Fix links and update figures (#26)

ASReviewLAB.qmd

@@ -105,7 +105,7 @@ bottom right corner.
 Select Validation Mode, fill out a project name and press ‘NEXT’. Note
 that you can fill out your name and a description as well.
 
-![](images/ASReviewLAB/Interface3.png){width=95%}
+![](https://raw.githubusercontent.com/asreview/asreview/main/docs/images/setup_project_modes.png){width=95%}
 
 For this exercise we are screening in the so-called ‘Validation Mode’
 of ASReview. By screening in the [Validation
@@ -189,7 +189,7 @@ To add the relevant records, you click on ‘Search’, copy and paste the title
 of these relevant records one by one in the search bar and add them as
 relevant.
 
-![](images/ASReviewLAB/Interface7.png){width=95%}
+![](https://raw.githubusercontent.com/asreview/asreview/main/docs/images/setup_prior_knowledge_random_validate.png){width=95%}
 
 
 After adding all five relevant records, you can add some irrelevant ones
@@ -343,7 +343,7 @@ Some suggestions:
     Github… +1 for open-science!)
 
 
-![](images/ASReviewLAB/card_game.png){width=95%}
+![](https://raw.githubusercontent.com/asreview/asreview/main/docs/images/game.png){width=95%}
 
 [^1]: Wang Z, Nayfeh T, Tetzlaff J, O’Blenis P, Murad MH (2020) Error
     rates of human reviewers during abstract screening in systematic

_quarto.yml

@@ -12,10 +12,9 @@ website:
    pinned: true
    align: left
    tools:
-      - icon: github
-        align: left
-        href: https://github.com/asreview/asreview-academy/
-        text: "GitHub organization"
+     - icon: github
+       href: https://github.com/asreview/asreview-academy/
+       text: "GitHub organization"
    style: "docked"
    search: true
    collapse-level: 1

