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script.js
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function toggleMenu(menuHeader) {
const submenu = menuHeader.nextElementSibling;
submenu.style.display = submenu.style.display === 'block' ? 'none' : 'block';
}
function loadContent(page) {
const content = {
overview: `
<h3 class="sidebar-title">Version: 3 October 2024 </h3>
<h3 class="sidebar-title">Authors: Mohamed Sillah Kanu, Sammy Oppong, Jaline Gerardin </h3>
<h2>Overview</h2>
<h3>Motivation</h3>
<p>SNT is here to stay: many NMCPs have found it useful and are continuing to embrace it and further develop it for their analytical needs. Since 2019, multiple individuals have supported the analysis portions of SNT. In most cases, individuals have built their own code in a variety of languages (Stata, R, and Python), sometimes building on others’ previous code and sometimes re-developed independently.
As SNT matures, more quality assurance is needed such that NMCPs can be confident that the analysis they use to inform their decisions is of high quality regardless of the individual supporting analyst. The continued rollout of SNT also means that analysis can become more efficient if analysts are better able to build on each other’s work rather than tempted to reinvent what has already been developed. Lastly, SNT analysis can become much more accessible if there is a common resource available to help those with intermediate coding skills quickly access the collective knowledge of the SNT analyst community.
.</p>
<h3>Objectives</h3>
<p>We will build a code library for SNT analysis to:
<p>1. Improve quality and reproducibility of SNT analysis by ensuring that analysts are using similar, correct approaches.</p>
<p>2. Improve efficiency of SNT analysis by minimizing duplication of effort.</p>
<p>3. Promote accessibility of SNT analysis by lowering barriers to entry.</p>
<h3>Target audience</h3>
<p>Anyone doing this kind of work. We assume some basic knowledge of Python, some understanding of the data, and a strong connection to the NMCP.</p>
<h3>Scope</h3>
<p>All analysis steps of SNT up to but not including mathematical modeling; some related analysis.</p>
`,
shapefiles: `
<div class="fixed-buttons">
<button class="text-button" onclick="scrollToSection('stepByStep')">Step by step</button>
<button class="text-button" onclick="scrollToSection('fullCode')">Full code</button>
</div>
<h3>A. Data Assembly and Management>A.1 Shapefiles</h3>
<h4 id="stepByStep">Step by step approach</h4>
<p>This section explains the workflow of importing and managing shapefiles using Python.</p>
<h5>Step 1: Install Necessary Libraries</h5>
<p>Before starting, ensure you have the required Python packages installed.</p>
<p>This can be done using the following code:</p>
<pre><code>
# Install necessary libraries
pip install geopandas matplotlib pandas
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p>This code installs the <code>geopandas</code> package for handling spatial data, <code>matplotlib</code> for data visualization, and <code>pandas</code> for data manipulation.</p>
<h3>Step 2: Load Necessary Libraries</h3>
<p>After installing the libraries, you need to load them into your Python environment:</p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
# Load necessary libraries
import geopandas as gpd
import pandas as pd
import matplotlib.pyplot as plt
</code></pre>
<p>This step makes the functions from these libraries available for use in your script.</p>
<h3>Step 3: Import Shapefiles</h3>
<p>You can import shapefiles using the <code>read_file</code> function from the <code>geopandas</code> package. Here’s a function to do that:</p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
# Import Shapefiles
def import_shapefile(filepath):
shapefile = gpd.read_file(filepath) # Read the shapefile
return shapefile # Return the loaded shapefile
</code></pre>
<p>This function takes a file path as input, reads the shapefile, and returns it as a spatial object.</p>
<h3>Step 4: Rename and Match Names</h3>
<p>Sometimes, the columns in your shapefile may need to be renamed for clarity or to match other datasets. You can do this as follows:</p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
# Rename and Match Names
def rename_shapefile_columns(shapefile, new_names):
shapefile.columns = new_names # Rename columns
return shapefile # Return the renamed shapefile
