diff --git a/.github/workflows/autobuild.yml b/.github/workflows/autobuild.yml index 463f0dd8..3c61e48e 100644 --- a/.github/workflows/autobuild.yml +++ b/.github/workflows/autobuild.yml @@ -7,8 +7,8 @@ on: # Triggers the workflow on push or pull request events but only for the gh-pages branch push: branches: [master] -# pull_request: -# branches: [master] + # pull_request: + # branches: [master] schedule: # * is a special character in YAML so you have to quote this string # run every night: @@ -27,12 +27,12 @@ jobs: # This workflow contains a single job called "build" build: # The type of runner that the job will run on - runs-on: ubuntu-18.04 + runs-on: ubuntu-22.04 # Steps represent a sequence of tasks that will be executed as part of the job steps: # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 # Runs a set of commands using the runners shell - name: CI Autobuild diff --git a/docs/.gitignore b/docs/.gitignore new file mode 100755 index 00000000..595e2151 --- /dev/null +++ b/docs/.gitignore @@ -0,0 +1,12 @@ +pids +logs +node_modules +npm-debug.log +coverage/ +run +dist +.DS_Store +.nyc_output +.basement +config.local.js +basement_dist diff --git a/docs/package.json b/docs/package.json new file mode 100755 index 00000000..91f7cced --- /dev/null +++ b/docs/package.json @@ -0,0 +1,19 @@ +{ + "name": "covid-sim", + "version": "0.0.1", + "description": "", + "main": "index.js", + "authors": { + "name": "", + "email": "" + }, + "repository": "/covid-sim", + "scripts": { + "dev": "vuepress dev src", + "build": "vuepress build src && cp -r ./src/.vuepress/dist/* ../public/docs" + }, + "license": "MIT", + "devDependencies": { + "vuepress": "^1.5.3" + } +} diff --git a/docs/src/.vuepress/components/Foo/Bar.vue b/docs/src/.vuepress/components/Foo/Bar.vue new file mode 100755 index 00000000..7ee8286a --- /dev/null +++ b/docs/src/.vuepress/components/Foo/Bar.vue @@ -0,0 +1,15 @@ + + + diff --git a/docs/src/.vuepress/components/OtherComponent.vue b/docs/src/.vuepress/components/OtherComponent.vue new file mode 100755 index 00000000..1d97c7ca --- /dev/null +++ b/docs/src/.vuepress/components/OtherComponent.vue @@ -0,0 +1,3 @@ + diff --git a/docs/src/.vuepress/components/demo-component.vue b/docs/src/.vuepress/components/demo-component.vue new file mode 100755 index 00000000..7d49de79 --- /dev/null +++ b/docs/src/.vuepress/components/demo-component.vue @@ -0,0 +1,15 @@ + + + diff --git a/docs/src/.vuepress/config.js b/docs/src/.vuepress/config.js new file mode 100755 index 00000000..3ef3ea47 --- /dev/null +++ b/docs/src/.vuepress/config.js @@ -0,0 +1,67 @@ +const { description } = require('../../package') + +module.exports = { + + base: '/docs/', + /** + * Ref：https://v1.vuepress.vuejs.org/config/#title + */ + title: 'COVID-SIM Documentation', + /** + * Ref：https://v1.vuepress.vuejs.org/config/#description + */ + description: description, + + /** + * Extra tags to be injected to the page HTML `` + * + * ref：https://v1.vuepress.vuejs.org/config/#head + */ + head: [ + ['meta', { name: 'theme-color', content: '#3eaf7c' }], + ['meta', { name: 'apple-mobile-web-app-capable', content: 'yes' }], + ['meta', { name: 'apple-mobile-web-app-status-bar-style', content: 'black' }] + ], + + /** + * Theme configuration, here is the default theme configuration for VuePress. + * + * ref：https://v1.vuepress.vuejs.org/theme/default-theme-config.html + */ + themeConfig: { + repo: '', + editLinks: true, + docsDir: '', + editLinkText: '', + lastUpdated: true, + nav: [ + { + text: 'Documentation', + link: '/documentation/', + } + ], + sidebar: { + '/documentation/': [ + { + title: 'Documentation', + collapsable: true, + children: [ + '', + 'run-setup', + 'configuration', + 'website', + 'plots', + ] + } + ], + } + }, + + /** + * Apply plugins，ref：https://v1.vuepress.vuejs.org/zh/plugin/ + */ + plugins: [ + '@vuepress/plugin-back-to-top', + '@vuepress/plugin-medium-zoom', + ] +} diff --git a/docs/src/.vuepress/enhanceApp.js b/docs/src/.vuepress/enhanceApp.js new file mode 100755 index 00000000..8452a868 --- /dev/null +++ b/docs/src/.vuepress/enhanceApp.js @@ -0,0 +1,14 @@ +/** + * Client app enhancement file. + * + * https://v1.vuepress.vuejs.org/guide/basic-config.html#app-level-enhancements + */ + +export default ({ + Vue, // the version of Vue being used in the VuePress app + options, // the options for the root Vue instance + router, // the router instance for the app + siteData // site metadata +}) => { + // ...apply enhancements for the site. +} diff --git a/docs/src/.vuepress/styles/index.styl b/docs/src/.vuepress/styles/index.styl new file mode 100755 index 00000000..420feb93 --- /dev/null +++ b/docs/src/.vuepress/styles/index.styl @@ -0,0 +1,8 @@ +/** + * Custom Styles here. + * + * ref：https://v1.vuepress.vuejs.org/config/#index-styl + */ + +.home .hero img + max-width 450px!important diff --git a/docs/src/.vuepress/styles/palette.styl b/docs/src/.vuepress/styles/palette.styl new file mode 100755 index 00000000..6490cb35 --- /dev/null +++ b/docs/src/.vuepress/styles/palette.styl @@ -0,0 +1,10 @@ +/** + * Custom palette here. + * + * ref：https://v1.vuepress.vuejs.org/zh/config/#palette-styl + */ + +$accentColor = #3eaf7c +$textColor = #2c3e50 +$borderColor = #eaecef +$codeBgColor = #282c34 diff --git a/docs/src/config/README.md b/docs/src/config/README.md new file mode 100755 index 00000000..63a04b9e --- /dev/null +++ b/docs/src/config/README.md @@ -0,0 +1,15 @@ +--- +sidebar: auto +--- + +# Config + +## foo + +- Type: `string` +- Default: `/` + +## bar + +- Type: `string` +- Default: `/` diff --git a/docs/src/documentation/README.md b/docs/src/documentation/README.md new file mode 100755 index 00000000..f0fcee75 --- /dev/null +++ b/docs/src/documentation/README.md @@ -0,0 +1,3 @@ +# Introduction + +Here you can find all the information for covid-sim.info. Among other things, how you can set up a new run, what configuration options are available, etc. \ No newline at end of file diff --git a/docs/src/documentation/configuration.md b/docs/src/documentation/configuration.md new file mode 100644 index 00000000..a6a7f07f --- /dev/null +++ b/docs/src/documentation/configuration.md @@ -0,0 +1,90 @@ +# Configuration + +Each run has a `config.yaml` file. In this file settings can be made. The following settings are possible: + +## YAML File + +| name | required | data type | description | +|------|-----------|----------|-------------| +| viewerVersion | false | number | There are several versions of covid-sim. The current version is 2. Possible versions are: 1 and 2. | +| city | true | string | Covid-sim can map data from different cities. Possible are: berlin and cologne. | +| info | true | string | Specifies the name of the file in which the run IDs are assigned to the settings. | +| readme | true | string | For the description to be displayed above the plots, the name of the Markdown file can be specified, which is located in the same folder as the YAML file. | +| zipFolder | true | string | For the data of the runs, the folder with the results can be specified here, which is located in the same folder as the YAML file. | +| timestamp | true | string | Specifies the date in the format `YYYY-MM-DD` on which the run was set up. | +| offset | false| number[] | desc... | +| startDate | false | string | Specifies the start date in the format `YYYY-MM-DD` when the run starts. One of the two values `startDate` and `defaultStartDate` must be set. | +| endDate | false | string | Specifies the start date in the format `YYYY-MM-DD` when the run ends. | +| defaultStartDate | false | string | One of the two values `startDate` and `defaultStartDate` must be set. | +| startDates | false | string[] | Are required if no `offset` has been specified. | +| ignoredPlots | false | string[] | Plots can be hidden for specific runs. For this purpose, the short name of the plot must be specified at this point. For the respective short names see: [Plots](plots.md#plots). | +| graphStartDate | true | string | Specifies the date in the format `YYYY-MM-DD` when the plots start. | +| heatMapMaxValue | false | number | So that the results of different runs can be compared with the heatmap. A maximum value must be set, which can be adjusted here. | +| rValueDate | false | string | The date for the displayed R-value can be set in the format 'YYYY-MM-DD'. The default date is: `2020-10-15`. | +| optionGroups | true | [optionGroups](#optiongroups)[] | desc... | + +### optionGroups + +| name | required | data type | description | +|------|-----------|----------|-------------| +| day | false | number | desc... | +| heading | true | string | desc... | +| subheading | false | string | desc... | +| measures | true | [measures](#measures)[] | desc... | + +### measures + +| name | required | data type | description | +|------|-----------|----------|-------------| +| measure | true | string | desc... | +| title | true | string | desc... | +| order | false | string | desc... | +| options | false | number[] | desc... | +| asPercent | false | boolean | desc... | + +### Example +This is an example YAML file which belongs to this [run](https://covid-sim.info/cologne/2022-11-16/3-variants). + +```yaml +--- +readme: notes.md +zip: summaries.zip +info: _info.txt +zipFolder: summaries +timestamp: 2022-11-18 +viewerVersion: 2 +city: cologne +runName: calibration +defaultStartDate: 2020-02-25 +graphStartDate: 2022-08-01 +endDate: 2024-09-30 +startDates: +- 2020-02-25 +optionGroups: +- day: -1 + heading: "" + subheading: "" + measures: + - title: Vac Camp + measure: vacCamp + - title: Strain A + measure: StrainA + - title: Strain A Date + measure: strainADate + - title: Esc + measure: esc + - title: Esc L + measure: escL + - title: Ci Corr + measure: ciCorr + - title: Days + measure: days + - title: Strain Rnd + measure: strainRnd + - title: Line B + measure: lineB + - title: Iga + measure: iga + - title: Seasonal + measure: seasonal +``` \ No newline at end of file diff --git a/docs/src/documentation/plots.md b/docs/src/documentation/plots.md new file mode 100644 index 00000000..1c8e9aaa --- /dev/null +++ b/docs/src/documentation/plots.md @@ -0,0 +1,160 @@ +# Plots + +The results of the runs are shown in the plots below. The following plots are available for visualization. The `RunId` describes the run currently selected via the buttons. Each run is contained as a .zip file in the summaries folder. The URL for the `PUBLIC_SVN` is: [https://svn.vsp.tu-berlin.de/repos/public-svn/matsim/scenarios/countries/de/episim]() + +| Plot name | Short name | File name | +|---------|--|--| +| [Activity Levels by Type](#activity-levels-by-type) | actLevPerTyp | ActivityLevelsPlot | +| [Disease Import](#disease-import) | disImp | DiseaseImport | +| [Hospitalization New Cases (post-process)](#hospitalization-new-cases-post-process) | hosNewCasPos | PostHospital | +| [Hospitalization Rate (post-process)](#hospitalization-rate-post-process) | hosRatPos | PostHospital | +| [Cases Comparison](#cases-comparison) | casCom | WeeklyInfectionsPlot | +| [Virus Strains](#virus-strains) | virStr | MutationsPlot | +| [Simulated R-Values](#simulated-r-values) | simRVal | RValuePlot | +| [Simulated R-Values by Purpose](#simulated-r-values-by-purpose) | simRValByPur | RValueTwo | +| [Infections by Activity Type](#infections-by-activity-type) | infByActTyp | InfectionsByActivityType | +| Vaccine Effectiveness (against infection) | vacEffAgaInf | Vaccination
EffectivenessPlot | +| Vaccine Effectiveness Vs. Strain | vacEffVsStr | VaccinationEffectiveness-
