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getting_started/compile.html

@@ -221,7 +221,7 @@ <h2 id="toc-title">Table of content</h2>
 
   <ul>
   <li><a href="#out-of-the-box-compilation" id="toc-out-of-the-box-compilation" class="nav-link active" data-scroll-target="#out-of-the-box-compilation">Out-of-the-box compilation</a></li>
-  <li><a href="#customise-generated-linelists" id="toc-customise-generated-linelists" class="nav-link" data-scroll-target="#customise-generated-linelists">Customise generated linelists</a>
+  <li><a href="#extra-customisations" id="toc-extra-customisations" class="nav-link" data-scroll-target="#extra-customisations">Extra customisations</a>
   <ul>
   <li><a href="#change-style" id="toc-change-style" class="nav-link" data-scroll-target="#change-style">Change style</a></li>
   <li><a href="#import-a-geobase" id="toc-import-a-geobase" class="nav-link" data-scroll-target="#import-a-geobase">Import a geobase</a></li>
@@ -288,8 +288,8 @@ <h2 class="anchored" data-anchor-id="out-of-the-box-compilation">Out-of-the-box
 </figure>
 </div>
 </section>
-<section id="customise-generated-linelists" class="level2">
-<h2 class="anchored" data-anchor-id="customise-generated-linelists">Customise generated linelists</h2>
+<section id="extra-customisations" class="level2">
+<h2 class="anchored" data-anchor-id="extra-customisations">Extra customisations</h2>
 <p>There are a couple of extra steps you can take.</p>
 <div id="fig-setup-ribbon" class="quarto-float quarto-figure quarto-figure-center anchored" data-fig-align="center">
 <figure class="quarto-float quarto-float-fig figure">
@@ -307,7 +307,7 @@ <h3 class="anchored" data-anchor-id="change-style">Change style</h3>
 </section>
 <section id="import-a-geobase" class="level3">
 <h3 class="anchored" data-anchor-id="import-a-geobase">Import a geobase</h3>
-<p>If you are compiling a linelist for a given country, you could generate the linelist with the geobase already imported. Click on the “Import de geobase” button to import a geobase in excel format (learn <a href="../how_to/import_geobase#sec-geobase-download">how to get</a> a geobase) before compiling.</p>
+<p>If you are compiling a linelist for a given country, you could generate the linelist with the geobase already imported. Click on the “Import de geobase” button to import a geobase in excel format (learn <a href="../how_to/import_geobase#sec-geobase-download">how to get a geobase</a>) before compiling.</p>
 <div class="callout callout-style-default callout-note callout-titled">
 <div class="callout-header d-flex align-content-center">
 <div class="callout-icon-container">
@@ -340,14 +340,14 @@ <h2 class="anchored" data-anchor-id="advanced-customisations">Advanced customisa
 </section>
 <section id="compilation-advice" class="level2">
 <h2 class="anchored" data-anchor-id="compilation-advice">Compilation advice</h2>
-<p>The linelist compilation relies on Excel VBA and can be a litle bit finicky. Here is some advice.</p>
+<p>The linelist compilation relies on Excel VBA and can be a bit <em>finicky.</em> Here is some advice.</p>
 <ul>
-<li><p><a href="../reference/ribbons.html#sec-check-setup">Run the checks</a> on the setup before attempting compilation to verify that everything is good.</p></li>
-<li><p>Make sure there are no hidden columns or filters on the sheets of the setup.</p></li>
+<li><p><a href="../reference/ribbons.html#sec-check-setup">Run the checks</a> on the setup before attempting compilation to verify that everything is ready.</p></li>
+<li><p>Make sure there are no hidden columns or filters on the sheets of the <strong>setup file</strong>.</p></li>
 <li><p>Pause Onedrive or work in a non-synchronised folder (see <a href="../getting_started/create_dic.html#sec-get-tools-ready">here</a> for more information)</p></li>
 <li><p>The compilation is sensitive to RAM limitations: if it fails it might be worth closing a couple of greedy applications and try again.<a href="#fn2" class="footnote-ref" id="fnref2" role="doc-noteref"><sup>2</sup></a></p></li>
 <li><p>In general, it is always worth trying again: sometimes an action you did in another applications perturbed the process.</p></li>
-<li><p>If it fails, start with a new designer file, in case the other got corrupted when compilation fails.</p></li>
+<li><p>If it fails, start with a new designer file, in case the previous one got corrupted when compilation failed.</p></li>
 <li><p>Excel VBA sometimes interact with other Office applications. If all goes well, no problem. But in case of unexpected failures, try avoiding using Office applications while compiling.</p></li>
 </ul>
 <div class="callout callout-style-default callout-tip callout-titled">
@@ -360,7 +360,7 @@ <h2 class="anchored" data-anchor-id="compilation-advice">Compilation advice</h2>
 </div>
 </div>
 <div class="callout-body-container callout-body">
-<p>One of the writer of this guide prepares the setup, the designer, and then copy both of them and use the copies to compile. If a compilation fails, delete both copies and start from fresh, just in case the failure to compile corrupted any of the file.</p>
+<p>I prepare the <strong>setup file</strong>, the <strong>designer file</strong>, and then copy both of them and use the copies to compile. If a compilation fails, I delete both copies and start from fresh, just in case the failure to compile corrupted any of the file.</p>
 </div>
 </div>
 

