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(v1.6.0.9014) as.rsi() for numeric values

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dr. M.S. (Matthijs) Berends 2021-04-30 13:18:48 +02:00
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4
DESCRIPTION
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Package: AMR Package: AMR
Version: 1.6.0.9013 Version: 1.6.0.9014
Date: 2021-04-29 Date: 2021-04-30
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

46
NEWS.md
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# AMR 1.6.0.9013 # `AMR` 1.6.0.9014
## <small>Last updated: 29 April 2021</small> ## <small>Last updated: 30 April 2021</small>
### New ### New
* Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()` * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
@ -31,9 +31,11 @@
* Fixed an installation error on R-3.0 * Fixed an installation error on R-3.0
* Added `info` argument to `as.mo()` to turn on/off the progress bar * Added `info` argument to `as.mo()` to turn on/off the progress bar
* Fixed a bug that `col_mo` for some functions (esp. `eucast_rules()` and `mdro()`) could not be column names of the `microorganisms` data set as it would throw an error * Fixed a bug that `col_mo` for some functions (esp. `eucast_rules()` and `mdro()`) could not be column names of the `microorganisms` data set as it would throw an error
* Fix for transforming numeric values to RSI (`as.rsi()`) when the `vctrs` package is loaded (i.e., when using tidyverse)
* Colour fix for using `barplot()` on an RSI class
# AMR 1.6.0 # `AMR` 1.6.0
### New ### New
* Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package. * Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
@ -127,7 +129,7 @@
* Loading the package (i.e., `library(AMR)`) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB) * Loading the package (i.e., `library(AMR)`) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)
# AMR 1.5.0 # `AMR` 1.5.0
### New ### New
* Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`): * Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):
@ -204,7 +206,7 @@
* Added CodeFactor as a continuous code review to this package: <https://www.codefactor.io/repository/github/msberends/amr/> * Added CodeFactor as a continuous code review to this package: <https://www.codefactor.io/repository/github/msberends/amr/>
* Added Dr. Rogier Schade as contributor * Added Dr. Rogier Schade as contributor
# AMR 1.4.0 # `AMR` 1.4.0
### New ### New
* Support for 'EUCAST Expert Rules' / 'EUCAST Intrinsic Resistance and Unusual Phenotypes' version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the `eucast_rules()` function can now correct for more than 180 different antibiotics and the `mdro()` function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The `eucast_rules()` function consequently gained the arguments `version_breakpoints` (at the moment defaults to v10.0, 2020) and `version_expertrules` (at the moment defaults to v3.2, 2020). The `example_isolates` data set now also reflects the change from v3.1 to v3.2. The `mdro()` function now accepts `guideline == "EUCAST3.1"` and `guideline == "EUCAST3.2"`. * Support for 'EUCAST Expert Rules' / 'EUCAST Intrinsic Resistance and Unusual Phenotypes' version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the `eucast_rules()` function can now correct for more than 180 different antibiotics and the `mdro()` function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The `eucast_rules()` function consequently gained the arguments `version_breakpoints` (at the moment defaults to v10.0, 2020) and `version_expertrules` (at the moment defaults to v3.2, 2020). The `example_isolates` data set now also reflects the change from v3.1 to v3.2. The `mdro()` function now accepts `guideline == "EUCAST3.1"` and `guideline == "EUCAST3.2"`.
@ -276,7 +278,7 @@
* Removed unnecessary references to the `base` package * Removed unnecessary references to the `base` package
* Added packages that could be useful for some functions to the `Suggests` field of the `DESCRIPTION` file * Added packages that could be useful for some functions to the `Suggests` field of the `DESCRIPTION` file
# AMR 1.3.0 # `AMR` 1.3.0
### New ### New
* Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally * Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
@ -329,7 +331,7 @@
### Other ### Other
* 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. * 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.
# AMR 1.2.0 # `AMR` 1.2.0
### Breaking ### Breaking
* Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users. * Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.
@ -367,7 +369,7 @@
* Removed previously deprecated function `p.symbol()` - it was replaced with `p_symbol()` * Removed previously deprecated function `p.symbol()` - it was replaced with `p_symbol()`
* Removed function `read.4d()`, that was only useful for reading data from an old test database. * Removed function `read.4d()`, that was only useful for reading data from an old test database.
# AMR 1.1.0 # `AMR` 1.1.0
### New ### New
* Support for easy principal component analysis for AMR, using the new `pca()` function * Support for easy principal component analysis for AMR, using the new `pca()` function
@ -389,7 +391,7 @@
* Support for the upcoming `dplyr` version 1.0.0 * Support for the upcoming `dplyr` version 1.0.0
* More robust assigning for classes `rsi` and `mic` * More robust assigning for classes `rsi` and `mic`
# AMR 1.0.1 # `AMR` 1.0.1
### Changed ### Changed
* Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline * Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline
@ -405,7 +407,7 @@
* Added `uti` (as abbreviation of urinary tract infections) as argument to `as.rsi()`, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs * Added `uti` (as abbreviation of urinary tract infections) as argument to `as.rsi()`, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs
* Info printing in functions `eucast_rules()`, `first_isolate()`, `mdro()` and `resistance_predict()` will now at default only print when R is in an interactive mode (i.e. not in RMarkdown) * Info printing in functions `eucast_rules()`, `first_isolate()`, `mdro()` and `resistance_predict()` will now at default only print when R is in an interactive mode (i.e. not in RMarkdown)
# AMR 1.0.0 # `AMR` 1.0.0
This software is now out of beta and considered stable. Nonetheless, this package will be developed continually. This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.
@ -453,7 +455,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
* Full support for the upcoming R 4.0 * Full support for the upcoming R 4.0
