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(v0.7.1.9016) deps

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dr. M.S. (Matthijs) Berends 2019-07-29 17:34:57 +02:00
parent 240f03a672
commit b7e2d7b9b8
18 changed files with 34 additions and 18 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.7.1.9015 Version: 0.7.1.9016
Date: 2019-07-29 Date: 2019-07-29
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

3
NAMESPACE
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@ -196,6 +196,7 @@ exportMethods(summary.mic)
exportMethods(summary.mo) exportMethods(summary.mo)
exportMethods(summary.rsi) exportMethods(summary.rsi)
importFrom(clean,freq) importFrom(clean,freq)
importFrom(clean,top_freq)
importFrom(crayon,bgGreen) importFrom(crayon,bgGreen)
importFrom(crayon,bgRed) importFrom(crayon,bgRed)
importFrom(crayon,bgYellow) importFrom(crayon,bgYellow)
@ -222,6 +223,7 @@ importFrom(dplyr,arrange_at)
importFrom(dplyr,between) importFrom(dplyr,between)
importFrom(dplyr,bind_rows) importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when) importFrom(dplyr,case_when)
importFrom(dplyr,desc)
importFrom(dplyr,distinct) importFrom(dplyr,distinct)
importFrom(dplyr,everything) importFrom(dplyr,everything)
importFrom(dplyr,filter) importFrom(dplyr,filter)
@ -250,6 +252,7 @@ importFrom(dplyr,summarise)
importFrom(dplyr,summarise_if) importFrom(dplyr,summarise_if)
importFrom(dplyr,tibble) importFrom(dplyr,tibble)
importFrom(dplyr,transmute) importFrom(dplyr,transmute)
importFrom(dplyr,ungroup)
importFrom(dplyr,vars) importFrom(dplyr,vars)
importFrom(graphics,arrows) importFrom(graphics,arrows)
importFrom(graphics,axis) importFrom(graphics,axis)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9015 # AMR 0.7.1.9016
### Breaking ### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. We decided to create a new package for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too. * Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. We decided to create a new package for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.

2
R/first_isolate.R
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@ -70,7 +70,7 @@
#' @keywords isolate isolates first #' @keywords isolate isolates first
#' @seealso \code{\link{key_antibiotics}} #' @seealso \code{\link{key_antibiotics}}
#' @export #' @export
#' @importFrom dplyr arrange_at lag between row_number filter mutate arrange pull #' @importFrom dplyr arrange_at lag between row_number filter mutate arrange pull ungroup
#' @importFrom crayon blue bold silver #' @importFrom crayon blue bold silver
#' @return Logical vector #' @return Logical vector
#' @source Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}. #' @source Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.

2
R/mic.R
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@ -51,6 +51,8 @@
#' #'
#' plot(mic_data) #' plot(mic_data)
#' barplot(mic_data) #' barplot(mic_data)
#'
#' library(clean)
#' freq(mic_data) #' freq(mic_data)
as.mic <- function(x, na.rm = FALSE) { as.mic <- function(x, na.rm = FALSE) {
if (is.mic(x)) { if (is.mic(x)) {

1
R/mo.R
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@ -1412,6 +1412,7 @@ print.mo <- function(x, ...) {
#' @exportMethod summary.mo #' @exportMethod summary.mo
#' @importFrom dplyr n_distinct #' @importFrom dplyr n_distinct
#' @importFrom clean freq top_freq
#' @export #' @export
#' @noRd #' @noRd
summary.mo <- function(object, ...) { summary.mo <- function(object, ...) {

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R/resistance_predict.R
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@ -58,7 +58,7 @@
#' @rdname resistance_predict #' @rdname resistance_predict
#' @export #' @export
#' @importFrom stats predict glm lm #' @importFrom stats predict glm lm
#' @importFrom dplyr %>% pull mutate mutate_at n group_by_at summarise filter filter_at all_vars n_distinct arrange case_when n_groups transmute #' @importFrom dplyr %>% pull mutate mutate_at n group_by_at summarise filter filter_at all_vars n_distinct arrange case_when n_groups transmute ungroup
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @examples #' @examples
#' x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010) #' x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010)