how_to/import_geobase.html

@@ -252,9 +252,9 @@ <h2 class="anchored" data-anchor-id="sec-geobase-download">Download a geobase</h
 <ol type="1">
 <li><p>In you internet browser, go to the <a href="https://reports.msf.net/secure/app/outbreak-tools-geoapp">Geoapp</a>.</p></li>
 <li><p>Use your account to connect. If you do not have one already, create one <a href="https://reports.msf.net/signup/">here</a> first then connect to the Geoapp.</p></li>
-<li><p>Select one or more countries from the dropdown menu in the top left of the screen. The Admin 1 regions of each country will be rendered on the map.</p></li>
-<li><p>Click on the regions you require geo data for. Once clicked, the region will turn red to indicate it has been selected. Alternatively, to select all regions currently rendered on the map, click the “Select all regions” button under the country dropdown menu. Once at least one region has been selected, buttons to inspect and download the data will appear below the country dropdown menu.</p></li>
-<li><p>Clicking the “Download Geobase” button will download the data for the selected regions in the excel format that can be directly imported into an Outbreak Tools Linelist.</p></li>
+<li><p>Select one <em>or more</em> countries from the dropdown menu in the top left of the screen. The Admin 1 regions of each country will be rendered on the map.</p></li>
+<li><p>Click on the regions you require geo data for. Selected regions turn red. If you want to select the whole country, click the “Select all regions” button under the country dropdown menu. Once one region has been selected, buttons to inspect and download the data will appear below the country dropdown menu.</p></li>
+<li><p>Clicking the “Download Geobase” button to download the data for the selected regions in an excel format that can be directly imported into an OutbreakTools Linelist.</p></li>
 </ol>
 <div class="callout callout-style-default callout-note callout-titled">
 <div class="callout-header d-flex align-content-center">
@@ -266,7 +266,7 @@ <h2 class="anchored" data-anchor-id="sec-geobase-download">Download a geobase</h
 </div>
 </div>
 <div class="callout-body-container callout-body">
-<p>The geospatial administrative boundary data used to build the Geobase can also be downloaded in the format of your choice, compatible with GIS software (e.g.&nbsp;QGIS, ArcGIS) and the R statistical software by clicking on the “Download geo Data” button</p>
+<p>The geospatial administrative boundary data used to build the geobase can also be downloaded in the format of your choice, compatible with GIS software (e.g.&nbsp;QGIS, ArcGIS) and the R statistical software by clicking on the “Download geo Data” button.</p>
 </div>
 </div>
 <div class="callout callout-style-default callout-tip callout-titled">
@@ -285,6 +285,12 @@ <h2 class="anchored" data-anchor-id="sec-geobase-download">Download a geobase</h
 </section>
 <section id="sec-geobase-import" class="level2">
 <h2 class="anchored" data-anchor-id="sec-geobase-import">Import a geobase in a linelist</h2>
+<p>Once you have downloaded a geobase from the <a href="https://reports.msf.net/secure/app/outbreak-tools-geoapp">Geoapp</a>, you can import it in an OBT linelist.</p>
+<ol type="1">
+<li>Open the linelist</li>
+<li>Go to the <a href="../reference/ribbons.qmdsec-linelist-ribbon">OutbreakTools Menu</a></li>
+<li>Click on the <a href="../reference/ribbons.html#sec-import-geobase">“Import geobase” button</a></li>
+</ol>
 
 
 </section>

how_to/show_hide_variables.html

@@ -240,7 +240,14 @@ <h1 class="title">Show or hide variables</h1>
 </header>
 
 
-<p>TODO</p>
+<p>TODO (copied stuff en vrac)</p>
+<p>Clicking on the “Show/hide variables” button opens a window listing all the variables in this linelist sheet.</p>
+<div class="quarto-figure quarto-figure-center">
+<figure class="figure">
+<p><img src="../reference/images/img-012-ll-show-hide.png" class="img-fluid figure-img"></p>
+<figcaption>OutbreakTools tab in the created linelist</figcaption>
+</figure>
+</div>
 <p><strong>1</strong></p>
 <p>The “optional, hidden” variables in the <strong>setup file</strong> appear as “Hidden” (by default). However, the user can change the status by choosing “Show”, in which case the column will become visible. <img src="images/im-027-example.png" class="img-fluid"></p>
 <p><strong>2</strong> <img src="images/im-028-example.png" class="img-fluid"></p>

reference/dictionary_sheet.html

@@ -262,7 +262,7 @@ <h2 id="toc-title">Table of content</h2>
   <li><a href="#sec-custom-dropdowns" id="toc-sec-custom-dropdowns" class="nav-link" data-scroll-target="#sec-custom-dropdowns">choice_custom</a></li>
   <li><a href="#sec-list-auto" id="toc-sec-list-auto" class="nav-link" data-scroll-target="#sec-list-auto">list_auto</a></li>
   </ul></li>
-  <li><a href="#sec-geo-data" id="toc-sec-geo-data" class="nav-link" data-scroll-target="#sec-geo-data">Special case of amdinistrative levels and health facilities</a>
+  <li><a href="#sec-geo-data" id="toc-sec-geo-data" class="nav-link" data-scroll-target="#sec-geo-data">Special case of administrative levels and health facilities</a>
   <ul class="collapse">
   <li><a href="#sec-geo-variable" id="toc-sec-geo-variable" class="nav-link" data-scroll-target="#sec-geo-variable">geo</a></li>
   <li><a href="#hf" id="toc-hf" class="nav-link" data-scroll-target="#hf">hf</a></li>
@@ -688,9 +688,9 @@ <h3 class="anchored" data-anchor-id="status">Status</h3>
 <li><p><em>mandatory</em>: variable displayed by default, <strong>it cannot be hidden</strong> in the linelist</p></li>
 <li><p><em>optional, visible</em>: variable displayed by default, it can be displayed or hidden by the linelist user</p></li>
 <li><p><em>optional, hidden</em>: variable hidden by default, it can be displayed or hidden by the linelist user</p></li>
-<li><p><em>hidden</em>: variable hidden by default, it cannot be displayed in the linelis</p></li>
+<li><p><em>hidden</em>: variable hidden by default, it cannot be displayed in the linelist</p></li>
 </ul>
-<p>Variables can be shown or hidden using the <a href="../how_to/show_hide_variables.html"><em>Show/Hide</em> button</a> in the <strong>linelist file</strong>.</p>
+<p>Variables can be shown or hidden using the “Show/Hide” button of the <a href="../reference/ribbons.html#sec-linelist-ribbon">linelist OutbreakTools menu</a> in the <strong>linelist file</strong>. See the <a href="../how_to/show_hide_variables.html">how to</a>.</p>
 <div class="callout callout-style-default callout-note callout-titled">
 <div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-13-contents" aria-controls="callout-13" aria-expanded="false" aria-label="Toggle callout">
 <div class="callout-icon-container">
@@ -958,7 +958,7 @@ <h5 class="anchored" data-anchor-id="sec-list-auto">list_auto</h5>
 </section>
 </section>
 <section id="sec-geo-data" class="level4">
-<h4 class="anchored" data-anchor-id="sec-geo-data">Special case of amdinistrative levels and health facilities</h4>
+<h4 class="anchored" data-anchor-id="sec-geo-data">Special case of administrative levels and health facilities</h4>
 <p>Two controls allow the user of the linelist to enter geographic information, or information about health facilities. While the created variables are technically dropdown menus, they are treated as a special type of variables in OubtbreakTools linelists, with dedicated tools and analyses.</p>
 <p>OutbreakTool linelists all have a button to <a href="../how_to/import_geobase.html">import a geobase</a>, a standardised file containing lists of administrative levels to describe places. Once the geobase is successfully imported, the values from its lists populate specific dropdown menus.</p>
 <section id="sec-geo-variable" class="level5">