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PaulC91 committed Feb 8, 2024
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2 changes: 1 addition & 1 deletion README.md
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## Adding an item to the gallery

New items can be added to the [`items.yml`](items.yml) file after which they will automatically appear on the website gallery when it is next generated.
New items can be added to the [`gallery.yml`](items/gallery.yml) file after which they will automatically appear on the website gallery when it is next generated.

Below is an example of an item entry:

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12 changes: 9 additions & 3 deletions _quarto.yml
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Expand Up @@ -7,14 +7,20 @@ website:
navbar:
background: light
left:
- href: index.qmd
- href: gallery.qmd
icon: search
text: Gallery
- href: software.qmd
icon: code-slash
text: Software

execute:
freeze: auto

format:
html:
theme: cosmo
html:
theme:
- default
- styles.scss
css: styles.css
toc: true
148 changes: 148 additions & 0 deletions epicentre_qmd_style.scss
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/*-- scss:defaults --*/

$col-primary: #2E4473;
$col-primary-light: #E4EDF3;
$col-secondary: #A1B8CF;
$col-secondary-bg: #F5F9FB;
$col-dark-grey: #C5C5C5;
$col-light-grey: #F8F8F8;
$col-red-prim : #C0392B;
$col-red-sec : #F9EBEA;
$col-yellow-prim : #FAB872;
$col-yellow-sec : #FEF6E7;

/* Table of content */

$toc-color: $col-primary;
$toc-inactive-color: $col-light-grey;
$content-padding-top: 1px;

/* titles font size and weight*/
$h1-font-size: 30px;
$h1-font-weight: 400;

$h2-font-size: 27px;
$h2-font-weight: 300;

$h3-font-size: 25px;
$h3-font-weight: 300;

$h4-font-size: 23px;
$h4-font-weight: 300;

/* font-weights */

$weight-title: 600;

$navbar-bg: $col-secondary-bg;

/* inline code */

$code-bg: $col-primary-light;
$code-color: $col-primary;

/* code block */
$code-block-bg: $col-primary-light ;

/*-- scss:rules --*/

h1, h2, h3 {
color: $col-primary;
}

h1.title {
font-size: 50px;
font-weight: 600;
color: $col-primary;
}

h1 {
font-weight: $h1-font-weight;
}

h2 {
font-weight: $h2-font-weight;
}

h3 {
font-weight: $h3-font-weight;
}

h4{
font-weight: $h4-font-weight;
}

p.subtitle {
font-style: italic;
color: darken($col-dark-grey, 50%);
}

/* BLOCKQUOTE */
.blockquote {
font-size: 1em;
color: $col-primary;
border-left-color: $col-primary;
}

/* Inline code */
code {
border-radius: 5px;

}

/* Inline code */
.quarto-title-block .quarto-title-banner {
background-image: url(assets/img/logo_epicentre.png);
background-size: 250px;
background-position: left;
background-repeat: no-repeat;
padding-left: 50px;
padding-right: 50px;
background-origin: content-box;
}

/* Customize code block and output */
.code {

border-radius: 1px;
}

/* call outs style */

div.callout-note.callout{
border-left-color: $col-primary;
background-color: $col-secondary-bg;
border-radius: 10px;
}

div.callout-caution.callout{
border-left-color: $col-yellow-prim;
background-color: $col-yellow-sec;
border-radius: 10px;
}

div.callout-important.callout{
border-left-color: $col-red-prim;
background-color: $col-red-sec;
border-radius: 10px;
}

/* TOC styling */

h2#toc-title{
font-weight: 700;
}

.nav-link {
border-left-color: $col-primary ;
border-left-width: thick;
border-radius: 3px;
}

.nav-link:hover, .nav-link:focus, .nav-link.active {
color: $col-primary;
background-color: $col-secondary-bg;
font-weight: 700;
}


6 changes: 5 additions & 1 deletion gallery.Rproj
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Expand Up @@ -5,9 +5,13 @@ SaveWorkspace: No
AlwaysSaveHistory: Default

EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8

RnwWeave: Sweave
LaTeX: pdfLaTeX

AutoAppendNewline: Yes
StripTrailingWhitespace: Yes
LineEndingConversion: Posix

35 changes: 35 additions & 0 deletions gallery.qmd
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---
page-layout: full
toc: false
listing:
id: gallery
template: epi-grid.ejs
contents: items/gallery.yml
categories: true
page-size: 1000
sort:
- "status"
- "date-modified desc"
sort-ui: [title, date-created, date-modified]
filter-ui: true
field-required: [title, href, status, access, author, date-created, date-modified]
field-types:
date-created: date
date-modified: date
field-display-names:
status: "Status"
access: "Access"
date-created: "Published"
date-modified: "Updated"
---

## Data Visualisation Gallery

Below is our collection of our interactive dashboards, reports and tools. Use the search bar and categories menu to filter to your areas of interest.

Items labelled as [INTERNAL]{.tag .status-internal} will require a login. If you are a member of the MSF network and have an msf.org email address you can [create an account to access our dashboards on our sign-up page](https://reports.msf.net/signup/){target="_blank"}. Note that some dashboards are limited to specific OCs, individual personel or project partners, so not all content will be accessible with your account.

---

::: {#gallery}
:::
51 changes: 18 additions & 33 deletions index.qmd
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@@ -1,37 +1,22 @@
---
page-layout: full
toc: false
listing:
id: gallery
template: epi-grid.ejs
contents: items.yml
categories: true
page-size: 1000
sort:
- "status"
- "date-modified desc"
sort-ui: [title, date-created, date-modified]
filter-ui: true
field-required: [title, href, status, access, author, date-created, date-modified]
field-types:
date-created: date
date-modified: date
field-display-names:
status: "Status"
access: "Access"
date-created: "Published"
date-modified: "Updated"
title: "Data Science Team"
about:
template: jolla
image: assets/img/logo_epicentre.png
image-shape: rectangle
image-width: 600px
links:
- icon: twitter
text: twitter
href: https://twitter.com/@Epicentre_MSF
- icon: github
text: Github
href: https://github.com/epicentre-msf
- icon: website
text: Website
href: https://epicentre.msf.org/
---

## Data Visualisation Gallery
From outbreaks to clinical trials, Epicentre's data science team (Epi DS) leverages its expertise in epidemiology, statistical analysis, GIS, programming and data visualisation to drive actionable insight from public health data.

From outbreaks to clinical trials, Epicentre's data science team (Epi DS) leverages its expertise in epidemiology, statistical analysis, programming and data visualisation to drive actionable insight from public health data.

Below is our collection of our interactive dashboards and reports. Use the search bar and categories menu to filter to your areas of interest.

Items labelled as [INTERNAL]{.tag .status-internal} will require a login. If you are a member of the MSF network and have an msf.org email address you can [create an account to access our dashboards on our sign-up page](https://reports.msf.net/signup/){target="_blank"}. Note that some dashboards are limited to specific OCs, individual personel or project partners, so not all content will be accessible with your account.

---

::: {#gallery}
:::
Explore our collection of web-apps, tools, interactive dashboards and reports on our [gallery page](/gallery.html), and our open-source software repository on our [software page](/software.html).
84 changes: 42 additions & 42 deletions items.yml → items/gallery.yml
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categories:
- study
- lassa
- title: ENABLE Interim Analysis
description: Report summarising the interim analysis for the Enable Lassa study
href: https://enable.epicentre-msf.org/app/lasv-interim-analysis
repo: https://github.com/epicentre-msf/enable-final-analysis
access: internal
status: active
author: Epi DS
image: assets/img/enable.png
date-created: '2022-06-26'
date-modified: '2023-11-15'
categories:
- study
- lassa
- title: ENABLE ELISA Analysis
description: Tool to measure IgG concentration in blood serum using an indirect
ELISA
Expand Down Expand Up @@ -285,20 +272,6 @@
categories:
- surveillance
- covid19
- id: covid19-additional-analysis
title: MSF COVID-19 Additional Analysis
description: Supplementary graphics and tables
href: https://reports.msf.net/secure/app/covid19-additional-analysis
repo: https://github.com/epicentre-msf/covid19-episitrep-overall
access: internal
status: archived
author: Epi DS
image: assets/img/covid19-linelist-dashboard.png
date-created: '2020-06-07'
date-modified: '2022-04-01'
categories:
- surveillance
- covid19
- id: covid19-modelling-tool
title: COVID-19 Modelling Tool
description: Estimate the demand for hospitalization and operational resources for COVID patients in locations of your choice
Expand Down Expand Up @@ -401,21 +374,6 @@
date-modified: '2023-10-01'
categories:
- hr
- id: drc-eb-001-en
title: DRC-EB-001 (Tujiokowe) Daily Situation Report (EN)
description: Daily data from the J&J vaccine trial in Kivu, DRC
href: https://reports.msf.net/secure/app/drc-eb-001-en
repo: https://github.com/epicentre-msf/tujiokowe
access: internal
status: archived
author: Epi DS
image: assets/img/drc-eb-001.png
date-created: '2019-12-01'
date-modified: '2019-12-01'
categories:
- trial
- ebola
- drc
- id: drc-eb-001-fr
title: DRC-EB-001 (Tujiokowe) Rapport de Situation Quotidien (FR)
description: Daily data from the J&J vaccine trial in Kivu, DRC
Expand Down Expand Up @@ -477,3 +435,45 @@
- trial
- ebola
- uganda
- title: ENABLE Interim Analysis
description: Report summarising the interim analysis for the Enable Lassa study
href: https://enable.epicentre-msf.org/app/lasv-interim-analysis
repo: https://github.com/epicentre-msf/enable-final-analysis
access: internal
status: active
author: Epi DS
image: assets/img/enable.png
date-created: '2022-06-26'
date-modified: '2023-11-15'
categories:
- study
- lassa
- id: covid19-additional-analysis
title: MSF COVID-19 Additional Analysis
description: Supplementary graphics and tables
href: https://reports.msf.net/secure/app/covid19-additional-analysis
repo: https://github.com/epicentre-msf/covid19-episitrep-overall
access: internal
status: archived
author: Epi DS
image: assets/img/covid19-linelist-dashboard.png
date-created: '2020-06-07'
date-modified: '2022-04-01'
categories:
- surveillance
- covid19
- id: drc-eb-001-en
title: DRC-EB-001 (Tujiokowe) Daily Situation Report (EN)
description: Daily data from the J&J vaccine trial in Kivu, DRC
href: https://reports.msf.net/secure/app/drc-eb-001-en
repo: https://github.com/epicentre-msf/tujiokowe
access: internal
status: archived
author: Epi DS
image: assets/img/drc-eb-001.png
date-created: '2019-12-01'
date-modified: '2019-12-01'
categories:
- trial
- ebola
- drc
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