All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.
@ -61,6 +61,7 @@ All functions in this package are now all considered to be stable. Updates to th
@@ -61,6 +61,7 @@ All functions in this package are now all considered to be stable. Updates to th
* Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is ggplot2 bug 4511, soon to be fixed)
* Fix for minor translation errors
* Fix for the MIC interpretation of *Morganellaceae* (such as *Morganella* and *Proteus*) when using the EUCAST 2021 guideline
* Improved algorithm of `as.mo()`
* Improved algorithm for generating random MICs with `random_mic()`
* Improved plot legends for MICs and disk diffusion values
* Improved speed of `as.ab()` and all `ab_*()` functions
@ -731,7 +732,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
@@ -731,7 +732,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
* Added support for *Blastocystis*
* Added support for 5,000 new fungi
* Added support for unknown yeasts and fungi
* Changed most microorganism IDs to improve readability. For example, the old code `B_ENTRC_FAE` could have been both *E. faecalis* and *E. faecium*. Its new code is `B_ENTRC_FCLS` and *E. faecium* has become `B_ENTRC_FACM`. Also, the Latin character æ (ae) is now preserved at the start of each genus and species abbreviation. For example, the old code for *Aerococcus urinae* was `B_ARCCC_NAE`. This is now `B_AERCC_URIN`.
* Changed most microorganism IDs to improve readability. For example, the old code `B_ENTRC_FAE` could have been both *E. faecalis* and *E. faecium*. Its new code is `B_ENTRC_FCLS` and *E. faecium* has become `B_ENTRC_FACM`. Also, the Latin character ae is now preserved at the start of each genus and species abbreviation. For example, the old code for *Aerococcus urinae* was `B_ARCCC_NAE`. This is now `B_AERCC_URIN`.
**IMPORTANT:** Old microorganism IDs are still supported, but support will be dropped in a future version. Use `as.mo()` on your old codes to transform them to the new format. Using functions from the `mo_*` family (like `mo_name()` and `mo_gramstain()`) on old codes, will throw a warning.
* More intelligent guessing for `as.ab()`, including bidirectional language support
* Added support for the German national guideline (3MRGN/4MRGN) in the `mdro()` function, to determine multi-drug resistant organisms
@ -789,7 +790,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
@@ -789,7 +790,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
* EIEC (Entero-Invasive *E. coli*)
* EPEC (Entero-Pathogenic *E. coli*)
* ETEC (Entero-Toxigenic *E. coli*)
* NMEC (Neonatal Meningitis‐causing *E. coli*)
* NMEC (Neonatal Meningitis-causing *E. coli*)
* STEC (Shiga-toxin producing *E. coli*)
* UPEC (Uropathogenic *E. coli*)
@ -1015,13 +1016,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
@@ -1015,13 +1016,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
Using `as.mo(..., allow_uncertain = 3)` could lead to very unreliable results.
* Implemented the latest publication of Becker *et al.* (2019), for categorising coagulase-negative *Staphylococci*
* All microbial IDs that found are now saved to a local file `~/.Rhistory_mo`. Use the new function `clean_mo_history()` to delete this file, which resets the algorithms.
* Incoercible results will now be considered 'unknown', MO code `UNKNOWN`. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:
```r
mo_genus("qwerty", language = "es")
# Warning:
# one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.
#> [1] "(género desconocido)"
```
* Incoercible results will now be considered 'unknown', MO code `UNKNOWN`. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese.
