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< h1 > Join a table with < code > microorganisms< / code > < / h1 >
< div class = "hidden name" > < code > join.Rd< / code > < / div >
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< div class = "ref-description" >
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< p > Join the dataset < code > < a href = 'microorganisms.html' > microorganisms< / a > < / code > easily to an existing table or character vector.< / p >
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< / div >
< pre class = "usage" > < span class = 'fu' > inner_join_microorganisms< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > by< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > suffix< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c< / a > < / span > (< span class = 'st' > "2"< / span > , < span class = 'st' > ""< / span > ), < span class = 'no' > ...< / span > )
< span class = 'fu' > left_join_microorganisms< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > by< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > suffix< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c< / a > < / span > (< span class = 'st' > "2"< / span > , < span class = 'st' > ""< / span > ), < span class = 'no' > ...< / span > )
< span class = 'fu' > right_join_microorganisms< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > by< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > suffix< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c< / a > < / span > (< span class = 'st' > "2"< / span > , < span class = 'st' > ""< / span > ), < span class = 'no' > ...< / span > )
< span class = 'fu' > full_join_microorganisms< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > by< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > suffix< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c< / a > < / span > (< span class = 'st' > "2"< / span > , < span class = 'st' > ""< / span > ), < span class = 'no' > ...< / span > )
< span class = 'fu' > semi_join_microorganisms< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > by< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > anti_join_microorganisms< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > by< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'no' > ...< / span > )< / pre >
< h2 class = "hasAnchor" id = "arguments" > < a class = "anchor" href = "#arguments" > < / a > Arguments< / h2 >
< table class = "ref-arguments" >
< colgroup > < col class = "name" / > < col class = "desc" / > < / colgroup >
< tr >
< th > x< / th >
< td > < p > existing table to join, or character vector< / p > < / td >
< / tr >
< tr >
< th > by< / th >
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< td > < p > a variable to join by - if left empty will search for a column with class < code > mo< / code > (created with < code > < a href = 'as.mo.html' > as.mo< / a > < / code > ) or will be < code > "mo"< / code > if that column name exists in < code > x< / code > , could otherwise be a column name of < code > x< / code > with values that exist in < code > microorganisms$mo< / code > (like < code > by = "bacteria_id"< / code > ), or another column in < code > < a href = 'microorganisms.html' > microorganisms< / a > < / code > (but then it should be named, like < code > by = c("my_genus_species" = "fullname")< / code > )< / p > < / td >
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< / tr >
< tr >
< th > suffix< / th >
< td > < p > if there are non-joined duplicate variables in < code > x< / code > and < code > y< / code > , these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.< / p > < / td >
< / tr >
< tr >
< th > ...< / th >
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< td > < p > other parameters to pass on to < code > dplyr::< a href = 'https://dplyr.tidyverse.org/reference/join.html' > join< / a > < / code > .< / p > < / td >
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< / tr >
< / table >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
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< p > < strong > Note:< / strong > As opposed to the < code > < a href = 'https://dplyr.tidyverse.org/reference/join.html' > join< / a > < / code > functions of < code > dplyr< / code > , characters vectors are supported and at default existing columns will get a suffix < code > "2"< / code > and the newly joined columns will not get a suffix. See < code > < a href = 'https://dplyr.tidyverse.org/reference/join.html' > join< / a > < / code > for more information.< / p >
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< h2 class = "hasAnchor" id = "read-more-on-our-website-" > < a class = "anchor" href = "#read-more-on-our-website-" > < / a > Read more on our website!< / h2 >
< p > < img src = 'figures/logo.png' height = 40px style = margin-bottom:5px / > < br / >
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On our website < a href = 'https://msberends.gitlab.io/AMR' > https://msberends.gitlab.io/AMR< / a > you can find < a href = 'https://msberends.gitlab.io/AMR/articles/AMR.html' > a comprehensive tutorial< / a > about how to conduct AMR analysis, the < a href = 'https://msberends.gitlab.io/AMR/reference' > complete documentation of all functions< / a > (which reads a lot easier than here in R) and < a href = 'https://msberends.gitlab.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > .< / p >
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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 >
< span class = 'fu' > left_join_microorganisms< / span > (< span class = 'fu' > < a href = 'as.mo.html' > as.mo< / a > < / span > (< span class = 'st' > "K. pneumoniae"< / span > ))
< span class = 'fu' > left_join_microorganisms< / span > (< span class = 'st' > "B_KLBSL_PNE"< / 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 = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span > < span class = 'fu' > left_join_microorganisms< / span > ()
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< span class = 'no' > df< / 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' > date< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/seq' > seq< / a > < / span > (< span class = 'kw' > from< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/as.Date' > as.Date< / a > < / span > (< span class = 'st' > "2018-01-01"< / span > ),
< span class = 'kw' > to< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/as.Date' > as.Date< / a > < / span > (< span class = 'st' > "2018-01-07"< / span > ),
< span class = 'kw' > by< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 1< / span > ),
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< span class = 'kw' > bacteria< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'as.mo.html' > as.mo< / a > < / span > (< span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c< / a > < / span > (< span class = 'st' > "S. aureus"< / span > , < span class = 'st' > "MRSA"< / span > , < span class = 'st' > "MSSA"< / span > , < span class = 'st' > "STAAUR"< / span > ,
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< span class = 'st' > "E. coli"< / span > , < span class = 'st' > "E. coli"< / span > , < span class = 'st' > "E. coli"< / span > )),
< span class = 'kw' > stringsAsFactors< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )
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< span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/colnames' > colnames< / a > < / span > (< span class = 'no' > df< / span > )
< span class = 'no' > df_joined< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > left_join_microorganisms< / span > (< span class = 'no' > df< / span > , < span class = 'st' > "bacteria"< / span > )
< span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/colnames' > colnames< / a > < / span > (< span class = 'no' > df_joined< / span > )
< span class = 'co' > # }< / span > < / pre >
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< li > < a href = "#read-more-on-our-website-" > Read more on our website!< / a > < / li >
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< p > Developed by < a href = 'https://www.rug.nl/staff/m.s.berends/' > Matthijs S. Berends< / a > , < a href = 'https://www.rug.nl/staff/c.f.luz/' > Christian F. Luz< / a > , < a href = 'https://www.rug.nl/staff/c.glasner/' > Corinna Glasner< / a > , < a href = 'https://www.rug.nl/staff/a.w.friedrich/' > Alex W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > .< / p >
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