diff --git a/dev/LICENSE-text.html b/dev/LICENSE-text.html
index 5cfd4cd..2b7ffcf 100644
--- a/dev/LICENSE-text.html
+++ b/dev/LICENSE-text.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">jmf</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9001</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">
diff --git a/dev/LICENSE.html b/dev/LICENSE.html
index b3daa6b..87089c6 100644
--- a/dev/LICENSE.html
+++ b/dev/LICENSE.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">jmf</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9001</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">
diff --git a/dev/authors.html b/dev/authors.html
index 9b58a87..2742fa8 100644
--- a/dev/authors.html
+++ b/dev/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">jmf</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9001</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">
@@ -55,14 +55,14 @@ <h2 id="citation">Citation</h2>
 
       <p>Hausmann B (2024).
 <em>jmf: JMF Utility Functions</em>.
-R package version 0.3.0.9000,
+R package version 0.3.0.9001,
 https://github.com/jmf-vienna/jmf-r, https://jmf.univie.ac.at/, <a href="https://jmf-vienna.github.io/jmf-r/">https://jmf-vienna.github.io/jmf-r/</a>.
 </p>
       <pre>@Manual{,
   title = {jmf: JMF Utility Functions},
   author = {Bela Hausmann},
   year = {2024},
-  note = {R package version 0.3.0.9000,
+  note = {R package version 0.3.0.9001,
     https://github.com/jmf-vienna/jmf-r, https://jmf.univie.ac.at/},
   url = {https://jmf-vienna.github.io/jmf-r/},
 }</pre>
diff --git a/dev/index.html b/dev/index.html
index 147a05c..58d6b65 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -30,7 +30,7 @@
 
     <a class="navbar-brand me-2" href="index.html">jmf</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9001</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">
@@ -141,7 +141,7 @@ <h3 id="validation-of-jmf-ids">Validation of JMF IDs<a class="anchor" aria-label
 <span><span class="co">#&gt; [1] FALSE</span></span></code></pre></div>
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="reference/validate-jmf-ids.html">jmf_project_id_regex</a></span><span class="op">(</span>internal <span class="op">=</span> <span class="st">"allow"</span><span class="op">)</span></span>
-<span><span class="co">#&gt; JMF-(?:(?:19(?:01|02|03|04|05|06|07|08|09|10|11|12|DM)-[1-9A-Z])|(?:20(?:01|02|03|04|05|06|07|08|09|10|11|12)-[1-9A-Z])|(?:(?:(?:2[1-9])|(?:[3-9][0-9]))(?:01|02|03|04|05|06|07|08|09|10|11|12)-(?:(?:0[1-9])|(?:[1-9][0-9])))|(?:(?:19NC|19PC|CTRL)-[1-9A-Z]))</span></span></code></pre></div>
+<span><span class="co">#&gt; JMF-(?:(?:(?:(?:19(?:01|02|03|04|05|06|07|08|09|10|11|12|DM|NC|PC))|(?:20(?:01|02|03|04|05|06|07|08|09|10|11|12))|(?:[A-Z]){4})-[1-9A-Z])|(?:(?:(?:2[1-9])|(?:[3-9][0-9]))(?:01|02|03|04|05|06|07|08|09|10|11|12)-(?:(?:0[1-9])|(?:[1-9][0-9]))))</span></span></code></pre></div>
 </div>
 </div>
 </div>
diff --git a/dev/news/index.html b/dev/news/index.html
index 681237a..2136e1c 100644
--- a/dev/news/index.html
+++ b/dev/news/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">jmf</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9001</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">
diff --git a/dev/pkgdown.yml b/dev/pkgdown.yml
index e583b14..3fae74f 100644
--- a/dev/pkgdown.yml
+++ b/dev/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 3.1.11
 pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-08-06T11:05Z
+last_built: 2024-08-13T07:46Z
 urls:
   reference: https://jmf-vienna.github.io/jmf-r/reference
   article: https://jmf-vienna.github.io/jmf-r/articles
diff --git a/dev/reference/index.html b/dev/reference/index.html
index aa88912..738afeb 100644
--- a/dev/reference/index.html
+++ b/dev/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">jmf</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9001</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">
diff --git a/dev/reference/jmf-package.html b/dev/reference/jmf-package.html
index 9b4f839..9daac3b 100644
--- a/dev/reference/jmf-package.html
+++ b/dev/reference/jmf-package.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">jmf</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9001</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">
diff --git a/dev/reference/na.html b/dev/reference/na.html
index cfaa7a8..9710ffa 100644
--- a/dev/reference/na.html
+++ b/dev/reference/na.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">jmf</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9001</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">
diff --git a/dev/reference/quiet.html b/dev/reference/quiet.html
index a20f67e..f5a5ca9 100644