* Fix for vector containing only empty values
* Finds better results when input is in other languages
* Better handling for subspecies
@ -1297,7 +1292,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
@@ -1297,7 +1292,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
* New Becker classification for *Staphylococcus* to categorise them into Coagulase Negative *Staphylococci* (CoNS) and Coagulase Positve *Staphylococci* (CoPS)
* New Lancefield classification for *Streptococcus* to categorise them into Lancefield groups
* For convience, new descriptive statistical functions `kurtosis` and `skewness` that are lacking in base R - they are generic functions and have support for vectors, data.frames and matrices
* Function `g.test` to perform the Χ<sup>2</sup> distributed [*G*-test](https://en.wikipedia.org/wiki/G-test), which use is the same as `chisq.test`
* Function `g.test` to perform the X<sup>2</sup> distributed [*G*-test](https://en.wikipedia.org/wiki/G-test), which use is the same as `chisq.test`
* ~~Function `ratio` to transform a vector of values to a preset ratio~~
* ~~For example: `ratio(c(10, 500, 10), ratio = "1:2:1")` would return `130, 260, 130`~~
* Support for Addins menu in RStudio to quickly insert `%in%` or `%like%` (and give them keyboard shortcuts), or to view the datasets that come with this package
#' List of Prokaryotic names with Standing in Nomenclature (`r CATALOGUE_OF_LIFE$yearmonth_LPSN`) as currently implemented in this `AMR` package:
#'
#' * Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}
#' * Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
#' * Parte, A.C. (2014). LPSN — List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613–D616; \doi{10.1093/nar/gkt1111}
#' * Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
#' * Parte, A.C. (2014). LPSN - List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613-D616; \doi{10.1093/nar/gkt1111}
#' * Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; \doi{10.1099/00207713-47-2-590}
#'
#' `r SNOMED_VERSION$current_source` as currently implemented in this `AMR` package:
@ -155,7 +155,7 @@
@@ -155,7 +155,7 @@
#' - `prevalence`\cr Prevalence of the microorganism, see [as.mo()]
#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]).
#'
#' Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
#' Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
#' @inheritSection AMR Reference Data Publicly Available
#' - **M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition**, 2014, *Clinical and Laboratory Standards Institute (CLSI)*. <https://clsi.org/standards/products/microbiology/documents/m39/>.
#'
#' - Hindler JF and Stelling J (2007). **Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.** Clinical Infectious Diseases, 44(6), 867–873. \doi{10.1086/511864}
#' - Hindler JF and Stelling J (2007). **Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.** Clinical Infectious Diseases, 44(6), 867-873. \doi{10.1086/511864}
#' @inheritSection AMR Read more on Our Website!
#' @examples
#' # `example_isolates` is a data set available in the AMR package.
#' 2. Becker K *et al.* **Implications of identifying the recently defined members of the *S. aureus* complex, *S. argenteus* and *S. schweitzeri*: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).** 2019. Clin Microbiol Infect; \doi{10.1016/j.cmi.2019.02.028}
#' 3. Becker K *et al.* **Emergence of coagulase-negative staphylococci** 2020. Expert Rev Anti Infect Ther. 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
#' 4. Lancefield RC **A serological differentiation of human and other groups of hemolytic streptococci**. 1933. J Exp Med. 57(4): 571–95; \doi{10.1084/jem.57.4.571}
#' 4. Lancefield RC **A serological differentiation of human and other groups of hemolytic streptococci**. 1933. J Exp Med. 57(4): 571-95; \doi{10.1084/jem.57.4.571}
#' 6. List of Prokaryotic names with Standing in Nomenclature (`r CATALOGUE_OF_LIFE$yearmonth_LPSN`), \doi{10.1099/ijsem.0.004332}
#' 7. `r SNOMED_VERSION$current_source`, retrieved from the `r SNOMED_VERSION$title`, OID `r SNOMED_VERSION$current_oid`, version `r SNOMED_VERSION$current_version`; url: <`r SNOMED_VERSION$url`>
<p>Many R users just ask questions on websites like <ahref="https://stackoverflow.com"class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <ahref="https://stackoverflow.com/questions/tagged/r?sort=votes"class="external-link">428,733 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
<p>Many R users just ask questions on websites like <ahref="https://stackoverflow.com"class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <ahref="https://stackoverflow.com/questions/tagged/r?sort=votes"class="external-link">429,535 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
</li>
<li>
<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
@ -308,7 +308,7 @@
@@ -308,7 +308,7 @@
<spanclass="co"># 8 10011 1 1 73.1</span>
<spanclass="co"># 9 10017 1 1 56.7</span>
<spanclass="co"># 10 10018 0 1 66.6</span>
<spanclass="co"># # … with 4,193 more rows</span>
<spanclass="co"># # ... with 4,193 more rows</span>
<h3id="last-updated-december-1-7-1-9073"><small>Last updated: 14 December 2021</small><aclass="anchor"aria-label="anchor"href="#last-updated-december-1-7-1-9073"></a></h3>
