")
+  expect_true(suppressWarnings("test" %like% c("^t", "^s")))
   expect_true("test" %like% "test")
   expect_true("test" %like% "TEST")
   expect_true(as.factor("test") %like% "TEST")

tests/testthat/test-print.R

@@ -3,6 +3,9 @@ context("print.R")
 
 test_that("tibble printing works", {
   library(dplyr)
+  library(data.table)
   expect_output(print(starwars))
+  expect_output(print(starwars %>% group_by(homeworld, gender)))
+  expect_output(print(starwars %>% as.data.table(), print.keys = TRUE))
   expect_output(print(septic_patients))
 })