VsStrain | +| [Incidence comparison between vaccinated and unvaccinated persons](#incidence-comparison-between-vaccinated-and-unvaccinated-persons) | incComVacAndUnvac | WeeklyInfection-
ByVaccination | +| [Vaccination Rates and Booster Rates](#vaccination-rates-and-booster-rates) | VacRatBooRat | VaccinationRates | +| [Vaccination per Type](#vaccination-per-type) | VacPerTyp | VaccinationPerType | +| Antibodies | Antibodies | Antibodies | +| [Hospitalization New Cases](#hospitalization-new-cases) | hospNewCas | Hospitalization7-
DayNewCasesPlot | +| [Hospitalization Rate Comparison](#hospitalization-rate-comparison) | hospRatComp | HospitalizationPlot | +| [Hospitalization Rate Comparison for vaccinated and unvaccinated persons](#hospitalization-rate-comparison-for-vaccinated-and-unvaccinated-persons) | hospRatCompVacAndUnvac | Hospitalization-
VaccinationComparison | +| [Simulated Health Outcomes Over Time](#simulated-health-outcomes-over-time) | simHealOutOveTim | HealthOutcomes | +| [7-Day Incidence by Age Group Over Time (Heatmap)](#7-day-incidence-by-age-group-over-time-heatmap) | inciHeatmap | HeatMap | +| [7-Day Incidence by Age Group Over Time (Linechart)](#7-day-incidence-by-age-group-over-time-linechart) | inciLinechart | AgeGroupLineChart | +| [Leisure Outdoor Fraction](#leisure-outdoor-fraction) | leiOutFra | LeisureOutdoorFraction | +| [Weekly Tests](#weekly-tests) | weekTest | WeeklyTests | + +## Activity Levels by Type + +![Activity Levels by Type Plot](./../images/activity-levels-per-type.png) + +Data basis: `RunId + '.restrictions.txt.csv'` + +## Disease Import + +![Disease Import Plot](./../images/disease-import.png) + +Data basis: `RunId + '.diseaseImport.tsv'` + +## Hospitalization New Cases (post-process) + +![Hospitalization New Cases (post-process) Plot](./../images/hosp-new-cases.png) + +Data basis: `RunId + '.post.hospital.tsv'` + +## Hospitalization Rate (post-process) + +![Hospitalization Rate (post-process) Plot](./../images/hosp-rate.png) + +Data basis: `RunId + '.post.hospital.tsv'` + +## Cases Comparison + +![DisCases Comparisonease Plot](./../images/case-comp.png) + +Data basis: +- Model data: `RunId + '.infections.txt.csv'` + +- Sewage data: `PUBLIC_SVN + 'original-data/Abwasser/CologneSewageDataCleaned.csv'` + + +## Virus Strains + +![Virus Strains Plot](./../images/virus-strains.png) + +Data basis: +- First plot: `PUBLIC_SVN + 'original-data/Fallzahlen/' + 'Cologne/VOC_Cologne_RKI.csv' respectively 'Berlin/VOC_Berlin.csv'` +- Second and third plot: `RunId + '.strains.tsv'` + +Add new data: +- As soon as new variants for Cologne are available, they will be added automatically. +- For the new variants only the name in the [file](https://github.com/matsim-vsp/covid-sim/blob/master/src/views/v2/MutationsPlot.vue) has to be adjusted (headerCologne[] line 292) +- In case new variants should not be displayed, the index must be added in the for loop (line 366) in the termination condition. + +## Simulated R-Values + +![Simulated R-Values Plot](./../images/sim-r-values.png) + +Data basis: `RunId + '.infections.txt.csv'` + +## Simulated R-Values by Purpose + +![Simulated R-Values by Purpose Plot](./../images/r-values-by-purpose.png) + +Data basis: `RunId + '.infections.txt.csv'` + +## Infections by Activity Type + +![Infections by Activity Type Plot](./../images/infection-by-activity-type.png) + +Data basis: `RunId + '.infectionsPerActivity.txt.tsv'` + +## Incidence comparison between vaccinated and unvaccinated persons + +![Incidence comparison between vaccinated and unvaccinated persons Plot](./../images/incidence-comp-vac-unvac.png) + +Data basis: `PUBLIC_SVN + 'original-data/Fallzahlen/RKI/' + e.g. 'cologne-cases.csv'` + +## Vaccination Rates and Booster Rates + +![Disease Plot](./../images/vac-rates-and-booster-rates.png) + +Data basis: `RunId + '.vaccinationsDetailed.tsv'` + +## Vaccination per Type + +![Vaccination Rates and Booster Rates Plot](./../images/vac-per-type.png) + +Data basis: `RunId + '.vaccinations.tsv'` + +## Hospitalization New Cases + +![Hospitalization New Cases Plot](./../images/hosp-new-cases-old.png) + +Data basis: `RunId + '.infections.txt.csv'` + +## Hospitalization Rate Comparison + +![Hospitalization Rate Comparison Plot](./../images/hosp-rate-old.png) + +Data basis: `RunId + '.infections.txt.csv'` + +## Hospitalization Rate Comparison for vaccinated and unvaccinated persons + +![Hospitalization Rate Comparison for vaccinated and unvaccinated persons Plot](./../images/hosp-rate-vac-and-unvac.png) + +Data basis: `RunId + '.infections.txt.csv'` + +## Simulated Health Outcomes Over Time + +![Simulated Health Outcomes Over Time Plot](./../images/sim-health-outcome.png) + +Data basis: `RunId + '.infections.txt.csv'` + +## 7-Day Incidence by Age Group Over Time (Heatmap) + +![7-Day Incidence by Age Group Over Time (Heatmap) Plot](./../images/heapmap.png) + +Data basis: `RunId + '.post.incidenceByAge.tsv'` + +## 7-Day Incidence by Age Group Over Time (Linechart) + +![7-Day Incidence by Age Group Over Time (Linechart) Plot](./../images/incidence-by-age.png) + +Data basis: `RunId + '.post.incidenceByAge.tsv'` + +## Leisure Outdoor Fraction + +![Leisure Outdoor Fraction Plot](./../images/leisure-outdoor-fraction.png) + +Data basis: `RunId + '.outdoorFraction.tsv'` + +## Weekly Tests + +![Weekly Tests Plot](./../images/weekly-tests.png) + +Data basis: `RunId + '.infections.txt.csv'` \ No newline at end of file diff --git a/docs/src/documentation/run-setup.md b/docs/src/documentation/run-setup.md new file mode 100644 index 00000000..fae9260a --- /dev/null +++ b/docs/src/documentation/run-setup.md @@ -0,0 +1,58 @@ +# MATSim Episim + +![Build