From e4d3288bc49adcfea0cbf28119881f0408a89206 Mon Sep 17 00:00:00 2001
From: "github-merge-queue[bot]"
 <github-merge-queue[bot]@users.noreply.github.com>
Date: Tue, 12 Dec 2023 16:38:12 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20Public-H?=
 =?UTF-8?q?ealth-Scotland/slfhelper@448b7218017081a1adf1f576e040094d183a67?=
 =?UTF-8?q?4e=20=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                           |  2 +-
 CODE_OF_CONDUCT.html               |  2 +-
 CONTRIBUTING.html                  |  2 +-
 LICENSE-text.html                  |  2 +-
 LICENSE.html                       |  2 +-
 SUPPORT.html                       |  2 +-
 articles/index.html                |  2 +-
 articles/variable-packs.html       |  2 +-
 authors.html                       |  6 +++---
 index.html                         | 23 +++++++++++++----------
 news/index.html                    |  7 ++++++-
 pkgdown.yml                        |  2 +-
 reference/check_has_access.html    |  2 +-
 reference/check_on_server.html     |  2 +-
 reference/check_year.html          |  2 +-
 reference/chi_cohort.html          |  2 +-
 reference/demog_vars.html          |  2 +-
 reference/ep_file_bedday_vars.html |  2 +-
 reference/ep_file_cost_vars.html   |  2 +-
 reference/ep_file_vars.html        |  2 +-
 reference/format_year.html         |  2 +-
 reference/gen_file_path.html       |  2 +-
 reference/get_anon_chi.html        |  2 +-
 reference/get_chi.html             |  2 +-
 reference/index.html               |  2 +-
 reference/indiv_file_vars.html     |  2 +-
 reference/ltc_vars.html            |  2 +-
 reference/partnerships.html        |  2 +-
 reference/pipe.html                |  2 +-
 reference/read_slf.html            |  4 ++--
 reference/read_slf_episode.html    |  4 ++--
 reference/read_slf_individual.html |  4 ++--
 reference/recids.html              |  2 +-
 reference/slfhelper-package.html   | 11 ++++++-----
 search.json                        |  2 +-
 35 files changed, 62 insertions(+), 53 deletions(-)

diff --git a/404.html b/404.html
index 4add4cf..96a55c4 100644
--- a/404.html
+++ b/404.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="https://public-health-scotland.github.io/slfhelper/index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 6baa919..279699b 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/CONTRIBUTING.html b/CONTRIBUTING.html
index a8daf3c..8f08147 100644
--- a/CONTRIBUTING.html
+++ b/CONTRIBUTING.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/LICENSE-text.html b/LICENSE-text.html
index 5c56da2..f23461a 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/LICENSE.html b/LICENSE.html
index 71937b6..dcb8f52 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/SUPPORT.html b/SUPPORT.html
index 1b26520..cfef79c 100644
--- a/SUPPORT.html
+++ b/SUPPORT.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/articles/index.html b/articles/index.html
index 2ef310b..9fd77db 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/articles/variable-packs.html b/articles/variable-packs.html
index 5b3b5d6..898d727 100644
--- a/articles/variable-packs.html
+++ b/articles/variable-packs.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/authors.html b/authors.html
index 99abc1d..b618d91 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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">
@@ -72,14 +72,14 @@ <h2 id="citation">Citation</h2>
 
       <p>McMahon J, McNicol M (2023).
 <em>slfhelper: Useful functions for working with the Source Linkage Files</em>.
-R package version 0.10.0, 
+R package version 0.10.0.9000, 
 https://github.com/Public-Health-Scotland/slfhelper, <a href="https://public-health-scotland.github.io/slfhelper/">https://public-health-scotland.github.io/slfhelper/</a>. 
 </p>
       <pre>@Manual{,
   title = {slfhelper: Useful functions for working with the Source Linkage Files},
   author = {James McMahon and Megan McNicol},
   year = {2023},
-  note = {R package version 0.10.0, 
+  note = {R package version 0.10.0.9000, 
 https://github.com/Public-Health-Scotland/slfhelper},
   url = {https://public-health-scotland.github.io/slfhelper/},
 }</pre>
diff --git a/index.html b/index.html
index 470b713..46746d4 100644
--- a/index.html
+++ b/index.html
@@ -32,7 +32,7 @@
     
     <a class="navbar-brand me-2" href="index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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">
@@ -76,12 +76,15 @@
 <div class="section level1">
 <div class="page-header"><h1 id="slfhelper">slfhelper<a class="anchor" aria-label="anchor" href="#slfhelper"></a>
 </h1></div>
-<p>The goal of slfhelper is to provide some easy-to-use functions that make working with the Source Linkage Files as painless and efficient as possible.</p>
+<p>The goal of slfhelper is to provide some easy-to-use functions that make working with the Source Linkage Files as painless and efficient as possible. It is only intended for use by PHS employees and will only work on the PHS R infrastructure.</p>
 <div class="section level2">
 <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
 </h2>
-<p>The preferred method of installation is to use the <a href="https://pak.r-lib.org/" class="external-link">{<code>pak</code>} package</a>, which does an excellent job of handling the errors which sometimes occur.</p>
+<p>The simplest way to install to the PHS Posit Workbench environment is to use the <a href="https://ppm.publichealthscotland.org/client/#/repos/3/packages/slfhelper" class="external-link">PHS Package Manager</a>, this will be the default setting and means you can install <code>slfhelper</code> as you would any other package.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"slfhelper"</span><span class="op">)</span></span></code></pre></div>
+<p>If this doesn’t work you can install it directly from GitHub, there are a number of ways to do this, we recommend the <a href="https://pak.r-lib.org/" class="external-link">{<code>pak</code>} package</a>.</p>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># Install pak (if needed)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"pak"</span><span class="op">)</span></span>
 <span></span>
@@ -94,9 +97,9 @@ <h2 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a>
 <div class="section level3">
 <h3 id="read-a-file">Read a file<a class="anchor" aria-label="anchor" href="#read-a-file"></a>
 </h3>
-<p><strong>Note:</strong> Reading a full file is quite slow and will use a lot of memory, we would always recommend doing a column selection to only keep the variables that you need for your analysis. Just doing this will dramatically speed up the read-time.</p>
-<p>We provide some data snippets to help with the column selection and filtering.</p>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<p><strong>Note:</strong> Reading a full file is quite slow and will use a lot of memory, we would always recommend doing a column selection to only keep the variables that you need for your analysis. Just doing this will dramatically speed up the read time.</p>
+<p>We provide some data snippets to help with column selection and filtering.</p>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://public-health-scotland.github.io/slfhelper/">slfhelper</a></span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># Get a list of the variables in a file</span></span>
@@ -108,7 +111,7 @@ <h3 id="read-a-file">Read a file<a class="anchor" aria-label="anchor" href="#rea
 <span></span>
 <span><span class="co"># See a list with descriptions for the recids</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/utils/View.html" class="external-link">View</a></span><span class="op">(</span><span class="va">recids</span><span class="op">)</span></span></code></pre></div>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://public-health-scotland.github.io/slfhelper/">slfhelper</a></span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># Read certain variables</span></span>
@@ -138,7 +141,7 @@ <h3 id="read-a-file">Read a file<a class="anchor" aria-label="anchor" href="#rea
 <div class="section level3">
 <h3 id="match-on-chi-numbers-to-anon_chi-or-vice-versa">Match on CHI numbers to Anon_CHI (or vice versa)<a class="anchor" aria-label="anchor" href="#match-on-chi-numbers-to-anon_chi-or-vice-versa"></a>
 </h3>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://public-health-scotland.github.io/slfhelper/">slfhelper</a></span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># Add real CHI numbers to a SLF</span></span>
@@ -147,11 +150,11 @@ <h3 id="match-on-chi-numbers-to-anon_chi-or-vice-versa">Match on CHI numbers to
 <span><span class="op">)</span> <span class="op"><a href="reference/pipe.html">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="reference/get_chi.html">get_chi</a></span><span class="op">(</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># Change chi numbers from data above back to anon_chi</span></span>
+<span><span class="co"># Change chi numbers from the data above back to anon_chi</span></span>
 <span><span class="va">ep_1718_anon</span> <span class="op">&lt;-</span> <span class="va">ep_1718</span> <span class="op"><a href="reference/pipe.html">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="reference/get_anon_chi.html">get_anon_chi</a></span><span class="op">(</span>chi_var <span class="op">=</span> <span class="st">"chi"</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># Add anon_chi to cohort sample</span></span>
+<span><span class="co"># Add anon_chi to the cohort sample</span></span>
 <span><span class="va">chi_cohort</span> <span class="op">&lt;-</span> <span class="va">chi_cohort</span> <span class="op"><a href="reference/pipe.html">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="reference/get_anon_chi.html">get_anon_chi</a></span><span class="op">(</span>chi_var <span class="op">=</span> <span class="st">"upi_number"</span><span class="op">)</span></span></code></pre></div>
 </div>
diff --git a/news/index.html b/news/index.html
index 8b59d5b..f0bd4ea 100644
--- a/news/index.html
+++ b/news/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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">
@@ -50,6 +50,9 @@
       <small>Source: <a href="https://github.com/Public-Health-Scotland/slfhelper/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="development version" id="slfhelper-development-version">slfhelper (development version)<a class="anchor" aria-label="anchor" href="#slfhelper-development-version"></a></h2>
+</div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.10.0" id="slfhelper-0100">slfhelper 0.10.0<a class="anchor" aria-label="anchor" href="#slfhelper-0100"></a></h2>
 <ul><li>
@@ -57,6 +60,8 @@ <h2 class="pkg-version" data-toc-text="0.10.0" id="slfhelper-0100">slfhelper 0.1
 <li>Dependency versions have been updated to the latest.</li>
 <li>
 <code><a href="../reference/get_chi.html">get_chi()</a></code> and <code><a href="../reference/get_anon_chi.html">get_anon_chi()</a></code> now properly match missing (<code>NA</code>) and blank (<code>""</code>) values.</li>
+<li>slfhelper now defaults to using the <code>.parquet</code> file versions, old versions of slfhelper will no longer work.</li>
+<li>There is now a <code>dev</code> parameter available when using the <code>read_slf_*</code> functions which allows reading the file from the development environment.</li>
 </ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.9.0" id="slfhelper-090">slfhelper 0.9.0<a class="anchor" aria-label="anchor" href="#slfhelper-090"></a></h2>
diff --git a/pkgdown.yml b/pkgdown.yml
index 389748c..64bda42 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   variable-packs: variable-packs.html
-last_built: 2023-12-12T15:18Z
+last_built: 2023-12-12T16:37Z
 urls:
   reference: https://public-health-scotland.github.io/slfhelper/reference
   article: https://public-health-scotland.github.io/slfhelper/articles
diff --git a/reference/check_has_access.html b/reference/check_has_access.html
index adf0d07..52eb026 100644
--- a/reference/check_has_access.html
