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remove reshape2 dependency
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parent
510e8f22aa
commit
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12
.travis.yml
12
.travis.yml
@ -2,18 +2,21 @@
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language: r
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jobs:
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include:
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- r: 3.1
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- r: 3.0
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os: linux
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warnings_are_errors: false
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- r: 3.0
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os: osx
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warnings_are_errors: false
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- r: 3.1
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os: linux
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- r: 3.1
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os: osx
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warnings_are_errors: false
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- r: 3.2
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os: linux
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warnings_are_errors: false
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- r: 3.2
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os: osx
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warnings_are_errors: false
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- r: 3.3
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os: linux
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- r: 3.3
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@ -43,12 +46,13 @@ cran: https://cran.rstudio.com
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before_install:
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# needed for clipboard function:
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# - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get -qq update; fi
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- if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get install -y xclip; fi
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# - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get install -y xclip; fi
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- if [ $TRAVIS_OS_NAME = osx ]; then brew install xclip; fi
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- if [ $TRAVIS_OS_NAME = osx ]; then brew install libgit2; fi
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# postrun
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after_success:
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# only run on osx, so clipboard functions can be checked
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- if [ $TRAVIS_OS_NAME = osx ]; then Rscript -e 'covr::codecov()'; fi
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notifications:
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email:
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.2.0.9017
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Date: 2018-07-28
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Version: 0.2.0.9018
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Date: 2018-07-30
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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@ -31,7 +31,6 @@ Imports:
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clipr,
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curl,
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dplyr (>= 0.7.0),
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reshape2 (>= 1.4.0),
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xml2 (>= 1.0.0),
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knitr (>= 1.0.0),
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Rcpp (>= 0.12.14),
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2
NEWS.md
2
NEWS.md
@ -28,7 +28,7 @@
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#### Changed
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* Improvements for forcasting with `resistance_predict` and added more examples
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* More antibiotics for EUCAST rules
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* Updated version of the `setic_patients` data set to better reflect the reality
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* Updated version of the `septic_patients` data set to better reflect the reality
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* Pretty printing for tibbles removed as it is not really the scope of this package
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* Improved speed of key antibiotics comparison for determining first isolates
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* 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
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21
R/bactid.R
21
R/bactid.R
@ -126,23 +126,27 @@ as.bactid <- function(x) {
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}
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if (tolower(x[i]) == '^h.*influenzae$') {
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# avoid detection of Haematobacter influenzae in case of H. influenzae
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x[i] <- 'Haemophilus influenzae'
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x[i] <- 'HAEINF'
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next
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}
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if (tolower(x[i]) == '^st.*au$'
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| tolower(x[i]) == '^stau$'
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| tolower(x[i]) == '^staaur$') {
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# avoid detection of Staphylococcus auricularis in case of S. aureus
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x[i] <- 'Staphylococcus aureus'
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x[i] <- 'STAAUR'
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next
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}
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if (tolower(x[i]) == '^p.*aer$') {
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# avoid detection of Pasteurella aerogenes in case of Pseudomonas aeruginosa
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x[i] <- 'Pseudomonas aeruginosa'
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x[i] <- 'PSEAER'
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next
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}
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if (tolower(x[i]) %like% 'coagulase'
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| tolower(x[i]) %like% 'cns'
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| tolower(x[i]) %like% 'cons') {
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# coerce S. coagulase negative, also as CNS and CoNS
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x[i] <- 'Coagulase Negative Staphylococcus (CNS)'
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x[i] <- 'STACNS'
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next
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}
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# translate known trivial names to genus+species
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@ -150,17 +154,20 @@ as.bactid <- function(x) {
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if (toupper(x.backup[i]) == 'MRSA'
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| toupper(x.backup[i]) == 'VISA'
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| toupper(x.backup[i]) == 'VRSA') {
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x[i] <- 'Staphylococcus aureus'
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x[i] <- 'STAAUR'
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next
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}
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if (toupper(x.backup[i]) == 'MRSE') {
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x[i] <- 'Staphylococcus epidermidis'
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}
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if (toupper(x.backup[i]) == 'VRE') {
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x[i] <- 'Enterococcus'
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x[i] <- 'ENC'
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next
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}
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if (toupper(x.backup[i]) == 'MRPA') {
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# multi resistant P. aeruginosa
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x[i] <- 'Pseudomonas aeruginosa'
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x[i] <- 'PSEAER'
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next
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}
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if (toupper(x.backup[i]) == 'PISP'
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| toupper(x.backup[i]) == 'PRSP') {
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