Status](https://github.com/matsim-org/matsim-episim-libs/workflows/build/badge.svg?branch=master) +![license](https://img.shields.io/github/license/matsim-org/matsim-episim.svg) +![JDK](https://img.shields.io/badge/JDK-11+-green.svg) +[![Join the chat at https://gitter.im/matsim-episim-libs/community](https://badges.gitter.im/matsim-episim-libs/community.svg)](https://gitter.im/matsim-episim-libs/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) + + +This repository contains an epidemic simulation based on MATSim, provided by the [Transport Systems Planning and Transport Telematics group](https://www.vsp.tu-berlin.de) of [Technische Universität Berlin](https://www.tu-berlin.de). + +Dissemination of some scenarios and results produced with the methods in this repository can be found at [https://matsim-vsp.github.io/covid-sim](). + + + +## How to use Episim + +In order perform an epidemic simulation you first need an MATSim events file. +To get started you can also use a provided event file from the [OpenBerlin Scenario](https://svn.vsp.tu-berlin.de/repos/public-svn/matsim/scenarios/countries/de/berlin/berlin-v5.4-1pct-schools/output-berlin-v5.4-1pct-schools/berlin-v5.4-1pct-schools.output_events_for_episim.xml.gz). + +It is best to run the scenarios with your IDE from the `org.matsim.run` package. +In `org.matsim.run.modules` you can find example scenarios that you may adapt or use to create your own configuration. + +To run them you can create a standalone jar file with: + + mvn package + +and run it with (where `OpenBerlinScenario` is the name of the scenario you want to run): + + java -jar matsim-episim-1.0-SNAPSHOT.jar --modules OpenBerlinScenario + + +## Generating mobility traces events file + +If you have a MATSim scenario you can also create your own event file to be used for an epidemic simulation. +All that is needed is the population and the event file of one iteration. + +Run `DownSampleScenario` to extract the necessary information: + + java -jar matsim-episim-1.0-SNAPSHOT.jar scenarioCreation downSample 0.1 \ + --population --events + +This example will write a 10% sample into `output` that can be used in the subsequent steps. + +## Licenses + +The **MATSim program code** in this repository is distributed under the terms of the [GNU Affero General Public License](https://www.gnu.org/licenses/agpl-3.0.html). The MATSim program code are files that reside in the `src` directory hierarchy and typically end with `*.java`. + +The **MATSim input files, output files, analysis data and visualizations** are licensed under a Creative Commons Attribution 4.0 International License. +Creative Commons License
MATSim input files are those that are used as input to run MATSim. They often, but not always, have a header pointing to matsim.org. They typically reside in the `scenarios` directory hierarchy. MATSim output files, analysis data, and visualizations are files generated by MATSim runs, or by postprocessing. They typically reside in a directory hierarchy starting with `output`. + +**Other data files**, in particular in `original-input-data`, have their own individual licenses that need to be individually clarified with the copyright holders. + + +## More information + +For more information about the methodology and preliminary results, see VSP working paper [https://dx.doi.org/10.14279/depositonce-9835](). + +For more information about MATSim, see here: [https://www.matsim.org](). \ No newline at end of file diff --git a/docs/src/documentation/website.md b/docs/src/documentation/website.md new file mode 100644 index 00000000..ac4af8e1 --- /dev/null +++ b/docs/src/documentation/website.md @@ -0,0 +1,91 @@ +# COVID Episim Website + +EpiSim + +This repo contains the visualization website for MATSim/EpiSim, available at [covid-sim.info](https://covid-sim.info). See that website for information on the use of MATSim for COVID-19 disease propagation, given various measures for combating its spread. + +This README details build instructions for the website itself. + +## Project pre-requisites + +The site uses npm and yarn, and was developed using VS Code. + +- You should install VS Code, npm, and yarn first. +- All code is TypeScript and shall remain so. + +The following VS Code plugins are used: + +- Prettier to force code style consistencey +- Vetur, for Vuejs support. This site is a [Vue](https://vuejs.org) SPA. +- Shader languages support + +## Foundational technologies + +You will need to know this tech in order to hack on this website: + +- [TypeScript](https://typescriptlang.org) - typesafe JavaScript +- [Vue](https://vuejs.org) - the glue that connects UI elements to code. Similar to React but lightweight and awesome +- [ThreeJS](https://threejs.org) - WebGL library for the fancy animations. +- [Pug](https://pugjs.org) - the template language used in Vue files. Pug uses Python-style indentation instead of open/close XML tags, which makes it far easier to read than bare HTML. + +## First time install + +One line fetches everything from the npm database: + +``` +yarn install +``` + +## Development Commands + +### Compiling and hot-reloads during development + +This command runs a local server with hot reload for testing, usually listens on http://localhost:8080 + +``` +yarn serve +``` + +### Compiles and minifies for production + +``` +yarn build +``` + +### Run your unit tests + +Well... I have not written tests but the infrastructure is there to use `jest`. + +``` +yarn test:unit +``` + +### Pushing to the live site + +Travis-CI is configured to automatically build the site with **every push to master**, so don't push to master until you are ready for your code to go live. + +- Travis config is in `.travis.yml` + +### Issues + +I (kn) need to fix the npm version on something older. The command is +``` +nvm use --lts +``` +Needed to install `nvm` to make this