remove reshape2 dependency

.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:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.2.0.9017
+Version: 0.2.0.9018
-Date: 2018-07-28
+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),

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

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') {