* Removed unnecessary `AMR::` calls * Removed unnecessary `AMR::` calls
# AMR 0.9.0 # `AMR` 0.9.0
### Breaking ### Breaking
* Adopted Adeolu *et al.* (2016), [PMID 27620848](https:/pubmed.ncbi.nlm.nih.gov/27620848/) for the `microorganisms` data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like *Morganellaceae* and *Yersiniaceae*). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with `mdro()` will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family. * Adopted Adeolu *et al.* (2016), [PMID 27620848](https:/pubmed.ncbi.nlm.nih.gov/27620848/) for the `microorganisms` data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like *Morganellaceae* and *Yersiniaceae*). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with `mdro()` will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.
@ -519,7 +521,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
* Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request * Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request
* Added Dr. Sofia Ny as contributor * Added Dr. Sofia Ny as contributor
# AMR 0.8.0 # `AMR` 0.8.0
### Breaking ### Breaking
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new argument `include_unknown`: * Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new argument `include_unknown`:
@ -648,7 +650,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
* Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors * Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors
* Cleaned the coding style of every single syntax line in this package with the help of the `lintr` package * Cleaned the coding style of every single syntax line in this package with the help of the `lintr` package
# AMR 0.7.1 # `AMR` 0.7.1
#### New #### New
* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates: * Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
@ -709,7 +711,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
#### Other #### Other
* Fixed a note thrown by CRAN tests * Fixed a note thrown by CRAN tests
# AMR 0.7.0 # `AMR` 0.7.0
#### New #### New
* Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use `as.rsi()` on an MIC value (created with `as.mic()`), a disk diffusion value (created with the new `as.disk()`) or on a complete date set containing columns with MIC or disk diffusion values. * Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use `as.rsi()` on an MIC value (created with `as.mic()`), a disk diffusion value (created with the new `as.disk()`) or on a complete date set containing columns with MIC or disk diffusion values.
@ -767,13 +769,13 @@ This software is now out of beta and considered stable. Nonetheless, this packag
#### Other #### Other
* Support for R 3.6.0 and later by providing support for [staged install](https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html) * Support for R 3.6.0 and later by providing support for [staged install](https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html)
# AMR 0.6.1 # `AMR` 0.6.1
#### Changed #### Changed
* Fixed a critical bug when using `eucast_rules()` with `verbose = TRUE` * Fixed a critical bug when using `eucast_rules()` with `verbose = TRUE`
* Coercion of microbial IDs are now written to the package namespace instead of the user's home folder, to comply with the CRAN policy * Coercion of microbial IDs are now written to the package namespace instead of the user's home folder, to comply with the CRAN policy
# AMR 0.6.0 # `AMR` 0.6.0
**New website!** **New website!**
@ -966,7 +968,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
#### Other #### Other
* Updated licence text to emphasise GPL 2.0 and that this is an R package. * Updated licence text to emphasise GPL 2.0 and that this is an R package.
# AMR 0.5.0 # `AMR` 0.5.0
#### New #### New
* Repository moved to GitLab * Repository moved to GitLab
@ -1049,7 +1051,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
* Updated vignettes to comply with README * Updated vignettes to comply with README
# AMR 0.4.0 # `AMR` 0.4.0
#### New #### New
* The data set `microorganisms` now contains **all microbial taxonomic data from ITIS** (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set `microorganisms.old` contains all previously known taxonomic names from those kingdoms. * The data set `microorganisms` now contains **all microbial taxonomic data from ITIS** (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set `microorganisms.old` contains all previously known taxonomic names from those kingdoms.
@ -1160,7 +1162,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
#### Other #### Other
* More unit tests to ensure better integrity of functions * More unit tests to ensure better integrity of functions
# AMR 0.3.0 # `AMR` 0.3.0
#### New #### New
* **BREAKING**: `rsi_df` was removed in favour of new functions `portion_R`, `portion_IR`, `portion_I`, `portion_SI` and `portion_S` to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old `rsi` function. The old function still works, but is deprecated. * **BREAKING**: `rsi_df` was removed in favour of new functions `portion_R`, `portion_IR`, `portion_I`, `portion_SI` and `portion_S` to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old `rsi` function. The old function still works, but is deprecated.
@ -1230,7 +1232,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
* Windows: https://ci.appveyor.com/project/msberends/amr * Windows: https://ci.appveyor.com/project/msberends/amr
* Added thesis advisors to DESCRIPTION file * Added thesis advisors to DESCRIPTION file
# AMR 0.2.0 # `AMR` 0.2.0
#### New #### New
* Full support for Windows, Linux and macOS * Full support for Windows, Linux and macOS
@ -1265,7 +1267,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
* Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR) * Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
* Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R) * Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
# AMR 0.1.1 # `AMR` 0.1.1
* `EUCAST_rules` applies for amoxicillin even if ampicillin is missing * `EUCAST_rules` applies for amoxicillin even if ampicillin is missing
* Edited column names to comply with GLIMS, the laboratory information system * Edited column names to comply with GLIMS, the laboratory information system
@ -1273,6 +1275,6 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
* Renamed 'Daily Defined Dose' to 'Defined Daily Dose' * Renamed 'Daily Defined Dose' to 'Defined Daily Dose'
* Added barplots for `rsi` and `mic` classes * Added barplots for `rsi` and `mic` classes
# AMR 0.1.0 # `AMR` 0.1.0
* First submission to CRAN. * First submission to CRAN.

