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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -160,65 +160,60 @@
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">availability</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> count available visual_availabilty resistant visual_resistance</span>
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<span class="r-out co"><span class="r-pr">#></span> date 2000 100.0% |################| </span>
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<span class="r-out co"><span class="r-pr">#></span> hospital_id 2000 100.0% |################| </span>
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<span class="r-out co"><span class="r-pr">#></span> ward_icu 2000 100.0% |################| </span>
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<span class="r-out co"><span class="r-pr">#></span> ward_clinical 2000 100.0% |################| </span>
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<span class="r-out co"><span class="r-pr">#></span> ward_outpatient 2000 100.0% |################| </span>
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<span class="r-out co"><span class="r-pr">#></span> age 2000 100.0% |################| </span>
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<span class="r-out co"><span class="r-pr">#></span> gender 2000 100.0% |################| </span>
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<span class="r-out co"><span class="r-pr">#></span> patient_id 2000 100.0% |################| </span>
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<span class="r-out co"><span class="r-pr">#></span> mo 2000 100.0% |################| </span>
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<span class="r-out co"><span class="r-pr">#></span> PEN 1629 81.5% |############----| 73.7% |###########-----|</span>
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<span class="r-out co"><span class="r-pr">#></span> OXA 365 18.3% |##--------------| 31.2% |#####-----------|</span>
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<span class="r-out co"><span class="r-pr">#></span> FLC 943 47.2% |#######---------| 29.5% |####------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMX 1350 67.5% |##########------| 59.6% |#########-------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMC 1879 94.0% |###############-| 23.7% |###-------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMP 1350 67.5% |##########------| 59.6% |#########-------|</span>
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<span class="r-out co"><span class="r-pr">#></span> TZP 1001 50.0% |########--------| 12.6% |##--------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CZO 446 22.3% |###-------------| 44.6% |#######---------|</span>
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<span class="r-out co"><span class="r-pr">#></span> FEP 724 36.2% |#####-----------| 14.2% |##--------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CXM 1789 89.5% |##############--| 26.3% |####------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> FOX 818 40.9% |######----------| 27.4% |####------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CTX 943 47.2% |#######---------| 15.5% |##--------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CAZ 1811 90.6% |##############--| 66.5% |##########------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CRO 943 47.2% |#######---------| 15.5% |##--------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> GEN 1855 92.8% |##############--| 24.6% |###-------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> TOB 1351 67.6% |##########------| 34.4% |#####-----------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMK 692 34.6% |#####-----------| 63.7% |##########------|</span>
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<span class="r-out co"><span class="r-pr">#></span> KAN 471 23.6% |###-------------| 100.0% |################|</span>
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<span class="r-out co"><span class="r-pr">#></span> TMP 1499 75.0% |############----| 38.1% |######----------|</span>
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<span class="r-out co"><span class="r-pr">#></span> SXT 1759 88.0% |##############--| 20.5% |###-------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> NIT 743 37.2% |#####-----------| 17.1% |##--------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> FOS 351 17.6% |##--------------| 42.2% |######----------|</span>
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<span class="r-out co"><span class="r-pr">#></span> LNZ 1023 51.2% |########--------| 69.3% |###########-----|</span>
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<span class="r-out co"><span class="r-pr">#></span> CIP 1409 70.5% |###########-----| 16.2% |##--------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> MFX 211 10.6% |#---------------| 33.6% |#####-----------|</span>
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<span class="r-out co"><span class="r-pr">#></span> VAN 1861 93.1% |##############--| 38.3% |######----------|</span>
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<span class="r-out co"><span class="r-pr">#></span> TEC 976 48.8% |#######---------| 75.7% |############----|</span>
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<span class="r-out co"><span class="r-pr">#></span> TCY 1200 60.0% |#########-------| 29.8% |####------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> TGC 798 39.9% |######----------| 12.7% |##--------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> DOX 1136 56.8% |#########-------| 27.7% |####------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> ERY 1894 94.7% |###############-| 57.2% |#########-------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CLI 1520 76.0% |############----| 61.2% |#########-------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AZM 1894 94.7% |###############-| 57.2% |#########-------|</span>
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<span class="r-out co"><span class="r-pr">#></span> IPM 889 44.5% |#######---------| 6.2% |----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> MEM 829 41.5% |######----------| 5.9% |----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> MTR 34 1.7% |----------------| 14.7% |##--------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CHL 154 7.7% |#---------------| 21.4% |###-------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> COL 1640 82.0% |#############---| 81.2% |############----|</span>
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<span class="r-out co"><span class="r-pr">#></span> MUP 270 13.5% |##--------------| 5.9% |----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> RIF 1003 50.2% |########--------| 69.6% |###########-----|</span>
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<span class="r-out co"><span class="r-pr">#></span> count available visual_availabilty resistant visual_resistance</span>
