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(v1.2.0.9010) documentation fix
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Package: AMR
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Version: 1.2.0.9009
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Version: 1.2.0.9010
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Date: 2020-06-17
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
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NEWS.md
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# AMR 1.2.0.9009
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# AMR 1.2.0.9010
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## <small>Last updated: 17-Jun-2020</small>
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### New
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@ -29,8 +29,8 @@
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#' @param x existing table to join, or character vector
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#' @param by a variable to join by - if left empty will search for a column with class [`mo`] (created with [as.mo()]) or will be `"mo"` if that column name exists in `x`, could otherwise be a column name of `x` with values that exist in `microorganisms$mo` (like `by = "bacteria_id"`), or another column in [microorganisms] (but then it should be named, like `by = c("my_genus_species" = "fullname")`)
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#' @param suffix if there are non-joined duplicate variables in `x` and `y`, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.
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#' @param ... other parameters to pass on to [dplyr::join()]
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#' @details **Note:** As opposed to the [join()] functions of `dplyr`, [`character`] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix.
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#' @param ... ignored
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#' @details **Note:** As opposed to the `join()` functions of `dplyr`, [`character`] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix.
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#'
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#' These functions rely on [merge()], a base R function to do joins.
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#' @inheritSection AMR Read more on our website!
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@ -165,7 +165,7 @@ resistance_predict <- function(x,
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year <- function(x) {
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# don't depend on lubridate or so, would be overkill for only this function
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if (all(grepl("^[0-9]{4}$", x))) {
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x
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as.integer(x)
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} else {
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as.integer(format(as.Date(x), "%Y"))
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}
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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.gitlab.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">1.2.0.9009</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9009</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9009</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9009</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</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">1.2.0.9009</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9009</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
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</span>
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</div>
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@ -229,9 +229,9 @@
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<small>Source: <a href='https://gitlab.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-1209009" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9009">
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<a href="#amr-1209009" class="anchor"></a>AMR 1.2.0.9009<small> Unreleased </small>
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<div id="amr-1209010" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9010">
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<a href="#amr-1209010" class="anchor"></a>AMR 1.2.0.9010<small> Unreleased </small>
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</h1>
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<div id="last-updated-17-jun-2020" class="section level2">
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<h2 class="hasAnchor">
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@ -10,7 +10,7 @@ articles:
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WHONET: WHONET.html
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benchmarks: benchmarks.html
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resistance_predict: resistance_predict.html
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last_built: 2020-06-17T14:24Z
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last_built: 2020-06-17T19:33Z
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urls:
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reference: https://msberends.gitlab.io/AMR/reference
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article: https://msberends.gitlab.io/AMR/articles
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9009</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
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</span>
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</div>
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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">1.2.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
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</span>
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</div>
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@ -264,7 +264,7 @@
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</tr>
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<tr>
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<th>...</th>
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<td><p>other parameters to pass on to <code><a href='https://dplyr.tidyverse.org/reference/join.html'>dplyr::join()</a></code></p></td>
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<td><p>ignored</p></td>
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</tr>
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</table>
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\item{suffix}{if there are non-joined duplicate variables in \code{x} and \code{y}, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.}
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\item{...}{other parameters to pass on to \code{\link[dplyr:join]{dplyr::join()}}}
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\item{...}{ignored}
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}
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\description{
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Join the data set \link{microorganisms} easily to an existing table or character vector.
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}
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\details{
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\strong{Note:} As opposed to the \code{\link[=join]{join()}} functions of \code{dplyr}, \code{\link{character}} vectors are supported and at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix.
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\strong{Note:} As opposed to the \code{join()} functions of \code{dplyr}, \code{\link{character}} vectors are supported and at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix.
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These functions rely on \code{\link[=merge]{merge()}}, a base R function to do joins.
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}
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