+++ b/reference/check_has_access.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/check_on_server.html b/reference/check_on_server.html
index 5ca5d1b..d8f6b8a 100644
--- a/reference/check_on_server.html
+++ b/reference/check_on_server.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/check_year.html b/reference/check_year.html
index 2c03345..0995da3 100644
--- a/reference/check_year.html
+++ b/reference/check_year.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/chi_cohort.html b/reference/chi_cohort.html
index 284fd8d..7de2db8 100644
--- a/reference/chi_cohort.html
+++ b/reference/chi_cohort.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/demog_vars.html b/reference/demog_vars.html
index 4c6a879..8704c78 100644
--- a/reference/demog_vars.html
+++ b/reference/demog_vars.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/ep_file_bedday_vars.html b/reference/ep_file_bedday_vars.html
index eb6fcb4..0d42363 100644
--- a/reference/ep_file_bedday_vars.html
+++ b/reference/ep_file_bedday_vars.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/ep_file_cost_vars.html b/reference/ep_file_cost_vars.html
index db573d2..b0e7f63 100644
--- a/reference/ep_file_cost_vars.html
+++ b/reference/ep_file_cost_vars.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/ep_file_vars.html b/reference/ep_file_vars.html
index 73cc3b0..e487ec4 100644
--- a/reference/ep_file_vars.html
+++ b/reference/ep_file_vars.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/format_year.html b/reference/format_year.html
index 5cec1d0..08d2756 100644
--- a/reference/format_year.html
+++ b/reference/format_year.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/gen_file_path.html b/reference/gen_file_path.html
index 71cae2f..80d7781 100644
--- a/reference/gen_file_path.html
+++ b/reference/gen_file_path.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/get_anon_chi.html b/reference/get_anon_chi.html
index 8c31291..33260f0 100644
--- a/reference/get_anon_chi.html
+++ b/reference/get_anon_chi.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/get_chi.html b/reference/get_chi.html
index 41a7f8c..c7ae9c1 100644
--- a/reference/get_chi.html
+++ b/reference/get_chi.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/index.html b/reference/index.html
index b44a12e..8849691 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/indiv_file_vars.html b/reference/indiv_file_vars.html
index dfcb84c..de64fe8 100644
--- a/reference/indiv_file_vars.html
+++ b/reference/indiv_file_vars.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/ltc_vars.html b/reference/ltc_vars.html
index 6b18635..632333a 100644
--- a/reference/ltc_vars.html
+++ b/reference/ltc_vars.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/partnerships.html b/reference/partnerships.html
index 5623d8c..ec4859c 100644
--- a/reference/partnerships.html
+++ b/reference/partnerships.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/pipe.html b/reference/pipe.html
index 9d5aa0c..8f4b49b 100644
--- a/reference/pipe.html
+++ b/reference/pipe.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/read_slf.html b/reference/read_slf.html
index 85e5758..1f3c0cf 100644
--- a/reference/read_slf.html
+++ b/reference/read_slf.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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">
@@ -100,7 +100,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt>as_data_frame</dt>
-<dd><p>Should the function return a <code>data.frame</code> (default) or
+<dd><p>Should the function return a <code>tibble</code> (default) or
 an Arrow <a href="https://arrow.apache.org/docs/r/reference/Table-class.html" class="external-link">Table</a>?</p></dd>
 
 
diff --git a/reference/read_slf_episode.html b/reference/read_slf_episode.html
index 4a003c9..94f2427 100644
--- a/reference/read_slf_episode.html
+++ b/reference/read_slf_episode.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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">
@@ -93,7 +93,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt>as_data_frame</dt>
-<dd><p>Should the function return a <code>data.frame</code> (default) or
+<dd><p>Should the function return a <code>tibble</code> (default) or
 an Arrow <a href="https://arrow.apache.org/docs/r/reference/Table-class.html" class="external-link">Table</a>?</p></dd>
 
 
diff --git a/reference/read_slf_individual.html b/reference/read_slf_individual.html
index e08442c..b5dd0b7 100644
--- a/reference/read_slf_individual.html
+++ b/reference/read_slf_individual.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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">
@@ -88,7 +88,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt>as_data_frame</dt>
-<dd><p>Should the function return a <code>data.frame</code> (default) or
+<dd><p>Should the function return a <code>tibble</code> (default) or
 an Arrow <a href="https://arrow.apache.org/docs/r/reference/Table-class.html" class="external-link">Table</a>?</p></dd>
 
 
diff --git a/reference/recids.html b/reference/recids.html
index 6a328a5..7da1070 100644
--- a/reference/recids.html
+++ b/reference/recids.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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/reference/slfhelper-package.html b/reference/slfhelper-package.html
index e739d77..27e59d3 100644
--- a/reference/slfhelper-package.html
+++ b/reference/slfhelper-package.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This package provides helper functions for working with the Source Linkage Files (SLFs). The functions are mainly focused on making the first steps of analysis easier. They can read and filter the files efficiently using minimal code."><title>slfhelper: Useful functions for working with the Source Linkage Files — slfhelper-package • slfhelper</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="slfhelper: Useful functions for working with the Source Linkage Files — slfhelper-package"><meta property="og:description" content="This package provides helper functions for working with the Source Linkage Files (SLFs). The functions are mainly focused on making the first steps of analysis easier. They can read and filter the files efficiently using minimal code."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">slfhelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.10.0.9000</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">
@@ -52,7 +52,7 @@
     </div>
 
     <div class="ref-description section level2">
-    <p>This package provides a few helper functions for working with the Source Linkage Files (SLFs). The functions are mainly focussed on making the first steps of analysis easier. They can read in and filter the files in an efficient way using minimal syntax. If you find a bug or have any ideas for new functions or improvements get in touch or submit a pull request.</p>
+    <p>This package provides helper functions for working with the Source Linkage Files (SLFs). The functions are mainly focused on making the first steps of analysis easier. They can read and filter the files efficiently using minimal code.</p>
     </div>
 
 
@@ -65,8 +65,9 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
     <div class="section level2">
     <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
-    <p><strong>Maintainer</strong>: James McMahon <a href="mailto:james.mcmahon@phs.scot">james.mcmahon@phs.scot</a> (<a href="https://orcid.org/0000-0002-5380-2029" class="external-link">ORCID</a>)</p>
-<p>Other contributors:</p><ul><li><p>Public Health Scotland <a href="mailto:phs.source@phs.scot">phs.source@phs.scot</a> [copyright holder]</p></li>
+    <p><strong>Maintainer</strong>: Megan McNicol <a href="mailto:megan.mcnicol2@phs.scot">megan.mcnicol2@phs.scot</a></p>
+<p>Authors:</p><ul><li><p>James McMahon <a href="mailto:james.mcmahon@phs.scot">james.mcmahon@phs.scot</a> (<a href="https://orcid.org/0000-0002-5380-2029" class="external-link">ORCID</a>)</p></li>
+</ul><p>Other contributors:</p><ul><li><p>Public Health Scotland <a href="mailto:phs.source@phs.scot">phs.source@phs.scot</a> [copyright holder]</p></li>
 </ul></div>
 
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/search.json b/search.json
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--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https:// www.contributor-covenant.org/translations.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to slfhelper","title":"Contributing to slfhelper","text":"outlines propose change slfhelper.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing to slfhelper","text":"can fix typos, spelling mistakes, grammatical errors documentation directly using GitHub web interface, long changes made source file. generally means ’ll need edit roxygen2 comments .R, .Rd file. can find .R file generates .Rd reading comment first line.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CONTRIBUTING.html","id":"bigger-changes","dir":"","previous_headings":"","what":"Bigger changes","title":"Contributing to slfhelper","text":"want make bigger change, ’s good idea first file issue make sure someone team agrees ’s needed. ’ve found bug, please file issue illustrates bug minimal reprex (also help write unit test, needed).","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"Bigger changes","what":"Pull request process","title":"Contributing to slfhelper","text":"Fork package clone onto computer. haven’t done , recommend using usethis::create_from_github(\"Public-Health-Scotland/slfhelper\", fork = TRUE). Install development dependences devtools::install_dev_deps(), make sure package passes R CMD check running devtools::check(). R CMD check doesn’t pass cleanly, ’s good idea ask help continuing. Create Git branch pull request (PR). recommend using usethis::pr_init(\"brief-description--change\"). Make changes, commit git, create PR running usethis::pr_push(), following prompts browser. title PR briefly describe change. body PR contain Fixes #issue-number. user-facing changes, add bullet top NEWS.md (.e. just first header). Follow style described https://style.tidyverse.org/news.html.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CONTRIBUTING.html","id":"code-style","dir":"","previous_headings":"Bigger changes","what":"Code style","title":"Contributing to slfhelper","text":"New code follow tidyverse style guide. can use styler package apply styles, please don’t restyle code nothing PR. use roxygen2, Markdown syntax, documentation. use testthat unit tests. Contributions test cases included easier accept.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing to slfhelper","text":"Please note slfhelper project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2019 James McMahon 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://public-health-scotland.github.io/slfhelper/SUPPORT.html","id":null,"dir":"","previous_headings":"","what":"Getting help with slfhelper","title":"Getting help with slfhelper","text":"Thanks using slfhelper! filing issue, places explore pieces put together make process smooth possible.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/SUPPORT.html","id":"make-a-reprex","dir":"","previous_headings":"","what":"Make a reprex","title":"Getting help with slfhelper","text":"Start making minimal reproducible example using reprex package. haven’t heard used reprex , ’re treat! Seriously, reprex make R-question-asking endeavors easier (pretty insane ROI five ten minutes ’ll take learn ’s ). additional reprex pointers, check Get help! section tidyverse site.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/SUPPORT.html","id":"where-to-ask","dir":"","previous_headings":"","what":"Where to ask?","title":"Getting help with slfhelper","text":"Armed reprex, next step figure ask. ’s question: start SLF Teams channel. ’s bug: ’re right place, file issue. ’re sure: feel free either! opening new issue, sure search issues pull requests make sure bug hasn’t reported /already fixed development version. default, search pre-populated :issue :open. can edit qualifiers (e.g. :pr, :closed) needed. example, ’d simply remove :open search issues repo, open closed.