From 7633733acc444cb449cc613b4d3833735633ee7a Mon Sep 17 00:00:00 2001 From: hugzsoubrier Date: Thu, 1 Feb 2024 18:37:05 +0100 Subject: [PATCH 1/5] new features Added tabs for Reports and Packages, also added skeleton for an About page --- _quarto.yml | 12 ++- about_index.qmd | 19 ++++ index.qmd => dashboard_index.qmd | 8 +- gallery.Rproj | 6 +- items.yml => items/dashboard_items.yml | 42 --------- items/pkg_items.yml | 119 +++++++++++++++++++++++++ items/report_items.yml | 42 +++++++++ pkg_index.qmd | 33 +++++++ report_index.qmd | 31 +++++++ 9 files changed, 261 insertions(+), 51 deletions(-) create mode 100644 about_index.qmd rename index.qmd => dashboard_index.qmd (80%) rename items.yml => items/dashboard_items.yml (90%) create mode 100644 items/pkg_items.yml create mode 100644 items/report_items.yml create mode 100644 pkg_index.qmd create mode 100644 report_index.qmd diff --git a/_quarto.yml b/_quarto.yml index 672a738..6712648 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -6,14 +6,20 @@ website: search: false navbar: left: - - href: index.qmd - text: Gallery + - href: about_index.qmd + text: About + - href: dashboard_index.qmd + text: Dashboard Gallery + - href: report_index.qmd + text: Reports + - href: pkg_index.qmd + text: Packages execute: freeze: auto format: - html: + html: theme: cosmo css: styles.css toc: true diff --git a/about_index.qmd b/about_index.qmd new file mode 100644 index 0000000..91d9321 --- /dev/null +++ b/about_index.qmd @@ -0,0 +1,19 @@ +--- +title: "Data Science Team" +about: + template: jolla + image: assets/img/logo_epicentre.png + image-width: 10em + 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/ +--- + +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. diff --git a/index.qmd b/dashboard_index.qmd similarity index 80% rename from index.qmd rename to dashboard_index.qmd index 1fa3083..09a506a 100644 --- a/index.qmd +++ b/dashboard_index.qmd @@ -2,9 +2,9 @@ page-layout: full toc: false listing: - id: gallery + id: dashboard-gallery template: epi-grid.ejs - contents: items.yml + contents: items/dashboard_items.yml categories: true page-size: 1000 sort: @@ -25,8 +25,6 @@ listing: ## Data Visualisation Gallery -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. @@ -34,4 +32,4 @@ Items labelled as [INTERNAL]{.tag .status-internal} will require a login. If you --- ::: {#gallery} -::: \ No newline at end of file +::: diff --git a/gallery.Rproj b/gallery.Rproj index 7bdb19d..c8daeb9 100644 --- a/gallery.Rproj +++ b/gallery.Rproj @@ -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 - diff --git a/items.yml b/items/dashboard_items.yml similarity index 90% rename from items.yml rename to items/dashboard_items.yml index fd62dc9..978a8a9 100644 --- a/items.yml +++ b/items/dashboard_items.yml @@ -230,19 +230,6 @@ 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 @@ -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 @@ -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 diff --git a/items/pkg_items.yml b/items/pkg_items.yml new file mode 100644 index 0000000..4bba7f9 --- /dev/null +++ b/items/pkg_items.yml @@ -0,0 +1,119 @@ +- title: Epivis + description: Tools for visualising epidemiological data. + href: https://epicentre-msf.github.io/epivis/ + repo: https://github.com/epicentre-msf/epivis + status: active + updated: daily + author: Epi DS + access: internal + date-created: '2023-10-01' + date-modified: '2023-11-29' + image: assets/img/logo_epicentre.png + categories: + - data visualisation + - ggplot +- title: Epishiny + description: Tools for interactive visualisation of epidemiological data + href: https://epicentre-msf.github.io/epishiny/ + repo: https://github.com/epicentre-msf/epishiny + status: active + updated: daily + author: Epi DS + access: internal + date-created: '2023-10-01' + date-modified: '2023-11-29' + image: assets/img/logo_epicentre.png + categories: + - data visualisation + - shiny +- title: Hmatch + description: Tools for cleaning and matching hierarchically-structured data + href: https://epicentre-msf.github.io/hmatch/ + repo: https://github.com/epicentre-msf/hmatch + status: active + updated: daily + author: Epi DS + access: internal + date-created: '2023-10-01' + date-modified: '2023-11-29' + image: assets/img/logo_epicentre.png + categories: + - data manipulation +- title: nmatch + description: Fuzzy matching for proper names + href: https://epicentre-msf.github.io/nmatch/ + repo: https://github.com/epicentre-msf/nmatch + status: active + updated: daily + author: Epi DS + access: internal + date-created: '2023-10-01' + date-modified: '2023-11-29' + image: assets/img/logo_epicentre.png + categories: + - data manipulation +- title: dbc + description: Dictionnary based cleaning + href: https://epicentre-msf.github.io/dbc/ + repo: https://github.com/epicentre-msf/dbc + status: active + updated: daily + author: Epi DS + access: internal + date-created: '2023-10-01' + date-modified: '2023-11-29' + image: assets/img/logo_epicentre.png + categories: + - data manipulation +- title: qxl + description: Write quick, customized .xlsx files + href: https://epicentre-msf.github.io/qxl/ + repo: https://github.com/epicentre-msf/qxl + status: active + updated: daily + author: Epi DS + access: internal + date-created: '2023-10-01' + date-modified: '2023-11-29' + image: assets/img/logo_epicentre.png + categories: + - excel +- title: rpxl + description: Read password-protected Excel files + href: https://epicentre-msf.github.io/rpxl/ + repo: https://github.com/epicentre-msf/rpxl + status: active + updated: daily + author: Epi DS + access: internal + date-created: '2023-10-01' + date-modified: '2023-11-29' + image: assets/img/logo_epicentre.png + categories: + - excel +- title: redcap + description: R utilities for interacting with Redcap + href: https://epicentre-msf.github.io/redcap/ + repo: https://github.com/epicentre-msf/redcap + status: active + updated: daily + author: Epi DS + access: internal + date-created: '2023-10-01' + date-modified: '2023-11-29' + image: assets/img/logo_epicentre.png + categories: + - redcap +- title: queryr + description: Data validation queries with tidy, stackable output + href: https://epicentre-msf.github.io/queryr/ + repo: https://github.com/epicentre-msf/queryr + status: active + updated: daily + author: Epi DS + access: internal + date-created: '2023-10-01' + date-modified: '2023-11-29' + image: assets/img/logo_epicentre.png + categories: + - data queries diff --git a/items/report_items.yml b/items/report_items.yml new file mode 100644 index 0000000..353aa82 --- /dev/null +++ b/items/report_items.yml @@ -0,0 +1,42 @@ +- 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 diff --git a/pkg_index.qmd b/pkg_index.qmd new file mode 100644 index 0000000..3975a30 --- /dev/null +++ b/pkg_index.qmd @@ -0,0 +1,33 @@ +--- +page-layout: full +toc: false +listing: + id: pckg-gallery + template: epi-grid.ejs + contents: items/pkg_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" +--- + +## EpiDS packages Gallery + +A description here + +--- + +::: {#gallery} +::: diff --git a/report_index.qmd b/report_index.qmd new file mode 100644 index 0000000..1ef84eb --- /dev/null +++ b/report_index.qmd @@ -0,0 +1,31 @@ +--- +page-layout: full +toc: false +listing: + id: report-gallery + template: epi-grid.ejs + contents: items/report_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" +--- + +## Reports Gallery + +--- + +::: {#gallery} +::: From 89f1005d915e0c008c651c43d8fc4616c551bf02 Mon Sep 17 00:00:00 2001 From: hugzsoubrier Date: Mon, 5 Feb 2024 10:58:19 +0100 Subject: [PATCH 2/5] updates based on comments taking into account comments on #1 --- _quarto.yml | 12 ++++---- dashboard_index.qmd => dashboard.qmd | 0 about_index.qmd => index.qmd | 3 +- items/dashboard_items.yml | 42 ++++++++++++++++++++++++++++ items/report_items.yml | 42 ---------------------------- pkg_index.qmd => pkg.qmd | 0 report_index.qmd | 31 -------------------- 7 files changed, 49 insertions(+), 81 deletions(-) rename dashboard_index.qmd => dashboard.qmd (100%) rename about_index.qmd => index.qmd (92%) delete mode 100644 items/report_items.yml rename pkg_index.qmd => pkg.qmd (100%) delete mode 100644 report_index.qmd diff --git a/_quarto.yml b/_quarto.yml index 6712648..97c78f8 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -6,14 +6,12 @@ website: search: false navbar: left: - - href: about_index.qmd + - href: index.qmd text: About - - href: dashboard_index.qmd - text: Dashboard Gallery - - href: report_index.qmd - text: Reports - - href: pkg_index.qmd - text: Packages + - href: dashboard.qmd + text: Dashboard & Reports Gallery + - href: pkg.qmd + text: R Packages execute: freeze: auto diff --git a/dashboard_index.qmd b/dashboard.qmd similarity index 100% rename from dashboard_index.qmd rename to dashboard.qmd diff --git a/about_index.qmd b/index.qmd similarity index 92% rename from about_index.qmd rename to index.qmd index 91d9321..d5e4b77 100644 --- a/about_index.qmd +++ b/index.qmd @@ -3,7 +3,8 @@ title: "Data Science Team" about: template: jolla image: assets/img/logo_epicentre.png - image-width: 10em + image-shape: rectangle + image-width: 600px links: - icon: twitter text: twitter diff --git a/items/dashboard_items.yml b/items/dashboard_items.yml index 978a8a9..e4b6ce7 100644 --- a/items/dashboard_items.yml +++ b/items/dashboard_items.yml @@ -435,3 +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 diff --git a/items/report_items.yml b/items/report_items.yml deleted file mode 100644 index 353aa82..0000000 --- a/items/report_items.yml +++ /dev/null @@ -1,42 +0,0 @@ -- 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 diff --git a/pkg_index.qmd b/pkg.qmd similarity index 100% rename from pkg_index.qmd rename to pkg.qmd diff --git a/report_index.qmd b/report_index.qmd deleted file mode 100644 index 1ef84eb..0000000 --- a/report_index.qmd +++ /dev/null @@ -1,31 +0,0 @@ ---- -page-layout: full -toc: false -listing: - id: report-gallery - template: epi-grid.ejs - contents: items/report_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" ---- - -## Reports Gallery - ---- - -::: {#gallery} -::: From b0eb2987804c797e9c4c74b34973ef17d6e200b6 Mon Sep 17 00:00:00 2001 From: hugzsoubrier Date: Wed, 7 Feb 2024 16:04:55 +0100 Subject: [PATCH 3/5] adding .scss --- _quarto.yml | 5 +- epicentre_qmd_style.scss | 148 +++++++++++++++++++++++++++++++++++++++ index.qmd | 3 + pkg.qmd | 4 +- 4 files changed, 156 insertions(+), 4 deletions(-) create mode 100644 epicentre_qmd_style.scss diff --git a/_quarto.yml b/_quarto.yml index 97c78f8..030a5f5 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -18,6 +18,7 @@ execute: format: html: - theme: cosmo - css: styles.css + theme: + - cosmo + - epicentre_qmd_style.scss toc: true diff --git a/epicentre_qmd_style.scss b/epicentre_qmd_style.scss new file mode 100644 index 0000000..c74ae48 --- /dev/null +++ b/epicentre_qmd_style.scss @@ -0,0 +1,148 @@ +/*-- 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; +} + + diff --git a/index.qmd b/index.qmd index d5e4b77..53129e7 100644 --- a/index.qmd +++ b/index.qmd @@ -18,3 +18,6 @@ about: --- 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. + + + diff --git a/pkg.qmd b/pkg.qmd index 3975a30..0faca3e 100644 --- a/pkg.qmd +++ b/pkg.qmd @@ -23,9 +23,9 @@ listing: date-modified: "Updated" --- -## EpiDS packages Gallery +## R packages gallery -A description here +Here is a list of R packages developped by members of the EpiDS team at Epicentre. --- From 36453bbd4f4780163d26734dd687f3d73038d68d Mon Sep 17 00:00:00 2001 From: Paul Campbell Date: Wed, 7 Feb 2024 17:19:48 +0100 Subject: [PATCH 4/5] tidy up --- _quarto.yml | 13 ++-- dashboard.qmd => gallery.qmd | 6 +- items/{dashboard_items.yml => gallery.yml} | 0 items/{pkg_items.yml => software.yml} | 86 +++++++++------------- pkg-grid.ejs | 67 +++++++++++++++++ pkg.qmd | 33 --------- software.qmd | 14 ++++ 7 files changed, 127 insertions(+), 92 deletions(-) rename dashboard.qmd => gallery.qmd (82%) rename items/{dashboard_items.yml => gallery.yml} (100%) rename items/{pkg_items.yml => software.yml} (68%) create mode 100644 pkg-grid.ejs delete mode 100644 pkg.qmd create mode 100644 software.qmd diff --git a/_quarto.yml b/_quarto.yml index 97c78f8..7200a0f 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -7,11 +7,14 @@ website: navbar: left: - href: index.qmd - text: About - - href: dashboard.qmd - text: Dashboard & Reports Gallery - - href: pkg.qmd - text: R Packages + icon: house-fill + text: Home + - href: gallery.qmd + icon: search + text: Gallery + - href: software.qmd + icon: code-slash + text: Software execute: freeze: auto diff --git a/dashboard.qmd b/gallery.qmd similarity index 82% rename from