<p>These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. <strong>
<td><p>an antimicrobial class, such as <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <ahref='antibiotics.html'>antibiotics</a> data set will be searched (case-insensitive) for this value.</p></td>
<td><p>a <ahref='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether only columns of class <code><rsi></code> must be selected (defaults to <code>FALSE</code>), see <code><ahref='as.rsi.html'>as.rsi()</a></code></p></td>
<p>These functions can be used in data set calls for selecting columns and filtering rows, see <em>Examples</em>. They support base R, but work more convenient in dplyr functions such as <code><ahref='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code>, <code><ahref='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> and <code><ahref='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>.</p>
<p>All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) in the <ahref='antibiotics.html'>antibiotics</a> data set. This means that a selector like e.g. <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
The <ahref='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2class="hasAnchor"id="reference-data-publicly-available"><aclass="anchor"href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <ahref='https://msberends.github.io/AMR/articles/datasets.html'>all download links on our website</a>, which is automatically updated with every code change.</p>
<p>On our website <ahref='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <ahref='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <ahref='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <ahref='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
</div><divclass='output co'>#><spanclass='message'></span><spanstyle='color: #0000BB;'>ℹ For </span><spanstyle='color: #0000BB;background-color: #E4E4E4;'>`aminoglycosides()`</span><spanstyle='color: #0000BB;'> using columns: '</span><spanstyle='color: #0000BB;font-weight: bold;'>AMK</span><spanstyle='color: #0000BB;'>' (amikacin), '</span><spanstyle='color: #0000BB;font-weight: bold;'>GEN</span><spanstyle='color: #0000BB;'>'</span>
#><spanclass='message'> (gentamicin), '</span><spanstyle='color: #0000BB;font-weight: bold;'>KAN</span><spanstyle='color: #0000BB;'>' (kanamycin) and '</span><spanstyle='color: #0000BB;font-weight: bold;'>TOB</span><spanstyle='color: #0000BB;'>' (tobramycin)</span><span></span></div><divclass='output co'>#> mo GEN TOB AMK KAN
