mirror of
https://github.com/msberends/AMR.git
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new git flow to repository
This commit is contained in:
parent
4ca00e1868
commit
6eb08a2ea3
1
.gitignore
vendored
1
.gitignore
vendored
@ -18,6 +18,5 @@ vignettes/*.R
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.DS_Store
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.DS_Store
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.Rprofile
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.Rprofile
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^CRAN-RELEASE$
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^CRAN-RELEASE$
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git_*.sh
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packrat/lib*/
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packrat/lib*/
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packrat/src/
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packrat/src/
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@ -1,5 +1,5 @@
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Package: AMR
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Package: AMR
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Version: 0.6.1.9003
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Version: 0.6.1.9033
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Date: 2019-05-20
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Date: 2019-05-20
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Title: Antimicrobial Resistance Analysis
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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Authors@R: c(
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3
R/mdro.R
3
R/mdro.R
@ -374,6 +374,9 @@ eucast_exceptional_phenotypes <- function(x, country = "EUCAST", ...) {
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}
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}
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# is_ESBL <- function(x, col_mo = NULL, ...) {
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# is_ESBL <- function(x, col_mo = NULL, ...) {
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# get_ab_col <- function(columns, ab) {
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# columns[names(columns) == ab]
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# }
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# col_mo <- get_column_mo(tbl = x, col_mo = col_mo)
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# col_mo <- get_column_mo(tbl = x, col_mo = col_mo)
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# cols_ab <- get_column_abx(tbl = x,
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# cols_ab <- get_column_abx(tbl = x,
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# soft_dependencies = c("AMX", "AMP"),
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# soft_dependencies = c("AMX", "AMP"),
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4
R/misc.R
4
R/misc.R
@ -154,10 +154,6 @@ search_type_in_df <- function(tbl, type) {
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found
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found
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}
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}
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get_ab_col <- function(columns, ab) {
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columns[names(columns) == ab]
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}
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get_column_abx <- function(x,
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get_column_abx <- function(x,
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soft_dependencies = NULL,
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soft_dependencies = NULL,
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hard_dependencies = NULL,
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hard_dependencies = NULL,
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10
README.md
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README.md
@ -13,12 +13,12 @@
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This is the **development source** of `AMR`, a free and open-source [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods.
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This is the **development source** of `AMR`, a free and open-source [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods.
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## Authors
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## Authors
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Matthijs S. Berends <a href="https://orcid.org/0000-0001-7620-1800"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,2,a</sup>,
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Matthijs S. Berends <a href="https://orcid.org/0000-0001-7620-1800"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,2,a</sup>,
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Christian F. Luz <a href="https://orcid.org/0000-0001-5809-5995"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,a</sup>,
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Christian F. Luz <a href="https://orcid.org/0000-0001-5809-5995"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,a</sup>,
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Erwin E.A. Hassing<sup>2</sup>,
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Erwin E.A. Hassing<sup>2</sup>,
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Corinna Glasner <a href="https://orcid.org/0000-0003-1241-1328"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
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Corinna Glasner <a href="https://orcid.org/0000-0003-1241-1328"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