docs/ASReviewLAB.html

@@ -121,7 +121,7 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation docked overflow-auto">
-    <div class="pt-lg-2 mt-2 text-center sidebar-header">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
       <a href="./index.html" class="sidebar-logo-link">
       <img src="./images/ASReviewLAB/Elas_afstudeerhoedje.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
       </a>
@@ -280,8 +280,8 @@ <h3 class="anchored" data-anchor-id="step-3-creating-a-project">Step 3: Creating
 <li><em>Project name;</em></li>
 </ol>
 <p>Select Validation Mode, fill out a project name and press ‘NEXT’. Note that you can fill out your name and a description as well.</p>
-<p><img src="images/ASReviewLAB/Interface3.png" class="img-fluid" style="width:95.0%"></p>
-<p>For this exercise we are screening in the so-called Validation Mode’ of ASReview. By screening in the <a href="https://asreview.readthedocs.io/en/latest/project_create.html#project-modes" target="_blank">Validation Mode</a>, we are going to make use of a <a href="https://asreview.readthedocs.io/en/latest/data_labeled.html#fully-labeled-data" target="_blank">benchmark dataset</a>. This means that all records in the dataset have already been labeled as relevant or irrelevant. This is indicated to the user through a banner above each article. Note that in ‘Oracle Mode’ - when screening your own dataset - the relevant papers will not be marked; you, the oracle, have to make the decisions.</p>
+<p><img src="https://raw.githubusercontent.com/asreview/asreview/main/docs/images/setup_project_modes.png" class="img-fluid" style="width:95.0%"></p>
+<p>For this exercise we are screening in the so-called ‘Validation Mode’ of ASReview. By screening in the <a href="https://asreview.readthedocs.io/en/latest/project_create.html#project-modes" target="_blank">Validation Mode</a>, we are going to make use of a <a href="https://asreview.readthedocs.io/en/latest/data_labeled.html#fully-labeled-data" target="_blank">benchmark dataset</a>. This means that all records in the dataset have already been labeled as relevant or irrelevant. This is indicated to the user through a banner above each article. Note that in ‘Oracle Mode’ - when screening your own dataset - the relevant papers will not be marked; you, the oracle, have to make the decisions.</p>
 <p>More detailed information about setting up a project can be found on <a href="https://asreview.readthedocs.io/en/latest/project_create.html#project-information" target="_blank">ReadTheDocs</a>.</p>
 <p><em>Have you started creating a new project? If so, you can proceed to step 4!</em></p>
 </section>
@@ -290,7 +290,7 @@ <h3 class="anchored" data-anchor-id="step-3-creating-a-project">Step 3: Creating
 <h2 class="anchored" data-anchor-id="project-setup">Project setup</h2>
 <section id="step-4-the-dataset" class="level3">
 <h3 class="anchored" data-anchor-id="step-4-the-dataset">Step 4: The dataset</h3>
-<p>Now that you have created your ASReview project (woohoo!), you need to set it up.Without data, we have nothing to screen. So, you need to tell ELAS which dataset you want to screen for relevant articles.</p>
+<p>Now that you have created your ASReview project (woohoo!), you need to set it up. Without data, we have nothing to screen. So, you need to tell ELAS which dataset you want to screen for relevant articles.</p>
 <p>Click on the ‘ADD’ button next to ‘Add dataset’. Now a menu appears where you can choose how to load the dataset. You can add your dataset by selecting a file or providing an URL. For this exercise, we will use a benchmark dataset.</p>
 <p>Go to the ‘Benchmark datasets’ button, open the first dataset (i.e.&nbsp;the Van de Schoot (2017) dataset about PTSD trajectories) and click on ‘SELECT’. After you select the dataset, click on ‘SAVE’.</p>
 <p><img src="images/ASReviewLAB/Interface5.png" class="img-fluid" style="width:95.0%"></p>
@@ -310,7 +310,7 @@ <h3 class="anchored" data-anchor-id="step-5-prior-knowledge">Step 5: Prior knowl
 <li>Trajectories of trauma symptoms and resilience in deployed US military service members: Prospective cohort study (DOI: <a href="https://doi.org/10.1192/bjp.bp.111.096552" target="_blank">10.1192/bjp.bp.111.096552</a>)</li>
 </ul>
 <p>To add the relevant records, you click on ‘Search’, copy and paste the titles of these relevant records one by one in the search bar and add them as relevant.</p>
-<p><img src="images/ASReviewLAB/Interface7.png" class="img-fluid" style="width:95.0%"></p>
+<p><img src="https://raw.githubusercontent.com/asreview/asreview/main/docs/images/setup_prior_knowledge_random_validate.png" class="img-fluid" style="width:95.0%"></p>
 <p>After adding all five relevant records, you can add some irrelevant ones by clicking the ‘Random’ button (use the arrow in the upper left corner to be able to select this button) and by changing ‘relevant’ to ‘irrelevant’. Select five irrelevant records and click on ‘CLOSE’.</p>
 <p><em>Have you selected five relevant and five irrelevant records? If so, you can proceed to step 6!</em></p>
 </section>
@@ -364,7 +364,7 @@ <h2 class="anchored" data-anchor-id="whats-next">What’s next?</h2>
 <li><p>Ready to start your own project? Upload <a href="https://asreview.readthedocs.io/en/latest/data.html" target="_blank">your own data</a> and start screening in the Oracle mode!</p></li>
 <li><p>Try to find the hidden memory game in ASReview (some people found it by going through the <a href="https://github.com/asreview/asreview/tree/master/asreview" target="_blank">source code</a> on Github… +1 for open-science!)</p></li>
 </ul>
-<p><img src="images/ASReviewLAB/card_game.png" class="img-fluid" style="width:95.0%"></p>
+<p><img src="https://raw.githubusercontent.com/asreview/asreview/main/docs/images/game.png" class="img-fluid" style="width:95.0%"></p>
 
 
 </section>

docs/LICENSE.html

@@ -86,7 +86,7 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation docked overflow-auto">
-    <div class="pt-lg-2 mt-2 text-center sidebar-header">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
       <a href="./index.html" class="sidebar-logo-link">
       <img src="./images/ASReviewLAB/Elas_afstudeerhoedje.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
       </a>