work. Can't remember how I did that; possibly through macports. + +## Project Layout + +- `/src`: all TypeScript and Vue files go here +- `/src/assets`: images, .csvs, etc that get packaged by webpack +- `/src/components`: shared Vue components go here +- `/src/HomeIndex.vue`: the front page. Add new thumbnails for pages or other content here. +- `/src/runs`: Each page has its own folder under the `/src/runs` folder. + - Connect up your new pages by adding a new folder here, and also adding a new URL to `/src/router.ts`. Anyone who knows the URL can then see the page. When you are ready for the public to also find it, add a link to `/src/components/TopBar.vue` and to the homepage. + - Each run should use a `readme.md` file under `/src/assets` so that researchers can add notes without having to learn the build system. +- `/scripts`: Python scripts go here, which are used for preprocessing EpiSim results +- `/public`: large .zip files, project notes, etc go in public. These files are pushed as-is by webpack; i.e. they are not packaged in any way + +## Thank you! + +Good luck and thanks for the help! -- [Billy](https://github.com/billyc) diff --git a/docs/src/images/activity-levels-per-type.png b/docs/src/images/activity-levels-per-type.png new file mode 100644 index 00000000..2413a373 Binary files /dev/null and b/docs/src/images/activity-levels-per-type.png differ diff --git a/docs/src/images/case-comp.png b/docs/src/images/case-comp.png new file mode 100644 index 00000000..acfc304f Binary files /dev/null and b/docs/src/images/case-comp.png differ diff --git a/docs/src/images/disease-import.png b/docs/src/images/disease-import.png new file mode 100644 index 00000000..fae347c3 Binary files /dev/null and b/docs/src/images/disease-import.png differ diff --git a/docs/src/images/heapmap.png b/docs/src/images/heapmap.png new file mode 100644 index 00000000..97671fc4 Binary files /dev/null and b/docs/src/images/heapmap.png differ diff --git a/docs/src/images/hosp-new-cases-old.png b/docs/src/images/hosp-new-cases-old.png new file mode 100644 index 00000000..0ee80cac Binary files /dev/null and b/docs/src/images/hosp-new-cases-old.png differ diff --git a/docs/src/images/hosp-new-cases.png b/docs/src/images/hosp-new-cases.png new file mode 100644 index 00000000..80834eca Binary files /dev/null and b/docs/src/images/hosp-new-cases.png differ diff --git a/docs/src/images/hosp-rate-old.png b/docs/src/images/hosp-rate-old.png new file mode 100644 index 00000000..481af6c4 Binary files /dev/null and b/docs/src/images/hosp-rate-old.png differ diff --git a/docs/src/images/hosp-rate-vac-and-unvac.png b/docs/src/images/hosp-rate-vac-and-unvac.png new file mode 100644 index 00000000..5eda02c4 Binary files /dev/null and b/docs/src/images/hosp-rate-vac-and-unvac.png differ diff --git a/docs/src/images/hosp-rate.png b/docs/src/images/hosp-rate.png new file mode 100644 index 00000000..f65d5bc0 Binary files /dev/null and b/docs/src/images/hosp-rate.png differ diff --git a/docs/src/images/incidence-by-age.png b/docs/src/images/incidence-by-age.png new file mode 100644 index 00000000..727aaabb Binary files /dev/null and b/docs/src/images/incidence-by-age.png differ diff --git a/docs/src/images/incidence-comp-vac-unvac.png b/docs/src/images/incidence-comp-vac-unvac.png new file mode 100644 index 00000000..41a82bf7 Binary files /dev/null and b/docs/src/images/incidence-comp-vac-unvac.png differ diff --git a/docs/src/images/infection-by-activity-type.png b/docs/src/images/infection-by-activity-type.png new file mode 100644 index 00000000..e4505ae6 Binary files /dev/null and b/docs/src/images/infection-by-activity-type.png differ diff --git a/docs/src/images/leisure-outdoor-fraction.png b/docs/src/images/leisure-outdoor-fraction.png new file mode 100644 index 00000000..cdf835de Binary files /dev/null and b/docs/src/images/leisure-outdoor-fraction.png differ diff --git a/docs/src/images/r-values-by-purpose.png b/docs/src/images/r-values-by-purpose.png new file mode 100644 index 00000000..027b10c7 Binary files /dev/null and b/docs/src/images/r-values-by-purpose.png differ diff --git a/docs/src/images/sim-health-outcome.png b/docs/src/images/sim-health-outcome.png new file mode 100644 index 00000000..8705ef04 Binary files /dev/null and b/docs/src/images/sim-health-outcome.png differ diff --git a/docs/src/images/sim-r-values.png b/docs/src/images/sim-r-values.png new file mode 100644 index 00000000..8eec5abe Binary files /dev/null and b/docs/src/images/sim-r-values.png differ diff --git a/docs/src/images/vac-per-type.png b/docs/src/images/vac-per-type.png new file mode 100644 index 00000000..f7610220 Binary files /dev/null and b/docs/src/images/vac-per-type.png differ diff --git a/docs/src/images/vac-rates-and-booster-rates.png b/docs/src/images/vac-rates-and-booster-rates.png new file mode 100644 index 00000000..8622acb5 Binary files /dev/null and b/docs/src/images/vac-rates-and-booster-rates.png differ diff --git a/docs/src/images/virus-strains.png b/docs/src/images/virus-strains.png new file mode 100644 index 00000000..93aa9c40 Binary files /dev/null and b/docs/src/images/virus-strains.png differ diff --git a/docs/src/images/weekly-tests.png b/docs/src/images/weekly-tests.png new file mode 100644 index 00000000..3d05acfa Binary files /dev/null and b/docs/src/images/weekly-tests.png differ diff --git a/docs/src/index.md b/docs/src/index.md new file mode 100755 index 00000000..300e1276 --- /dev/null +++ b/docs/src/index.md @@ -0,0 +1,15 @@ +--- +home: true +heroImage: https://github.com/matsim-vsp/covid-sim/raw/master/src/assets/images/readme-banner.jpg +tagline: +actionText: Documentation +actionLink: /documentation/ +# features: +# - 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COVID-SIM Documentation