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"selecting-only-specified-variables","dir":"Articles","previous_headings":"","what":"Selecting only specified variables","title":"Using variable packs","text":"recommended choose variables need reading Source Linkage File. can achieved specifying column argument relevant read_slf_ function. result data read much faster well easy work . full episode individual files 200+ 100+ variables respectively!","code":"library(slfhelper)  ep_data <- read_slf_episode(year = 1920, columns = c(\"year\", \"anon_chi\", \"recid\"))  indiv_data <- read_slf_individual(year = 1920, columns = c(\"year\", \"anon_chi\", \"nsu\"))"},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"looking-up-variable-names","dir":"Articles","previous_headings":"","what":"Looking up variable names","title":"Using variable packs","text":"help task picking variables might need analysis, well getting spelling correct, provide lists variable names package.","code":"# Show the first few variables from the episode file head(ep_file_vars) #> [1] \"year\"            \"recid\"           \"record_keydate1\" \"record_keydate2\" #> [5] \"smrtype\"         \"gender\"  # Do the same for the individual file head(indiv_file_vars) #> [1] \"anon_chi\"        \"gender\"          \"postcode\"        \"dob\"             #> [5] \"gpprac\"          \"ch_cis_episodes\""},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"variable-packs","dir":"Articles","previous_headings":"","what":"Variable packs","title":"Using variable packs","text":"great can still lot effort copy/pasting every time, especially need quite variables analysis. assist , number ‘variable packs’, groups variables commonly needed together can accessed simple name. Currently four packs; demog_vars, ltc_vars, ep_file_bedday_vars ep_file_cost_vars. Let’s see contain.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"demographic-variables","dir":"Articles","previous_headings":"Variable packs","what":"Demographic variables","title":"Using variable packs","text":"demographic variables specific CHI can used episode individual file.","code":"demog_vars #>  [1] \"anon_chi\"                     \"gender\"                       #>  [3] \"dob\"                          \"age\"                          #>  [5] \"gpprac\"                       \"hbpraccode\"                   #>  [7] \"postcode\"                     \"hbrescode\"                    #>  [9] \"hscp2018\"                     \"lca\"                          #> [11] \"ca2018\"                       \"locality\"                     #> [13] \"datazone2011\"                 \"hb2019\"                       #> [15] \"hscp2019\"                     \"ca2019\"                       #> [17] \"simd2020v2_rank\"              \"simd2020v2_sc_decile\"         #> [19] \"simd2020v2_sc_quintile\"       \"simd2020v2_hb2019_decile\"     #> [21] \"simd2020v2_hb2019_quintile\"   \"simd2020v2_hscp2019_decile\"   #> [23] \"simd2020v2_hscp2019_quintile\" \"ur8_2016\"                     #> [25] \"ur6_2016\"                     \"ur3_2016\"                     #> [27] \"ur2_2016\"                     \"cluster\"                      #> [29] \"demographic_cohort\"           \"service_use_cohort\""},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"long-term-condition-ltc-variables","dir":"Articles","previous_headings":"Variable packs","what":"Long Term Condition (LTC) variables","title":"Using variable packs","text":"Long Term Condition flag variables specific CHI can used episode individual file.","code":"ltc_vars #>  [1] \"arth\"       \"asthma\"     \"atrialfib\"  \"cancer\"     \"cvd\"        #>  [6] \"liver\"      \"copd\"       \"dementia\"   \"diabetes\"   \"epilepsy\"   #> [11] \"chd\"        \"hefailure\"  \"ms\"         \"parkinsons\" \"refailure\"  #> [16] \"congen\"     \"bloodbfo\"   \"endomet\"    \"digestive\""},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"bedday-variables","dir":"Articles","previous_headings":"Variable packs","what":"Bedday variables","title":"Using variable packs","text":"variables detailing beddays, specific episode can used episode file.","code":"ep_file_bedday_vars #>  [1] \"yearstay\"    \"stay\"        \"apr_beddays\" \"may_beddays\" \"jun_beddays\" #>  [6] \"jul_beddays\" \"aug_beddays\" \"sep_beddays\" \"oct_beddays\" \"nov_beddays\" #> [11] \"dec_beddays\" \"jan_beddays\" \"feb_beddays\" \"mar_beddays\""},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"cost-variables","dir":"Articles","previous_headings":"Variable packs","what":"Cost variables","title":"Using variable packs","text":"variables detailing costs, specific episode can used episode file.","code":"ep_file_cost_vars #>  [1] \"cost_total_net\"         \"cost_total_net_incdnas\" \"apr_cost\"               #>  [4] \"may_cost\"               \"jun_cost\"               \"jul_cost\"               #>  [7] \"aug_cost\"               \"sep_cost\"               \"oct_cost\"               #> [10] \"nov_cost\"               \"dec_cost\"               \"jan_cost\"               #> [13] \"feb_cost\"               \"mar_cost\""},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"using-variable-packs","dir":"Articles","previous_headings":"","what":"Using variable packs","title":"Using variable packs","text":"variable packs can used column selection simplify code substantially. example take demographic data LTC flags individual file. get bedday information Acute records episode file.","code":"library(slfhelper)  indiv_ltc_data <- read_slf_individual(year = 1920, columns = c(\"year\", demog_vars, ltc_vars)) library(slfhelper)  acute_beddays <- read_slf_episode(   year = 1920,   columns = c(\"year\", \"anon_chi\", \"hbtreatcode\", \"recid\", ep_file_bedday_vars, \"cij_pattype\"),   recid = c(\"01B\", \"GLS\") )"},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"conclusion","dir":"Articles","previous_headings":"","what":"Conclusion","title":"Using variable packs","text":"using column argument reading data increase read speed, reduce amount data loading R. slfhelper provides number helpers make picking using variables need easier. like changes made existing packs, please open issue GitHub. like suggest additional variable packs, either open issue, even submit pull request!","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Public Health Scotland. Copyright holder. James McMahon. Author. Megan McNicol. Maintainer, author.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"McMahon J, McNicol M (2023). slfhelper: Useful functions working Source Linkage Files. R package version 0.10.0,  https://github.com/Public-Health-Scotland/slfhelper, https://public-health-scotland.github.io/slfhelper/.","code":"@Manual{,   title = {slfhelper: Useful functions for working with the Source Linkage Files},   author = {James McMahon and Megan McNicol},   year = {2023},   note = {R package version 0.10.0,  https://github.com/Public-Health-Scotland/slfhelper},   url = {https://public-health-scotland.github.io/slfhelper/}, }"},{"path":"https://public-health-scotland.github.io/slfhelper/index.html","id":"slfhelper","dir":"","previous_headings":"","what":"Useful functions for working with the Source Linkage Files","title":"Useful functions for working with the Source Linkage Files","text":"goal slfhelper provide easy--use functions make working Source Linkage Files painless efficient possible.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Useful functions for working with the Source Linkage Files","text":"preferred method installation use {pak} package, excellent job handling errors sometimes occur.","code":"# Install pak (if needed) install.packages(\"pak\")  # Use pak to install slfhelper pak::pak(\"Public-Health-Scotland/slfhelper\")"},{"path":[]},{"path":"https://public-health-scotland.github.io/slfhelper/index.html","id":"read-a-file","dir":"","previous_headings":"Usage","what":"Read a file","title":"Useful functions for working with the Source Linkage Files","text":"Note: Reading full file quite slow use lot memory, always recommend column selection keep variables need analysis. Just dramatically speed read-time. provide data snippets help column selection filtering. options reading files can () combined required.","code":"library(slfhelper)  # Get a list of the variables in a file ep_file_vars indiv_file_vars  # See a lookup of Partnership names to HSCP_2018 codes View(partnerships)  # See a list with descriptions for the recids View(recids) library(slfhelper)  # Read certain variables # It's much faster to choose variables like this indiv_1718 <- read_slf_individual(year = \"1718\", col_select = c(\"anon_chi\", \"hri_scot\"))  # Read multiple years # This will use dplyr::bind_rows() and return the files added together as a single tibble episode_data <- read_slf_episode(   year = c(\"1516\", \"1617\", \"1718\", \"1819\"),   col_select = c(\"anon_chi\", \"yearstay\") )  # Read only data for a certain partnership (HSCP_2018 code) # This can be a single partnership or multiple by supplying a vector e.g. c(...) indiv_1718 <- read_slf_individual(   year = \"1718\",   partnerships = \"S37000001\", # Aberdeen City   col_select = c(\"anon_chi\", \"hri_scot\") )  # Read only data for a certain recid # This can be a single recid or multiple by supplying a vector e.g. c(...) ep_1718 <- read_slf_episode(\"1718\", recid = c(\"01B\", \"GLS\"), col_select = c(\"anon_chi\", \"yearstay\"))"},{"path":"https://public-health-scotland.github.io/slfhelper/index.html","id":"match-on-chi-numbers-to-anon_chi-or-vice-versa","dir":"","previous_headings":"Usage","what":"Match on CHI numbers to Anon_CHI (or vice versa)","title":"Useful functions for working with the Source Linkage Files","text":"","code":"library(slfhelper)  # Add real CHI numbers to a SLF ep_1718 <- read_slf_episode(c(\"1718\", \"1819\", \"1920\"),   col_select = c(\"year\", \"anon_chi\", \"demographic_cohort\") ) %>%   get_chi()  # Change chi numbers from data above back to anon_chi ep_1718_anon <- ep_1718 %>%   get_anon_chi(chi_var = \"chi\")  # Add anon_chi to cohort sample chi_cohort <- chi_cohort %>%   get_anon_chi(chi_var = \"upi_number\")"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_has_access.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if the current user is in a UNIX group — check_has_access","title":"Check if the current user is in a UNIX group — check_has_access","text":"Check current user UNIX group","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_has_access.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if the current user is in a UNIX group — check_has_access","text":"","code":"check_has_access(group = \"hscdiip\")"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_has_access.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if the current user is in a UNIX group — check_has_access","text":"group group check, default hscdiip","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_has_access.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if the current user is in a UNIX group — check_has_access","text":"Boolean","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_on_server.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if it's a server session — check_on_server","title":"Check if it's a server session — check_on_server","text":"Check server session","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_on_server.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if it's a server session — check_on_server","text":"","code":"check_on_server()"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_on_server.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if it's a server session — check_on_server","text":"Boolean","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_year.html","id":null,"dir":"Reference","previous_headings":"","what":"Check the year(s) supplied are valid — check_year","title":"Check the year(s) supplied are valid — check_year","text":"Check year(s) supplied valid","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_year.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check the year(s) supplied are valid — check_year","text":"","code":"check_year(year, call = rlang::caller_env())"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_year.