docs/datatools.html

@@ -121,7 +121,7 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation docked overflow-auto">
-    <div class="pt-lg-2 mt-2 text-center sidebar-header">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
       <a href="./index.html" class="sidebar-logo-link">
       <img src="./images/ASReviewLAB/Elas_afstudeerhoedje.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
       </a>
@@ -234,17 +234,18 @@ <h3 class="anchored" data-anchor-id="step-1-create-a-folder-structure">Step 1: C
 <h3 class="anchored" data-anchor-id="step-2-choose-a-dataset">Step 2: Choose a dataset</h3>
 <p>Before we get started, we need a dataset that is already labeled. You can use a dataset from the SYNERGY dataset via the synergy-dataset Python package.</p>
 <ol type="1">
-<li><p><em>Open the command prompt, by typing ‘cmd’ (for Windows) or ‘terminal’ (for Apple) in your computer’s search bar;</em></p></li>
+<li><p><em>Open the command prompt, by typing ‘cmd’ (for Windows) or ‘terminal’ (for MacOS) in your computer’s search bar;</em></p></li>
 <li><p><em>Navigate to the folder structure;</em></p></li>
 </ol>
 <p>You can navigate to your folder structure with:</p>
 <div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> <span class="pp">[</span><span class="ss">file_path</span><span class="pp">]</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<p>For MacOS: 1. Right-click on created folder. 2. Click “New Terminal at Folder”. Then the data set will be automatically be put into the designated data folder.</p>
 <ol start="3" type="1">
 <li><em>Install the synergy-dataset Python package with:</em></li>
 </ol>
 <div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pip</span> install synergy-dataset</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <ol start="4" type="1">
-<li><em>Built the dataset.</em></li>
+<li><em>Build the dataset.</em></li>
 </ol>
 <p>To download and build the SYNERGY dataset, run the following command in the command line:</p>
 <div class="sourceCode" id="cb3"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="ex">python</span> <span class="at">-m</span> synergy_dataset get <span class="at">-o</span> data</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
@@ -256,7 +257,7 @@ <h3 class="anchored" data-anchor-id="step-3-write-and-run-the-script">Step 3: Wr
 <div class="sourceCode" id="cb4"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pip</span> install asreview-datatools</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <p>Note: if you installed ASReview datatools before, make sure you install the latest version. You can do so with:</p>
 <div class="sourceCode" id="cb5"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pip</span> install <span class="at">--upgrade</span> asreview-datatools</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-<p>Before you are going to write your script, here is a general explaination of how you can get started with ASReview datatools. The parts between the brackets need to be filled out by you when using ASReview Datatools.</p>
+<p>Before you are going to write your script, here is a general explanation of how you can get started with ASReview datatools. The parts between the brackets need to be filled out by you when using ASReview Datatools.</p>
 <div class="sourceCode" id="cb6"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="ex">asreview</span> data <span class="pp">[</span><span class="ss">name_of_tool</span><span class="pp">]</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <p>where <code>[name_of_tool]</code> is the name of the tool you want to use (<code>describe</code>, <code>convert</code>, <code>dedup</code>, <code>vstack</code>, or <code>compose</code>) followed by positional arguments and optional arguments.</p>
 <p>Each tool has its own help description which is available with:</p>
@@ -271,7 +272,7 @@ <h3 class="anchored" data-anchor-id="tool-1-describe">Tool 1: Describe</h3>
 </section>
 <section id="tool-2-compose" class="level3">
 <h3 class="anchored" data-anchor-id="tool-2-compose">Tool 2: Compose</h3>
-<p>Next, you are going to compose a dataset out of two datasets; a labeled and an unlabeled dataset. The code starts similary to the code of the Describe tool (<code>asreview data compose</code>), but now the output path should always be specified (<code>output/[name_of_your_output_file.csv]</code>) and you need to assign a corresponsing proporty to the datasets you want to merge. The labeled dataset you need to assign the argument <code>-l</code> and the unlabeled dataset you need to assign a <code>-u</code>.</p>
+<p>Next, you are going to compose a dataset out of two datasets; a labeled and an unlabeled dataset. The code starts similarly to the code of the Describe tool (<code>asreview data compose</code>), but now the output path should always be specified (<code>output/[name_of_your_output_file.csv]</code>) and you need to assign a corresponding property to the datasets you want to merge. To the labeled dataset you need to assign the argument <code>-l</code>, and to the unlabeled dataset you need to assign a <code>-u</code>.</p>
 <p>Furthermore, in case of conflict, you need to determine which label to keep (<code>-c</code>). Let’s say you want to keep one of the labels, you can do so with the <code>keep_one</code> command. By default the hierarchy in determining which label to keep is: relevant, irrelevant, unlabeled.</p>
 <p>See the <a href="https://github.com/asreview/asreview-datatools#data-compose-experimental" target="_blank">Datatools README</a> for other possible arguments.</p>
 <p>You can compose a dataset with:</p>

docs/index.html

@@ -86,7 +86,7 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation docked overflow-auto">
-    <div class="pt-lg-2 mt-2 text-center sidebar-header">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
       <a href="./index.html" class="sidebar-logo-link">
       <img src="./images/ASReviewLAB/Elas_afstudeerhoedje.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
       </a>