<h3id="last-updated-december-1-7-1-9074"><small>Last updated: 14 December 2021</small><aclass="anchor"aria-label="anchor"href="#last-updated-december-1-7-1-9074"></a></h3>
<p>All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.</p>
<ul><li>Removed <code>p_symbol()</code> and all <code>filter_*()</code> functions (except for <code><ahref="../reference/first_isolate.html">filter_first_isolate()</a></code>), which were all deprecated in a previous package version</li>
<li>Removed the <code>key_antibiotics()</code> and <code>key_antibiotics_equal()</code> functions, which were deprecated and superseded by <code><ahref="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> and <code><ahref="../reference/key_antimicrobials.html">antimicrobials_equal()</a></code>
</li>
@ -171,7 +171,7 @@
@@ -171,7 +171,7 @@
<li>Renamed function <code>get_locale()</code> to <code><ahref="../reference/translate.html">get_AMR_locale()</a></code> to prevent conflicts with other packages</li>
<ul><li><p>Support for the CLSI 2021 guideline for interpreting MIC/disk diffusion values, which are incorporated in the <code>rsi_translation</code> data set. This data set now more strictly follows the WHONET software as well.</p></li>
<li><p>Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021). This is now the default EUCAST guideline in the package (all older guidelines are still available) for <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><ahref="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> and <code><ahref="../reference/mdro.html">mdro()</a></code>. The <code>intrinsic_resistant</code> data set was also updated accordingly.</p></li>
<li><p>Support for all antimicrobial drug (group) names and colloquial microorganism names in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish</p></li>
@ -186,7 +186,7 @@
@@ -186,7 +186,7 @@
<li><p>Function <code><ahref="../reference/ab_property.html">ab_ddd_units()</a></code> to get units of DDDs (daily defined doses), deprecating the use of <code>ab_ddd(..., units = TRUE)</code> to be more consistent in data types of function output</p></li>
<ul><li>Updated the bacterial taxonomy to 5 October 2021 (according to <ahref="https://lpsn.dsmz.de"class="external-link">LPSN</a>), including all 11 new staphylococcal species named since 1 January last year</li>
<li>The <code>antibiotics</code> data set now contains <strong>all ATC codes</strong> that are available through the <ahref="https://www.whocc.no"class="external-link">WHOCC website</a>, regardless of drugs being present in more than one ATC group. This means that:
<li>Fix for legends created with <code><ahref="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code> when using <code>ggplot2</code> v3.3.4 or higher (this is ggplot2 bug 4511, soon to be fixed)</li>
<li>Fix for minor translation errors</li>
<li>Fix for the MIC interpretation of <em>Morganellaceae</em> (such as <em>Morganella</em> and <em>Proteus</em>) when using the EUCAST 2021 guideline</li>
<li>Improved algorithm of <code><ahref="../reference/as.mo.html">as.mo()</a></code>
</li>
<li>Improved algorithm for generating random MICs with <code><ahref="../reference/random.html">random_mic()</a></code>
</li>
<li>Improved plot legends for MICs and disk diffusion values</li>
@ -256,7 +258,7 @@
@@ -256,7 +258,7 @@
<code><ahref="../reference/get_episode.html">get_episode()</a></code> and <code><ahref="../reference/get_episode.html">is_new_episode()</a></code> can now cope with <code>NA</code>s</li>
<ul><li>This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations.</li>
</ul></div>
</div>
@ -1073,7 +1075,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1073,7 +1075,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>Added support for 5,000 new fungi</li>
<li>Added support for unknown yeasts and fungi</li>
<li>Changed most microorganism IDs to improve readability. For example, the old code <code>B_ENTRC_FAE</code> could have been both <em>E. faecalis</em> and <em>E. faecium</em>. Its new code is <code>B_ENTRC_FCLS</code> and <em>E. faecium</em> has become <code>B_ENTRC_FACM</code>. Also, the Latin character æ (ae) is now preserved at the start of each genus and species abbreviation. For example, the old code for <em>Aerococcus urinae</em> was <code>B_ARCCC_NAE</code>. This is now <code>B_AERCC_URIN</code>. <strong>IMPORTANT:</strong> Old microorganism IDs are still supported, but support will be dropped in a future version. Use <code><ahref="../reference/as.mo.html">as.mo()</a></code> on your old codes to transform them to the new format. Using functions from the <code>mo_*</code> family (like <code><ahref="../reference/mo_property.html">mo_name()</a></code> and <code><ahref="../reference/mo_property.html">mo_gramstain()</a></code>) on old codes, will throw a warning.</li>
