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atc_ functions
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@ -385,34 +385,34 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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<span class='co'># you could also use `select` or `pull` to get your variables</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>mo</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'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%>%</span>
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<span class='fu'>freq</span>()
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<span class='co'># multiple selected variables will be pasted together</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='no'>left_join_microorganisms</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"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'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</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='co'># group a variable and analyse another</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'>freq</span>(<span class='no'>gender</span>)
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<span class='co'># get top 10 bugs of hospital A as a vector</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"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'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</span>
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<span class='fu'>freq</span>(<span class='no'>mo</span>) <span class='kw'>%>%</span>
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<span class='fu'>top_freq</span>(<span class='fl'>10</span>)
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<span class='co'># save frequency table to an object</span>
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<span class='no'>years</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%>%</span>
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<span class='fu'>freq</span>(<span class='no'>year</span>)
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@ -463,11 +463,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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<span class='co'># only get selected columns</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>)
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>)
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</span>)
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</span>)
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<span class='co'># check differences between frequency tables</span>
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