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(v1.2.0.9032) Permanently move to GitHub
This commit is contained in:
parent
a438dcc884
commit
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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# as long as GitLab used - make sure the website will be updated
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stages:
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- deploy
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pages:
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stage: deploy
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allow_failure: true
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when: always
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only:
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- master
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script:
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- mv docs public
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artifacts:
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paths:
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- public
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.2.0.9031
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Version: 1.2.0.9032
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Date: 2020-07-09
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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4
NEWS.md
4
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.2.0.9031
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# AMR 1.2.0.9032
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## <small>Last updated: 09-Jul-2020</small>
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### New
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@ -38,7 +38,7 @@
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* Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
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### Other
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* Project moved to GitHub
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* Moved primary location of this project from GitLab to [GitHub](https://github.com/msberends/AMR), giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.
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# AMR 1.2.0
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@ -126,7 +126,7 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
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# check if text to look for is in one of the patterns
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any_form_in_patterns <- tryCatch(any(from %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")),
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error = function(e) {
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warning("Translation not possible. Please open an issue on GitLab (https://github.com/msberends/AMR/issues) or GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
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warning("Translation not possible. Please open an issue on GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
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return(FALSE)
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})
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if (NROW(df_trans) == 0 | !any_form_in_patterns) {
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@ -1,18 +1,18 @@
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% AMR (for R)
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# `AMR` (for R)
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<img src="man/figures/logo.png" align="right" height="120px" />
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<img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
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This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR](https://msberends.github.io/AMR) to read about this package.
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*NOTE: this source code is on GitHub (https://github.com/msberends/AMR) and GitLab (https://gitlab.com/msberends/AMR).*
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*NOTE: this source code is on GitHub (https://github.com/msberends/AMR), but also automatically mirrored to GitLab (https://gitlab.com/msberends/AMR).*
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### How to get this package
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Please see [our website](https://msberends.github.io/AMR/#get-this-package).
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### Copyright
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This R package is licensed under the [GNU General Public License (GPL) v2.0](https://gitlab.com/msberends/AMR/blob/master/LICENSE). In a nutshell, this means that this package:
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This R package is licensed under the [GNU General Public License (GPL) v2.0](https://github.com/msberends/AMR/blob/master/LICENSE). In a nutshell, this means that this package:
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- May be used for commercial purposes
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@ -3,7 +3,7 @@
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
|
||||
# (c) 2018-2020 Berends MS, Luz CF et al. #
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@ -16,7 +16,7 @@
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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||||
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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# Read and format data ----------------------------------------------------
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@ -3,7 +3,7 @@
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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||||
# #
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||||
# LICENCE #
|
||||
# (c) 2018-2020 Berends MS, Luz CF et al. #
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@ -16,7 +16,7 @@
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||||
# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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# Run this file to update the package using: -------------------------------
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@ -3,7 +3,7 @@
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2020 Berends MS, Luz CF et al. #
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||||
@ -16,7 +16,7 @@
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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||||
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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# last updated: 20 January 2020 - Loinc_2.67
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@ -3,7 +3,7 @@
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
|
||||
# (c) 2018-2020 Berends MS, Luz CF et al. #
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@ -16,7 +16,7 @@
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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||||
# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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||||
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# ------------------------------------------------
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|
@ -3,7 +3,7 @@
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2020 Berends MS, Luz CF et al. #
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||||
@ -16,7 +16,7 @@
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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||||
# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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library(openxlsx)
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@ -3,7 +3,7 @@
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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||||
# LICENCE #
|
||||
# (c) 2018-2020 Berends MS, Luz CF et al. #
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@ -16,7 +16,7 @@
|
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# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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library(dplyr)
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
|
||||
# (c) 2018-2020 Berends MS, Luz CF et al. #
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@ -16,7 +16,7 @@
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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# get all data from the WHOCC website
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@ -3,7 +3,7 @@
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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||||
# https://gitlab.com/msberends/AMR #
|
||||
# https://github.com/msberends/AMR #
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||||
# #
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||||
# LICENCE #
|
||||
# (c) 2018-2020 Berends MS, Luz CF et al. #
|
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@ -16,7 +16,7 @@
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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patients <- unlist(lapply(LETTERS, paste0, 1:10))
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@ -3,7 +3,7 @@
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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||||
# https://gitlab.com/msberends/AMR #
|
||||