--- a/dev/reference/quiet.html
+++ b/dev/reference/quiet.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">jmf</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9001</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">
diff --git a/dev/reference/uniques.html b/dev/reference/uniques.html
index 7952959..71a7dfc 100644
--- a/dev/reference/uniques.html
+++ b/dev/reference/uniques.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">jmf</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9001</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">
diff --git a/dev/reference/validate-jmf-ids.html b/dev/reference/validate-jmf-ids.html
index f5182cc..6b52d77 100644
--- a/dev/reference/validate-jmf-ids.html
+++ b/dev/reference/validate-jmf-ids.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">jmf</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.3.0.9001</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">
diff --git a/dev/search.json b/dev/search.json
index 81bc326..6316de0 100644
--- a/dev/search.json
+++ b/dev/search.json
@@ -1 +1 @@
-[{"path":"https://jmf-vienna.github.io/jmf-r/dev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 jmf authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Bela Hausmann. Author. Joint Microbiome Facility (JMF) Medical University Vienna University Vienna. Maintainer, funder.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Hausmann B (2024). jmf: JMF Utility Functions. R package version 0.3.0.9000, https://github.com/jmf-vienna/jmf-r, https://jmf.univie.ac./, https://jmf-vienna.github.io/jmf-r/.","code":"@Manual{,   title = {jmf: JMF Utility Functions},   author = {Bela Hausmann},   year = {2024},   note = {R package version 0.3.0.9000,     https://github.com/jmf-vienna/jmf-r, https://jmf.univie.ac.at/},   url = {https://jmf-vienna.github.io/jmf-r/}, }"},{"path":[]},{"path":"https://jmf-vienna.github.io/jmf-r/dev/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"JMF Utility Functions","text":"Install latest release GitHub using pak: install development version:","code":"pak::pak(\"jmf-vienna/jmf-r@*release\") pak::pak(\"jmf-vienna/jmf-r\")"},{"path":[]},{"path":"https://jmf-vienna.github.io/jmf-r/dev/index.html","id":"reduce-verbosity","dir":"","previous_headings":"Usage","what":"Reduce verbosity","title":"JMF Utility Functions","text":"","code":"library(jmf) quiet() library(tidyverse)"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/index.html","id":"utils","dir":"","previous_headings":"Usage","what":"Utils","title":"JMF Utility Functions","text":"Stable combined unique() sort():","code":"x <- c(   \"a\", \"vector\", \"of\", \"strings\",   \"and\", \"some\", \"letters\", \":\", NA,   \"a\", \"b\", \"c\", \"and\", \"A\", \"B\", \"C\" )  x |> uniques() #>  [1] \":\"       \"A\"       \"B\"       \"C\"       \"a\"       \"and\"     \"b\"       #>  [8] \"c\"       \"letters\" \"of\"      \"some\"    \"strings\" \"vector\"  NA"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/index.html","id":"shortcuts","dir":"","previous_headings":"Usage","what":"Shortcuts","title":"JMF Utility Functions","text":"available (.e., NA): () available (.e., NA): na()","code":"starwars |>   select(name, birth_year, hair_color) |>   filter(a(birth_year), na(hair_color)) #> # A tibble: 4 × 3 #>   name                  birth_year hair_color #>   <chr>                      <dbl> <chr>      #> 1 C-3PO                        112 <NA>       #> 2 R2-D2                         33 <NA>       #> 3 Greedo                        44 <NA>       #> 4 Jabba Desilijic Tiure        600 <NA>"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/index.html","id":"validation-of-jmf-ids","dir":"","previous_headings":"Usage","what":"Validation of JMF IDs","title":"JMF Utility Functions","text":"","code":"# valid JMF project ID: is_jmf_project_id(\"JMF-2401-42\") #> [1] TRUE  # this is a JMF sample ID: is_jmf_project_id(\"JMF-2401-42-0001\") #> [1] FALSE jmf_project_id_regex(internal = \"allow\") #> JMF-(?:(?:19(?:01|02|03|04|05|06|07|08|09|10|11|12|DM)-[1-9A-Z])|(?:20(?:01|02|03|04|05|06|07|08|09|10|11|12)-[1-9A-Z])|(?:(?:(?:2[1-9])|(?:[3-9][0-9]))(?:01|02|03|04|05|06|07|08|09|10|11|12)-(?:(?:0[1-9])|(?:[1-9][0-9])))|(?:(?:19NC|19PC|CTRL)-[1-9A-Z]))"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/jmf-package.html","id":null,"dir":"Reference","previous_headings":"","what":"jmf: JMF Utility Functions — jmf-package","title":"jmf: JMF Utility Functions — jmf-package","text":"assortment utilities, helpers, common functions used Joint Microbiome Facility (JMF).","code":""},{"path":[]},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/jmf-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"jmf: JMF Utility Functions — jmf-package","text":"Maintainer: Joint Microbiome Facility (JMF) Medical University Vienna University Vienna info.jmf@univie.ac.