mirror of
https://github.com/msberends/AMR.git
synced 2025-07-10 00:23:03 +02:00
website update
This commit is contained in:
@ -309,9 +309,49 @@
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># NOT RUN {</span>
|
||||
<span class='no'>a</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>septic_patients</span>)
|
||||
|
||||
<pre class="examples"><div class='input'><span class='no'>a</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>septic_patients</span>)</div><div class='output co'>#> <span class='message'><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>mo</span><span style='color: #0000BB;'>` as input for `col_mo`.</span><span></span></div><div class='output co'>#> <span class='warning'>Warning: These columns do not exist and will be ignored: azlo, aztr, cefa, cfra, clar, dapt, erta, fusi, levo, linc, mezl, mino, nali, neom, neti, novo, norf, oflo, pipe, poly, pris, qida, roxi, siso, tica.</span>
|
||||
#> <span class='warning'>THIS MAY STRONGLY INFLUENCE THE OUTCOME.</span></div><div class='output co'>#>
|
||||
#> Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
|
||||
#> </span><span style='font-weight: bold;'>
|
||||
#> EUCAST Clinical Breakpoints (v8.1, 2018)
|
||||
#> </span><span>Enterobacteriales (Order)</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Staphylococcus</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Enterococcus</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Streptococcus</span><span> groups A, B, C, G</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Streptococcus pneumoniae</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Viridans group streptococci</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Haemophilus influenzae</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Moraxella catarrhalis</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Anaerobic Gram positives</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Anaerobic Gram negatives</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Pasteurella multocida</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Campylobacter jejuni</span><span> and </span><span style='font-style: italic;'>C. coli</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Aerococcus sanguinicola</span><span> and </span><span style='font-style: italic;'>A. urinae</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Kingella kingae</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-weight: bold;'>
|
||||
#> EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)
|
||||
#> </span><span>Table 1: Intrinsic resistance in </span><span style='font-style: italic;'>Enterobacteriaceae</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 3: Intrinsic resistance in other Gram-negative bacteria</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 4: Intrinsic resistance in Gram-positive bacteria</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 9: Interpretive rules for B-lactam agents and Gram-negative rods</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 12: Interpretive rules for aminoglycosides</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 13: Interpretive rules for quinolones</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-weight: bold;'>
|
||||
#> Other rules
|
||||
#> </span><span>Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-weight: bold;'>
|
||||
#> => EUCAST rules affected 1,980 out of 2,000 rows -> </span><span style='color: #00BB00;font-weight: bold;'>changed 0 test results.
|
||||
#>
|
||||
#> </span><span></div><div class='input'>
|
||||
<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>,
|
||||
<span class='st'>"Enterococcus faecalis"</span>,
|
||||
<span class='st'>"Escherichia coli"</span>,
|
||||
@ -326,24 +366,72 @@
|
||||
<span class='kw'>cfox</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
|
||||
<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='no'>a</span>
|
||||
<span class='co'># mo vanc amox coli cfta cfur peni cfox</span>
|
||||
<span class='no'>a</span></div><div class='output co'>#> mo vanc amox coli cfta cfur peni cfox
|
||||
#> 1 Staphylococcus aureus - - - - - S S
|
||||
#> 2 Enterococcus faecalis - - - - - S S
|
||||
#> 3 Escherichia coli - - - - - S S
|
||||
#> 4 Klebsiella pneumoniae - - - - - S S
|
||||
#> 5 Pseudomonas aeruginosa - - - - - S S</div><div class='input'><span class='co'># mo vanc amox coli cfta cfur peni cfox</span>
|
||||
<span class='co'># 1 Staphylococcus aureus - - - - - S S</span>
|
||||
<span class='co'># 2 Enterococcus faecalis - - - - - S S</span>
|
||||
<span class='co'># 3 Escherichia coli - - - - - S S</span>
|
||||
<span class='co'># 4 Klebsiella pneumoniae - - - - - S S</span>
|
||||
<span class='co'># 5 Pseudomonas aeruginosa - - - - - S S</span>
|
||||
|
||||
<span class='no'>b</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='st'>"mo"</span>) <span class='co'># 18 results are forced as R or S</span>
|
||||
|
||||
<span class='no'>b</span>
|
||||