# https://github.com/msberends/AMR #
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||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2020 Berends MS, Luz CF et al. #
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@ -16,7 +16,7 @@
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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# Reproduction of the `microorganisms` data set
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|
@ -3,7 +3,7 @@
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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||||
# https://github.com/msberends/AMR #
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# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2020 Berends MS, Luz CF et al. #
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@ -16,7 +16,7 @@
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# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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library(AMR)
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<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">1.2.0.9031</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9031</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
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</span>
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</div>
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|
@ -39,7 +39,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9030</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
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</span>
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</div>
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@ -39,7 +39,7 @@
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</button>
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<span class="navbar-brand">
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<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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
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</span>
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</div>
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@ -202,7 +202,7 @@
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<p>An example syntax could look like this:</p>
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<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">readxl</span>)
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<span class="no">data</span> <span class="kw"><-</span> <span class="fu"><a href="https://readxl.tidyverse.org/reference/read_excel.html">read_excel</a></span>(<span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/your/file.xlsx"</span>)</pre></body></html></div>
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<p>This package comes with an <a href="https://msberends.gitlab.io/AMR/reference/WHONET.html">example data set <code>WHONET</code></a>. We will use it for this analysis.</p>
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||||
<p>This package comes with an <a href="https://msberends.github.io/AMR/reference/WHONET.html">example data set <code>WHONET</code></a>. We will use it for this analysis.</p>
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</div>
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<div id="preparation" class="section level3">
|
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<h3 class="hasAnchor">
|
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@ -214,7 +214,7 @@
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<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">cleaner</span>) <span class="co"># to create frequency tables</span></pre></body></html></div>
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<p>We will have to transform some variables to simplify and automate the analysis:</p>
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<ul>
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<li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="https://msberends.gitlab.io/AMR/reference/catalogue_of_life">our Catalogue of Life reference data set</a>, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
|
||||
<li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="https://msberends.github.io/AMR/reference/catalogue_of_life">our Catalogue of Life reference data set</a>, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
|
||||
<li>Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values <code>"S"</code>, <code>"I"</code> or <code>"R"</code>. That is exactly where the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function is for.</li>
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||||
</ul>
|
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<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="co"># transform variables</span>
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@ -81,7 +81,7 @@
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</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">1.2.0.9031</span>
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||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
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</span>
|
||||
</div>
|
||||
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||||
|
@ -81,7 +81,7 @@
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</button>
|
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<span class="navbar-brand">
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||||
<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">1.2.0.9031</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
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</span>
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</div>
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||||
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||||
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@ -43,7 +43,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
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||||
<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">1.2.0.9031</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
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@ -81,7 +81,7 @@
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</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">1.2.0.9031</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
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</div>
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@ -229,9 +229,9 @@
|
||||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-1209031" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.2.0.9031">
|
||||
<a href="#amr-1209031" class="anchor"></a>AMR 1.2.0.9031<small> Unreleased </small>
|
||||
<div id="amr-1209032" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.2.0.9032">
|
||||
<a href="#amr-1209032" class="anchor"></a>AMR 1.2.0.9032<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-09-jul-2020" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
@ -292,7 +292,7 @@
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>Project moved to GitHub</li>
|
||||
<li>Moved primary location of this project from GitLab to <a href="https://github.com/msberends/AMR">GitHub</a>, giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
@ -10,7 +10,7 @@ articles:
|
||||
WHONET: WHONET.html
|
||||
benchmarks: benchmarks.html
|
||||
resistance_predict: resistance_predict.html
|
||||
last_built: 2020-07-09T14:11Z
|
||||
last_built: 2020-07-09T18:06Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR/reference
|
||||
article: https://msberends.github.io/AMR/articles
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -83,7 +83,7 @@ This function requires an internet connection." />
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -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">1.2.0.9031</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</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">1.2.0.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
BIN
docs/works_great_on.png
Normal file
BIN
docs/works_great_on.png
Normal file
Binary file not shown.
After Width: | Height: | Size: 87 KiB |
BIN
pkgdown/logos/works_great_on.png
Normal file
BIN
pkgdown/logos/works_great_on.png
Normal file
Binary file not shown.
After Width: | Height: | Size: 87 KiB |
@ -34,7 +34,7 @@ library(readxl)
|
||||
data <- read_excel(path = "path/to/your/file.xlsx")
|
||||
```
|
||||
|
||||
This package comes with an [example data set `WHONET`](https://msberends.gitlab.io/AMR/reference/WHONET.html). We will use it for this analysis.
|
||||
This package comes with an [example data set `WHONET`](https://msberends.github.io/AMR/reference/WHONET.html). We will use it for this analysis.
|
||||
|
||||
### Preparation
|
||||
|
||||
@ -49,7 +49,7 @@ library(cleaner) # to create frequency tables
|
||||
|
||||
We will have to transform some variables to simplify and automate the analysis:
|
||||
|
||||
* Microorganisms should be transformed to our own microorganism IDs (called an `mo`) using [our Catalogue of Life reference data set](https://msberends.gitlab.io/AMR/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms.
|
||||
* Microorganisms should be transformed to our own microorganism IDs (called an `mo`) using [our Catalogue of Life reference data set](https://msberends.github.io/AMR/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms.
|
||||
* Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values `"S"`, `"I"` or `"R"`. That is exactly where the `as.rsi()` function is for.
|
||||
|
||||
```{r}
|
||||
|
Loading…
Reference in New Issue
Block a user