# Configuration

Each run has a config.yaml file. In this file settings can be made. The following settings are possible:

# YAML File

name required data type description
viewerVersion false number There are several versions of covid-sim. The current version is 2. Possible versions are: 1 and 2.
city true string Covid-sim can map data from different cities. Possible are: berlin and cologne.
info true string Specifies the name of the file in which the run IDs are assigned to the settings.
readme true string For the description to be displayed above the plots, the name of the Markdown file can be specified, which is located in the same folder as the YAML file.
zipFolder true string For the data of the runs, the folder with the results can be specified here, which is located in the same folder as the YAML file.
timestamp true string Specifies the date in the format YYYY-MM-DD on which the run was set up.
offset false number[] desc...
startDate false string Specifies the start date in the format YYYY-MM-DD when the run starts. One of the two values startDate and defaultStartDate must be set.
endDate false string Specifies the start date in the format YYYY-MM-DD when the run ends.
defaultStartDate false string One of the two values startDate and defaultStartDate must be set.
startDates false string[] Are required if no offset has been specified.
ignoredPlots false string[] Plots can be hidden for specific runs. For this purpose, the short name of the plot must be specified at this point. For the respective short names see: Plots.
graphStartDate true string Specifies the date in the format YYYY-MM-DD when the plots start.
heatMapMaxValue false number So that the results of different runs can be compared with the heatmap. A maximum value must be set, which can be adjusted here.
rValueDate false string The date for the displayed R-value can be set in the format 'YYYY-MM-DD'. The default date is: 2020-10-15.
optionGroups true optionGroups[] desc...

# optionGroups

name required data type description
day false number desc...
heading true string desc...
subheading false string desc...
measures true measures[] desc...

# measures

name required data type description
measure true string desc...
title true string desc...
order false string desc...
options false number[] desc...
asPercent false boolean desc...

# Example

This is an example YAML file which belongs to this run (opens new window).

