mirror of https://github.com/msberends/AMR.git
(v1.2.0.9010) documentation fix
This commit is contained in:
parent
f18389d5d6
commit
e88d7853f5
|
@ -1,5 +1,5 @@
|
||||||
Package: AMR
|
Package: AMR
|
||||||
Version: 1.2.0.9009
|
Version: 1.2.0.9010
|
||||||
Date: 2020-06-17
|
Date: 2020-06-17
|
||||||
Title: Antimicrobial Resistance Analysis
|
Title: Antimicrobial Resistance Analysis
|
||||||
Authors@R: c(
|
Authors@R: c(
|
||||||
|
|
2
NEWS.md
2
NEWS.md
|
@ -1,4 +1,4 @@
|
||||||
# AMR 1.2.0.9009
|
# AMR 1.2.0.9010
|
||||||
## <small>Last updated: 17-Jun-2020</small>
|
## <small>Last updated: 17-Jun-2020</small>
|
||||||
|
|
||||||
### New
|
### New
|
||||||
|
|
|
@ -29,8 +29,8 @@
|
||||||
#' @param x existing table to join, or character vector
|
#' @param x existing table to join, or character vector
|
||||||
#' @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$mo` (like `by = "bacteria_id"`), or another column in [microorganisms] (but then it should be named, like `by = c("my_genus_species" = "fullname")`)
|
#' @param by a variable to join by - if left empty will search for a column with class [`mo`] (created with [as.mo()]) or will be `"mo"` if that column name exists in `x`, could otherwise be a column name of `x` with values that exist in `microorganisms$mo` (like `by = "bacteria_id"`), or another column in [microorganisms] (but then it should be named, like `by = c("my_genus_species" = "fullname")`)
|
||||||
#' @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.
|
#' @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.
|
||||||
#' @param ... other parameters to pass on to [dplyr::join()]
|
#' @param ... ignored
|
||||||
#' @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.
|
#' @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.
|
||||||
#'
|
#'
|
||||||
#' These functions rely on [merge()], a base R function to do joins.
|
#' These functions rely on [merge()], a base R function to do joins.
|
||||||
#' @inheritSection AMR Read more on our website!
|
#' @inheritSection AMR Read more on our website!
|
||||||
|
|
|
@ -165,7 +165,7 @@ resistance_predict <- function(x,
|
||||||
year <- function(x) {
|
year <- function(x) {
|
||||||
# don't depend on lubridate or so, would be overkill for only this function
|
# don't depend on lubridate or so, would be overkill for only this function
|
||||||
if (all(grepl("^[0-9]{4}$", x))) {
|
if (all(grepl("^[0-9]{4}$", x))) {
|
||||||
x
|
as.integer(x)
|
||||||
} else {
|
} else {
|
||||||
as.integer(format(as.Date(x), "%Y"))
|
as.integer(format(as.Date(x), "%Y"))
|
||||||
}
|
}
|
||||||
|
|
|
@ -81,7 +81,7 @@
|
||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
|
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9009</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|
|
@ -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">1.2.0.9009</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|
|
@ -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">1.2.0.9009</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|
|
@ -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">1.2.0.9009</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|
|
@ -43,7 +43,7 @@
|
||||||
</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">1.2.0.9009</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|
|
@ -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">1.2.0.9009</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -229,9 +229,9 @@
|
||||||
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div id="amr-1209009" class="section level1">
|
<div id="amr-1209010" class="section level1">
|
||||||
<h1 class="page-header" data-toc-text="1.2.0.9009">
|
<h1 class="page-header" data-toc-text="1.2.0.9010">
|
||||||
<a href="#amr-1209009" class="anchor"></a>AMR 1.2.0.9009<small> Unreleased </small>
|
<a href="#amr-1209010" class="anchor"></a>AMR 1.2.0.9010<small> Unreleased </small>
|
||||||
</h1>
|
</h1>
|
||||||
<div id="last-updated-17-jun-2020" class="section level2">
|
<div id="last-updated-17-jun-2020" class="section level2">
|
||||||
<h2 class="hasAnchor">
|
<h2 class="hasAnchor">
|
||||||
|
|
|
@ -10,7 +10,7 @@ articles:
|
||||||
WHONET: WHONET.html
|
WHONET: WHONET.html
|
||||||
benchmarks: benchmarks.html
|
benchmarks: benchmarks.html
|
||||||
resistance_predict: resistance_predict.html
|
resistance_predict: resistance_predict.html
|
||||||
last_built: 2020-06-17T14:24Z
|
last_built: 2020-06-17T19:33Z
|
||||||
urls:
|
urls:
|
||||||
reference: https://msberends.gitlab.io/AMR/reference
|
reference: https://msberends.gitlab.io/AMR/reference
|
||||||
article: https://msberends.gitlab.io/AMR/articles
|
article: https://msberends.gitlab.io/AMR/articles
|
||||||
|
|
|
@ -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">1.2.0.9009</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|
|
@ -82,7 +82,7 @@
|
||||||
</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">1.2.0</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -264,7 +264,7 @@
|
||||||
</tr>
|
</tr>
|
||||||
<tr>
|
<tr>
|
||||||
<th>...</th>
|
<th>...</th>
|
||||||
<td><p>other parameters to pass on to <code><a href='https://dplyr.tidyverse.org/reference/join.html'>dplyr::join()</a></code></p></td>
|
<td><p>ignored</p></td>
|
||||||
</tr>
|
</tr>
|
||||||
</table>
|
</table>
|
||||||
|
|
||||||
|
|
|
@ -30,13 +30,13 @@ anti_join_microorganisms(x, by = NULL, ...)
|
||||||
|
|
||||||
\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.}
|
\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.}
|
||||||
|
|
||||||
\item{...}{other parameters to pass on to \code{\link[dplyr:join]{dplyr::join()}}}
|
\item{...}{ignored}
|
||||||
}
|
}
|
||||||
\description{
|
\description{
|
||||||
Join the data set \link{microorganisms} easily to an existing table or character vector.
|
Join the data set \link{microorganisms} easily to an existing table or character vector.
|
||||||
}
|
}
|
||||||
\details{
|
\details{
|
||||||
\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.
|
\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.
|
||||||
|
|
||||||
These functions rely on \code{\link[=merge]{merge()}}, a base R function to do joins.
|
These functions rely on \code{\link[=merge]{merge()}}, a base R function to do joins.
|
||||||
}
|
}
|
||||||
|
|
Loading…
Reference in New Issue