</div><divclass='output co'>#><spanclass='message'></span><spanstyle='color: #0000BB;'>ℹ Assuming a filter on all 2 carbapenems. Wrap around </span><spanstyle='color: #0000BB;background-color: #E4E4E4;'>`all()`</span><spanstyle='color: #0000BB;'> or </span><spanstyle='color: #0000BB;background-color: #E4E4E4;'>`any()`</span><spanstyle='color: #0000BB;'> to</span>
#><spanclass='message'> prevent this note.</span><span></span></div><divclass='output co'>#> date hospital_id ward_icu ward_clinical ward_outpatient age gender
</div><divclass='output co'>#><spanclass='message'></span><spanstyle='color: #0000BB;'>ℹ Assuming a filter on all 2 carbapenems. Wrap around </span><spanstyle='color: #0000BB;background-color: #E4E4E4;'>`all()`</span><spanstyle='color: #0000BB;'> or </span><spanstyle='color: #0000BB;background-color: #E4E4E4;'>`any()`</span><spanstyle='color: #0000BB;'> to</span>
#><spanclass='message'> prevent this note.</span><span></span></div><divclass='output co'>#> date hospital_id ward_icu ward_clinical ward_outpatient age gender
</div><divclass='output co'>#><spanclass='message'></span><spanstyle='color: #0000BB;'>ℹ Filtering any of columns '</span><spanstyle='color: #0000BB;font-weight: bold;'>IPM</span><spanstyle='color: #0000BB;'>' and '</span><spanstyle='color: #0000BB;font-weight: bold;'>MEM</span><spanstyle='color: #0000BB;'>' to contain value "R", "S" or "I"</span><span></span></div><divclass='output co'>#> date hospital_id ward_icu ward_clinical ward_outpatient age gender
#> 13 2002-01-19 D FALSE TRUE FALSE 71 M
#> 14 2002-01-19 D FALSE TRUE FALSE 71 M
#> 16 2002-01-22 B TRUE FALSE FALSE 50 M
#> 17 2002-01-22 B TRUE FALSE FALSE 50 M
#> 22 2002-02-05 B TRUE FALSE FALSE 45 F
#> 23 2002-02-05 B TRUE FALSE FALSE 45 F
#> 24 2002-02-05 B TRUE FALSE FALSE 45 F
#> 33 2002-02-27 D FALSE TRUE FALSE 85 F
#> 34 2002-02-27 D FALSE TRUE FALSE 85 F
#> 35 2002-03-08 C FALSE TRUE FALSE 69 M
#> 36 2002-03-16 C FALSE TRUE FALSE 69 M
#> 38 2002-04-01 B TRUE FALSE FALSE 46 F
#> 39 2002-04-01 B TRUE FALSE FALSE 46 F
#> 45 2002-04-08 A TRUE TRUE FALSE 78 M
#> 48 2002-04-14 C FALSE FALSE TRUE 73 M
#> 49 2002-04-23 B TRUE FALSE FALSE 69 F
#> 50 2002-04-23 B TRUE FALSE FALSE 69 F
#> 51 2002-04-26 D FALSE TRUE FALSE 79 M
#> 65 2002-06-05 D FALSE TRUE FALSE 20 F
#> 66 2002-06-06 D FALSE TRUE FALSE 20 F
#> patient_id mo PEN OXA FLC AMX AMC AMP TZP CZO FEP CXM FOX
#> 13 738003 B_ESCHR_COLI R <NA><NA><NA> I <NA><NA><NA><NA> S <NA>
#> 14 738003 B_ESCHR_COLI R <NA><NA><NA> I <NA><NA><NA><NA> S <NA>
#> 16 F35553 B_PROTS_MRBL R <NA><NA><NA> I <NA><NA><NA><NA> S <NA>
#> 17 F35553 B_PROTS_MRBL R <NA><NA><NA> I <NA><NA><NA><NA> S <NA>
#> 22 067927 B_SERRT_MRCS R <NA><NA> R R R <NA> R <NA> R R