[funder] Authors: Bela Hausmann (ORCID)","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/na.html","id":null,"dir":"Reference","previous_headings":"","what":"Shortcuts for is.na() — a","title":"Shortcuts for is.na() — a","text":"(x) !.na(x) na() alias .na().","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shortcuts for is.na() — a","text":"","code":"a(x)  na(x)"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shortcuts for is.na() — a","text":"x vector tested.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shortcuts for is.na() — a","text":"logical vector.","code":""},{"path":[]},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Shortcuts for is.na() — a","text":"","code":"a(c(1, NA, 3)) #> [1]  TRUE FALSE  TRUE na(c(1, NA, 3)) #> [1] FALSE  TRUE FALSE"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/quiet.html","id":null,"dir":"Reference","previous_headings":"","what":"Decreases tidyverse verbosity — quiet","title":"Decreases tidyverse verbosity — quiet","text":"Disables: tidyverse startup messages readr column specification messages","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/quiet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Decreases tidyverse verbosity — quiet","text":"","code":"quiet()"},{"path":[]},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/quiet.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Decreases tidyverse verbosity — quiet","text":"","code":"quiet() library(tidyverse) # so quiet :) x <- read_csv(readr_example(\"mtcars.csv\")) # so quiet :)"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/uniques.html","id":null,"dir":"Reference","previous_headings":"","what":"Unique and sorted vectors — uniques","title":"Unique and sorted vectors — uniques","text":"Like unique(), also sorted.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/uniques.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Unique and sorted vectors — uniques","text":"","code":"uniques(x)"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/uniques.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Unique and sorted vectors — uniques","text":"x vector.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/uniques.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Unique and sorted vectors — uniques","text":"sorted vector without duplicates.","code":""},{"path":[]},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/uniques.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Unique and sorted vectors — uniques","text":"","code":"base::unique(c(3, 1, 2, 3)) #> [1] 3 1 2 uniques(c(3, 1, 2, 3)) #> [1] 1 2 3"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/validate-jmf-ids.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for valid JMF IDs — is_jmf_project_id","title":"Check for valid JMF IDs — is_jmf_project_id","text":"is_jmf_project_id(): checks valid JMF project IDs. jmf_project_id_regex(): returns underlying regular expression.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/validate-jmf-ids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for valid JMF IDs — is_jmf_project_id","text":"","code":"is_jmf_project_id(string, internal = \"deny\")  jmf_project_id_regex(internal = \"deny\")"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/validate-jmf-ids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for valid JMF IDs — is_jmf_project_id","text":"string Input vector passed str_detect(). internal \"allow\" \"deny\" internal IDs.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/validate-jmf-ids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check for valid JMF IDs — is_jmf_project_id","text":"is_jmf_project_id(): logical vector length string. jmf_project_id_regex(): rex() regular expression.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/validate-jmf-ids.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for valid JMF IDs — is_jmf_project_id","text":"","code":"# valid JMF project ID: is_jmf_project_id(\"JMF-2401-42\") #> [1] TRUE  # this is a JMF sample ID: is_jmf_project_id(\"JMF-2401-42-0001\") #> [1] FALSE  # extract JMF project ID from text: stringr::str_extract(   \"my sample id is JMF-2401-42-0001\",   jmf_project_id_regex() ) #> [1] \"JMF-2401-42\""},{"path":[]},{"path":"https://jmf-vienna.github.io/jmf-r/dev/news/index.html","id":"jmf-030","dir":"Changelog","previous_headings":"","what":"jmf 0.3.0","title":"jmf 0.3.0","text":"Added is_jmf_project_id() jmf_project_id_regex().","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/news/index.html","id":"jmf-021","dir":"Changelog","previous_headings":"","what":"jmf 0.2.1","title":"jmf 0.2.1","text":"uniques() keeps NAs sorts using LC_COLLATE=C.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/news/index.html","id":"jmf-020","dir":"Changelog","previous_headings":"","what":"jmf 0.2.0","title":"jmf 0.2.0","text":"Added uniques(). Added quiet().","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/news/index.html","id":"jmf-010","dir":"Changelog","previous_headings":"","what":"jmf 0.1.0","title":"jmf 0.1.0","text":"Added () na().","code":""}]