<li>Changed most microorganism IDs to improve readability. For example, the old code <code>B_ENTRC_FAE</code> could have been both <em>E. faecalis</em> and <em>E. faecium</em>. Its new code is <code>B_ENTRC_FCLS</code> and <em>E. faecium</em> has become <code>B_ENTRC_FACM</code>. Also, the Latin character ae is now preserved at the start of each genus and species abbreviation. For example, the old code for <em>Aerococcus urinae</em> was <code>B_ARCCC_NAE</code>. This is now <code>B_AERCC_URIN</code>. <strong>IMPORTANT:</strong> Old microorganism IDs are still supported, but support will be dropped in a future version. Use <code><ahref="../reference/as.mo.html">as.mo()</a></code> on your old codes to transform them to the new format. Using functions from the <code>mo_*</code> family (like <code><ahref="../reference/mo_property.html">mo_name()</a></code> and <code><ahref="../reference/mo_property.html">mo_gramstain()</a></code>) on old codes, will throw a warning.</li>
</ul></li>
<li>More intelligent guessing for <code><ahref="../reference/as.ab.html">as.ab()</a></code>, including bidirectional language support</li>
<li>Added support for the German national guideline (3MRGN/4MRGN) in the <code><ahref="../reference/mdro.html">mdro()</a></code> function, to determine multi-drug resistant organisms</li>
@ -1141,7 +1143,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1141,7 +1143,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</ul><p>All these lead to the microbial ID of <em>E. coli</em>:</p>
@ -1414,15 +1416,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1414,15 +1416,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li><p>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em></p></li>
<li><p>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</p></li>
<li>
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
<spanclass="fu"><ahref="../reference/mo_property.html">mo_genus</a></span><spanclass="op">(</span><spanclass="st">"qwerty"</span>, language <spanclass="op">=</span><spanclass="st">"es"</span><spanclass="op">)</span>
<spanclass="co"># Warning: </span>
<spanclass="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span>
<li><p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese.</p></li>
<li><p>Fix for vector containing only empty values</p></li>
<li><p>Finds better results when input is in other languages</p></li>
<li><p>Better handling for subspecies</p></li>
@ -1460,7 +1454,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1460,7 +1454,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<spanclass="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
<spanclass="co"># OLD WAY</span>
@ -1530,7 +1524,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1530,7 +1524,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Fewer than 3 characters as input for <code>as.mo</code> will return NA</p></li>
<li>
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
@ -1546,7 +1540,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1546,7 +1540,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@ -1554,7 +1548,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1554,7 +1548,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@ -1621,7 +1615,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1621,7 +1615,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Author and year: <code>mo_ref</code>
</li>
</ul><p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
@ -1632,7 +1626,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1632,7 +1626,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<spanclass="fu"><ahref="../reference/mo_property.html">mo_fullname</a></span><spanclass="op">(</span><spanclass="st">"S. group A"</span>, language <spanclass="op">=</span><spanclass="st">"pt"</span><spanclass="op">)</span><spanclass="co"># Portuguese</span>
<spanclass="co"># [1] "Streptococcus grupo A"</span></code></pre></div>
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
<spanclass="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span>
@ -1645,7 +1639,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1645,7 +1639,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %>% mutate_if(is.rsi.eligible, as.rsi)</code></p></li>
<li>
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
@ -1654,7 +1648,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1654,7 +1648,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<spanclass="fu"><ahref="../reference/as.mo.html">as.mo</a></span><spanclass="op">(</span><spanclass="st">"S group A"</span><spanclass="op">)</span>
<spanclass="fu">microbenchmark</span><spanclass="fu">::</span><spanclass="fu"><ahref="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html"class="external-link">microbenchmark</a></span><spanclass="op">(</span><spanclass="fu"><ahref="../reference/as.mo.html">as.mo</a></span><spanclass="op">(</span><spanclass="va">thousands_of_E_colis</span><spanclass="op">)</span>, unit <spanclass="op">=</span><spanclass="st">"s"</span><spanclass="op">)</span>
@ -1683,7 +1677,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1683,7 +1677,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul><li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
<li>
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
@ -1700,7 +1694,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1700,7 +1694,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added arguments <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code></p></li>
<li>
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
@ -1720,12 +1714,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1720,12 +1714,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added longest en shortest character length in the frequency table (<code>freq</code>) header of class <code>character</code></p></li>