#> 23 067927 B_SERRT_MRCS R <NA><NA> R R R <NA> R <NA> R R
#> 24 067927 B_SERRT_MRCS R <NA><NA> R R R <NA> R <NA> R R
#> 33 066895 B_KLBSL_PNMN R <NA><NA> R I R <NA><NA><NA> S <NA>
#> 34 066895 B_KLBSL_PNMN R <NA><NA> R I R <NA><NA><NA> S <NA>
#> 35 4FC193 B_ESCHR_COLI R <NA><NA> R R R <NA><NA><NA> R <NA>
#> 36 4FC193 B_PSDMN_AERG R <NA><NA> R R R <NA> R <NA> R R
#> 38 496896 B_ESCHR_COLI R <NA><NA><NA> I <NA><NA><NA><NA> I <NA>
#> 39 496896 B_ESCHR_COLI R <NA><NA><NA> I <NA><NA><NA><NA> I <NA>
#> 45 130252 B_ENTRC_FCLS <NA><NA><NA><NA> S <NA><NA> R R R R
#> 48 F30196 B_STRPT_GRPB S <NA> S S S S S S S S S
#> 49 EE2510 B_ESCHR_COLI R <NA><NA><NA> I <NA> R <NA><NA> I <NA>
#> 50 EE2510 B_ESCHR_COLI R <NA><NA><NA> I <NA> R <NA><NA> I <NA>
#> 51 D10443 B_KLBSL_PNMN R <NA><NA> R S R <NA><NA><NA> S <NA>
#> 65 24D393 B_ESCHR_COLI R <NA><NA><NA> I <NA><NA><NA><NA> S <NA>
#> 66 24D393 B_ESCHR_COLI R <NA><NA><NA> I <NA><NA><NA><NA> S <NA>
#> CTX CAZ CRO GEN TOB AMK KAN TMP SXT NIT FOS LNZ CIP MFX VAN TEC
#> 13 S <NA> S <NA> S <NA><NA> S S <NA><NA> R <NA><NA> R R
#> 14 S <NA> S <NA> S <NA><NA> S S <NA><NA> R <NA><NA> R R
#> 16 S S S <NA><NA><NA><NA> S S R <NA> R S <NA> R R
#> 17 S S S <NA><NA><NA><NA> S S R <NA> R S <NA> R R
#> 22 <NA><NA><NA><NA><NA><NA><NA> S S R <NA> R S <NA> R R
#> 23 <NA><NA><NA><NA><NA><NA><NA> S S R <NA> R S <NA> R R
#> 24 <NA><NA><NA><NA><NA><NA><NA> S S R <NA> R S <NA> R R
#> 33 S S S S S <NA><NA> S S S <NA> R S <NA> R R
#> 34 S S S S S <NA><NA> S S S <NA> R S <NA> R R
#> 35 S S S S <NA><NA><NA> S S <NA><NA> R S <NA> R R
#> 36 R R R I S <NA> R R R <NA><NA> R I <NA> R R
#> 38 S S S S S <NA><NA> S S S <NA> R S <NA> R R
#> 39 S S S S S <NA><NA> S S S <NA> R S <NA> R R
#> 45 R R R R R R R R R <NA><NA><NA><NA><NA> S <NA>
#> 48 S R S R R R R S S <NA><NA><NA><NA><NA> S <NA>
#> 49 S S S S S <NA><NA> R R R <NA> R R R R R
#> 50 S S S S S <NA><NA> R R R <NA> R R R R R
#> 51 S S S S S <NA><NA> S S S <NA> R S <NA> R R
#> 65 S S S S S <NA><NA> S S S <NA> R S <NA> R R
#> 66 S S S S S <NA><NA> S S S <NA> R S <NA> R R
#> TCY TGC DOX ERY CLI AZM IPM MEM MTR CHL COL MUP RIF
#> 13 <NA><NA><NA> R R R S <NA><NA><NA><NA><NA> R
#> 14 <NA><NA><NA> R R R S <NA><NA><NA><NA><NA> R
#> 16 R R R R R R S <NA><NA><NA> R <NA> R
#> 17 R R R R R R S <NA><NA><NA> R <NA> R
#> 22 R R R R R R S <NA><NA><NA> R <NA> R
#> 23 R R R R R R S <NA><NA><NA> R <NA> R
#> 24 R R R R R R S <NA><NA><NA> R <NA> R
#> 33 <NA><NA><NA> R R R S <NA><NA><NA><NA><NA> R
#> 34 <NA><NA><NA> R R R S <NA><NA><NA><NA><NA> R
#> 35 <NA><NA><NA> R R R S <NA><NA><NA><NA><NA> R
#> 36 R R R R R R S <NA><NA> R <NA><NA> R