dashboard.qmd rename to gallery.qmd index 09a506a..a345c74 100644 --- a/dashboard.qmd +++ b/gallery.qmd @@ -2,9 +2,9 @@ page-layout: full toc: false listing: - id: dashboard-gallery + id: gallery template: epi-grid.ejs - contents: items/dashboard_items.yml + contents: items/gallery.yml categories: true page-size: 1000 sort: @@ -25,7 +25,7 @@ listing: ## Data Visualisation Gallery -Below is our collection of our interactive dashboards and reports. Use the search bar and categories menu to filter to your areas of interest. +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. diff --git a/items/dashboard_items.yml b/items/gallery.yml similarity index 100% rename from items/dashboard_items.yml rename to items/gallery.yml diff --git a/items/pkg_items.yml b/items/software.yml similarity index 68% rename from items/pkg_items.yml rename to items/software.yml index 4bba7f9..fa380fd 100644 --- a/items/pkg_items.yml +++ b/items/software.yml @@ -1,119 +1,103 @@ -- title: Epivis - description: Tools for visualising epidemiological data. - href: https://epicentre-msf.github.io/epivis/ - repo: https://github.com/epicentre-msf/epivis +- title: Outbreak Tools + description: Quickly build a linelist from an excel designer. + href: https://github.com/epicentre-msf/outbreak-tools + repo: https://github.com/epicentre-msf/outbreak-tools status: active - updated: daily author: Epi DS - access: internal - date-created: '2023-10-01' - date-modified: '2023-11-29' image: assets/img/logo_epicentre.png categories: - - data visualisation - - ggplot -- title: Epishiny + - data collection + - excel +- title: epishiny description: Tools for interactive visualisation of epidemiological data href: https://epicentre-msf.github.io/epishiny/ repo: https://github.com/epicentre-msf/epishiny status: active - updated: daily - author: Epi DS - access: internal - date-created: '2023-10-01' - date-modified: '2023-11-29' + author: P. Campbell image: assets/img/logo_epicentre.png categories: - data visualisation - shiny -- title: Hmatch + - R +- title: epivis + description: Tools for visualising epidemiological data + href: https://epicentre-msf.github.io/epivis/ + repo: https://github.com/epicentre-msf/epivis + status: active + author: Epi DS + image: assets/img/logo_epicentre.png + categories: + - data visualisation + - ggplot + - R +- title: hmatch description: Tools for cleaning and matching hierarchically-structured data href: https://epicentre-msf.github.io/hmatch/ repo: https://github.com/epicentre-msf/hmatch status: active - updated: daily - author: Epi DS - access: internal - date-created: '2023-10-01' - date-modified: '2023-11-29' + author: P. Barks image: assets/img/logo_epicentre.png categories: - data manipulation + - R - title: nmatch description: Fuzzy matching for proper names href: https://epicentre-msf.github.io/nmatch/ repo: https://github.com/epicentre-msf/nmatch status: active updated: daily - author: Epi DS - access: internal - date-created: '2023-10-01' - date-modified: '2023-11-29' + author: P. Barks image: assets/img/logo_epicentre.png categories: - data manipulation + - R - title: dbc description: Dictionnary based cleaning href: https://epicentre-msf.github.io/dbc/ repo: https://github.com/epicentre-msf/dbc status: active - updated: daily - author: Epi DS - access: internal - date-created: '2023-10-01' - date-modified: '2023-11-29' + author: P. Barks image: assets/img/logo_epicentre.png categories: - data manipulation + - R - title: qxl description: Write quick, customized .xlsx files href: https://epicentre-msf.github.io/qxl/ repo: https://github.com/epicentre-msf/qxl status: active - updated: daily - author: Epi DS - access: internal - date-created: '2023-10-01' - date-modified: '2023-11-29' + author: P. Barks image: assets/img/logo_epicentre.png categories: - excel + - R - title: rpxl description: Read password-protected Excel files href: https://epicentre-msf.github.io/rpxl/ repo: https://github.com/epicentre-msf/rpxl status: active - updated: daily - author: Epi DS - access: internal - date-created: '2023-10-01' - date-modified: '2023-11-29' + author: P. Barks image: assets/img/logo_epicentre.png categories: - excel + - R - title: redcap description: R utilities for interacting with Redcap