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p>This function takes a shapefile and a list of new names, renaming the columns accordingly.</p>
<h3>Step 5: Link Shapefiles to Relevant Scales</h3>
<p>Link your shapefile to relevant scales or metadata by merging it with another data frame:</p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
# Link Shapefiles to Relevant Scales
def link_shapefiles_to_scales(shapefile, scales_df, link_col):
linked_shapefile = shapefile.merge(scales_df, on=link_col) # Merge shapefile with scales
return linked_shapefile # Return the linked shapefile
</code></pre>
<p>This function performs a merge between the shapefile and a data frame containing scale information based on a specified linking column.</p>
<h3>Step 6: Visualizing Shapefiles and Making Basic Maps</h3>
<p>Finally, you can visualize the shapefile using <code>matplotlib</code> and <code>geopandas</code>. Here’s a function to do that:</p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
# Visualizing Shapefiles and Making Basic Maps
def visualize_shapefile(shapefile, variable):
shapefile.plot(column=variable, cmap='viridis', legend=True)
plt.title(f'Shapefile Visualization: {variable}')
plt.show()
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p>This function creates a simple map visualization using the spatial data. Replace <code>variable</code> with the name of the variable you want to visualize in the fill aesthetic.</p>
<h3 id="fullCode">Full code</h3>
<pre id="codeBlock">
<code>
# Install necessary libraries
pip install geopandas matplotlib pandas
# Load necessary libraries
import geopandas as gpd
import pandas as pd
import matplotlib.pyplot as plt
# Import Shapefiles
def import_shapefile(filepath):
shapefile = gpd.read_file(filepath) # Read the shapefile
return shapefile # Return the loaded shapefile
# Rename and Match Names
def rename_shapefile_columns(shapefile, new_names):
shapefile.columns = new_names # Rename columns
return shapefile # Return the renamed shapefile
# Link Shapefiles to Relevant Scales
def link_shapefiles_to_scales(shapefile, scales_df, link_col):
linked_shapefile = shapefile.merge(scales_df, on=link_col) # Merge shapefile with scales
return linked_shapefile # Return the linked shapefile
# Visualizing Shapefiles and Making Basic Maps
def visualize_shapefile(shapefile, variable):
shapefile.plot(column=variable, cmap='viridis', legend=True)
plt.title(f'Shapefile Visualization: {variable}')
plt.show()
</code>
<button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here -->
</pre>
`,
hf: `
<div class="fixed-buttons">
<button class="text-button" onclick="scrollToSection('stepByStep')">Step by step</button>
<button class="text-button" onclick="scrollToSection('fullCode')">Full code</button>
</div>
<h3>A. Data Assembly and Manangement>A.2 Health Facilities</h3>
<h4 id="stepByStep">Step by step approach</h4>
<p></p>
<h5>Step 1: </h5>
<p></p>
<pre><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h5>Step 2: </h5>
<p> </p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h5>Step 3: </h5>
<p> </p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h5>Step 4: </h5>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h5>Step 5: </h5>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h5>Step 6: </h5>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h3 id="fullCode">Full code</h3>
<pre id="codeBlock">
<code>
Code block
</code>
<button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here -->
</pre>
`,
dhis2: `
<div class="fixed-buttons">
<button class="text-button" onclick="scrollToSection('stepByStep')">Step by step</button>
<button class="text-button" onclick="scrollToSection('fullCode')">Full code</button>
</div>
<h3>A. Data Assembly and Manangement>A.3 Routine Case Data from DHIS2</h3>
<h4 id="stepByStep">Step by step approach</h4>
<p></p>
<h5>Step 1: </h5>
<p></p>
<pre><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h5>Step 2: </h5>
<p> </p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h5>Step 3: </h5>
<p> </p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h5>Step 4: </h5>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h5>Step 5: </h5>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h5>Step 6: </h5>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h3 id="fullCode">Full code</h3>
<pre id="codeBlock">
<code>
Code block
</code>
<button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here -->
</pre>
`,
dhs: `
<div class="fixed-buttons">