<li>
<p>Support for types (classes) list and matrix for <code>freq</code></p>
@ -1769,7 +1763,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1769,7 +1763,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>New Lancefield classification for <em>Streptococcus</em> to categorise them into Lancefield groups</li>
</ul></li>
<li>For convience, new descriptive statistical functions <code>kurtosis</code> and <code>skewness</code> that are lacking in base R - they are generic functions and have support for vectors, data.frames and matrices</li>
<li>Function <code>g.test</code> to perform the Χ<sup>2</sup> distributed <ahref="https://en.wikipedia.org/wiki/G-test"class="external-link"><em>G</em>-test</a>, which use is the same as <code>chisq.test</code>
<li>Function <code>g.test</code> to perform the X<sup>2</sup> distributed <ahref="https://en.wikipedia.org/wiki/G-test"class="external-link"><em>G</em>-test</a>, which use is the same as <code>chisq.test</code>
</li>
<li>
<del>Function <code>ratio</code> to transform a vector of values to a preset ratio</del>
<li><p>Becker K <em>et al.</em><strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect; doi: <ahref="https://doi.org/10.1016/j.cmi.2019.02.028"class="external-link">10.1016/j.cmi.2019.02.028</a></p></li>
<li><p>Becker K <em>et al.</em><strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366; doi: <ahref="https://doi.org/10.1080/14787210.2020.1730813"class="external-link">10.1080/14787210.2020.1730813</a></p></li>
<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95; doi: <ahref="https://doi.org/10.1084/jem.57.4.571"class="external-link">10.1084/jem.57.4.571</a></p></li>
<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571-95; doi: <ahref="https://doi.org/10.1084/jem.57.4.571"class="external-link">10.1084/jem.57.4.571</a></p></li>
<li><p>Catalogue of Life: 2019 Annual Checklist, <ahref="http://www.catalogueoflife.org"class="external-link">http://www.catalogueoflife.org</a></p></li>
<li><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021), doi: <ahref="https://doi.org/10.1099/ijsem.0.004332"class="external-link">10.1099/ijsem.0.004332</a></p></li>
<li><p>US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <ahref="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009"class="external-link">https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
<p>Methodology of this function is strictly based on:</p><ul><li><p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition</strong>, 2014, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <ahref="https://clsi.org/standards/products/microbiology/documents/m39/"class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
<li><p>Hindler JF and Stelling J (2007). <strong>Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.</strong> Clinical Infectious Diseases, 44(6), 867–873. doi: <ahref="https://doi.org/10.1086/511864"class="external-link">10.1086/511864</a></p></li>
<li><p>Hindler JF and Stelling J (2007). <strong>Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.</strong> Clinical Infectious Diseases, 44(6), 867-873. doi: <ahref="https://doi.org/10.1086/511864"class="external-link">10.1086/511864</a></p></li>
ab <spanclass="op">=</span><spanclass="fu"><ahref="ab_property.html">ab_name</a></span><spanclass="op">(</span><spanclass="va">mo</span><spanclass="op">)</span><spanclass="op">)</span>
<p>Catalogue of Life: 2019 Annual Checklist as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Annual Checklist (public online taxonomic database), <ahref="http://www.catalogueoflife.org"class="external-link">http://www.catalogueoflife.org</a></p></li>
</ul><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; doi: <ahref="https://doi.org/10.1099/ijsem.0.004332"class="external-link">10.1099/ijsem.0.004332</a></p></li>
<li><p>Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: <ahref="https://doi.org/10.1099/ijsem.0.002786"class="external-link">10.1099/ijsem.0.002786</a></p></li>
<li><p>Parte, A.C. (2014). LPSN — List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613–D616; doi: <ahref="https://doi.org/10.1093/nar/gkt1111"class="external-link">10.1093/nar/gkt1111</a></p></li>
<li><p>Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: <ahref="https://doi.org/10.1099/ijsem.0.002786"class="external-link">10.1099/ijsem.0.002786</a></p></li>
<li><p>Parte, A.C. (2014). LPSN - List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613-D616; doi: <ahref="https://doi.org/10.1093/nar/gkt1111"class="external-link">10.1093/nar/gkt1111</a></p></li>
<li><p>Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; doi: <ahref="https://doi.org/10.1099/00207713-47-2-590"class="external-link">10.1099/00207713-47-2-590</a></p></li>
</ul><p>US Edition of SNOMED CT from 1 September 2020 as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <ahref="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009"class="external-link">https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <ahref="http://www.catalogueoflife.org"class="external-link">http://www.catalogueoflife.org</a> (check included annual version with <code><ahref="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>).</p>