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@ -586,6 +586,8 @@ barplot.rsi <- function(height,
if (length(colours_RSI) == 1) { if (length(colours_RSI) == 1) {
colours_RSI <- rep(colours_RSI, 3) colours_RSI <- rep(colours_RSI, 3)
} else {
colours_RSI <- c(colours_RSI[2], colours_RSI[3], colours_RSI[1])
} }
main <- gsub(" +", " ", paste0(main, collapse = " ")) main <- gsub(" +", " ", paste0(main, collapse = " "))

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R/rsi.R
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@ -259,9 +259,10 @@ as.rsi.default <- function(x, ...) {
} }
if (inherits(x, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) { if (inherits(x, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) {
x[x == 1] <- "S" x <- as.character(x) # this is needed to prevent the vctrs pkg to throw an error
x[x == 2] <- "I" x[x == "1"] <- "S"
x[x == 3] <- "R" x[x == "2"] <- "I"
x[x == "3"] <- "R"
} else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R")) && !all(x %in% c("R", "S", "I", NA))) { } else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R")) && !all(x %in% c("R", "S", "I", NA))) {

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <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">1.6.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
</span> </span>
</div> </div>

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</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="Latest development version">1.6.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
</span> </span>
</div> </div>

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</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="Latest development version">1.6.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
</span> </span>
</div> </div>