#> 38 <NA><NA><NA> R R R S <NA><NA><NA><NA><NA> R
#> 39 <NA><NA><NA> R R R S <NA><NA><NA><NA><NA> R
#> 45 R <NA><NA> R R R S <NA><NA><NA> R <NA><NA>
#> 48 S <NA> S S <NA> S S S <NA><NA> R <NA><NA>
#> 49 <NA><NA><NA> R R R S <NA><NA><NA><NA><NA> R
#> 50 <NA><NA><NA> R R R S <NA><NA><NA><NA><NA> R
#> 51 <NA><NA><NA> R R R S <NA><NA><NA><NA><NA> R
#> 65 <NA><NA><NA> R R R S <NA><NA><NA><NA><NA> R
#> 66 <NA><NA><NA> R R R S <NA><NA><NA><NA><NA> R
</div><divclass='output co'>#><spanclass='message'></span><spanstyle='color: #0000BB;'>ℹ Filtering all of columns '</span><spanstyle='color: #0000BB;font-weight: bold;'>IPM</span><spanstyle='color: #0000BB;'>' and '</span><spanstyle='color: #0000BB;font-weight: bold;'>MEM</span><spanstyle='color: #0000BB;'>' to contain value "R", "S" or "I"</span><span></span></div><divclass='output co'>#> date hospital_id ward_icu ward_clinical ward_outpatient age gender
#> 48 2002-04-14 C FALSE FALSE TRUE 73 M
#> 153 2003-04-08 B TRUE FALSE FALSE 74 M
#> 154 2003-04-08 B TRUE FALSE FALSE 74 M
#> 155 2003-04-08 B TRUE FALSE FALSE 74 M
#> 207 2003-08-14 D FALSE TRUE FALSE 0 F
#> 237 2003-10-16 B TRUE FALSE FALSE 63 F
#> 240 2003-10-20 B TRUE FALSE FALSE 52 M
#> 242 2003-10-20 B TRUE FALSE FALSE 52 M
#> 246 2003-11-04 B TRUE FALSE FALSE 87 F
#> 247 2003-11-04 B TRUE FALSE FALSE 87 F
#> 248 2003-11-04 B TRUE FALSE FALSE 87 F
#> 251 2003-11-21 B TRUE FALSE FALSE 77 F
#> 278 2004-02-10 B TRUE FALSE FALSE 71 F
#> 279 2004-02-10 B TRUE FALSE FALSE 71 F
#> 280 2004-02-10 B TRUE FALSE FALSE 71 F
#> 298 2004-03-03 D FALSE TRUE FALSE 74 M
#> 299 2004-03-03 D FALSE TRUE FALSE 74 M
#> 309 2004-04-07 C FALSE TRUE FALSE 86 F
#> 313 2004-04-15 B TRUE FALSE FALSE 87 F
#> 314 2004-04-15 B TRUE FALSE FALSE 87 F
#> patient_id mo PEN OXA FLC AMX AMC AMP TZP CZO FEP CXM FOX
#> 48 F30196 B_STRPT_GRPB S <NA> S S S S S S S S S
#> 153 114570 B_STRPT_PYGN S <NA> S S S S S S S S S
#> 154 114570 B_STRPT_GRPA S <NA> S S S S S S S S S
#> 155 114570 B_STRPT_GRPA S <NA> S S S S S S S S S
#> 207 F71508 B_STRPT_GRPB S <NA> S S S S S S S S S
#> 237 650870 B_ESCHR_COLI R <NA><NA> R R R S <NA> S S S
#> 240 F35553 B_ENTRBC_CLOC R <NA><NA> R R R S R S R R
#> 242 F35553 B_ENTRBC_CLOC R <NA><NA> R R R S R S R R
#> 246 2FC253 B_ESCHR_COLI R <NA><NA><NA> S <NA> S <NA> S S S
#> 247 2FC253 B_ESCHR_COLI R <NA><NA><NA> S <NA> S <NA> S S S
#> 248 2FC253 B_ESCHR_COLI R <NA><NA><NA> S <NA> S <NA> S S S
#> 251 550406 B_ESCHR_COLI R <NA><NA> R R R S <NA> S I R
#> 278 F24801 B_STRPT_GRPB S <NA> S S S S S S S S S
#> 279 F24801 B_STRPT_AGLC S <NA> S S S S S S S S S
#> 280 F24801 B_STRPT_GRPB S <NA> S S S S S S S S S