4
R/rsi.R
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@ -50,7 +50,7 @@
#' @return Ordered factor with new class \code{rsi} #' @return Ordered factor with new class \code{rsi}
#' @keywords rsi #' @keywords rsi
#' @export #' @export
#' @importFrom dplyr %>% #' @importFrom dplyr %>% desc arrange filter
#' @seealso \code{\link{as.mic}} #' @seealso \code{\link{as.mic}}
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @examples #' @examples
@ -73,6 +73,8 @@
#' #'
#' plot(rsi_data) # for percentages #' plot(rsi_data) # for percentages
#' barplot(rsi_data) # for frequencies #' barplot(rsi_data) # for frequencies
#'
#' library(clean)
#' freq(rsi_data) # frequency table with informative header #' freq(rsi_data) # frequency table with informative header
#' #'
#' # using dplyr's mutate #' # using dplyr's mutate

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docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9016</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9016</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9016</span>
</span> </span>
</div> </div>

2
docs/index.html
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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">0.7.1.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9016</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9016</span>
</span> </span>
</div> </div>
@ -225,9 +225,9 @@
</div> </div>
<div id="amr-0-7-1-9015" class="section level1"> <div id="amr-0-7-1-9016" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9015" class="anchor"></a>AMR 0.7.1.9015<small> Unreleased </small> <a href="#amr-0-7-1-9016" class="anchor"></a>AMR 0.7.1.9016<small> Unreleased </small>
</h1> </h1>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -1198,7 +1198,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9015">0.7.1.9015</a></li> <li><a href="#amr-0-7-1-9016">0.7.1.9016</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li> <li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li> <li><a href="#amr-0-6-1">0.6.1</a></li>

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docs/reference/as.mic.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9016</span>
</span> </span>
</div> </div>
@ -289,7 +289,9 @@
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>mic_data</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>mic_data</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/barplot'>barplot</a></span>(<span class='no'>mic_data</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/barplot'>barplot</a></span>(<span class='no'>mic_data</span>)
<span class='fu'>freq</span>(<span class='no'>mic_data</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>clean</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/clean/topics/freq'>freq</a></span>(<span class='no'>mic_data</span>)
<span class='co'># }</span></pre> <span class='co'># }</span></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

6
docs/reference/as.rsi.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9016</span>
</span> </span>
</div> </div>
@ -336,7 +336,9 @@
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for percentages</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for percentages</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/barplot'>barplot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for frequencies</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/barplot'>barplot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for frequencies</span>
<span class='fu'>freq</span>(<span class='no'>rsi_data</span>) <span class='co'># frequency table with informative header</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>clean</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/clean/topics/freq'>freq</a></span>(<span class='no'>rsi_data</span>) <span class='co'># frequency table with informative header</span>
<span class='co'># using dplyr's mutate</span> <span class='co'># using dplyr's mutate</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)

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docs/reference/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9016</span>
</span> </span>
</div> </div>

2
man/as.mic.Rd
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@ -47,6 +47,8 @@ as.rsi(x = as.mic(4),
plot(mic_data) plot(mic_data)
barplot(mic_data) barplot(mic_data)
library(clean)
freq(mic_data) freq(mic_data)
} }
\seealso{ \seealso{

2
man/as.rsi.Rd
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@ -90,6 +90,8 @@ as.rsi(x = as.mic(4),
plot(rsi_data) # for percentages plot(rsi_data) # for percentages
barplot(rsi_data) # for frequencies barplot(rsi_data) # for frequencies
library(clean)
freq(rsi_data) # frequency table with informative header freq(rsi_data) # frequency table with informative header
# using dplyr's mutate # using dplyr's mutate