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</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="Latest development version">1.6.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
</span> </span>
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@ -40,13 +40,18 @@ $(document).ready(function() {
window.location.replace(url_new); window.location.replace(url_new);
} }
// Edit title of manual
$('.template-reference-index h1').text('Manual');
// replace 'Value' in manual with 'Returned value' // replace 'Value' in manual with 'Returned value'
$(".template-reference-topic h2#value").text("Returned value"); $(".template-reference-topic h2#value").text("Returned value");
// replace \donttest and \dontrun texts in Examples // replace \donttest and \dontrun texts in Examples
$("pre.examples").html($("pre.examples").html().replaceAll("# \\donttest{", "")); if ($("pre.examples").length > 0) {
$("pre.examples").html($("pre.examples").html().replaceAll("# \\dontrun{", "")); $("pre.examples").html($("pre.examples").html().replaceAll("# \\donttest{", ""));
$("pre.examples").html($("pre.examples").html().replaceAll("# }", "")); $("pre.examples").html($("pre.examples").html().replaceAll("# \\dontrun{", ""));
$("pre.examples").html($("pre.examples").html().replaceAll("# }", ""));
}
// PR for 'R for Data Science' on How To pages // PR for 'R for Data Science' on How To pages
if ($(".template-article").length > 0) { if ($(".template-article").length > 0) {
@ -106,9 +111,6 @@ $(document).ready(function() {
$('.template-citation-authors h1').eq(1).html("All contributors of the <code>AMR</code> package"); $('.template-citation-authors h1').eq(1).html("All contributors of the <code>AMR</code> package");
$(".developers").html(doct_tit($(".developers").html())); $(".developers").html(doct_tit($(".developers").html()));
$(".developers a[href='authors.html']").text("All contributors..."); $(".developers a[href='authors.html']").text("All contributors...");
// Edit title of manual
$('.template-reference-index h1').text('Manual');
}); });
$('head').append("<!-- Global site tag (gtag.js) - Google Analytics --> <script async src=\"https://www.googletagmanager.com/gtag/js?id=UA-172114740-1\"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-172114740-1'); </script><!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.msberends.github.io/AMR']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s); })();</script><!-- End Matomo Code -->"); $('head').append("<!-- Global site tag (gtag.js) - Google Analytics --> <script async src=\"https://www.googletagmanager.com/gtag/js?id=UA-172114740-1\"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-172114740-1'); </script><!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.msberends.github.io/AMR']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s); })();</script><!-- End Matomo Code -->");

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@ -42,7 +42,7 @@
</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="Latest development version">1.6.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
</span> </span>
</div> </div>