#> 298 1435C8 B_ESCHR_COLI R <NA><NA> S S S S <NA> S S S
#> 299 1435C8 B_ESCHR_COLI R <NA><NA> S S S S <NA> S S S
#> 309 765860 B_STRPT_GRPA S <NA> S S S S S S S S S
#> 313 386739 B_ESCHR_COLI R <NA><NA> R I R S <NA> S S S
#> 314 386739 B_ESCHR_COLI R <NA><NA> R I R S <NA> S S S
#> CTX CAZ CRO GEN TOB AMK KAN TMP SXT NIT FOS LNZ CIP MFX VAN TEC
#> 48 S R S R R R R S S <NA><NA><NA><NA><NA> S <NA>
#> 153 S R S R R R R S S <NA><NA><NA><NA><NA> S <NA>
#> 154 S R S R R R R S S <NA><NA><NA><NA><NA> S <NA>
#> 155 S R S R R R R S S <NA><NA><NA><NA><NA> S <NA>
#> 207 S R S R R R R S S <NA><NA><NA><NA><NA> S <NA>
#> 237 S S S S S S <NA><NA> S S <NA> R S <NA> R R
#> 240 <NA><NA><NA> S S S <NA><NA> S R <NA> R S <NA> R R
#> 242 <NA><NA><NA> S S S <NA><NA> S R <NA> R S <NA> R R
#> 246 S S S S S S <NA><NA> S S <NA> R S <NA> R R
#> 247 S S S S S S <NA><NA> S S <NA> R S <NA> R R
#> 248 S S S S S S <NA><NA> S S <NA> R S <NA> R R
#> 251 S S S S S S <NA><NA> S S <NA> R S <NA> R R
#> 278 S R S R R R R R <NA><NA><NA><NA><NA><NA> S <NA>
#> 279 S R S R R R R R <NA><NA><NA><NA><NA><NA> S <NA>
#> 280 S R S R R R R R <NA><NA><NA><NA><NA><NA> S <NA>
#> 298 S S S S S S <NA><NA> S S <NA> R S <NA> R R
#> 299 S S S S S S <NA><NA> S S <NA> R S <NA> R R
#> 309 S R S R R R R S S <NA><NA><NA><NA><NA> S <NA>
#> 313 S S S S S S <NA><NA> S S <NA> R S <NA> R R
#> 314 S S S S S S <NA><NA> S S <NA> R S <NA> R R
#> TCY TGC DOX ERY CLI AZM IPM MEM MTR CHL COL MUP RIF
#> 48 S <NA> S S <NA> S S S <NA><NA> R <NA><NA>
#> 153 S <NA> S S S S S S <NA><NA> R <NA><NA>
#> 154 S <NA> S S S S S S <NA><NA> R <NA><NA>
#> 155 S <NA> S S S S S S <NA><NA> R <NA><NA>
#> 207 R <NA><NA> S <NA> S S S <NA><NA> R <NA><NA>
#> 237 <NA><NA><NA> R R R S S <NA><NA><NA><NA> R
#> 240 <NA><NA><NA> R R R S S <NA><NA><NA><NA> R
#> 242 <NA><NA><NA> R R R S S <NA><NA><NA><NA> R
#> 246 <NA><NA><NA> R R R S S <NA><NA><NA><NA> R
#> 247 <NA><NA><NA> R R R S S <NA><NA><NA><NA> R
#> 248 <NA><NA><NA> R R R S S <NA><NA><NA><NA> R
#> 251 <NA><NA><NA> R R R S S <NA><NA><NA><NA> R
#> 278 R <NA><NA> S <NA> S S S <NA><NA> R <NA><NA>
#> 279 R <NA><NA> S <NA> S S S <NA><NA> R <NA><NA>
#> 280 R <NA><NA> S <NA> S S S <NA><NA> R <NA><NA>
#> 298 <NA><NA><NA> R R R S S <NA><NA><NA><NA> R
#> 299 <NA><NA><NA> R R R S S <NA><NA><NA><NA> R
#> 309 R <NA><NA> S S S S S <NA><NA> R <NA><NA>
#> 313 <NA><NA><NA> R R R S S <NA><NA><NA><NA> R
#> 314 <NA><NA><NA> R R R S S <NA><NA><NA><NA> R
</div><divclass='output co'>#><spanclass='message'></span><spanstyle='color: #0000BB;'>ℹ Assuming a filter on all 6 carbapenems, aminoglycosides. Wrap around</span>