<button class="text-button" onclick="scrollToSection('stepByStep')">Step by step</button>
<button class="text-button" onclick="scrollToSection('fullCode')">Full code</button>
</div>
<h3>A. Data Assembly and Manangement>A.4 DHS Data</h3>
<h4 id="stepByStep">Step by step approach</h4>
<p></p>
<h5>Step 1: </h5>
<p></p>
<pre><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h5>Step 2: </h5>
<p> </p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h5>Step 3: </h5>
<p> </p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h5>Step 4: </h5>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h3>Step 5: </h3>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h3>Step 6: </h3>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h3 id="fullCode">Full code</h3>
<pre id="codeBlock">
<code>
Code block
</code>
<button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here -->
</pre>
`,
pop: `
<div class="fixed-buttons">
<button class="text-button" onclick="scrollToSection('stepByStep')">Step by step</button>
<button class="text-button" onclick="scrollToSection('fullCode')">Full code</button>
</div>
<h3>A. Data Assembly and Manangement>A.5 Population Data</h3>
<h3 id="stepByStep">Step by step approach</h3>
<p></p>
<h3>Step 1: </h3>
<p></p>
<pre><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h3>Step 2: </h3>
<p> </p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h3>Step 3: </h3>
<p> </p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h3>Step 4: </h3>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h3>Step 5: </h3>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h3>Step 6: </h3>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h3 id="fullCode">Full code</h3>
<pre id="codeBlock">
<code>
Code block
</code>
<button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here -->
</pre>
`,
climate: `
<div class="fixed-buttons">
<button class="text-button" onclick="scrollToSection('stepByStep')">Step by step</button>
<button class="text-button" onclick="scrollToSection('fullCode')">Full code</button>
</div>
<h3>A. Data Assembly and Manangement>A.6 Climate Data</h3>
<h3 id="stepByStep">Step by step approach</h3>
<p></p>
<h3>Step 1: </h3>
<p></p>
<pre><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h3>Step 2: </h3>
<p> </p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h3>Step 3: </h3>
<p> </p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h3>Step 4: </h3>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h3>Step 5: </h3>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h3>Step 6: </h3>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h3 id="fullCode">Full code</h3>
<pre id="codeBlock">
<code>
Code block
</code>
<button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here -->
</pre>
`,
lmis: `
<div class="fixed-buttons">
<button class="text-button" onclick="scrollToSection('stepByStep')">Step by step</button>
<button class="text-button" onclick="scrollToSection('fullCode')">Full code</button>
</div>
<h3>A. Data Assembly and Manangement>A.7 LMIS Data</h3>
<h3 id="stepByStep">Step by step approach</h3>
<p></p>
<h3>Step 1: </h3>
<p></p>
<pre><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h3>Step 2: </h3>
<p> </p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h3>Step 3: </h3>
<p> </p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h3>Step 4: </h3>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h3>Step 5: </h3>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h3>Step 6: </h3>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h3 id="fullCode">Full code</h3>
<pre id="codeBlock">
<code>
Code block
</code>
<button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here -->
</pre>
`,
model: `
<div class="fixed-buttons">
<button class="text-button" onclick="scrollToSection('stepByStep')">Step by step</button>
<button class="text-button" onclick="scrollToSection('fullCode')">Full code</button>
</div>
<h3>A. Data Assembly and Manangement>A.8 Modeled Data</h3>
<h3 id="stepByStep">Step by step approach</h3>
<p></p>
<h3>Step 1: </h3>
<p></p>
<pre><code>
Code block
</code><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --></pre>
<p></p>
<h3>Step 2: </h3>
<p> </p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h3>Step 3: </h3>
<p> </p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block
</code></pre>
<p></p>
<h3>Step 4: </h3>
<p></p>
<pre><button class="copy-button" onclick="copyCode()">Copy Code</button> <!-- Copy button positioned here --><code>
Code block