<span class='co'># mo vanc amox coli cfta cfur peni cfox</span>
|
||||
<span class='co'># 1 Staphylococcus aureus - S R R S S S</span>
|
||||
<span class='co'># 2 Enterococcus faecalis - - R R R S R</span>
|
||||
<span class='co'># 3 Escherichia coli R - - - - R S</span>
|
||||
<span class='co'># 4 Klebsiella pneumoniae R R - - - R S</span>
|
||||
<span class='co'># 5 Pseudomonas aeruginosa R R - - R R R</span>
|
||||
<span class='co'># }</span></pre>
|
||||
<span class='no'>b</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='st'>"mo"</span>) <span class='co'># 18 results are forced as R or S</span></div><div class='output co'>#> <span class='warning'>Warning: These columns do not exist and will be ignored: amcl, amik, ampi, azit, azlo, aztr, cefa, cfra, cfep, cfot, cftr, chlo, cipr, clar, clin, clox, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, novo, norf, oflo, oxac, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu.</span>
|
||||
#> <span class='warning'>THIS MAY STRONGLY INFLUENCE THE OUTCOME.</span></div><div class='output co'>#>
|
||||
#> Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)</div><div class='output co'>#> <span class='message'></span><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>amox</span><span style='color: #0000BB;'>` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.</span><span></span></div><div class='output co'>#> </span><span style='font-weight: bold;'>
|
||||
#> EUCAST Clinical Breakpoints (v8.1, 2018)
|
||||
#> </span><span>Enterobacteriales (Order)</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Staphylococcus</span><span style='color: #0000BB;'> (2 changes)
|
||||
#> </span><span style='font-style: italic;'>Enterococcus</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Streptococcus</span><span> groups A, B, C, G</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Streptococcus pneumoniae</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Viridans group streptococci</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Haemophilus influenzae</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Moraxella catarrhalis</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Anaerobic Gram positives</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Anaerobic Gram negatives</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Pasteurella multocida</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Campylobacter jejuni</span><span> and </span><span style='font-style: italic;'>C. coli</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Aerococcus sanguinicola</span><span> and </span><span style='font-style: italic;'>A. urinae</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-style: italic;'>Kingella kingae</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-weight: bold;'>
|
||||
#> EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)
|
||||
#> </span><span>Table 1: Intrinsic resistance in </span><span style='font-style: italic;'>Enterobacteriaceae</span><span style='color: #0000BB;'> (5 changes)
|
||||
#> </span><span>Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria</span><span style='color: #0000BB;'> (5 changes)
|
||||
#> </span><span>Table 3: Intrinsic resistance in other Gram-negative bacteria</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 4: Intrinsic resistance in Gram-positive bacteria</span><span style='color: #0000BB;'> (6 changes)
|
||||
#> </span><span>Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 9: Interpretive rules for B-lactam agents and Gram-negative rods</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 12: Interpretive rules for aminoglycosides</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Table 13: Interpretive rules for quinolones</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-weight: bold;'>
|
||||
#> Other rules
|
||||
#> </span><span>Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span>Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S</span><span style='color: #00BB00;'> (no changes)
|
||||
#> </span><span style='font-weight: bold;'>
|
||||
#> => EUCAST rules affected 5 out of 5 rows -> </span><span style='color: #0000BB;font-weight: bold;'>changed 18 test results.
|
||||
#>
|
||||
#> </span><span></div><div class='input'>
|
||||
<span class='no'>b</span></div><div class='output co'>#> mo vanc amox coli cfta cfur peni cfox
|
||||
#> 1 Staphylococcus aureus - S R R S S S
|
||||
#> 2 Enterococcus faecalis - - R R R S R
|
||||
#> 3 Escherichia coli R - - - - R S
|
||||
#> 4 Klebsiella pneumoniae R R - - - R S
|
||||
#> 5 Pseudomonas aeruginosa R R - - R R R</div><div class='input'># mo vanc amox coli cfta cfur peni cfox
|
||||
# 1 Staphylococcus aureus - S R R S S S
|
||||
# 2 Enterococcus faecalis - - R R R S R
|
||||
# 3 Escherichia coli R - - - - R S
|
||||
# 4 Klebsiella pneumoniae R R - - - R S
|
||||
# 5 Pseudomonas aeruginosa R R - - R R R
|
||||
</div></span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
|
||||
Reference in New Issue
Block a user