<p>Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: <ahref="https://doi.org/10.1099/ijsem.0.002786"class="external-link">10.1099/ijsem.0.002786</a></p>
<p>Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: <ahref="https://doi.org/10.1099/ijsem.0.002786"class="external-link">10.1099/ijsem.0.002786</a></p>
@ -292,10 +292,10 @@ This package contains the complete taxonomic tree of almost all microorganisms (
@@ -292,10 +292,10 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<li><p>Becker K <em>et al.</em><strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect; doi: <ahref="https://doi.org/10.1016/j.cmi.2019.02.028"class="external-link">10.1016/j.cmi.2019.02.028</a></p></li>
<li><p>Becker K <em>et al.</em><strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366; doi: <ahref="https://doi.org/10.1080/14787210.2020.1730813"class="external-link">10.1080/14787210.2020.1730813</a></p></li>
<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95; doi: <ahref="https://doi.org/10.1084/jem.57.4.571"class="external-link">10.1084/jem.57.4.571</a></p></li>
<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571-95; doi: <ahref="https://doi.org/10.1084/jem.57.4.571"class="external-link">10.1084/jem.57.4.571</a></p></li>
<li><p>Catalogue of Life: 2019 Annual Checklist, <ahref="http://www.catalogueoflife.org"class="external-link">http://www.catalogueoflife.org</a></p></li>
<li><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021), doi: <ahref="https://doi.org/10.1099/ijsem.0.004332"class="external-link">10.1099/ijsem.0.004332</a></p></li>
<li><p>US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <ahref="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009"class="external-link">https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
@ -126,10 +126,10 @@ The intelligent rules consider the prevalence of microorganisms in humans groupe
@@ -126,10 +126,10 @@ The intelligent rules consider the prevalence of microorganisms in humans groupe
\item Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect; \doi{10.1016/j.cmi.2019.02.028}
\item Becker K \emph{et al.} \strong{Emergence of coagulase-negative staphylococci} 2020. Expert Rev Anti Infect Ther. 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95; \doi{10.1084/jem.57.4.571}
\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571-95; \doi{10.1084/jem.57.4.571}
\item Catalogue of Life: 2019 Annual Checklist, \url{http://www.catalogueoflife.org}
\item List of Prokaryotic names with Standing in Nomenclature (5 October 2021), \doi{10.1099/ijsem.0.004332}
\item US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: \url{https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009}
Methodology of this function is strictly based on:
\itemize{
\item \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
\item Hindler JF and Stelling J (2007). \strong{Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.} Clinical Infectious Diseases, 44(6), 867–873. \doi{10.1086/511864}
\item Hindler JF and Stelling J (2007). \strong{Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.} Clinical Infectious Diseases, 44(6), 867-873. \doi{10.1086/511864}
@ -33,15 +33,13 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
@@ -33,15 +33,13 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
@ -27,8 +27,8 @@ Catalogue of Life: 2019 Annual Checklist as currently implemented in this \code{
@@ -27,8 +27,8 @@ Catalogue of Life: 2019 Annual Checklist as currently implemented in this \code{
List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this \code{AMR} package:
\itemize{
\item Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}
\item Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
\item Parte, A.C. (2014). LPSN — List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613–D616; \doi{10.1093/nar/gkt1111}
\item Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
\item Parte, A.C. (2014). LPSN - List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613-D616; \doi{10.1093/nar/gkt1111}
\item Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; \doi{10.1099/00207713-47-2-590}
@ -16,7 +16,7 @@ A \link{data.frame} with 14,338 observations and 4 variables:
@@ -16,7 +16,7 @@ A \link{data.frame} with 14,338 observations and 4 variables:
\source{
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
@ -181,10 +181,10 @@ This package contains the complete taxonomic tree of almost all microorganisms (
@@ -181,10 +181,10 @@ This package contains the complete taxonomic tree of almost all microorganisms (
\item Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect; \doi{10.1016/j.cmi.2019.02.028}
\item Becker K \emph{et al.} \strong{Emergence of coagulase-negative staphylococci} 2020. Expert Rev Anti Infect Ther. 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95; \doi{10.1084/jem.57.4.571}
\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571-95; \doi{10.1084/jem.57.4.571}
\item Catalogue of Life: 2019 Annual Checklist, \url{http://www.catalogueoflife.org}
\item List of Prokaryotic names with Standing in Nomenclature (5 October 2021), \doi{10.1099/ijsem.0.004332}
\item US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: \url{https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009}