79
docs/news/index.html
View File

@ -81,7 +81,7 @@
</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="Latest development version">1.6.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
</span> </span>
</div> </div>
@ -236,13 +236,12 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1609013" class="section level1"> <div id="amr-1609014" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9013"> <h1 class="page-header" data-toc-text="1.6.0.9014">
<a href="#amr-1609013" class="anchor"></a>AMR 1.6.0.9013<small> Unreleased </small> <a href="#amr-1609014" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9014</h1>
</h1> <div id="last-updated-30-april-2021" class="section level2">
<div id="last-updated-29-april-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-29-april-2021" class="anchor"></a><small>Last updated: 29 April 2021</small> <a href="#last-updated-30-april-2021" class="anchor"></a><small>Last updated: 30 April 2021</small>
</h2> </h2>
<div id="new" class="section level3"> <div id="new" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -296,14 +295,15 @@
<li>Fixed an installation error on R-3.0</li> <li>Fixed an installation error on R-3.0</li>
<li>Added <code>info</code> argument to <code><a href="../reference/as.mo.html">as.mo()</a></code> to turn on/off the progress bar</li> <li>Added <code>info</code> argument to <code><a href="../reference/as.mo.html">as.mo()</a></code> to turn on/off the progress bar</li>
<li>Fixed a bug that <code>col_mo</code> for some functions (esp. <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>) could not be column names of the <code>microorganisms</code> data set as it would throw an error</li> <li>Fixed a bug that <code>col_mo</code> for some functions (esp. <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>) could not be column names of the <code>microorganisms</code> data set as it would throw an error</li>
<li>Fix for transforming numeric values to RSI (<code><a href="../reference/as.rsi.html">as.rsi()</a></code>) when the <code>vctrs</code> package is loaded (i.e., when using tidyverse)</li>
<li>Colour fix for using <code><a href="https://rdrr.io/r/graphics/barplot.html">barplot()</a></code> on an RSI class</li>
</ul> </ul>
</div> </div>
</div> </div>
</div> </div>
<div id="amr-160" class="section level1"> <div id="amr-160" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0"> <h1 class="page-header" data-toc-text="1.6.0">
<a href="#amr-160" class="anchor"></a>AMR 1.6.0<small> 2021-03-14 </small> <a href="#amr-160" class="anchor"></a><small> 2021-03-14 </small><code>AMR</code> 1.6.0</h1>
</h1>
<div id="new-1" class="section level3"> <div id="new-1" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#new-1" class="anchor"></a>New</h3> <a href="#new-1" class="anchor"></a>New</h3>
@ -339,7 +339,7 @@
<span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div> <span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
</li> </li>
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li> <li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li> <li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li> <li>
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p> <p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
@ -396,7 +396,7 @@
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li> <li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li> <li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li> <li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li> <li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
</ul> </ul>
</li> </li>
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li> <li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
@ -440,8 +440,7 @@
</div> </div>
<div id="amr-150" class="section level1"> <div id="amr-150" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0"> <h1 class="page-header" data-toc-text="1.5.0">
<a href="#amr-150" class="anchor"></a>AMR 1.5.0<small> 2021-01-06 </small> <a href="#amr-150" class="anchor"></a><small> 2021-01-06 </small><code>AMR</code> 1.5.0</h1>
</h1>
<div id="new-2" class="section level3"> <div id="new-2" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#new-2" class="anchor"></a>New</h3> <a href="#new-2" class="anchor"></a>New</h3>
@ -554,8 +553,7 @@
</div> </div>
<div id="amr-140" class="section level1"> <div id="amr-140" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0"> <h1 class="page-header" data-toc-text="1.4.0">
<a href="#amr-140" class="anchor"></a>AMR 1.4.0<small> 2020-10-08 </small> <a href="#amr-140" class="anchor"></a><small> 2020-10-08 </small><code>AMR</code> 1.4.0</h1>
</h1>
<div id="new-3" class="section level3"> <div id="new-3" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#new-3" class="anchor"></a>New</h3> <a href="#new-3" class="anchor"></a>New</h3>
@ -658,8 +656,7 @@
</div> </div>
<div id="amr-130" class="section level1"> <div id="amr-130" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0"> <h1 class="page-header" data-toc-text="1.3.0">
