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2026-04-25 12:49:42 +00:00
parent cc4e9bab4b
commit e12355b4a8
16 changed files with 127 additions and 113 deletions
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20
reference/age.html
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@@ -112,16 +112,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 26 26.81644 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.23288 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.38356 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.14795 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.47671 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.18904 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.17534 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.28493 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.65753 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.24110 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 26 26.81918 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.23562 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.38630 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.15068 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.47945 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.19178 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.17808 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.28767 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.66027 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.24384 21</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

20
reference/age.md
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@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
df
#> birth_date age age_exact age_at_y2k
#> 1 1999-06-30 26 26.81644 0
#> 2 1968-01-29 58 58.23288 31
#> 3 1965-12-05 60 60.38356 34
#> 4 1980-03-01 46 46.14795 19
#> 5 1949-11-01 76 76.47671 50
#> 6 1947-02-14 79 79.18904 52
#> 7 1940-02-19 86 86.17534 59
#> 8 1988-01-10 38 38.28493 11
#> 9 1997-08-27 28 28.65753 2
#> 10 1978-01-26 48 48.24110 21
#> 1 1999-06-30 26 26.81918 0
#> 2 1968-01-29 58 58.23562 31
#> 3 1965-12-05 60 60.38630 34
#> 4 1980-03-01 46 46.15068 19
#> 5 1949-11-01 76 76.47945 50
#> 6 1947-02-14 79 79.19178 52
#> 7 1940-02-19 86 86.17808 59
#> 8 1988-01-10 38 38.28767 11
#> 9 1997-08-27 28 28.66027 2
#> 10 1978-01-26 48 48.24384 21
```

2
reference/amr-tidymodels.html
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@@ -184,7 +184,7 @@ may affect the computations for subsequent operations.</p></dd>
<span class="r-in"><span> <span class="va">metrics</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: tidymodels</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Attaching packages</span> ────────────────────────────────────── tidymodels 1.4.1 ──</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Attaching packages</span> ────────────────────────────────────── tidymodels 1.5.0 ──</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom </span> 1.0.12 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample </span> 1.3.2 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials </span> 1.4.3 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tailor </span> 0.1.0 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer </span> 1.1.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr </span> 1.3.2 </span>

2
reference/amr-tidymodels.md
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@@ -163,7 +163,7 @@ if (require("tidymodels")) {
metrics
}
#> Loading required package: tidymodels
#> ── Attaching packages ────────────────────────────────────── tidymodels 1.4.1 ──
#> ── Attaching packages ────────────────────────────────────── tidymodels 1.5.0 ──
#> ✔ broom 1.0.12 ✔ rsample 1.3.2
#> ✔ dials 1.4.3 ✔ tailor 0.1.0
#> ✔ infer 1.1.0 ✔ tidyr 1.3.2

3
reference/antimicrobial_selectors.html
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@@ -687,6 +687,9 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-msg co"><span class="r-pr">#&gt;</span> The following objects are masked from ‘package:AMR’:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> %like%, like</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> The following object is masked from ‘package:base’:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> %notin%</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>It should never be needed to print an antimicrobial selector class. Are you</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> using <span style="color: #0000BB;">data.table</span>? Then add the argument `with = FALSE`, see our examples at</span>

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@@ -1060,6 +1060,9 @@ if (require("data.table")) {
#> The following objects are masked from ‘package:AMR’:
#>
#> %like%, like
#> The following object is masked from ‘package:base’:
#>
#> %notin%
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> Warning: It should never be needed to print an antimicrobial selector class. Are you
#> using data.table? Then add the argument `with = FALSE`, see our examples at

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reference/as.sir.html
