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(v1.4.0.9018) reference_data in as.rsi()
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.github/workflows/check.yaml
vendored
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.github/workflows/check.yaml
vendored
@ -64,6 +64,7 @@ jobs:
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- {os: ubuntu-16.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.4', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.4.0.9017
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Version: 1.4.0.9018
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Date: 2020-11-11
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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 1.4.0.9017
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# AMR 1.4.0.9018
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## <small>Last updated: 11 November 2020</small>
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### New
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@ -11,7 +11,7 @@
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* Functions `%not_like%` and `%not_like_case%` as wrappers around `%like%` and `%like_case%`. The RStudio addin to insert the text " %like% " as provided in this package now iterates over all like variants. So if you have defined the keyboard shortcut Ctrl/Cmd + L to this addin, it will first insert ` %like% ` and by pressing it again it will be replaced with ` %not_like% `, etc.
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### Changed
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* Reference data used for `as.rsi()` can now be set by the user, using the `reference_data` parameter.
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* Reference data used for `as.rsi()` can now be set by the user, using the `reference_data` parameter. This allows for using own interpretation guidelines.
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* For all function parameters in the code, it is now defined what the exact type of user input should be (inspired by the [`typed`](https://github.com/moodymudskipper/typed) package). If the user input for a certain function does not meet the requirements for a specific parameter (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 400 arguments were defined.
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* Deprecated function `p_symbol()` that not really fits the scope of this package. It will be removed in a future version. See [here](https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R) for the source code to preserve it.
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* Better determination of disk zones and MIC values when running `as.rsi()` on a data.frame
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27
R/rsi.R
27
R/rsi.R
@ -36,7 +36,7 @@
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#' @param guideline defaults to the latest included EUCAST guideline, see Details for all options
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#' @param conserve_capped_values a logical to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
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#' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a logical to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version `r EUCAST_VERSION_EXPERT_RULES`.
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#' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this parameter allows for using own interpretation guidelines. This parameter must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the 'guideline' column in this data set must contain values set in the 'guideline' parameter of [as.rsi()].
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#' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this parameter allows for using own interpretation guidelines. This parameter must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the `guideline` parameter will be ignored when `reference_data` is manually set.
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#' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples*
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#' @param ... for using on a [data.frame]: names of columns to apply [as.rsi()] on (supports tidy selection like `AMX:VAN`). Otherwise: parameters passed on to methods.
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#' @details
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@ -67,7 +67,7 @@
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#'
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#' For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the `guideline` parameter are: `r paste0('"', sort(unique(AMR::rsi_translation$guideline)), '"', collapse = ", ")`.
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#'
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#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline. You can set your own data set using the `reference_data` parameter.
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#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline. You can set your own data set using the `reference_data` parameter. The `guideline` parameter will then be ignored.
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#'
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#' ## After interpretation
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#'
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@ -359,7 +359,10 @@ as.rsi.mic <- function(x,
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message_("=> Interpreting MIC values of `", font_bold(ab), "` (",
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ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
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ab_name(ab_coerced, tolower = TRUE), ")", mo_var_found,
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" according to ", font_bold(guideline_coerced), " ... ",
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" according to ", ifelse(identical(reference_data, AMR::rsi_translation),
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font_bold(guideline_coerced),
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"manually defined 'reference_data'"),
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" ... ",
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appendLF = FALSE,
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as_note = FALSE)
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@ -445,9 +448,14 @@ as.rsi.disk <- function(x,
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message_("=> Interpreting disk zones of `", font_bold(ab), "` (",
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ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
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ab_name(ab_coerced, tolower = TRUE), ") using guideline ", font_bold(guideline_coerced), " ... ",
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ab_name(ab_coerced, tolower = TRUE), ")", mo_var_found,
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" according to ", ifelse(identical(reference_data, AMR::rsi_translation),
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font_bold(guideline_coerced),
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"manually defined 'reference_data'"),
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" ... ",
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appendLF = FALSE,
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as_note = FALSE)
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result <- exec_as.rsi(method = "disk",
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x = x,
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mo = mo_coerced,
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@ -622,6 +630,9 @@ as.rsi.data.frame <- function(x,
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}
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get_guideline <- function(guideline, reference_data) {
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if (!identical(reference_data, AMR::rsi_translation)) {
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return(guideline)
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}
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guideline_param <- toupper(guideline)
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if (guideline_param %in% c("CLSI", "EUCAST")) {
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guideline_param <- rev(sort(subset(reference_data, guideline %like% guideline_param)$guideline))[1L]
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@ -646,7 +657,8 @@ exec_as.rsi <- function(method,
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guideline,
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uti,
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conserve_capped_values,
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add_intrinsic_resistance) {
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add_intrinsic_resistance,
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reference_data) {
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metadata_mo <- get_mo_failures_uncertainties_renamed()
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@ -687,8 +699,13 @@ exec_as.rsi <- function(method,
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new_rsi <- rep(NA_character_, length(x))
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ab_param <- ab
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if (identical(reference_data, AMR::rsi_translation)) {
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trans <- reference_data %pm>%
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subset(guideline == guideline_coerced & method == method_param & ab == ab_param)
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} else {
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trans <- reference_data %pm>%
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subset(method == method_param & ab == ab_param)
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}
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trans$lookup <- paste(trans$mo, trans$ab)
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lookup_mo <- paste(mo, ab)
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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>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</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">1.4.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</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">1.4.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</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">1.4.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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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">1.4.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</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">1.4.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
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</span>
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</div>
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@ -236,9 +236,9 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1409017" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9017">
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<a href="#amr-1409017" class="anchor"></a>AMR 1.4.0.9017<small> Unreleased </small>
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<div id="amr-1409018" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9018">
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<a href="#amr-1409018" class="anchor"></a>AMR 1.4.0.9018<small> Unreleased </small>
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</h1>
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<div id="last-updated-11-november-2020" class="section level2">
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<h2 class="hasAnchor">
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@ -262,7 +262,7 @@
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<h3 class="hasAnchor">
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<a href="#changed" class="anchor"></a>Changed</h3>
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<ul>
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<li>Reference data used for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> can now be set by the user, using the <code>reference_data</code> parameter.</li>
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<li>Reference data used for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> can now be set by the user, using the <code>reference_data</code> parameter. This allows for using own interpretation guidelines.</li>
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<li>For all function parameters in the code, it is now defined what the exact type of user input should be (inspired by the <a href="https://github.com/moodymudskipper/typed"><code>typed</code></a> package). If the user input for a certain function does not meet the requirements for a specific parameter (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 400 arguments were defined.</li>
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<li>Deprecated function <code><a href="../reference/AMR-deprecated.html">p_symbol()</a></code> that not really fits the scope of this package. It will be removed in a future version. See <a href="https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R">here</a> for the source code to preserve it.</li>
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<li>Better determination of disk zones and MIC values when running <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame</li>
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@ -12,7 +12,7 @@ articles:
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2020-11-11T15:44Z
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last_built: 2020-11-11T17:53Z
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urls:
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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@ -82,7 +82,7 @@
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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">1.4.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
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</span>
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</div>
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@ -327,7 +327,7 @@ list(version_txt = "v3.2", year = 2020, title = "EUCAST Expert Rules / EUCAST In
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</tr>
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<tr>
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<th>reference_data</th>
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<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> to be used for interpretation, which defaults to the <a href='rsi_translation.html'>rsi_translation</a> data set. Changing this parameter allows for using own interpretation guidelines. This parameter must contain a data set that is equal in structure to the <a href='rsi_translation.html'>rsi_translation</a> data set (same column names and column types). Please note that the 'guideline' column in this data set must contain values set in the 'guideline' parameter of <code>as.rsi()</code>.</p></td>
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<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> to be used for interpretation, which defaults to the <a href='rsi_translation.html'>rsi_translation</a> data set. Changing this parameter allows for using own interpretation guidelines. This parameter must contain a data set that is equal in structure to the <a href='rsi_translation.html'>rsi_translation</a> data set (same column names and column types). Please note that the <code>guideline</code> parameter will be ignored when <code>reference_data</code> is manually set.</p></td>
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</tr>
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<tr>
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<th>col_mo</th>
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@ -365,7 +365,7 @@ list(version_txt = "v3.2", year = 2020, title = "EUCAST Expert Rules / EUCAST In
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<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020".</p>
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<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline. You can set your own data set using the <code>reference_data</code> parameter.</p>
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<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline. You can set your own data set using the <code>reference_data</code> parameter. The <code>guideline</code> parameter will then be ignored.</p>
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<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>After interpretation</h3>
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@ -81,7 +81,7 @@
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</button>
|
||||
<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">1.4.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</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">1.4.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
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</span>
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</div>
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@ -70,7 +70,7 @@ is.rsi.eligible(x, threshold = 0.05)
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\item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a logical to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version list(version_txt = "v3.1", year = 2016, title = "EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes")
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list(version_txt = "v3.2", year = 2020, title = "EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes").}
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\item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{rsi_translation} data set. Changing this parameter allows for using own interpretation guidelines. This parameter must contain a data set that is equal in structure to the \link{rsi_translation} data set (same column names and column types). Please note that the 'guideline' column in this data set must contain values set in the 'guideline' parameter of \code{\link[=as.rsi]{as.rsi()}}.}
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\item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{rsi_translation} data set. Changing this parameter allows for using own interpretation guidelines. This parameter must contain a data set that is equal in structure to the \link{rsi_translation} data set (same column names and column types). Please note that the \code{guideline} parameter will be ignored when \code{reference_data} is manually set.}
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\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
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}
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@ -107,7 +107,7 @@ your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
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For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020".
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Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline. You can set your own data set using the \code{reference_data} parameter.
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Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline. You can set your own data set using the \code{reference_data} parameter. The \code{guideline} parameter will then be ignored.
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}
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\subsection{After interpretation}{
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