<a href="#amr-130" class="anchor"></a>AMR 1.3.0<small> 2020-07-31 </small> <a href="#amr-130" class="anchor"></a><small> 2020-07-31 </small><code>AMR</code> 1.3.0</h1>
</h1>
<div id="new-4" class="section level3"> <div id="new-4" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#new-4" class="anchor"></a>New</h3> <a href="#new-4" class="anchor"></a>New</h3>
@ -741,8 +738,7 @@
</div> </div>
<div id="amr-120" class="section level1"> <div id="amr-120" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0"> <h1 class="page-header" data-toc-text="1.2.0">
<a href="#amr-120" class="anchor"></a>AMR 1.2.0<small> 2020-05-28 </small> <a href="#amr-120" class="anchor"></a><small> 2020-05-28 </small><code>AMR</code> 1.2.0</h1>
</h1>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3> <a href="#breaking" class="anchor"></a>Breaking</h3>
@ -805,8 +801,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-110" class="section level1"> <div id="amr-110" class="section level1">
<h1 class="page-header" data-toc-text="1.1.0"> <h1 class="page-header" data-toc-text="1.1.0">
<a href="#amr-110" class="anchor"></a>AMR 1.1.0<small> 2020-04-15 </small> <a href="#amr-110" class="anchor"></a><small> 2020-04-15 </small><code>AMR</code> 1.1.0</h1>
</h1>
<div id="new-5" class="section level3"> <div id="new-5" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#new-5" class="anchor"></a>New</h3> <a href="#new-5" class="anchor"></a>New</h3>
@ -847,8 +842,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-101" class="section level1"> <div id="amr-101" class="section level1">
<h1 class="page-header" data-toc-text="1.0.1"> <h1 class="page-header" data-toc-text="1.0.1">
<a href="#amr-101" class="anchor"></a>AMR 1.0.1<small> 2020-02-23 </small> <a href="#amr-101" class="anchor"></a><small> 2020-02-23 </small><code>AMR</code> 1.0.1</h1>
</h1>
<div id="changed-7" class="section level3"> <div id="changed-7" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#changed-7" class="anchor"></a>Changed</h3> <a href="#changed-7" class="anchor"></a>Changed</h3>
@ -872,8 +866,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-100" class="section level1"> <div id="amr-100" class="section level1">
<h1 class="page-header" data-toc-text="1.0.0"> <h1 class="page-header" data-toc-text="1.0.0">
<a href="#amr-100" class="anchor"></a>AMR 1.0.0<small> 2020-02-17 </small> <a href="#amr-100" class="anchor"></a><small> 2020-02-17 </small><code>AMR</code> 1.0.0</h1>
</h1>
<p>This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.</p> <p>This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.</p>
<div id="new-6" class="section level3"> <div id="new-6" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -951,8 +944,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-090" class="section level1"> <div id="amr-090" class="section level1">
<h1 class="page-header" data-toc-text="0.9.0"> <h1 class="page-header" data-toc-text="0.9.0">
<a href="#amr-090" class="anchor"></a>AMR 0.9.0<small> 2019-11-29 </small> <a href="#amr-090" class="anchor"></a><small> 2019-11-29 </small><code>AMR</code> 0.9.0</h1>
</h1>
<div id="breaking-1" class="section level3"> <div id="breaking-1" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#breaking-1" class="anchor"></a>Breaking</h3> <a href="#breaking-1" class="anchor"></a>Breaking</h3>
@ -1059,8 +1051,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-080" class="section level1"> <div id="amr-080" class="section level1">
<h1 class="page-header" data-toc-text="0.8.0"> <h1 class="page-header" data-toc-text="0.8.0">
<a href="#amr-080" class="anchor"></a>AMR 0.8.0<small> 2019-10-15 </small> <a href="#amr-080" class="anchor"></a><small> 2019-10-15 </small><code>AMR</code> 0.8.0</h1>
</h1>
<div id="breaking-2" class="section level3"> <div id="breaking-2" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#breaking-2" class="anchor"></a>Breaking</h3> <a href="#breaking-2" class="anchor"></a>Breaking</h3>
@ -1225,8 +1216,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-071" class="section level1"> <div id="amr-071" class="section level1">
<h1 class="page-header" data-toc-text="0.7.1"> <h1 class="page-header" data-toc-text="0.7.1">
<a href="#amr-071" class="anchor"></a>AMR 0.7.1<small> 2019-06-23 </small> <a href="#amr-071" class="anchor"></a><small> 2019-06-23 </small><code>AMR</code> 0.7.1</h1>
</h1>
<div id="new-9" class="section level4"> <div id="new-9" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#new-9" class="anchor"></a>New</h4> <a href="#new-9" class="anchor"></a>New</h4>
@ -1310,8 +1300,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-070" class="section level1"> <div id="amr-070" class="section level1">
<h1 class="page-header" data-toc-text="0.7.0"> <h1 class="page-header" data-toc-text="0.7.0">
<a href="#amr-070" class="anchor"></a>AMR 0.7.0<small> 2019-06-03 </small> <a href="#amr-070" class="anchor"></a><small> 2019-06-03 </small><code>AMR</code> 0.7.0</h1>
</h1>