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<span class="r-out co"><span class="r-pr">#></span> date 2000 100.0% |####################| </span>
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<span class="r-out co"><span class="r-pr">#></span> patient 2000 100.0% |####################| </span>
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<span class="r-out co"><span class="r-pr">#></span> age 2000 100.0% |####################| </span>
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<span class="r-out co"><span class="r-pr">#></span> gender 2000 100.0% |####################| </span>
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<span class="r-out co"><span class="r-pr">#></span> ward 2000 100.0% |####################| </span>
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<span class="r-out co"><span class="r-pr">#></span> mo 2000 100.0% |####################| </span>
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<span class="r-out co"><span class="r-pr">#></span> PEN 1629 81.5% |################----| 73.7% |##############------|</span>
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<span class="r-out co"><span class="r-pr">#></span> OXA 365 18.3% |###-----------------| 31.2% |######--------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> FLC 943 47.2% |#########-----------| 29.5% |#####---------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMX 1350 67.5% |#############-------| 59.6% |###########---------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMC 1879 94.0% |##################--| 23.7% |####----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMP 1350 67.5% |#############-------| 59.6% |###########---------|</span>
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<span class="r-out co"><span class="r-pr">#></span> TZP 1001 50.0% |##########----------| 12.6% |##------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CZO 446 22.3% |####----------------| 44.6% |########------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> FEP 724 36.2% |#######-------------| 14.2% |##------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CXM 1789 89.5% |#################---| 26.3% |#####---------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> FOX 818 40.9% |########------------| 27.4% |#####---------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CTX 943 47.2% |#########-----------| 15.5% |###-----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CAZ 1811 90.6% |##################--| 66.5% |#############-------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CRO 943 47.2% |#########-----------| 15.5% |###-----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> GEN 1855 92.8% |##################--| 24.6% |####----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> TOB 1351 67.6% |#############-------| 34.4% |######--------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMK 692 34.6% |######--------------| 63.7% |############--------|</span>
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<span class="r-out co"><span class="r-pr">#></span> KAN 471 23.6% |####----------------| 100.0% |####################|</span>
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<span class="r-out co"><span class="r-pr">#></span> TMP 1499 75.0% |###############-----| 38.1% |#######-------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> SXT 1759 88.0% |#################---| 20.5% |####----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> NIT 743 37.2% |#######-------------| 17.1% |###-----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> FOS 351 17.6% |###-----------------| 42.2% |########------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> LNZ 1023 51.2% |##########----------| 69.3% |#############-------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CIP 1409 70.5% |#############-------| 16.2% |###-----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> MFX 211 10.6% |##------------------| 33.6% |######--------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> VAN 1861 93.1% |##################--| 38.3% |#######-------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> TEC 976 48.8% |#########-----------| 75.7% |###############-----|</span>
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<span class="r-out co"><span class="r-pr">#></span> TCY 1200 60.0% |###########---------| 29.8% |#####---------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> TGC 798 39.9% |########------------| 12.7% |##------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> DOX 1136 56.8% |###########---------| 27.7% |#####---------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> ERY 1894 94.7% |##################--| 57.2% |###########---------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CLI 1520 76.0% |###############-----| 61.2% |############--------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AZM 1894 94.7% |##################--| 57.2% |###########---------|</span>
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<span class="r-out co"><span class="r-pr">#></span> IPM 889 44.5% |########------------| 6.2% |#-------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> MEM 829 41.5% |########------------| 5.9% |#-------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> MTR 34 1.7% |--------------------| 14.7% |##------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CHL 154 7.7% |#-------------------| 21.4% |####----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> COL 1640 82.0% |################----| 81.2% |################----|</span>
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<span class="r-out co"><span class="r-pr">#></span> MUP 270 13.5% |##------------------| 5.9% |#-------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> RIF 1003 50.2% |##########----------| 69.6% |#############-------|</span>
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">mo</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">mo</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select_all.html" class="external-link">select_if</a></span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu">availability</span><span class="op">(</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
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<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
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<span class="r-out co"><span class="r-pr">#></span> count available visual_availabilty resistant visual_resistance</span>
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<span class="r-out co"><span class="r-pr">#></span> PEN 467 100.0% |######################| 100.0% |######################|</span>
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<span class="r-out co"><span class="r-pr">#></span> OXA 0 0.0% |----------------------| </span>
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