mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 18:01:50 +02:00
cli-147-2111
This commit is contained in:
github-actions
@ -24,7 +24,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9044</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@ -603,19 +603,19 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 13 × 14</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_user mo_user ab mo input</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-06-10 <span style="color: #949494;">13:14:36</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-06-10 <span style="color: #949494;">13:14:36</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-06-10 <span style="color: #949494;">13:14:36</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-06-10 <span style="color: #949494;">13:14:36</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-06-10 <span style="color: #949494;">13:14:32</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-06-10 <span style="color: #949494;">13:14:32</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-06-10 <span style="color: #949494;">13:14:32</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-06-10 <span style="color: #949494;">13:14:32</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-06-10 <span style="color: #949494;">13:14:31</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-06-10 <span style="color: #949494;">13:14:31</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> 2024-06-10 <span style="color: #949494;">13:14:31</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> 2024-06-10 <span style="color: #949494;">13:14:31</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> 2024-06-10 <span style="color: #949494;">13:14:31</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-06-12 <span style="color: #949494;">08:38:59</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-06-12 <span style="color: #949494;">08:38:59</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-06-12 <span style="color: #949494;">08:38:59</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-06-12 <span style="color: #949494;">08:38:59</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-06-12 <span style="color: #949494;">08:38:55</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-06-12 <span style="color: #949494;">08:38:55</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-06-12 <span style="color: #949494;">08:38:55</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-06-12 <span style="color: #949494;">08:38:55</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-06-12 <span style="color: #949494;">08:38:54</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-06-12 <span style="color: #949494;">08:38:54</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> 2024-06-12 <span style="color: #949494;">08:38:54</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> 2024-06-12 <span style="color: #949494;">08:38:54</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> 2024-06-12 <span style="color: #949494;">08:38:54</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 7 more variables: outcome <sir>, method <chr>, breakpoint_S_R <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># guideline <chr>, host <chr>, ref_table <chr>, uti <lgl></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
@ -782,7 +782,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column for NIT, EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2023...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> thus assuming uti = TRUE. See ?as.sir.</span>
|
||||
@ -794,7 +794,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column for NIT, EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2023...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> thus assuming uti = TRUE. See ?as.sir.</span>
|
||||
|
||||
Reference in New Issue
Block a user