<div id="new-10" class="section level4"> <div id="new-10" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#new-10" class="anchor"></a>New</h4> <a href="#new-10" class="anchor"></a>New</h4>
@ -1407,8 +1396,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-061" class="section level1"> <div id="amr-061" class="section level1">
<h1 class="page-header" data-toc-text="0.6.1"> <h1 class="page-header" data-toc-text="0.6.1">
<a href="#amr-061" class="anchor"></a>AMR 0.6.1<small> 2019-03-29 </small> <a href="#amr-061" class="anchor"></a><small> 2019-03-29 </small><code>AMR</code> 0.6.1</h1>
</h1>
<div id="changed-11" class="section level4"> <div id="changed-11" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#changed-11" class="anchor"></a>Changed</h4> <a href="#changed-11" class="anchor"></a>Changed</h4>
@ -1421,8 +1409,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-060" class="section level1"> <div id="amr-060" class="section level1">
<h1 class="page-header" data-toc-text="0.6.0"> <h1 class="page-header" data-toc-text="0.6.0">
<a href="#amr-060" class="anchor"></a>AMR 0.6.0<small> 2019-03-27 </small> <a href="#amr-060" class="anchor"></a><small> 2019-03-27 </small><code>AMR</code> 0.6.0</h1>
</h1>
<p><strong>New website!</strong></p> <p><strong>New website!</strong></p>
<p>We’ve got a new website: <a href="https://msberends.gitlab.io/AMR/">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)</p> <p>We’ve got a new website: <a href="https://msberends.gitlab.io/AMR/">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)</p>
<ul> <ul>
@ -1673,8 +1660,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-050" class="section level1"> <div id="amr-050" class="section level1">
<h1 class="page-header" data-toc-text="0.5.0"> <h1 class="page-header" data-toc-text="0.5.0">
<a href="#amr-050" class="anchor"></a>AMR 0.5.0<small> 2018-11-30 </small> <a href="#amr-050" class="anchor"></a><small> 2018-11-30 </small><code>AMR</code> 0.5.0</h1>
</h1>
<div id="new-12" class="section level4"> <div id="new-12" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#new-12" class="anchor"></a>New</h4> <a href="#new-12" class="anchor"></a>New</h4>
@ -1797,8 +1783,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-040" class="section level1"> <div id="amr-040" class="section level1">
<h1 class="page-header" data-toc-text="0.4.0"> <h1 class="page-header" data-toc-text="0.4.0">
<a href="#amr-040" class="anchor"></a>AMR 0.4.0<small> 2018-10-01 </small> <a href="#amr-040" class="anchor"></a><small> 2018-10-01 </small><code>AMR</code> 0.4.0</h1>
</h1>
<div id="new-13" class="section level4"> <div id="new-13" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#new-13" class="anchor"></a>New</h4> <a href="#new-13" class="anchor"></a>New</h4>
@ -1946,8 +1931,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-030" class="section level1"> <div id="amr-030" class="section level1">
<h1 class="page-header" data-toc-text="0.3.0"> <h1 class="page-header" data-toc-text="0.3.0">
<a href="#amr-030" class="anchor"></a>AMR 0.3.0<small> 2018-08-14 </small> <a href="#amr-030" class="anchor"></a><small> 2018-08-14 </small><code>AMR</code> 0.3.0</h1>
</h1>
<div id="new-14" class="section level4"> <div id="new-14" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#new-14" class="anchor"></a>New</h4> <a href="#new-14" class="anchor"></a>New</h4>
@ -2083,8 +2067,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-020" class="section level1"> <div id="amr-020" class="section level1">
<h1 class="page-header" data-toc-text="0.2.0"> <h1 class="page-header" data-toc-text="0.2.0">
<a href="#amr-020" class="anchor"></a>AMR 0.2.0<small> 2018-05-03 </small> <a href="#amr-020" class="anchor"></a><small> 2018-05-03 </small><code>AMR</code> 0.2.0</h1>
</h1>
<div id="new-15" class="section level4"> <div id="new-15" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#new-15" class="anchor"></a>New</h4> <a href="#new-15" class="anchor"></a>New</h4>
@ -2141,8 +2124,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-011" class="section level1"> <div id="amr-011" class="section level1">
<h1 class="page-header" data-toc-text="0.1.1"> <h1 class="page-header" data-toc-text="0.1.1">
<a href="#amr-011" class="anchor"></a>AMR 0.1.1<small> 2018-03-14 </small> <a href="#amr-011" class="anchor"></a><small> 2018-03-14 </small><code>AMR</code> 0.1.1</h1>
</h1>
<ul> <ul>
<li> <li>
<code>EUCAST_rules</code> applies for amoxicillin even if ampicillin is missing</li> <code>EUCAST_rules</code> applies for amoxicillin even if ampicillin is missing</li>
@ -2154,8 +2136,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div> </div>
<div id="amr-010" class="section level1"> <div id="amr-010" class="section level1">
<h1 class="page-header" data-toc-text="0.1.0"> <h1 class="page-header" data-toc-text="0.1.0">
<a href="#amr-010" class="anchor"></a>AMR 0.1.0<small> 2018-02-22 </small> <a href="#amr-010" class="anchor"></a><small> 2018-02-22 </small><code>AMR</code> 0.1.0</h1>
</h1>
<ul> <ul>
<li>First submission to CRAN.</li> <li>First submission to CRAN.</li>
</ul> </ul>