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@@ -370,20 +370,20 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span><span class="op">)</span> <span class="co"># see all SIR results at a glance</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Min. :2002-01-02 Length:2000 Min. : 0.00 Length:2000 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1st Qu.:2005-07-31 Class :character 1st Qu.:63.00 Class :character </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Median :2009-07-31 Mode :character Median :74.00 Mode :character </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Mean :2009-11-20 Mean :70.69 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3rd Qu.:2014-05-30 3rd Qu.:82.00 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Max. :2017-12-28 Max. :97.00 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward mo PEN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Length:2000 Class :mo Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class :character &lt;NA&gt; :0 %S :25.6% (n=417) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Mode :character Unique:90 %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> #1 :B_ESCHR_COLI %I : 0.7% (n=11) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> #2 :B_STPHY_CONS %R :73.7% (n=1201) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> #3 :B_STPHY_AURS %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Min. :2002-01-02 Length :2000 Min. : 0.00 Length :2000 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1st Qu.:2005-07-31 N.unique : 981 1st Qu.:63.00 N.unique : 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Median :2009-07-31 N.blank : 0 Median :74.00 N.blank : 0 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Mean :2009-11-20 Min.nchar: 6 Mean :70.69 Min.nchar: 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3rd Qu.:2014-05-30 Max.nchar: 6 3rd Qu.:82.00 Max.nchar: 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Max. :2017-12-28 Max. :97.00 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward mo PEN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Length :2000 Class :mo Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> N.unique : 3 &lt;NA&gt; :0 %S :25.6% (n=417) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> N.blank : 0 Unique:90 %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Min.nchar: 3 #1 :B_ESCHR_COLI %I : 0.7% (n=11) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Max.nchar: 10 #2 :B_STPHY_CONS %R :73.7% (n=1201) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> #3 :B_STPHY_AURS %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :68.8% (n=251) %S :70.5% (n=665) %S :40.2% (n=543) </span>
@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-04-24 <span style="color: #949494;">22:41:17</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-04-24 <span style="color: #949494;">22:41:17</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-04-24 <span style="color: #949494;">22:41:18</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-04-24 <span style="color: #949494;">22:41:18</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-04-25 <span style="color: #949494;">12:45:43</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-04-25 <span style="color: #949494;">12:45:43</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-04-25 <span style="color: #949494;">12:45:44</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-04-25 <span style="color: #949494;">12:45:44</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>

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reference/as.sir.md
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@@ -606,20 +606,20 @@ example_isolates
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
summary(example_isolates[, 1:10]) # see all SIR results at a glance
#> date patient age gender
#> Min. :2002-01-02 Length:2000 Min. : 0.00 Length:2000
#> 1st Qu.:2005-07-31 Class :character 1st Qu.:63.00 Class :character
#> Median :2009-07-31 Mode :character Median :74.00 Mode :character
#> Mean :2009-11-20 Mean :70.69
#> 3rd Qu.:2014-05-30 3rd Qu.:82.00
#> Max. :2017-12-28 Max. :97.00
#> ward mo PEN
#> Length:2000 Class :mo Class:sir
#> Class :character <NA> :0 %S :25.6% (n=417)
#> Mode :character Unique:90 %SDD : 0.0% (n=0)
#> #1 :B_ESCHR_COLI %I : 0.7% (n=11)
#> #2 :B_STPHY_CONS %R :73.7% (n=1201)
#> #3 :B_STPHY_AURS %NI : 0.0% (n=0)
#> date patient age gender
#> Min. :2002-01-02 Length :2000 Min. : 0.00 Length :2000
#> 1st Qu.:2005-07-31 N.unique : 981 1st Qu.:63.00 N.unique : 2
#> Median :2009-07-31 N.blank : 0 Median :74.00 N.blank : 0
#> Mean :2009-11-20 Min.nchar: 6 Mean :70.69 Min.nchar: 1
#> 3rd Qu.:2014-05-30 Max.nchar: 6 3rd Qu.:82.00 Max.nchar: 1
#> Max. :2017-12-28 Max. :97.00
#> ward mo PEN
#> Length :2000 Class :mo Class:sir
#> N.unique : 3 <NA> :0 %S :25.6% (n=417)
#> N.blank : 0 Unique:90 %SDD : 0.0% (n=0)
#> Min.nchar: 3 #1 :B_ESCHR_COLI %I : 0.7% (n=11)
#> Max.nchar: 10 #2 :B_STPHY_CONS %R :73.7% (n=1201)
#> #3 :B_STPHY_AURS %NI : 0.0% (n=0)
#> OXA FLC AMX
#> Class:sir Class:sir Class:sir
#> %S :68.8% (n=251) %S :70.5% (n=665) %S :40.2% (n=543)
@@ -660,10 +660,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2026-04-24 22:41:17 1 MIC amoxicillin Escherich… human 8
#> 2 2026-04-24 22:41:17 1 MIC cipro Escherich… human 0.256
#> 3 2026-04-24 22:41:18 1 DISK tobra Escherich… human 16
#> 4 2026-04-24 22:41:18 1 DISK genta Escherich… human 18
#> 1 2026-04-25 12:45:43 1 MIC amoxicillin Escherich… human 8
#> 2 2026-04-25 12:45:43 1 MIC cipro Escherich… human 0.256
#> 3 2026-04-25 12:45:44 1 DISK tobra Escherich… human 16
#> 4 2026-04-25 12:45:44 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr>