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(v0.7.1.9018) deps
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Package: AMR
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Version: 0.7.1.9017
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Date: 2019-07-29
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Version: 0.7.1.9018
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Date: 2019-07-30
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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2
NEWS.md
2
NEWS.md
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# AMR 0.7.1.9017
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# AMR 0.7.1.9018
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### Breaking
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* 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.
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@ -139,8 +139,6 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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#' }
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' a <- eucast_rules(septic_patients)
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#'
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#' a <- data.frame(mo = c("Staphylococcus aureus",
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#' "Enterococcus faecalis",
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#' "Escherichia coli",
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@ -176,7 +174,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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#' # 5 Pseudomonas aeruginosa R R - - R R R
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#'
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#'
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#' # do not apply EUCAST rules, but rather get a a data.frame
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#' # do not apply EUCAST rules, but rather get a data.frame
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#' # with 18 rows, containing all details about the transformations:
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#' c <- eucast_rules(a, verbose = TRUE)
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eucast_rules <- function(x,
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1
R/like.R
1
R/like.R
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#'
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#' # get frequencies of bacteria whose name start with 'Ent' or 'ent'
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#' library(dplyr)
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#' library(clean)
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#' septic_patients %>%
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#' left_join_microorganisms() %>%
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#' filter(genus %like% '^ent') %>%
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@ -78,7 +78,7 @@
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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">0.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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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">0.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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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">0.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
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</span>
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</div>
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@ -42,7 +42,7 @@
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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">0.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
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</span>
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</div>
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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">0.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
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</span>
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</div>
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@ -225,9 +225,9 @@
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</div>
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<div id="amr-0-7-1-9017" class="section level1">
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<div id="amr-0-7-1-9018" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0-7-1-9017" class="anchor"></a>AMR 0.7.1.9017<small> Unreleased </small>
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<a href="#amr-0-7-1-9018" class="anchor"></a>AMR 0.7.1.9018<small> Unreleased </small>
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</h1>
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<div id="breaking" class="section level3">
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<h3 class="hasAnchor">
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@ -1198,7 +1198,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<div id="tocnav">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0-7-1-9017">0.7.1.9017</a></li>
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<li><a href="#amr-0-7-1-9018">0.7.1.9018</a></li>
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<li><a href="#amr-0-7-1">0.7.1</a></li>
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<li><a href="#amr-0-7-0">0.7.0</a></li>
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<li><a href="#amr-0-6-1">0.6.1</a></li>
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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">0.7.1.9015</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
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</span>
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</div>
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@ -374,8 +374,6 @@
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># NOT RUN {</span>
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<span class='no'>a</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>septic_patients</span>)
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<span class='no'>a</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>,
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<span class='st'>"Enterococcus faecalis"</span>,
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<span class='st'>"Escherichia coli"</span>,
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<span class='co'># 5 Pseudomonas aeruginosa R R - - R R R</span>
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<span class='co'># do not apply EUCAST rules, but rather get a a data.frame</span>
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<span class='co'># do not apply EUCAST rules, but rather get a data.frame</span>
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<span class='co'># with 18 rows, containing all details about the transformations:</span>
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<span class='no'>c</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
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<span class='co'># }</span></pre>
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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">0.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
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</span>
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</div>
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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">0.7.1.9015</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
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</span>
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</div>
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<span class='co'># get frequencies of bacteria whose name start with 'Ent' or 'ent'</span>
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<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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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>clean</span>)
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='join.html'>left_join_microorganisms</a></span>() <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%>%</span>
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<span class='fu'>freq</span>(<span class='no'>genus</span>, <span class='no'>species</span>)
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<span class='fu'><a href='https://www.rdocumentation.org/packages/clean/topics/freq'>freq</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)
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<span class='co'># }</span></pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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@ -135,8 +135,6 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
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}
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\examples{
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a <- eucast_rules(septic_patients)
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a <- data.frame(mo = c("Staphylococcus aureus",
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"Enterococcus faecalis",
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"Escherichia coli",
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# 5 Pseudomonas aeruginosa R R - - R R R
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# do not apply EUCAST rules, but rather get a a data.frame
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# do not apply EUCAST rules, but rather get a data.frame
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# with 18 rows, containing all details about the transformations:
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c <- eucast_rules(a, verbose = TRUE)
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}
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# get frequencies of bacteria whose name start with 'Ent' or 'ent'
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library(dplyr)
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library(clean)
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septic_patients \%>\%
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left_join_microorganisms() \%>\%
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filter(genus \%like\% '^ent') \%>\%
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