2
docs/pkgdown.yml
View File

@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-04-29T15:15Z last_built: 2021-04-30T08:14Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

2
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</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="Latest development version">1.6.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
</span> </span>
</div> </div>

2
docs/survey.html
View File

@ -81,7 +81,7 @@
</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="Latest development version">1.6.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
</span> </span>
</div> </div>

2
git_premaster.sh
View File

@ -99,7 +99,7 @@ else
fi fi
# set version number to DESCRIPTION and NEWS files # set version number to DESCRIPTION and NEWS files
sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION
sed -i -- "1s/.*/# AMR ${new_version}/" NEWS.md sed -i -- "1s/.*/# \`AMR\` ${new_version}/" NEWS.md
rm *-- || true rm *-- || true
echo "• First 3 lines of DESCRIPTION:" echo "• First 3 lines of DESCRIPTION:"
head -3 DESCRIPTION head -3 DESCRIPTION

14
pkgdown/extra.js
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@ -40,13 +40,18 @@ $(document).ready(function() {
window.location.replace(url_new); window.location.replace(url_new);
} }
// Edit title of manual
$('.template-reference-index h1').text('Manual');
// replace 'Value' in manual with 'Returned value' // replace 'Value' in manual with 'Returned value'
$(".template-reference-topic h2#value").text("Returned value"); $(".template-reference-topic h2#value").text("Returned value");
// replace \donttest and \dontrun texts in Examples // replace \donttest and \dontrun texts in Examples
$("pre.examples").html($("pre.examples").html().replaceAll("# \\donttest{", "")); if ($("pre.examples").length > 0) {
$("pre.examples").html($("pre.examples").html().replaceAll("# \\dontrun{", "")); $("pre.examples").html($("pre.examples").html().replaceAll("# \\donttest{", ""));
$("pre.examples").html($("pre.examples").html().replaceAll("# }", "")); $("pre.examples").html($("pre.examples").html().replaceAll("# \\dontrun{", ""));
$("pre.examples").html($("pre.examples").html().replaceAll("# }", ""));
}
// PR for 'R for Data Science' on How To pages // PR for 'R for Data Science' on How To pages
if ($(".template-article").length > 0) { if ($(".template-article").length > 0) {
@ -106,9 +111,6 @@ $(document).ready(function() {
$('.template-citation-authors h1').eq(1).html("All contributors of the <code>AMR</code> package"); $('.template-citation-authors h1').eq(1).html("All contributors of the <code>AMR</code> package");
$(".developers").html(doct_tit($(".developers").html())); $(".developers").html(doct_tit($(".developers").html()));
$(".developers a[href='authors.html']").text("All contributors..."); $(".developers a[href='authors.html']").text("All contributors...");
// Edit title of manual
$('.template-reference-index h1').text('Manual');
}); });
$('head').append("<!-- Global site tag (gtag.js) - Google Analytics --> <script async src=\"https://www.googletagmanager.com/gtag/js?id=UA-172114740-1\"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-172114740-1'); </script><!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.msberends.github.io/AMR']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s); })();</script><!-- End Matomo Code -->"); $('head').append("<!-- Global site tag (gtag.js) - Google Analytics --> <script async src=\"https://www.googletagmanager.com/gtag/js?id=UA-172114740-1\"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-172114740-1'); </script><!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.msberends.github.io/AMR']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s); })();</script><!-- End Matomo Code -->");

2
tests/testthat/test-first_isolate.R
View File

@ -175,7 +175,7 @@ test_that("first isolates work", {
# shortcuts # shortcuts
expect_identical(filter_first_isolate(example_isolates), expect_identical(filter_first_isolate(example_isolates),
subset(example_isolates, first_isolate(example_isolates, method = "episode-based"))) subset(example_isolates, first_isolate(example_isolates)))
# notice that all mo's are distinct, so all are TRUE # notice that all mo's are distinct, so all are TRUE