+[{"path":"https://jmf-vienna.github.io/jmf-r/dev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 jmf authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Bela Hausmann. Author. Joint Microbiome Facility (JMF) Medical University Vienna University Vienna. Maintainer, funder.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Hausmann B (2024). jmf: JMF Utility Functions. R package version 0.3.0.9001, https://github.com/jmf-vienna/jmf-r, https://jmf.univie.ac./, https://jmf-vienna.github.io/jmf-r/.","code":"@Manual{,   title = {jmf: JMF Utility Functions},   author = {Bela Hausmann},   year = {2024},   note = {R package version 0.3.0.9001,     https://github.com/jmf-vienna/jmf-r, https://jmf.univie.ac.at/},   url = {https://jmf-vienna.github.io/jmf-r/}, }"},{"path":[]},{"path":"https://jmf-vienna.github.io/jmf-r/dev/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"JMF Utility Functions","text":"Install latest release GitHub using pak: install development version:","code":"pak::pak(\"jmf-vienna/jmf-r@*release\") pak::pak(\"jmf-vienna/jmf-r\")"},{"path":[]},{"path":"https://jmf-vienna.github.io/jmf-r/dev/index.html","id":"reduce-verbosity","dir":"","previous_headings":"Usage","what":"Reduce verbosity","title":"JMF Utility Functions","text":"","code":"library(jmf) quiet() library(tidyverse)"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/index.html","id":"utils","dir":"","previous_headings":"Usage","what":"Utils","title":"JMF Utility Functions","text":"Stable combined unique() sort():","code":"x <- c(   \"a\", \"vector\", \"of\", \"strings\",   \"and\", \"some\", \"letters\", \":\", NA,   \"a\", \"b\", \"c\", \"and\", \"A\", \"B\", \"C\" )  x |> uniques() #>  [1] \":\"       \"A\"       \"B\"       \"C\"       \"a\"       \"and\"     \"b\"       #>  [8] \"c\"       \"letters\" \"of\"      \"some\"    \"strings\" \"vector\"  NA"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/index.html","id":"shortcuts","dir":"","previous_headings":"Usage","what":"Shortcuts","title":"JMF Utility Functions","text":"available (.e., NA): () available (.e., NA): na()","code":"starwars |>   select(name, birth_year, hair_color) |>   filter(a(birth_year), na(hair_color)) #> # A tibble: 4 × 3 #>   name                  birth_year hair_color #>   <chr>                      <dbl> <chr>      #> 1 C-3PO                        112 <NA>       #> 2 R2-D2                         33 <NA>       #> 3 Greedo                        44 <NA>       #> 4 Jabba Desilijic Tiure        600 <NA>"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/index.html","id":"validation-of-jmf-ids","dir":"","previous_headings":"Usage","what":"Validation of JMF IDs","title":"JMF Utility Functions","text":"","code":"# valid JMF project ID: is_jmf_project_id(\"JMF-2401-42\") #> [1] TRUE  # this is a JMF sample ID: is_jmf_project_id(\"JMF-2401-42-0001\") #> [1] FALSE jmf_project_id_regex(internal = \"allow\") #> JMF-(?:(?:(?:(?:19(?:01|02|03|04|05|06|07|08|09|10|11|12|DM|NC|PC))|(?:20(?:01|02|03|04|05|06|07|08|09|10|11|12))|(?:[A-Z]){4})-[1-9A-Z])|(?:(?:(?:2[1-9])|(?:[3-9][0-9]))(?:01|02|03|04|05|06|07|08|09|10|11|12)-(?:(?:0[1-9])|(?:[1-9][0-9]))))"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/jmf-package.html","id":null,"dir":"Reference","previous_headings":"","what":"jmf: JMF Utility Functions — jmf-package","title":"jmf: JMF Utility Functions — jmf-package","text":"assortment utilities, helpers, common functions used Joint Microbiome Facility (JMF).","code":""},{"path":[]},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/jmf-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"jmf: JMF Utility Functions — jmf-package","text":"Maintainer: Joint Microbiome Facility (JMF) Medical University Vienna University Vienna info.jmf@univie.ac.[funder] Authors: Bela Hausmann (ORCID)","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/na.html","id":null,"dir":"Reference","previous_headings":"","what":"Shortcuts for is.na() — a","title":"Shortcuts for is.na() — a","text":"(x) !.na(x) na() alias .na().","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shortcuts for is.na() — a","text":"","code":"a(x)  na(x)"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shortcuts for is.na() — a","text":"x vector tested.