From 211e3bae143adb5900ad34815c144e8e51ce87a9 Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Mon, 30 Jul 2018 01:18:40 +0200
Subject: [PATCH] remove reshape2 dependency

---
 .travis.yml | 12 ++++++++----
 DESCRIPTION |  5 ++---
 NEWS.md     |  2 +-
 R/bactid.R  | 21 ++++++++++++++-------
 4 files changed, 25 insertions(+), 15 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index be9022e0..444b597d 100755
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,18 +2,21 @@
 language: r
 jobs:
   include:
-  - r: 3.1
+  - r: 3.0
     os: linux
     warnings_are_errors: false
+  - r: 3.0
+    os: osx
+    warnings_are_errors: false
+  - r: 3.1
+    os: linux
   - r: 3.1
     os: osx
     warnings_are_errors: false
   - r: 3.2
     os: linux
-    warnings_are_errors: false
   - r: 3.2
     os: osx
-    warnings_are_errors: false
   - r: 3.3
     os: linux
   - r: 3.3
@@ -43,12 +46,13 @@ cran: https://cran.rstudio.com
 before_install:
   # needed for clipboard function:
   # - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get -qq update; fi
-  - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get install -y xclip; fi
+  # - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get install -y xclip; fi
   - if [ $TRAVIS_OS_NAME = osx ]; then brew install xclip; fi
   - if [ $TRAVIS_OS_NAME = osx ]; then brew install libgit2; fi
 
 # postrun
 after_success:
+  # only run on osx, so clipboard functions can be checked
   - if [ $TRAVIS_OS_NAME = osx ]; then Rscript -e 'covr::codecov()'; fi
 notifications:
   email:
diff --git a/DESCRIPTION b/DESCRIPTION
index 5e206ebb..df6100cc 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.2.0.9017
-Date: 2018-07-28
+Version: 0.2.0.9018
+Date: 2018-07-30
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(
@@ -31,7 +31,6 @@ Imports:
     clipr,
     curl,
     dplyr (>= 0.7.0),
-    reshape2 (>= 1.4.0),
     xml2 (>= 1.0.0),
     knitr (>= 1.0.0),
     Rcpp (>= 0.12.14),
diff --git a/NEWS.md b/NEWS.md
index 210f2071..2115ce73 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -28,7 +28,7 @@
 #### Changed
 * Improvements for forcasting with `resistance_predict` and added more examples
 * More antibiotics for EUCAST rules
-* Updated version of the `setic_patients` data set to better reflect the reality
+* Updated version of the `septic_patients` data set to better reflect the reality
 * Pretty printing for tibbles removed as it is not really the scope of this package
 * Improved speed of key antibiotics comparison for determining first isolates
 * Column names for the `key_antibiotics` function are now generic: 6 for broadspectrum ABs, 6 for Gram-positive specific and 6 for Gram-negative specific ABs
diff --git a/R/bactid.R b/R/bactid.R
index 868aa09c..ba677b59 100644
--- a/R/bactid.R
+++ b/R/bactid.R
@@ -126,23 +126,27 @@ as.bactid <- function(x) {
     }
     if (tolower(x[i]) == '^h.*influenzae$') {
       # avoid detection of Haematobacter influenzae in case of H. influenzae
-      x[i] <- 'Haemophilus influenzae'
+      x[i] <- 'HAEINF'
+      next
     }
     if (tolower(x[i]) == '^st.*au$'
         | tolower(x[i]) == '^stau$'
         | tolower(x[i]) == '^staaur$') {
       # avoid detection of Staphylococcus auricularis in case of S. aureus
-      x[i] <- 'Staphylococcus aureus'
+      x[i] <- 'STAAUR'
+      next
     }
     if (tolower(x[i]) == '^p.*aer$') {
       # avoid detection of Pasteurella aerogenes in case of Pseudomonas aeruginosa
-      x[i] <- 'Pseudomonas aeruginosa'
+      x[i] <- 'PSEAER'
+      next
     }
     if (tolower(x[i]) %like% 'coagulase'
         | tolower(x[i]) %like% 'cns'
         | tolower(x[i]) %like% 'cons') {
       # coerce S. coagulase negative, also as CNS and CoNS
-      x[i] <- 'Coagulase Negative Staphylococcus (CNS)'
+      x[i] <- 'STACNS'
+      next
     }
 
     # translate known trivial names to genus+species
@@ -150,17 +154,20 @@ as.bactid <- function(x) {
       if (toupper(x.backup[i]) == 'MRSA'
           | toupper(x.backup[i]) == 'VISA'
           | toupper(x.backup[i]) == 'VRSA') {
-        x[i] <- 'Staphylococcus aureus'
+        x[i] <- 'STAAUR'
+        next
       }
       if (toupper(x.backup[i]) == 'MRSE') {
         x[i] <- 'Staphylococcus epidermidis'
       }
       if (toupper(x.backup[i]) == 'VRE') {
-        x[i] <- 'Enterococcus'
+        x[i] <- 'ENC'
+        next
       }
       if (toupper(x.backup[i]) == 'MRPA') {
         # multi resistant P. aeruginosa
-        x[i] <- 'Pseudomonas aeruginosa'
+        x[i] <- 'PSEAER'
+        next
       }
       if (toupper(x.backup[i]) == 'PISP'
           | toupper(x.backup[i]) == 'PRSP') {