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check the year(s) supplied are valid — check_year","text":"year Year file read, can specify multiple years returned one file. converted short FY using format_year(). call Supply environment top-level function make error messages useful.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_year.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check the year(s) supplied are valid — check_year","text":"TRUE year valid newer year, FALSE older still valid years. Otherwise throws error.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/chi_cohort.html","id":null,"dir":"Reference","previous_headings":"","what":"A tibble containing an example\ncohort of CHI numbers under different variable names.\nIt is used for testing and to illustrate examples.\nIt is likely that many of the 'chi numbers' are not valid. — chi_cohort","title":"A tibble containing an example\ncohort of CHI numbers under different variable names.\nIt is used for testing and to illustrate examples.\nIt is likely that many of the 'chi numbers' are not valid. — chi_cohort","text":"tibble containing example cohort CHI numbers different variable names. used testing illustrate examples. likely many 'chi numbers' valid.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/chi_cohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A tibble containing an example\ncohort of CHI numbers under different variable names.\nIt is used for testing and to illustrate examples.\nIt is likely that many of the 'chi numbers' are not valid. — chi_cohort","text":"","code":"chi_cohort"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/chi_cohort.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"A tibble containing an example\ncohort of CHI numbers under different variable names.\nIt is used for testing and to illustrate examples.\nIt is likely that many of the 'chi numbers' are not valid. — chi_cohort","text":"object class tbl_df (inherits tbl, data.frame) 100 rows 2 columns.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/demog_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Demographic variables — demog_vars","title":"Demographic variables — demog_vars","text":"vector containing names demographic variables.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/demog_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Demographic variables — demog_vars","text":"","code":"demog_vars"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/demog_vars.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Demographic variables — demog_vars","text":"object class character length 30.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_bedday_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Episode file bedday variables — ep_file_bedday_vars","title":"Episode file bedday variables — ep_file_bedday_vars","text":"vector containing names bedday related variables episode file.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_bedday_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Episode file bedday variables — ep_file_bedday_vars","text":"","code":"ep_file_bedday_vars"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_bedday_vars.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Episode file bedday variables — ep_file_bedday_vars","text":"object class character length 14.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_cost_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Episode file cost variables — ep_file_cost_vars","title":"Episode file cost variables — ep_file_cost_vars","text":"vector containing names cost related variables episode file.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_cost_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Episode file cost variables — ep_file_cost_vars","text":"","code":"ep_file_cost_vars"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_cost_vars.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Episode file cost variables — ep_file_cost_vars","text":"object class character length 14.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Episode file variables — ep_file_vars","title":"Episode file variables — ep_file_vars","text":"names variables episode files, correct order.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Episode file variables — ep_file_vars","text":"","code":"ep_file_vars"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_vars.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Episode file variables — ep_file_vars","text":"object class character length 239.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/format_year.html","id":null,"dir":"Reference","previous_headings":"","what":"Format a year into the correct short FY format — format_year","title":"Format a year into the correct short FY format — format_year","text":"Format year correct short FY format","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/format_year.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format a year into the correct short FY format — format_year","text":"","code":"format_year(year)"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/format_year.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format a year into the correct short FY format — format_year","text":"year Year file read, can specify multiple years returned one file. converted short FY using format_year().","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/format_year.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format a year into the correct short FY format — format_year","text":"Year correctly formatted short FY e.g. '1718'","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/gen_file_path.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a Source Linkage File, file path — gen_file_path","title":"Generate a Source Linkage File, file path — gen_file_path","text":"Generate Source Linkage File, file path","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/gen_file_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a Source Linkage File, file path — gen_file_path","text":"","code":"gen_file_path(year, file_version, call, dev = FALSE, ext = \"parquet\")"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/gen_file_path.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a Source Linkage File, file path — gen_file_path","text":"year Year file read, can specify multiple years returned one file. converted short FY using format_year(). file_version Version file (individual / episode). call Supply environment top-level function make error messages useful. dev Whether get file development area (/conf/sourcedev/Source_Linkage_File_Updates). default (FALSE) get production file usual area. ext file extension read.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/gen_file_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a Source Linkage File, file path — gen_file_path","text":"fs_path object.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_anon_chi.html","id":null,"dir":"Reference","previous_headings":"","what":"Match on anon_chi to a dataset using CHI numbers — get_anon_chi","title":"Match on anon_chi to a dataset using CHI numbers — get_anon_chi","text":"Match anon_chi dataset using CHI numbers","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_anon_chi.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Match on anon_chi to a dataset using CHI numbers — get_anon_chi","text":"","code":"get_anon_chi(chi_cohort, chi_var = \"chi\", drop = TRUE, check = TRUE)"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_anon_chi.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Match on anon_chi to a dataset using CHI numbers — get_anon_chi","text":"chi_cohort tibble data frame. chi_var CHI variable: name variable containing CHI (default chi). drop Optional boolean indicating whether existing chi_var dropped - default TRUE. check Optional boolean, CHIs checked using phsmethods::chi_check() - default TRUE.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_anon_chi.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Match on anon_chi to a dataset using CHI numbers — get_anon_chi","text":"tibble","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_anon_chi.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Match on anon_chi to a dataset using CHI numbers — get_anon_chi","text":"","code":"if (FALSE) { chi_cohort %>% get_anon_chi() chi_cohort %>% get_anon_chi(chi_var = \"upi_number\") }"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_chi.html","id":null,"dir":"Reference","previous_headings":"","what":"Match on CHI numbers to a dataset using anon_chi — get_chi","title":"Match on CHI numbers to a dataset using anon_chi — get_chi","text":"Match CHI numbers dataset using anon_chi","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_chi.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Match on CHI numbers to a dataset using anon_chi — get_chi","text":"","code":"get_chi(data, anon_chi_var = \"anon_chi\", drop = TRUE)"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_chi.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Match on CHI numbers to a dataset using anon_chi — get_chi","text":"data tibble data frame anon_chi_var Anon CHI variable: name variable containing anonymised CHI (default anon_chi) drop Optional boolean indicating whether existing anon_chi_var dropped - default TRUE","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_chi.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Match on CHI numbers to a dataset using anon_chi — get_chi","text":"tibble","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_chi.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Match on CHI numbers to a dataset using anon_chi — get_chi","text":"","code":"if (FALSE) { slf_1718 <- read_slf_individual(\"1718\") get_chi(slf_1718) get_chi(slf_1718, drop = FALSE) }"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/indiv_file_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Individual file variables — indiv_file_vars","title":"Individual file variables — indiv_file_vars","text":"names variables individual files, correct order.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/indiv_file_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Individual file variables — indiv_file_vars","text":"","code":"indiv_file_vars"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/indiv_file_vars.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Individual file variables — indiv_file_vars","text":"object class character length 180.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ltc_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"LTC variables — ltc_vars","title":"LTC variables — ltc_vars","text":"vector containing names Long Term Condition (LTC) variables.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ltc_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"LTC variables — ltc_vars","text":"","code":"ltc_vars"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ltc_vars.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"LTC variables — ltc_vars","text":"object class character length 19.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/partnerships.html","id":null,"dir":"Reference","previous_headings":"","what":"HSCP name / code lookup — partnerships","title":"HSCP name / code lookup — partnerships","text":"tibble containing names codes (hscp2018 configuration) partnerships. used partnership parameter reading files.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/partnerships.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"HSCP name / code lookup — partnerships","text":"","code":"partnerships"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/partnerships.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"HSCP name / code lookup — partnerships","text":"tibble 31 rows 2 variables: partnership_name official name Partnership hscp2018 hscp2018 standard code S370000??","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf.html","id":null,"dir":"Reference","previous_headings":"","what":"Read a Source Linkage File — read_slf","title":"Read a Source Linkage File — read_slf","text":"Read Source Linkage File","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read a Source Linkage File — read_slf","text":"","code":"read_slf(   year,   file_version = c(\"episode\", \"individual\"),   dev = FALSE,   col_select = NULL,   columns = lifecycle::deprecated(),   as_data_frame = TRUE,   partnerships = NULL,   recids = NULL )"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read a Source Linkage File — read_slf","text":"year Year file read, can specify multiple years returned one file. converted short FY using format_year(). file_version Version file (individual / episode). dev Whether get file development area (/conf/sourcedev/Source_Linkage_File_Updates). default (FALSE) get production file usual area. col_select character vector column names keep, \"select\" argument data.table::fread(), tidy selection specification columns, used dplyr::select(). columns columns longer used, use col_select instead. as_data_frame function return data.frame (default) Arrow Table? partnerships Optional specify partnership (hscp2018) partnerships select. recids Optional specify recid recids select.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read a Source Linkage File — read_slf","text":"requested SLF data tibble Arrow Table.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_episode.html","id":null,"dir":"Reference","previous_headings":"","what":"Read a Source Linkage episode file — read_slf_episode","title":"Read a Source Linkage episode file — read_slf_episode","text":"Read Source Linkage episode file","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_episode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read a Source Linkage episode file — read_slf_episode","text":"","code":"read_slf_episode(   year,   col_select = NULL,   partnerships = NULL,   recids = NULL,   as_data_frame = TRUE,   dev = FALSE,   columns = lifecycle::deprecated() )"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_episode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read a Source Linkage episode file — read_slf_episode","text":"year Year file read, can specify multiple years returned one file. converted short FY using format_year(). col_select character vector column names keep, \"select\" argument data.table::fread(), tidy selection specification columns, used dplyr::select(). partnerships Optional specify partnership (hscp2018) partnerships select. recids Optional specify recid recids select. as_data_frame function return data.frame (default) Arrow Table? dev Whether get file development area (/conf/sourcedev/Source_Linkage_File_Updates). default (FALSE) get production file usual area. columns columns longer used, use col_select instead.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_episode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read a Source Linkage episode file — read_slf_episode","text":"requested SLF data tibble Arrow Table.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_episode.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read a Source Linkage episode file — read_slf_episode","text":"","code":"if (FALSE) { read_slf_episode(\"1718\",   col_select = c(\"anon_chi\", \"dob\", \"demographic_cohort\") )  read_slf_episode(c(\"1718\", \"1819\"),   col_select = c(\"anon_chi\", \"dob\", \"demographic_cohort\"),   as_data_frame = FALSE ) }"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_individual.html","id":null,"dir":"Reference","previous_headings":"","what":"Read a Source Linkage individual file — read_slf_individual","title":"Read a Source Linkage individual file — read_slf_individual","text":"Read Source Linkage individual file","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_individual.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read a Source Linkage individual file — read_slf_individual","text":"","code":"read_slf_individual(   year,   col_select = NULL,   partnerships = NULL,   as_data_frame = TRUE,   dev = FALSE,   columns = lifecycle::deprecated() )"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_individual.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read a Source Linkage individual file — read_slf_individual","text":"year Year file read, can specify multiple years returned one file. converted short FY using format_year(). col_select character vector column names keep, \"select\" argument data.table::fread(), tidy selection specification columns, used dplyr::select(). partnerships Optional specify partnership (hscp2018) partnerships select. as_data_frame function return data.frame (default) Arrow Table? dev Whether get file development area (/conf/sourcedev/Source_Linkage_File_Updates). default (FALSE) get production file usual area. columns columns longer used, use col_select instead.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_individual.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read a Source Linkage individual file — read_slf_individual","text":"requested SLF data tibble Arrow Table.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_individual.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read a Source Linkage individual file — read_slf_individual","text":"","code":"if (FALSE) { read_slf_individual(\"1718\",   col_select = c(\"anon_chi\", \"dob\", \"hri_scot\") ) read_slf_individual(c(\"1718\", \"1819\"),   col_select = c(\"anon_chi\", \"dob\", \"hri_scot\"),   as_data_frame = FALSE ) }"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/recids.html","id":null,"dir":"Reference","previous_headings":"","what":"Recid name / description lookup — recids","title":"Recid name / description lookup — recids","text":"tibble containing names description recids. used recid parameter reading episode files.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/recids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Recid name / description lookup — recids","text":"","code":"recids"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/recids.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Recid name / description lookup — recids","text":"tibble 18 rows 2 variables: recid short-form recid Description description recid","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/slfhelper-package.html","id":null,"dir":"Reference","previous_headings":"","what":"slfhelper: Useful functions for working with the Source Linkage Files — slfhelper-package","title":"slfhelper: Useful functions for working with the Source Linkage Files — slfhelper-package","text":"package provides helper functions working Source Linkage Files (SLFs). functions mainly focussed making first steps analysis easier. can read filter files efficient way using minimal syntax. find bug ideas new functions improvements get touch submit pull request.","code":""},{"path":[]},{"path":"https://public-health-scotland.github.io/slfhelper/reference/slfhelper-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"slfhelper: Useful functions for working with the Source Linkage Files — slfhelper-package","text":"Maintainer: James McMahon james.mcmahon@phs.scot (ORCID) contributors: Public Health Scotland phs.source@phs.scot [copyright holder]","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-0100","dir":"Changelog","previous_headings":"","what":"slfhelper 0.10.0","title":"slfhelper 0.10.0","text":"{glue} longer dependency required functionality can provided `stringr::str_glue(). Dependency versions updated latest. get_chi() get_anon_chi() now properly match missing (NA) blank (\"\") values.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-090","dir":"Changelog","previous_headings":"","what":"slfhelper 0.9.0","title":"slfhelper 0.9.0","text":"{openssl} now required. get_chi() get_anon_chi() now much faster (>100X) use significantly less memory. year parameter now checked early process, invalid year supplied error message much informative.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-082","dir":"Changelog","previous_headings":"","what":"slfhelper 0.8.2","title":"slfhelper 0.8.2","text":"ep_file_vars indiv_file_vars updated correct variables.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-081","dir":"Changelog","previous_headings":"","what":"slfhelper 0.8.1","title":"slfhelper 0.8.1","text":"Use cli nicer error messages warning.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-080","dir":"Changelog","previous_headings":"","what":"slfhelper 0.8.0","title":"slfhelper 0.8.0","text":"Add number ‘variable packs’ easily selecting sets variables: demog_vars, ltc_vars, ep_file_bedday_vars ep_file_cost_vars. Add new vignette introducing variable packs.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-071","dir":"Changelog","previous_headings":"","what":"slfhelper 0.7.1","title":"slfhelper 0.7.1","text":"Add check server hscdiip access package load. Add recid lookup use recid filtering parameter. using get_anon_chi() now use phsmethods::chi_check (available) warn lot CHI numbers return invalid. Update variable lists new Home Care related variables.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-070","dir":"Changelog","previous_headings":"","what":"slfhelper 0.7.0","title":"slfhelper 0.7.0","text":"Now depends R >= 3.5 ep_file_vars indiv_file_vars updated latest variable names. now also return character vector instead list. read_slf_ now returns tibble.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-060","dir":"Changelog","previous_headings":"","what":"slfhelper 0.6.0","title":"slfhelper 0.6.0","text":"Fix bug selecting partnerships/recids also selecting multiple years (#13) (#14)","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-053","dir":"Changelog","previous_headings":"","what":"slfhelper 0.5.3","title":"slfhelper 0.5.3","text":"Added NEWS.md file track changes package. Moved use Rmd version readme. Bump dplyr version requirement 1.0.0 enable use across() new things. Add checks year","code":""}]
+[{"path":[]},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https:// www.contributor-covenant.org/translations.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to slfhelper","title":"Contributing to slfhelper","text":"outlines propose change slfhelper.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing to slfhelper","text":"can fix typos, spelling mistakes, grammatical errors documentation directly using GitHub web interface, long changes made source file. generally means ’ll need edit roxygen2 comments .R, .Rd file. can find .R file generates .Rd reading comment first line.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CONTRIBUTING.html","id":"bigger-changes","dir":"","previous_headings":"","what":"Bigger changes","title":"Contributing to slfhelper","text":"want make bigger change, ’s good idea first file issue make sure someone team agrees ’s needed. ’ve found bug, please file issue illustrates bug minimal reprex (also help write unit test, needed).","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"Bigger changes","what":"Pull request process","title":"Contributing to slfhelper","text":"Fork package clone onto computer. haven’t done , recommend using usethis::create_from_github(\"Public-Health-Scotland/slfhelper\", fork = TRUE). Install development dependences devtools::install_dev_deps(), make sure package passes R CMD check running devtools::check(). R CMD check doesn’t pass cleanly, ’s good idea ask help continuing. Create Git branch pull request (PR). recommend using usethis::pr_init(\"brief-description--change\"). Make changes, commit git, create PR running usethis::pr_push(), following prompts browser. title PR briefly describe change. body PR contain Fixes #issue-number. user-facing changes, add bullet top NEWS.md (.e. just first header). Follow style described https://style.tidyverse.org/news.html.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CONTRIBUTING.html","id":"code-style","dir":"","previous_headings":"Bigger changes","what":"Code style","title":"Contributing to slfhelper","text":"New code follow tidyverse style guide. can use styler package apply styles, please don’t restyle code nothing PR. use roxygen2, Markdown syntax, documentation. use testthat unit tests. Contributions test cases included easier accept.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing to slfhelper","text":"Please note slfhelper project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2019 James McMahon 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://public-health-scotland.github.io/slfhelper/SUPPORT.html","id":null,"dir":"","previous_headings":"","what":"Getting help with slfhelper","title":"Getting help with slfhelper","text":"Thanks using slfhelper! filing issue, places explore pieces put together make process smooth possible.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/SUPPORT.html","id":"make-a-reprex","dir":"","previous_headings":"","what":"Make a reprex","title":"Getting help with slfhelper","text":"Start making minimal reproducible example using reprex package. haven’t heard used reprex , ’re treat! Seriously, reprex make R-question-asking endeavors easier (pretty insane ROI five ten minutes ’ll take learn ’s ). additional reprex pointers, check Get help! section tidyverse site.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/SUPPORT.html","id":"where-to-ask","dir":"","previous_headings":"","what":"Where to ask?","title":"Getting help with slfhelper","text":"Armed reprex, next step figure ask. ’s question: start SLF Teams channel. ’s bug: ’re right place, file issue. ’re sure: feel free either! opening new issue, sure search issues pull requests make sure bug hasn’t reported /already fixed development version. default, search pre-populated :issue :open. can edit qualifiers (e.g. :pr, :closed) needed. example, ’d simply remove :open search issues repo, open closed.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"selecting-only-specified-variables","dir":"Articles","previous_headings":"","what":"Selecting only specified variables","title":"Using variable packs","text":"recommended choose variables need reading Source Linkage File. can achieved specifying column argument relevant read_slf_ function. result data read much faster well easy work . full episode individual files 200+ 100+ variables respectively!","code":"library(slfhelper)  ep_data <- read_slf_episode(year = 1920, columns = c(\"year\", \"anon_chi\", \"recid\"))  indiv_data <- read_slf_individual(year = 1920, columns = c(\"year\", \"anon_chi\", \"nsu\"))"},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"looking-up-variable-names","dir":"Articles","previous_headings":"","what":"Looking up variable names","title":"Using variable packs","text":"help task picking variables might need analysis, well getting spelling correct, provide lists variable names package.","code":"# Show the first few variables from the episode file head(ep_file_vars) #> [1] \"year\"            \"recid\"           \"record_keydate1\" \"record_keydate2\" #> [5] \"smrtype\"         \"gender\"  # Do the same for the individual file head(indiv_file_vars) #> [1] \"anon_chi\"        \"gender\"          \"postcode\"        \"dob\"             #> [5] \"gpprac\"          \"ch_cis_episodes\""},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"variable-packs","dir":"Articles","previous_headings":"","what":"Variable packs","title":"Using variable packs","text":"great can still lot effort copy/pasting every time, especially need quite variables analysis. assist , number ‘variable packs’, groups variables commonly needed together can accessed simple name. Currently four packs; demog_vars, ltc_vars, ep_file_bedday_vars ep_file_cost_vars. Let’s see contain.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"demographic-variables","dir":"Articles","previous_headings":"Variable packs","what":"Demographic variables","title":"Using variable packs","text":"demographic variables specific CHI can used episode individual file.","code":"demog_vars #>  [1] \"anon_chi\"                     \"gender\"                       #>  [3] \"dob\"                          \"age\"                          #>  [5] \"gpprac\"                       \"hbpraccode\"                   #>  [7] \"postcode\"                     \"hbrescode\"                    #>  [9] \"hscp2018\"                     \"lca\"                          #> [11] \"ca2018\"                       \"locality\"                     #> [13] \"datazone2011\"                 \"hb2019\"                       #> [15] \"hscp2019\"                     \"ca2019\"                       #> [17] \"simd2020v2_rank\"              \"simd2020v2_sc_decile\"         #> [19] \"simd2020v2_sc_quintile\"       \"simd2020v2_hb2019_decile\"     #> [21] \"simd2020v2_hb2019_quintile\"   \"simd2020v2_hscp2019_decile\"   #> [23] \"simd2020v2_hscp2019_quintile\" \"ur8_2016\"                     #> [25] \"ur6_2016\"                     \"ur3_2016\"                     #> [27] \"ur2_2016\"                     \"cluster\"                      #> [29] \"demographic_cohort\"           \"service_use_cohort\""},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"long-term-condition-ltc-variables","dir":"Articles","previous_headings":"Variable packs","what":"Long Term Condition (LTC) variables","title":"Using variable packs","text":"Long Term Condition flag variables specific CHI can used episode individual file.","code":"ltc_vars #>  [1] \"arth\"       \"asthma\"     \"atrialfib\"  \"cancer\"     \"cvd\"        #>  [6] \"liver\"      \"copd\"       \"dementia\"   \"diabetes\"   \"epilepsy\"   #> [11] \"chd\"        \"hefailure\"  \"ms\"         \"parkinsons\" \"refailure\"  #> [16] \"congen\"     \"bloodbfo\"   \"endomet\"    \"digestive\""},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"bedday-variables","dir":"Articles","previous_headings":"Variable packs","what":"Bedday variables","title":"Using variable packs","text":"variables detailing beddays, specific episode can used episode file.","code":"ep_file_bedday_vars #>  [1] \"yearstay\"    \"stay\"        \"apr_beddays\" \"may_beddays\" \"jun_beddays\" #>  [6] \"jul_beddays\" \"aug_beddays\" \"sep_beddays\" \"oct_beddays\" \"nov_beddays\" #> [11] \"dec_beddays\" \"jan_beddays\" \"feb_beddays\" \"mar_beddays\""},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"cost-variables","dir":"Articles","previous_headings":"Variable packs","what":"Cost variables","title":"Using variable packs","text":"variables detailing costs, specific episode can used episode file.","code":"ep_file_cost_vars #>  [1] \"cost_total_net\"         \"cost_total_net_incdnas\" \"apr_cost\"               #>  [4] \"may_cost\"               \"jun_cost\"               \"jul_cost\"               #>  [7] \"aug_cost\"               \"sep_cost\"               \"oct_cost\"               #> [10] \"nov_cost\"               \"dec_cost\"               \"jan_cost\"               #> [13] \"feb_cost\"               \"mar_cost\""},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"using-variable-packs","dir":"Articles","previous_headings":"","what":"Using variable packs","title":"Using variable packs","text":"variable packs can used column selection simplify code substantially. example take demographic data LTC flags individual file. get bedday information Acute records episode file.","code":"library(slfhelper)  indiv_ltc_data <- read_slf_individual(year = 1920, columns = c(\"year\", demog_vars, ltc_vars)) library(slfhelper)  acute_beddays <- read_slf_episode(   year = 1920,   columns = c(\"year\", \"anon_chi\", \"hbtreatcode\", \"recid\", ep_file_bedday_vars, \"cij_pattype\"),   recid = c(\"01B\", \"GLS\") )"},{"path":"https://public-health-scotland.github.io/slfhelper/articles/variable-packs.html","id":"conclusion","dir":"Articles","previous_headings":"","what":"Conclusion","title":"Using variable packs","text":"using column argument reading data increase read speed, reduce amount data loading R. slfhelper provides number helpers make picking using variables need easier. like changes made existing packs, please open issue GitHub. like suggest additional variable packs, either open issue, even submit pull request!","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Public Health Scotland. Copyright holder. James McMahon. Author. Megan McNicol. Maintainer, author.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"McMahon J, McNicol M (2023). slfhelper: Useful functions working Source Linkage Files. R package version 0.10.0.9000,  https://github.com/Public-Health-Scotland/slfhelper, https://public-health-scotland.github.io/slfhelper/.","code":"@Manual{,   title = {slfhelper: Useful functions for working with the Source Linkage Files},   author = {James McMahon and Megan McNicol},   year = {2023},   note = {R package version 0.10.0.9000,  https://github.com/Public-Health-Scotland/slfhelper},   url = {https://public-health-scotland.github.io/slfhelper/}, }"},{"path":"https://public-health-scotland.github.io/slfhelper/index.html","id":"slfhelper","dir":"","previous_headings":"","what":"Useful functions for working with the Source Linkage Files","title":"Useful functions for working with the Source Linkage Files","text":"goal slfhelper provide easy--use functions make working Source Linkage Files painless efficient possible. intended use PHS employees work PHS R infrastructure.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Useful functions for working with the Source Linkage Files","text":"simplest way install PHS Posit Workbench environment use PHS Package Manager, default setting means can install slfhelper package. doesn’t work can install directly GitHub, number ways , recommend {pak} package.","code":"install.packages(\"slfhelper\") # Install pak (if needed) install.packages(\"pak\")  # Use pak to install slfhelper pak::pak(\"Public-Health-Scotland/slfhelper\")"},{"path":[]},{"path":"https://public-health-scotland.github.io/slfhelper/index.html","id":"read-a-file","dir":"","previous_headings":"Usage","what":"Read a file","title":"Useful functions for working with the Source Linkage Files","text":"Note: Reading full file quite slow use lot memory, always recommend column selection keep variables need analysis. Just dramatically speed read time. provide data snippets help column selection filtering. options reading files can () combined required.","code":"library(slfhelper)  # Get a list of the variables in a file ep_file_vars indiv_file_vars  # See a lookup of Partnership names to HSCP_2018 codes View(partnerships)  # See a list with descriptions for the recids View(recids) library(slfhelper)  # Read certain variables # It's much faster to choose variables like this indiv_1718 <- read_slf_individual(year = \"1718\", col_select = c(\"anon_chi\", \"hri_scot\"))  # Read multiple years # This will use dplyr::bind_rows() and return the files added together as a single tibble episode_data <- read_slf_episode(   year = c(\"1516\", \"1617\", \"1718\", \"1819\"),   col_select = c(\"anon_chi\", \"yearstay\") )  # Read only data for a certain partnership (HSCP_2018 code) # This can be a single partnership or multiple by supplying a vector e.g. c(...) indiv_1718 <- read_slf_individual(   year = \"1718\",   partnerships = \"S37000001\", # Aberdeen City   col_select = c(\"anon_chi\", \"hri_scot\") )  # Read only data for a certain recid # This can be a single recid or multiple by supplying a vector e.g. c(...) ep_1718 <- read_slf_episode(\"1718\", recid = c(\"01B\", \"GLS\"), col_select = c(\"anon_chi\", \"yearstay\"))"},{"path":"https://public-health-scotland.github.io/slfhelper/index.html","id":"match-on-chi-numbers-to-anon_chi-or-vice-versa","dir":"","previous_headings":"Usage","what":"Match on CHI numbers to Anon_CHI (or vice versa)","title":"Useful functions for working with the Source Linkage Files","text":"","code":"library(slfhelper)  # Add real CHI numbers to a SLF ep_1718 <- read_slf_episode(c(\"1718\", \"1819\", \"1920\"),   col_select = c(\"year\", \"anon_chi\", \"demographic_cohort\") ) %>%   get_chi()  # Change chi numbers from the data above back to anon_chi ep_1718_anon <- ep_1718 %>%   get_anon_chi(chi_var = \"chi\")  # Add anon_chi to the cohort sample chi_cohort <- chi_cohort %>%   get_anon_chi(chi_var = \"upi_number\")"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_has_access.