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shortcuts for is.na() — a","text":"logical vector.","code":""},{"path":[]},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Shortcuts for is.na() — a","text":"","code":"a(c(1, NA, 3)) #> [1]  TRUE FALSE  TRUE na(c(1, NA, 3)) #> [1] FALSE  TRUE FALSE"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/quiet.html","id":null,"dir":"Reference","previous_headings":"","what":"Decreases tidyverse verbosity — quiet","title":"Decreases tidyverse verbosity — quiet","text":"Disables: tidyverse startup messages readr column specification messages","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/quiet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Decreases tidyverse verbosity — quiet","text":"","code":"quiet()"},{"path":[]},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/quiet.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Decreases tidyverse verbosity — quiet","text":"","code":"quiet() library(tidyverse) # so quiet :) x <- read_csv(readr_example(\"mtcars.csv\")) # so quiet :)"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/uniques.html","id":null,"dir":"Reference","previous_headings":"","what":"Unique and sorted vectors — uniques","title":"Unique and sorted vectors — uniques","text":"Like unique(), also sorted.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/uniques.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Unique and sorted vectors — uniques","text":"","code":"uniques(x)"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/uniques.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Unique and sorted vectors — uniques","text":"x vector.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/uniques.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Unique and sorted vectors — uniques","text":"sorted vector without duplicates.","code":""},{"path":[]},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/uniques.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Unique and sorted vectors — uniques","text":"","code":"base::unique(c(3, 1, 2, 3)) #> [1] 3 1 2 uniques(c(3, 1, 2, 3)) #> [1] 1 2 3"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/validate-jmf-ids.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for valid JMF IDs — is_jmf_project_id","title":"Check for valid JMF IDs — is_jmf_project_id","text":"is_jmf_project_id(): checks valid JMF project IDs. jmf_project_id_regex(): returns underlying regular expression.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/validate-jmf-ids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for valid JMF IDs — is_jmf_project_id","text":"","code":"is_jmf_project_id(string, internal = \"deny\")  jmf_project_id_regex(internal = \"deny\")"},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/validate-jmf-ids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for valid JMF IDs — is_jmf_project_id","text":"string Input vector passed str_detect(). internal \"allow\" \"deny\" internal IDs.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/validate-jmf-ids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check for valid JMF IDs — is_jmf_project_id","text":"is_jmf_project_id(): logical vector length string. jmf_project_id_regex(): rex() regular expression.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/reference/validate-jmf-ids.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for valid JMF IDs — is_jmf_project_id","text":"","code":"# valid JMF project ID: is_jmf_project_id(\"JMF-2401-42\") #> [1] TRUE  # this is a JMF sample ID: is_jmf_project_id(\"JMF-2401-42-0001\") #> [1] FALSE  # extract JMF project ID from text: stringr::str_extract(   \"my sample id is JMF-2401-42-0001\",   jmf_project_id_regex() ) #> [1] \"JMF-2401-42\""},{"path":[]},{"path":"https://jmf-vienna.github.io/jmf-r/dev/news/index.html","id":"jmf-030","dir":"Changelog","previous_headings":"","what":"jmf 0.3.0","title":"jmf 0.3.0","text":"Added is_jmf_project_id() jmf_project_id_regex().","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/news/index.html","id":"jmf-021","dir":"Changelog","previous_headings":"","what":"jmf 0.2.1","title":"jmf 0.2.1","text":"uniques() keeps NAs sorts using LC_COLLATE=C.","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/news/index.html","id":"jmf-020","dir":"Changelog","previous_headings":"","what":"jmf 0.2.0","title":"jmf 0.2.0","text":"Added uniques(). Added quiet().","code":""},{"path":"https://jmf-vienna.github.io/jmf-r/dev/news/index.html","id":"jmf-010","dir":"Changelog","previous_headings":"","what":"jmf 0.1.0","title":"jmf 0.1.0","text":"Added () na().","code":""}]