#><spanclass='message'></span><spanstyle='color: #0000BB;background-color: #E4E4E4;'>`all()`</span><spanstyle='color: #0000BB;'> or </span><spanstyle='color: #0000BB;background-color: #E4E4E4;'>`any()`</span><spanstyle='color: #0000BB;'> to prevent this note.</span><span></span></div><divclass='output co'>#> date hospital_id ward_icu ward_clinical ward_outpatient age gender
#> 381 2004-11-03 B TRUE FALSE FALSE 80 F
#> 463 2005-04-22 B TRUE FALSE FALSE 82 F
#> 698 2007-02-21 D FALSE TRUE FALSE 61 F
#> 799 2007-12-15 A FALSE TRUE FALSE 72 M
#> 918 2008-12-06 D FALSE TRUE FALSE 43 F
#> 1172 2011-05-09 D TRUE TRUE FALSE 82 F
#> 1262 2012-03-12 B TRUE TRUE FALSE 80 M
#> 1281 2012-05-19 A FALSE FALSE TRUE 89 F
#> 1302 2012-07-17 D TRUE TRUE FALSE 83 M
#> 1307 2012-07-20 D FALSE TRUE FALSE 66 F
#> 1308 2012-07-20 D FALSE TRUE FALSE 66 F
#> 1324 2012-09-18 D FALSE TRUE FALSE 62 M
#> 1328 2012-10-04 D FALSE TRUE FALSE 62 M
#> 1334 2012-10-18 D TRUE TRUE FALSE 65 F
#> 1449 2014-01-14 B FALSE TRUE FALSE 81 M
#> 1450 2014-01-14 B FALSE TRUE FALSE 81 M
#> 1624 2015-10-06 B TRUE TRUE FALSE 79 F
#> 1625 2015-10-07 B TRUE TRUE FALSE 79 F
#> 1626 2015-10-07 B TRUE TRUE FALSE 79 F
#> 1690 2016-03-27 D FALSE TRUE FALSE 47 M
#> patient_id mo PEN OXA FLC AMX AMC AMP TZP CZO FEP CXM FOX
#> 381 D65308 B_STNTR_MLTP R <NA><NA> R R R R R <NA> R R
#> 463 452212 B_ENTRC_FACM <NA><NA><NA><NA><NA><NA> R R R R R
#> 698 8BBC46 B_ENTRC_FACM <NA><NA><NA><NA><NA><NA> R R R R R
#> 799 401043 B_ENTRC_FACM <NA><NA><NA><NA><NA><NA> R R R R R
#> 918 501361 B_STNTR_MLTP R <NA><NA> R R R R R <NA> R R
#> 1172 207325 B_ENTRC_FACM <NA><NA><NA><NA><NA><NA> R R R R R
#> 1262 582258 B_STPHY_CONS R R R R R R R R R R R
#> 1281 C25552 B_STPHY_CONS R R R R R R R R R R R
#> 1302 F05015 B_STPHY_CONS R R R R R R R R R R R
#> 1307 404299 B_STPHY_CONS R R R R R R R R R R R
#> 1308 404299 B_STPHY_CONS R R R R R R R R R R R
#> 1324 431647 B_STPHY_CONS R R R R R R R R R R R
#> 1328 431647 B_STPHY_CONS R R R R R R R R R R R
#> 1334 E4F322 B_ENTRC_FACM R R R R R R R R R R R
#> 1449 8F77B2 B_ENTRC_FACM R R R R R R R R R R R
#> 1450 8F77B2 B_ENTRC_FACM R R R R R R R R R R R
#> 1624 A76045 B_ENTRC_FACM R R R R R R R R R R R
#> 1625 A76045 B_ENTRC_FACM R R R R R R R R R R R
#> 1626 A76045 B_ENTRC_FACM R R R R R R R R R R R
#> 1690 960787 B_ENTRC_FACM R R R R R R R R R R R
#> CTX CAZ CRO GEN TOB AMK KAN TMP SXT NIT FOS LNZ CIP MFX VAN TEC
#> 381 R R R R R R R R S <NA> R R <NA><NA> R R
#> 463 R R R R R R R R R <NA><NA><NA><NA><NA> S <NA>
#> 698 R R R R R R R R R <NA><NA><NA><NA><NA> S <NA>
#> 799 R R R R R R R R R <NA><NA><NA> R <NA> S <NA>
#> 918 R R R R R R R R S R R R S <NA> R R