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if the current user is in a UNIX group — check_has_access","title":"Check if the current user is in a UNIX group — check_has_access","text":"Check current user UNIX group","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_has_access.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if the current user is in a UNIX group — check_has_access","text":"","code":"check_has_access(group = \"hscdiip\")"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_has_access.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if the current user is in a UNIX group — check_has_access","text":"group group check, default hscdiip","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_has_access.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if the current user is in a UNIX group — check_has_access","text":"Boolean","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_on_server.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if it's a server session — check_on_server","title":"Check if it's a server session — check_on_server","text":"Check server session","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_on_server.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if it's a server session — check_on_server","text":"","code":"check_on_server()"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_on_server.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if it's a server session — check_on_server","text":"Boolean","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_year.html","id":null,"dir":"Reference","previous_headings":"","what":"Check the year(s) supplied are valid — check_year","title":"Check the year(s) supplied are valid — check_year","text":"Check year(s) supplied valid","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_year.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check the year(s) supplied are valid — check_year","text":"","code":"check_year(year, call = rlang::caller_env())"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_year.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check the year(s) supplied are valid — check_year","text":"year Year file read, can specify multiple years returned one file. converted short FY using format_year(). call Supply environment top-level function make error messages useful.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/check_year.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check the year(s) supplied are valid — check_year","text":"TRUE year valid newer year, FALSE older still valid years. Otherwise throws error.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/chi_cohort.html","id":null,"dir":"Reference","previous_headings":"","what":"A tibble containing an example\ncohort of CHI numbers under different variable names.\nIt is used for testing and to illustrate examples.\nIt is likely that many of the 'chi numbers' are not valid. — chi_cohort","title":"A tibble containing an example\ncohort of CHI numbers under different variable names.\nIt is used for testing and to illustrate examples.\nIt is likely that many of the 'chi numbers' are not valid. — chi_cohort","text":"tibble containing example cohort CHI numbers different variable names. used testing illustrate examples. likely many 'chi numbers' valid.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/chi_cohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A tibble containing an example\ncohort of CHI numbers under different variable names.\nIt is used for testing and to illustrate examples.\nIt is likely that many of the 'chi numbers' are not valid. — chi_cohort","text":"","code":"chi_cohort"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/chi_cohort.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"A tibble containing an example\ncohort of CHI numbers under different variable names.\nIt is used for testing and to illustrate examples.\nIt is likely that many of the 'chi numbers' are not valid. — chi_cohort","text":"object class tbl_df (inherits tbl, data.frame) 100 rows 2 columns.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/demog_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Demographic variables — demog_vars","title":"Demographic variables — demog_vars","text":"vector containing names demographic variables.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/demog_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Demographic variables — demog_vars","text":"","code":"demog_vars"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/demog_vars.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Demographic variables — demog_vars","text":"object class character length 30.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_bedday_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Episode file bedday variables — ep_file_bedday_vars","title":"Episode file bedday variables — ep_file_bedday_vars","text":"vector containing names bedday related variables episode file.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_bedday_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Episode file bedday variables — ep_file_bedday_vars","text":"","code":"ep_file_bedday_vars"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_bedday_vars.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Episode file bedday variables — ep_file_bedday_vars","text":"object class character length 14.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_cost_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Episode file cost variables — ep_file_cost_vars","title":"Episode file cost variables — ep_file_cost_vars","text":"vector containing names cost related variables episode file.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_cost_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Episode file cost variables — ep_file_cost_vars","text":"","code":"ep_file_cost_vars"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_cost_vars.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Episode file cost variables — ep_file_cost_vars","text":"object class character length 14.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Episode file variables — ep_file_vars","title":"Episode file variables — ep_file_vars","text":"names variables episode files, correct order.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Episode file variables — ep_file_vars","text":"","code":"ep_file_vars"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ep_file_vars.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Episode file variables — ep_file_vars","text":"object class character length 239.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/format_year.html","id":null,"dir":"Reference","previous_headings":"","what":"Format a year into the correct short FY format — format_year","title":"Format a year into the correct short FY format — format_year","text":"Format year correct short FY format","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/format_year.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format a year into the correct short FY format — format_year","text":"","code":"format_year(year)"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/format_year.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format a year into the correct short FY format — format_year","text":"year Year file read, can specify multiple years returned one file. converted short FY using format_year().","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/format_year.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format a year into the correct short FY format — format_year","text":"Year correctly formatted short FY e.g. '1718'","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/gen_file_path.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a Source Linkage File, file path — gen_file_path","title":"Generate a Source Linkage File, file path — gen_file_path","text":"Generate Source Linkage File, file path","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/gen_file_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a Source Linkage File, file path — gen_file_path","text":"","code":"gen_file_path(year, file_version, call, dev = FALSE, ext = \"parquet\")"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/gen_file_path.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a Source Linkage File, file path — gen_file_path","text":"year Year file read, can specify multiple years returned one file. converted short FY using format_year(). file_version Version file (individual / episode). call Supply environment top-level function make error messages useful. dev Whether get file development area (/conf/sourcedev/Source_Linkage_File_Updates). default (FALSE) get production file usual area. ext file extension read.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/gen_file_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a Source Linkage File, file path — gen_file_path","text":"fs_path object.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_anon_chi.html","id":null,"dir":"Reference","previous_headings":"","what":"Match on anon_chi to a dataset using CHI numbers — get_anon_chi","title":"Match on anon_chi to a dataset using CHI numbers — get_anon_chi","text":"Match anon_chi dataset using CHI numbers","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_anon_chi.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Match on anon_chi to a dataset using CHI numbers — get_anon_chi","text":"","code":"get_anon_chi(chi_cohort, chi_var = \"chi\", drop = TRUE, check = TRUE)"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_anon_chi.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Match on anon_chi to a dataset using CHI numbers — get_anon_chi","text":"chi_cohort tibble data frame. chi_var CHI variable: name variable containing CHI (default chi). drop Optional boolean indicating whether existing chi_var dropped - default TRUE. check Optional boolean, CHIs checked using phsmethods::chi_check() - default TRUE.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_anon_chi.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Match on anon_chi to a dataset using CHI numbers — get_anon_chi","text":"tibble","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_anon_chi.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Match on anon_chi to a dataset using CHI numbers — get_anon_chi","text":"","code":"if (FALSE) { chi_cohort %>% get_anon_chi() chi_cohort %>% get_anon_chi(chi_var = \"upi_number\") }"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_chi.html","id":null,"dir":"Reference","previous_headings":"","what":"Match on CHI numbers to a dataset using anon_chi — get_chi","title":"Match on CHI numbers to a dataset using anon_chi — get_chi","text":"Match CHI numbers dataset using anon_chi","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_chi.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Match on CHI numbers to a dataset using anon_chi — get_chi","text":"","code":"get_chi(data, anon_chi_var = \"anon_chi\", drop = TRUE)"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_chi.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Match on CHI numbers to a dataset using anon_chi — get_chi","text":"data tibble data frame anon_chi_var Anon CHI variable: name variable containing anonymised CHI (default anon_chi) drop Optional boolean indicating whether existing anon_chi_var dropped - default TRUE","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_chi.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Match on CHI numbers to a dataset using anon_chi — get_chi","text":"tibble","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/get_chi.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Match on CHI numbers to a dataset using anon_chi — get_chi","text":"","code":"if (FALSE) { slf_1718 <- read_slf_individual(\"1718\") get_chi(slf_1718) get_chi(slf_1718, drop = FALSE) }"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/indiv_file_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Individual file variables — indiv_file_vars","title":"Individual file variables — indiv_file_vars","text":"names variables individual files, correct order.