---
+readme: notes.md
+zip: summaries.zip
+info: _info.txt
+zipFolder: summaries
+timestamp: 2022-11-18
+viewerVersion: 2
+city: cologne
+runName: calibration
+defaultStartDate: 2020-02-25
+graphStartDate: 2022-08-01
+endDate: 2024-09-30
+startDates:
+- 2020-02-25
+optionGroups:
+- day: -1
+  heading: ""
+  subheading: ""
+  measures:
+  - title: Vac Camp
+    measure: vacCamp
+  - title: Strain A
+    measure: StrainA
+  - title: Strain A Date
+    measure: strainADate
+  - title: Esc
+    measure: esc
+  - title: Esc L
+    measure: escL
+  - title: Ci Corr
+    measure: ciCorr
+  - title: Days
+    measure: days
+  - title: Strain Rnd
+    measure: strainRnd
+  - title: Line B
+    measure: lineB
+  - title: Iga
+    measure: iga
+  - title: Seasonal
+    measure: seasonal
+
Last Updated: 2/27/2023, 1:40:00 PM

+ ← + + COVID Episim Website + + → +

+ + + diff --git a/public/docs/documentation/index.html b/public/docs/documentation/index.html new file mode 100644 index 00000000..70593972 --- /dev/null +++ b/public/docs/documentation/index.html @@ -0,0 +1,29 @@ + + + + + + Introduction | COVID-SIM Documentation + + + + + + + + + + + +
COVID-SIM Documentation

# Introduction

Here you can find all the information for covid-sim.info. Among other things, how you can set up a new run, what configuration options are available, etc.

Last Updated: 2/27/2023, 1:14:20 PM

+ MATSim Episim + + → +

+ + + diff --git a/public/docs/documentation/plots.html b/public/docs/documentation/plots.html new file mode 100644 index 00000000..99ba699b --- /dev/null +++ b/public/docs/documentation/plots.html @@ -0,0 +1,29 @@ + + + + + + Plots | COVID-SIM Documentation + + + + + + + + + + + +
COVID-SIM Documentation

# Plots

The results of the runs are shown in the plots below. The following plots are available for visualization. The RunId describes the run currently selected via the buttons. Each run is contained as a .zip file in the summaries folder. The URL for the PUBLIC_SVN is: https://svn.vsp.tu-berlin.de/repos/public-svn/matsim/scenarios/countries/de/episim

Plot name Short name File name
Activity Levels by Type actLevPerTyp ActivityLevelsPlot
Disease Import disImp DiseaseImport
Hospitalization New Cases (post-process) hosNewCasPos PostHospital
Hospitalization Rate (post-process) hosRatPos PostHospital
Cases Comparison casCom WeeklyInfectionsPlot
Virus Strains virStr MutationsPlot
Simulated R-Values simRVal RValuePlot
Simulated R-Values by Purpose simRValByPur RValueTwo
Infections by Activity Type infByActTyp InfectionsByActivityType
Vaccine Effectiveness (against infection) vacEffAgaInf Vaccination
EffectivenessPlot
Vaccine Effectiveness Vs. Strain vacEffVsStr VaccinationEffectiveness-
VsStrain
Incidence comparison between vaccinated and unvaccinated persons incComVacAndUnvac WeeklyInfection-
ByVaccination
Vaccination Rates and Booster Rates VacRatBooRat VaccinationRates
Vaccination per Type VacPerTyp VaccinationPerType
Antibodies Antibodies Antibodies
Hospitalization New Cases hospNewCas Hospitalization7-
DayNewCasesPlot
Hospitalization Rate Comparison hospRatComp HospitalizationPlot
Hospitalization Rate Comparison for vaccinated and unvaccinated persons hospRatCompVacAndUnvac Hospitalization-
VaccinationComparison
Simulated Health Outcomes Over Time simHealOutOveTim HealthOutcomes
7-Day Incidence by Age Group Over Time (Heatmap) inciHeatmap HeatMap
7-Day Incidence by Age Group Over Time (Linechart) inciLinechart AgeGroupLineChart
Leisure Outdoor Fraction leiOutFra LeisureOutdoorFraction
Weekly Tests weekTest WeeklyTests

# Activity Levels by Type

Activity Levels by Type Plot

Data basis: RunId + '.restrictions.txt.csv'

# Disease Import

Disease Import Plot

Data basis: RunId + '.diseaseImport.tsv'

# Hospitalization New Cases (post-process)

Hospitalization New Cases (post-process) Plot

Data basis: RunId + '.post.hospital.tsv'

# Hospitalization Rate (post-process)

Hospitalization Rate (post-process) Plot

Data basis: RunId + '.post.hospital.tsv'

# Cases Comparison

DisCases Comparisonease Plot

Data basis:

  • Model data: RunId + '.infections.txt.csv'
  • Sewage data: PUBLIC_SVN + 'original-data/Abwasser/CologneSewageDataCleaned.csv'

# Virus Strains

Virus Strains Plot

Data basis:

  • First plot: PUBLIC_SVN + 'original-data/Fallzahlen/' + 'Cologne/VOC_Cologne_RKI.csv' respectively 'Berlin/VOC_Berlin.csv'
  • Second and third plot: RunId + '.strains.tsv'

# Simulated R-Values

Simulated R-Values Plot

Data basis: RunId + '.infections.txt.csv'

# Simulated R-Values by Purpose

Simulated R-Values by Purpose Plot

Data basis: RunId + '.infections.txt.csv'

# Infections by Activity Type

Infections by Activity Type Plot

Data basis: RunId + '.infectionsPerActivity.txt.tsv'

# Incidence comparison between vaccinated and unvaccinated persons

Incidence comparison between vaccinated and unvaccinated persons Plot

Data basis: PUBLIC_SVN + 'original-data/Fallzahlen/RKI/' + e.g. 'cologne-cases.csv'

# Vaccination Rates and Booster Rates

Disease Plot

Data basis: RunId + '.vaccinationsDetailed.tsv'