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Alex W. Friedrich <a href="https://orcid.org/0000-0003-4881-038X"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
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Alex W. Friedrich <a href="https://orcid.org/0000-0003-4881-038X"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
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Bhanu N.M. Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>
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Bhanu N.M. Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,b</sup>
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<sup>1</sup> Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - [rug.nl](http://www.rug.nl) [umcg.nl](http://www.umcg.nl)<br>
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<sup>1</sup> Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - [rug.nl](http://www.rug.nl) [umcg.nl](http://www.umcg.nl)<br>
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<sup>2</sup> Certe Medical Diagnostics & Advice, Groningen, the Netherlands - [certe.nl](http://www.certe.nl)<br>
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<sup>2</sup> Certe Medical Diagnostics & Advice, Groningen, the Netherlands - [certe.nl](http://www.certe.nl)<br>
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@ -78,7 +78,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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</span>
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</span>
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</div>
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</div>
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@ -78,7 +78,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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</span>
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</span>
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</div>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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</span>
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</span>
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</div>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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</span>
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</span>
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</div>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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</span>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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</span>
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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</span>
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<span class="navbar-brand">
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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</span>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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</span>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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</span>
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</span>
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</div>
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<span class="navbar-brand">
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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</span>
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<span class="navbar-brand">
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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</span>
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<span class="navbar-brand">
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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</span>
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<span class="navbar-brand">
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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</button>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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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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<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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
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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="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
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</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -78,7 +78,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9033</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
38
git_commit.sh
Executable file
38
git_commit.sh
Executable file
@ -0,0 +1,38 @@
|
|||||||
|
#######################################################################
|
||||||
|
# To push new commits to the premaster branch, run: #
|
||||||
|
# bash git_premaster.sh "commit message" #
|
||||||
|
# #
|
||||||
|
# After successful CRAN checks, merge it to the master branch with: #
|
||||||
|
# bash git_merge.sh #
|
||||||
|
#######################################################################
|
||||||
|
|
||||||
|
if [ -z "$1" ]; then
|
||||||
|
echo "FATAL - no commit message"
|
||||||
|
exit 1
|
||||||
|
fi
|
||||||
|
|
||||||
|
echo "••••••••••••••••••••••••••••••••••••••••••••"
|
||||||
|
echo "• Updating package date and version number •"
|
||||||
|
echo "••••••••••••••••••••••••••••••••••••••••••••"
|
||||||
|
sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
|
||||||
|
# get latest tags
|
||||||
|
git pull --tags --quiet
|
||||||
|
# get version number: latest tag + .90 + number of commits (like 0.6.1.9033)
|
||||||
|
newversion=`git describe --tags | sed 's/-/.90/' | sed 's/-.*//' | sed 's/v//'`