href: https://epicentre-msf.github.io/redcap/ repo: https://github.com/epicentre-msf/redcap status: active - updated: daily - author: Epi DS - access: internal - date-created: '2023-10-01' - date-modified: '2023-11-29' + author: P. Barks image: assets/img/logo_epicentre.png categories: - redcap + - R - title: queryr description: Data validation queries with tidy, stackable output href: https://epicentre-msf.github.io/queryr/ repo: https://github.com/epicentre-msf/queryr status: active - updated: daily - author: Epi DS - access: internal - date-created: '2023-10-01' - date-modified: '2023-11-29' + author: P. Barks image: assets/img/logo_epicentre.png categories: - data queries + - R diff --git a/pkg-grid.ejs b/pkg-grid.ejs new file mode 100644 index 0000000..4f9e427 --- /dev/null +++ b/pkg-grid.ejs @@ -0,0 +1,67 @@ +```{=html} + +<% +// Number of columns +const cols = 3; + +// Card alignment +const align = "left"; + +// Cap Options +const imgHeight = "100%"; +%> + +
+<% for (const item of items) { %> +
> +
+ +
+ + <%= item.title %> + +
+ + +
+ <% if (item.image) { %> + <%= item.title %> + <% } else { %> + <%= item.title %> + <% } %> +
+ + +
+ + <% if(item.categories) { %> +
+ <% for (const cat of item.categories) { %> +
+ + <%= cat %> + +
+ <% } %> +
+ <% } %> + + <% if (item.description) { %> +
<%= item.description %>
+ <% } %> +
+ +
+
+ <% if ('author') { %>
<%= item.author %>
<% } %> +
+
+ +
+
+<% } %> +
+ +``` \ No newline at end of file diff --git a/pkg.qmd b/pkg.qmd deleted file mode 100644 index 3975a30..0000000 --- a/pkg.qmd +++ /dev/null @@ -1,33 +0,0 @@ ---- -page-layout: full -toc: false -listing: - id: pckg-gallery - template: epi-grid.ejs - contents: items/pkg_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" ---- - -## EpiDS packages Gallery - -A description here - ---- - -::: {#gallery} -::: diff --git a/software.qmd b/software.qmd new file mode 100644 index 0000000..a1c4639 --- /dev/null +++ b/software.qmd @@ -0,0 +1,14 @@ +--- +page-layout: full +toc: false +listing: + id: gallery + template: pkg-grid.ejs + contents: items/software.yml + categories: true + page-size: 1000 + filter-ui: true + field-required: [title, href, author] + field-display-names: + status: "Status" +--- From e977bfa091726bc1d6277cd60596b4cbf75e5beb Mon Sep 17 00:00:00 2001 From: Paul Campbell Date: Wed, 7 Feb 2024 19:03:30 +0100 Subject: [PATCH 5/5] theming --- README.md | 2 +- _quarto.yml | 9 ++++----- index.qmd | 5 ++--- styles.scss | 23 +++++++++++++++++++++++ 4 files changed, 30 insertions(+), 9 deletions(-) create mode 100644 styles.scss diff --git a/README.md b/README.md index 54c6941..ab4ea8e 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ ## 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: diff --git a/_quarto.yml b/_quarto.yml index ff313a7..753fec0 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -5,10 +5,8 @@ website: title: "Epicentre Data Science" search: false navbar: + background: primary left: - - href: index.qmd - icon: house-fill - text: Home - href: gallery.qmd icon: search text: Gallery @@ -22,6 +20,7 @@ execute: format: html: theme: - - cosmo - - epicentre_qmd_style.scss + - default + - styles.scss + css: styles.css toc: true diff --git a/index.qmd b/index.qmd index 53129e7..796a493 100644 --- a/index.qmd +++ b/index.qmd @@ -17,7 +17,6 @@ about: href: https://epicentre.msf.org/ --- -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. - - +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. +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). diff --git a/styles.scss b/styles.scss new file mode 100644 index 0000000..0276216 --- /dev/null +++ b/styles.scss @@ -0,0 +1,23 @@ +/*-- scss:defaults --*/ + +// +// Color system +// + +$blue: #2E569E !default; +$orange: #D37331 !default; +$green: #94BA3B !default; + +$primary: $blue !default; +$success: $green !default; +$warning: $orange !default; + +// Variables + +$web-font-path: "https://fonts.googleapis.com/css2?family=Roboto:wght@400;500;700&display=swap" !default; + +@if $web-font-path { + @import url($web-font-path); +} + +$font-family-sans-serif: Roboto, -apple-system, BlinkMacSystemFont, "Segoe UI", "Helvetica Neue", Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol" !default;