#> 1172 R R R R R R R R R <NA><NA><NA><NA><NA> S <NA>
#> 1262 R R R R R R R R <NA><NA><NA><NA> S <NA> S <NA>
#> 1281 R R R R R R R R R <NA><NA><NA> R <NA> S <NA>
#> 1302 R R R R R R R S S <NA><NA><NA> S <NA> S <NA>
#> 1307 R R R R R R R R S <NA><NA><NA> S <NA><NA><NA>
#> 1308 R R R R R R R R R <NA><NA><NA> R <NA> S <NA>
#> 1324 R R R R R R R R R <NA><NA><NA> R <NA> S <NA>
#> 1328 R R R R R R R R R S <NA><NA> R <NA><NA><NA>
#> 1334 R R R R R R R R R S <NA> S <NA><NA> S <NA>
#> 1449 R R R R R R R R R S <NA> S <NA><NA> S S
#> 1450 R R R R R R R R R S <NA> S <NA><NA> S S
#> 1624 R R R R R R R R R S <NA> S <NA><NA> S S
#> 1625 R R R R R R R R R S <NA> S <NA><NA> S S
#> 1626 R R R R R R R R R S <NA> S <NA><NA> S S
#> 1690 R R R R R R R R R S <NA> S <NA><NA> S S
#> TCY TGC DOX ERY CLI AZM IPM MEM MTR CHL COL MUP RIF
#> 381 R <NA> R R R R R R <NA><NA> R <NA> R
#> 463 R <NA><NA> R R R R R <NA><NA> R <NA><NA>
#> 698 S <NA><NA> R R R R R <NA><NA> R <NA><NA>
#> 799 S <NA><NA> R R R R R <NA><NA> R <NA><NA>
#> 918 R <NA> R R R R R R <NA><NA> R <NA> R
#> 1172 <NA><NA> S R R R R R <NA><NA> R <NA><NA>
#> 1262 <NA><NA> S R R R R R <NA><NA> R <NA><NA>
#> 1281 <NA><NA><NA> R R R R R <NA><NA> R <NA><NA>
#> 1302 <NA><NA> R R R R R R <NA><NA> R <NA><NA>
#> 1307 <NA><NA> R R R R R R <NA><NA> R <NA><NA>
#> 1308 <NA><NA> S R S R R R <NA><NA> R <NA><NA>
#> 1324 <NA><NA> R R S R R R <NA><NA> R <NA><NA>
#> 1328 R <NA> R R R R R R <NA><NA> R S S
#> 1334 <NA><NA><NA> R R R R R <NA><NA> R <NA><NA>
#> 1449 <NA> S <NA> R R R R R <NA><NA> R <NA><NA>
#> 1450 <NA> S <NA> R R R R R <NA><NA> R <NA><NA>
#> 1624 <NA> S <NA> R R R R R <NA><NA> R <NA><NA>
#> 1625 <NA> S <NA> R R R R R <NA><NA> R <NA><NA>
#> 1626 <NA> S <NA> R R R R R <NA><NA> R <NA><NA>
#> 1690 <NA> S <NA> R R R R R <NA><NA> R <NA><NA>
J01CA01 <spanclass='op'>=</span><spanclass='st'>"S"</span><spanclass='op'>)</span><spanclass='op'>%>%</span><spanclass='co'># ATC code of ampicillin</span>
<spanclass='fu'><ahref='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><spanclass='op'>(</span><spanclass='fu'>penicillins</span><spanclass='op'>(</span><spanclass='op'>)</span><spanclass='op'>)</span><spanclass='co'># only the 'J01CA01' column will be selected</span>
<p>Developed by <ahref='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <ahref='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <ahref='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <ahref='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <ahref='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <ahref='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