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/indiv_file_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Individual file variables — indiv_file_vars","text":"","code":"indiv_file_vars"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/indiv_file_vars.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Individual file variables — indiv_file_vars","text":"object class character length 180.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ltc_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"LTC variables — ltc_vars","title":"LTC variables — ltc_vars","text":"vector containing names Long Term Condition (LTC) variables.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ltc_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"LTC variables — ltc_vars","text":"","code":"ltc_vars"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/ltc_vars.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"LTC variables — ltc_vars","text":"object class character length 19.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/partnerships.html","id":null,"dir":"Reference","previous_headings":"","what":"HSCP name / code lookup — partnerships","title":"HSCP name / code lookup — partnerships","text":"tibble containing names codes (hscp2018 configuration) partnerships. used partnership parameter reading files.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/partnerships.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"HSCP name / code lookup — partnerships","text":"","code":"partnerships"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/partnerships.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"HSCP name / code lookup — partnerships","text":"tibble 31 rows 2 variables: partnership_name official name Partnership hscp2018 hscp2018 standard code S370000??","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf.html","id":null,"dir":"Reference","previous_headings":"","what":"Read a Source Linkage File — read_slf","title":"Read a Source Linkage File — read_slf","text":"Read Source Linkage File","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read a Source Linkage File — read_slf","text":"","code":"read_slf(   year,   file_version = c(\"episode\", \"individual\"),   dev = FALSE,   col_select = NULL,   columns = lifecycle::deprecated(),   as_data_frame = TRUE,   partnerships = NULL,   recids = NULL )"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read a Source Linkage File — read_slf","text":"year Year file read, can specify multiple years returned one file. converted short FY using format_year(). file_version Version file (individual / episode). dev Whether get file development area (/conf/sourcedev/Source_Linkage_File_Updates). default (FALSE) get production file usual area. col_select character vector column names keep, \"select\" argument data.table::fread(), tidy selection specification columns, used dplyr::select(). columns columns longer used, use col_select instead. as_data_frame function return tibble (default) Arrow Table? partnerships Optional specify partnership (hscp2018) partnerships select. recids Optional specify recid recids select.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read a Source Linkage File — read_slf","text":"requested SLF data tibble Arrow Table.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_episode.html","id":null,"dir":"Reference","previous_headings":"","what":"Read a Source Linkage episode file — read_slf_episode","title":"Read a Source Linkage episode file — read_slf_episode","text":"Read Source Linkage episode file","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_episode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read a Source Linkage episode file — read_slf_episode","text":"","code":"read_slf_episode(   year,   col_select = NULL,   partnerships = NULL,   recids = NULL,   as_data_frame = TRUE,   dev = FALSE,   columns = lifecycle::deprecated() )"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_episode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read a Source Linkage episode file — read_slf_episode","text":"year Year file read, can specify multiple years returned one file. converted short FY using format_year(). col_select character vector column names keep, \"select\" argument data.table::fread(), tidy selection specification columns, used dplyr::select(). partnerships Optional specify partnership (hscp2018) partnerships select. recids Optional specify recid recids select. as_data_frame function return tibble (default) Arrow Table? dev Whether get file development area (/conf/sourcedev/Source_Linkage_File_Updates). default (FALSE) get production file usual area. columns columns longer used, use col_select instead.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_episode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read a Source Linkage episode file — read_slf_episode","text":"requested SLF data tibble Arrow Table.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_episode.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read a Source Linkage episode file — read_slf_episode","text":"","code":"if (FALSE) { read_slf_episode(\"1718\",   col_select = c(\"anon_chi\", \"dob\", \"demographic_cohort\") )  read_slf_episode(c(\"1718\", \"1819\"),   col_select = c(\"anon_chi\", \"dob\", \"demographic_cohort\"),   as_data_frame = FALSE ) }"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_individual.html","id":null,"dir":"Reference","previous_headings":"","what":"Read a Source Linkage individual file — read_slf_individual","title":"Read a Source Linkage individual file — read_slf_individual","text":"Read Source Linkage individual file","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_individual.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read a Source Linkage individual file — read_slf_individual","text":"","code":"read_slf_individual(   year,   col_select = NULL,   partnerships = NULL,   as_data_frame = TRUE,   dev = FALSE,   columns = lifecycle::deprecated() )"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_individual.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read a Source Linkage individual file — read_slf_individual","text":"year Year file read, can specify multiple years returned one file. converted short FY using format_year(). col_select character vector column names keep, \"select\" argument data.table::fread(), tidy selection specification columns, used dplyr::select(). partnerships Optional specify partnership (hscp2018) partnerships select. as_data_frame function return tibble (default) Arrow Table? dev Whether get file development area (/conf/sourcedev/Source_Linkage_File_Updates). default (FALSE) get production file usual area. columns columns longer used, use col_select instead.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_individual.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read a Source Linkage individual file — read_slf_individual","text":"requested SLF data tibble Arrow Table.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/read_slf_individual.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read a Source Linkage individual file — read_slf_individual","text":"","code":"if (FALSE) { read_slf_individual(\"1718\",   col_select = c(\"anon_chi\", \"dob\", \"hri_scot\") ) read_slf_individual(c(\"1718\", \"1819\"),   col_select = c(\"anon_chi\", \"dob\", \"hri_scot\"),   as_data_frame = FALSE ) }"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/recids.html","id":null,"dir":"Reference","previous_headings":"","what":"Recid name / description lookup — recids","title":"Recid name / description lookup — recids","text":"tibble containing names description recids. used recid parameter reading episode files.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/recids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Recid name / description lookup — recids","text":"","code":"recids"},{"path":"https://public-health-scotland.github.io/slfhelper/reference/recids.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Recid name / description lookup — recids","text":"tibble 18 rows 2 variables: recid short-form recid Description description recid","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/reference/slfhelper-package.html","id":null,"dir":"Reference","previous_headings":"","what":"slfhelper: Useful functions for working with the Source Linkage Files — slfhelper-package","title":"slfhelper: Useful functions for working with the Source Linkage Files — slfhelper-package","text":"package provides helper functions working Source Linkage Files (SLFs). functions mainly focused making first steps analysis easier. can read filter files efficiently using minimal code.","code":""},{"path":[]},{"path":"https://public-health-scotland.github.io/slfhelper/reference/slfhelper-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"slfhelper: Useful functions for working with the Source Linkage Files — slfhelper-package","text":"Maintainer: Megan McNicol megan.mcnicol2@phs.scot Authors: James McMahon james.mcmahon@phs.scot (ORCID) contributors: Public Health Scotland phs.source@phs.scot [copyright holder]","code":""},{"path":[]},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-0100","dir":"Changelog","previous_headings":"","what":"slfhelper 0.10.0","title":"slfhelper 0.10.0","text":"{glue} longer dependency required functionality can provided `stringr::str_glue(). Dependency versions updated latest. get_chi() get_anon_chi() now properly match missing (NA) blank (\"\") values. slfhelper now defaults using .parquet file versions, old versions slfhelper longer work. now dev parameter available using read_slf_* functions allows reading file development environment.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-090","dir":"Changelog","previous_headings":"","what":"slfhelper 0.9.0","title":"slfhelper 0.9.0","text":"{openssl} now required. get_chi() get_anon_chi() now much faster (>100X) use significantly less memory. year parameter now checked early process, invalid year supplied error message much informative.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-082","dir":"Changelog","previous_headings":"","what":"slfhelper 0.8.2","title":"slfhelper 0.8.2","text":"ep_file_vars indiv_file_vars updated correct variables.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-081","dir":"Changelog","previous_headings":"","what":"slfhelper 0.8.1","title":"slfhelper 0.8.1","text":"Use cli nicer error messages warning.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-080","dir":"Changelog","previous_headings":"","what":"slfhelper 0.8.0","title":"slfhelper 0.8.0","text":"Add number ‘variable packs’ easily selecting sets variables: demog_vars, ltc_vars, ep_file_bedday_vars ep_file_cost_vars. Add new vignette introducing variable packs.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-071","dir":"Changelog","previous_headings":"","what":"slfhelper 0.7.1","title":"slfhelper 0.7.1","text":"Add check server hscdiip access package load. Add recid lookup use recid filtering parameter. using get_anon_chi() now use phsmethods::chi_check (available) warn lot CHI numbers return invalid. Update variable lists new Home Care related variables.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-070","dir":"Changelog","previous_headings":"","what":"slfhelper 0.7.0","title":"slfhelper 0.7.0","text":"Now depends R >= 3.5 ep_file_vars indiv_file_vars updated latest variable names. now also return character vector instead list. read_slf_ now returns tibble.","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-060","dir":"Changelog","previous_headings":"","what":"slfhelper 0.6.0","title":"slfhelper 0.6.0","text":"Fix bug selecting partnerships/recids also selecting multiple years (#13) (#14)","code":""},{"path":"https://public-health-scotland.github.io/slfhelper/news/index.html","id":"slfhelper-053","dir":"Changelog","previous_headings":"","what":"slfhelper 0.5.3","title":"slfhelper 0.5.3","text":"Added NEWS.md file track changes package. Moved use Rmd version readme. Bump dplyr version requirement 1.0.0 enable use across() new things. Add checks year","code":""}]