|
||||||
|
sed -i -- "s/^Version: .*/Version: ${newversion}/" DESCRIPTION
|
||||||
|
echo "First 3 lines of DESCRIPTION:"
|
||||||
|
head -3 DESCRIPTION
|
||||||
|
echo
|
||||||
|
echo "•••••••••••••••••••••••"
|
||||||
|
echo "• Documenting package •"
|
||||||
|
echo "•••••••••••••••••••••••"
|
||||||
|
Rscript -e "devtools::document()"
|
||||||
|
echo
|
||||||
|
echo "••••••••••••••"
|
||||||
|
echo "• Committing •"
|
||||||
|
echo "••••••••••••••"
|
||||||
|
git add .
|
||||||
|
git commit -a -m "$1" --quiet
|
||||||
|
|
||||||
|
echo
|
||||||
|
echo "Done."
|
26
git_merge.sh
Executable file
26
git_merge.sh
Executable file
@ -0,0 +1,26 @@
|
|||||||
|
#######################################################################
|
||||||
|
# To push new commits to the premaster branch, run: #
|
||||||
|
# bash git_premaster.sh "commit message" #
|
||||||
|
# #
|
||||||
|
# After successful CRAN checks, merge it to the master branch with: #
|
||||||
|
# bash git_merge.sh #
|
||||||
|
#######################################################################
|
||||||
|
|
||||||
|
# stash current changes
|
||||||
|
# git stash --quiet
|
||||||
|
|
||||||
|
# go to master
|
||||||
|
git checkout master --quiet
|
||||||
|
echo "changed branch to master"
|
||||||
|
# import everything from premaster
|
||||||
|
git merge premaster
|
||||||
|
# and send it to git
|
||||||
|
git push
|
||||||
|
# echo "pushed changes to master"
|
||||||
|
# return to premaster
|
||||||
|
git checkout premaster --quiet
|
||||||
|
echo "changed branch back to premaster"
|
||||||
|
|
||||||
|
# and get stashed changes back
|
||||||
|
# git stash apply --quiet
|
||||||
|
|
62
git_premaster.sh
Executable file
62
git_premaster.sh
Executable file
@ -0,0 +1,62 @@
|
|||||||
|
#######################################################################
|
||||||
|
# To push new commits to the premaster branch, run: #
|
||||||
|
# bash git_premaster.sh "commit message" #
|
||||||
|
# #
|
||||||
|
# After successful CRAN checks, merge it to the master branch with: #
|
||||||
|
# bash git_merge.sh #
|
||||||
|
#######################################################################
|
||||||
|
|
||||||
|
if [ -z "$1" ]; then
|
||||||
|
echo "FATAL - no commit message"
|
||||||
|
exit 1
|
||||||
|
fi
|
||||||
|
|
||||||
|
echo "••••••••••••••••••••••••••••••••••••••••••••"
|
||||||
|
echo "• Updating package date and version number •"
|
||||||
|
echo "••••••••••••••••••••••••••••••••••••••••••••"
|
||||||
|
sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
|
||||||
|
# get latest tags
|
||||||
|
git pull --tags --quiet
|
||||||
|
# get version number: latest tag + .90 + number of commits (like 0.6.1.9033)
|
||||||
|
newversion=`git describe --tags | sed 's/-/.90/' | sed 's/-.*//' | sed 's/v//'`
|
||||||
|
sed -i -- "s/^Version: .*/Version: ${newversion}/" DESCRIPTION
|
||||||
|
echo "First 3 lines of DESCRIPTION:"
|
||||||
|
head -3 DESCRIPTION
|
||||||
|
echo
|
||||||
|
echo "•••••••••••••••••••••••••••••••••"
|
||||||
|
echo "• Reloading/Documenting package •"
|
||||||
|
echo "•••••••••••••••••••••••••••••••••"
|
||||||
|
Rscript -e "devtools::load_all(quiet = TRUE)"
|
||||||
|
Rscript -e "suppressMessages(devtools::document())"
|
||||||
|
Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
|
||||||
|
echo
|
||||||
|
echo "•••••••••••••••••"
|
||||||
|
echo "• Building site •"
|
||||||
|
echo "•••••••••••••••••"
|
||||||
|
Rscript -e "suppressMessages(pkgdown::build_site(lazy = TRUE, examples = FALSE))"
|
||||||
|
|
||||||
|
echo
|
||||||
|
echo "•••••••••••••••••••••••••"
|
||||||
|
echo "• List of changed files •"
|
||||||
|
echo "•••••••••••••••••••••••••"
|
||||||
|
git status --short
|
||||||
|
echo
|
||||||
|
|
||||||
|
read -p "Continue (Y/n)? " choice
|
||||||
|
case "$choice" in
|
||||||
|
n|N ) exit 1;;
|
||||||
|
* ) ;;
|
||||||
|
esac
|
||||||
|
|
||||||
|
echo
|
||||||
|
echo "•••••••••••••••••••••••••••"
|
||||||
|
echo "• Uploading to repository •"
|
||||||
|
echo "•••••••••••••••••••••••••••"
|
||||||
|
git add .
|
||||||
|
git commit -a -m "$1" --quiet
|
||||||
|
git push --quiet
|
||||||
|
echo "Comparison:"
|
||||||
|
echo "https://gitlab.com/msberends/AMR/compare/master...premaster?view=inline"
|
||||||
|
|
||||||
|
echo
|
||||||
|
echo "Done."
|
38
git_siteonly.sh
Executable file
38
git_siteonly.sh
Executable file
@ -0,0 +1,38 @@
|
|||||||
|
#######################################################################
|
||||||
|
# To push new commits to the premaster branch, run: #
|
||||||
|
# bash git_premaster.sh "commit message" #
|
||||||
|
# #
|
||||||
|
# After successful CRAN checks, merge it to the master branch with: #
|
||||||
|
# bash git_merge.sh #
|
||||||
|
#######################################################################
|
||||||
|
|
||||||
|
echo "•••••••••••••••••••••"
|
||||||
|
echo "• Reloading package •"
|
||||||
|
echo "•••••••••••••••••••••"
|
||||||
|
Rscript -e "devtools::load_all()"
|
||||||
|
Rscript -e "devtools::document()"
|
||||||
|
Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
|
||||||
|
echo
|
||||||
|
echo "•••••••••••••••••"
|
||||||
|
echo "• Building site •"
|
||||||
|
echo "•••••••••••••••••"
|
||||||
|
Rscript -e "suppressMessages(pkgdown::build_site(lazy = TRUE, examples = FALSE))"
|
||||||
|
|
||||||
|
echo
|
||||||
|
read -p "Continue (Y/n)? " choice
|
||||||
|
case "$choice" in
|
||||||
|
n|N ) exit 1;;
|
||||||
|
* ) ;;
|
||||||
|
esac
|
||||||
|
|
||||||
|
echo
|
||||||
|
echo "•••••••••••••••••••••••••••"
|
||||||
|
echo "• Uploading to repository •"
|
||||||
|
echo "•••••••••••••••••••••••••••"
|
||||||
|
git add .
|
||||||
|
git commit -a -m "website update" --quiet
|
||||||
|
# git push --quiet
|
||||||
|
git checkout master
|
||||||
|
git merge premaster
|
||||||
|
git push --quiet
|
||||||
|
git checkout premaster
|
Loading…
Reference in New Issue
Block a user