# Vaccination per Type

Vaccination Rates and Booster Rates Plot

Data basis: RunId + '.vaccinations.tsv'

# Hospitalization New Cases

Hospitalization New Cases Plot

Data basis: RunId + '.infections.txt.csv'

# Hospitalization Rate Comparison

Hospitalization Rate Comparison Plot

Data basis: RunId + '.infections.txt.csv'

# Hospitalization Rate Comparison for vaccinated and unvaccinated persons

Hospitalization Rate Comparison for vaccinated and unvaccinated persons Plot

Data basis: RunId + '.infections.txt.csv'

# Simulated Health Outcomes Over Time

Simulated Health Outcomes Over Time Plot

Data basis: RunId + '.infections.txt.csv'

# 7-Day Incidence by Age Group Over Time (Heatmap)

7-Day Incidence by Age Group Over Time (Heatmap) Plot

Data basis: RunId + '.post.incidenceByAge.tsv'

# 7-Day Incidence by Age Group Over Time (Linechart)

7-Day Incidence by Age Group Over Time (Linechart) Plot

Data basis: RunId + '.post.incidenceByAge.tsv'

# Leisure Outdoor Fraction

Leisure Outdoor Fraction Plot

Data basis: RunId + '.outdoorFraction.tsv'

# Weekly Tests

Weekly Tests Plot

Data basis: RunId + '.infections.txt.csv'

Last Updated: 2/27/2023, 1:40:00 PM

+ ← +

+ + + diff --git a/public/docs/documentation/run-setup.html b/public/docs/documentation/run-setup.html new file mode 100644 index 00000000..1cb0d1a8 --- /dev/null +++ b/public/docs/documentation/run-setup.html @@ -0,0 +1,41 @@ + + + + + + MATSim Episim | COVID-SIM Documentation + + + + + + + + + + + +
COVID-SIM Documentation

# MATSim Episim

Build Status license JDK Join the chat at https://gitter.im/matsim-episim-libs/community (opens new window)

This repository contains an epidemic simulation based on MATSim, provided by the Transport Systems Planning and Transport Telematics group (opens new window) of Technische Universität Berlin (opens new window).

Dissemination of some scenarios and results produced with the methods in this repository can be found at https://matsim-vsp.github.io/covid-sim.

# How to use Episim

In order perform an epidemic simulation you first need an MATSim events file. +To get started you can also use a provided event file from the OpenBerlin Scenario (opens new window).

It is best to run the scenarios with your IDE from the org.matsim.run package. +In org.matsim.run.modules you can find example scenarios that you may adapt or use to create your own configuration.

To run them you can create a standalone jar file with:

mvn package
+

and run it with (where OpenBerlinScenario is the name of the scenario you want to run):

java -jar matsim-episim-1.0-SNAPSHOT.jar --modules OpenBerlinScenario
+

# Generating mobility traces events file

If you have a MATSim scenario you can also create your own event file to be used for an epidemic simulation. +All that is needed is the population and the event file of one iteration.

Run DownSampleScenario to extract the necessary information:

java -jar matsim-episim-1.0-SNAPSHOT.jar scenarioCreation downSample 0.1 \
+    --population <Path to plans.xml> --events <Path to events.xml>
+

This example will write a 10% sample into output that can be used in the subsequent steps.

# Licenses

The MATSim program code in this repository is distributed under the terms of the GNU Affero General Public License (opens new window). The MATSim program code are files that reside in the src directory hierarchy and typically end with *.java.

The MATSim input files, output files, analysis data and visualizations are licensed under a Creative Commons Attribution 4.0 International License. +Creative Commons License
MATSim input files are those that are used as input to run MATSim. They often, but not always, have a header pointing to matsim.org. They typically reside in the scenarios directory hierarchy. MATSim output files, analysis data, and visualizations are files generated by MATSim runs, or by postprocessing. They typically reside in a directory hierarchy starting with output.

Other data files, in particular in original-input-data, have their own individual licenses that need to be individually clarified with the copyright holders.

# More information

For more information about the methodology and preliminary results, see VSP working paper https://dx.doi.org/10.14279/depositonce-9835.

For more information about MATSim, see here: https://www.matsim.org.

Last Updated: 2/27/2023, 1:14:20 PM

+ ← + + Configuration + + → +

+ + + diff --git a/public/docs/documentation/website.html b/public/docs/documentation/website.html new file mode 100644 index 00000000..5fb537a3 --- /dev/null +++ b/public/docs/documentation/website.html @@ -0,0 +1,39 @@ + + + + + + COVID Episim Website | COVID-SIM Documentation + + + + + + + + + + + +
COVID-SIM Documentation

# COVID Episim Website

EpiSim

This repo contains the visualization website for MATSim/EpiSim, available at covid-sim.info (opens new window). See that website for information on the use of MATSim for COVID-19 disease propagation, given various measures for combating its spread.

This README details build instructions for the website itself.

# Project pre-requisites

The site uses npm and yarn, and was developed using VS Code.

  • You should install VS Code, npm, and yarn first.
  • All code is TypeScript and shall remain so.

The following VS Code plugins are used:

  • Prettier to force code style consistencey
  • Vetur, for Vuejs support. This site is a Vue (opens new window) SPA.
  • Shader languages support

# Foundational technologies

You will need to know this tech in order to hack on this website:

# First time install

One line fetches everything from the npm database:

yarn install
+

# Development Commands

# Compiling and hot-reloads during development

This command runs a local server with hot reload for testing, usually listens on http://localhost:8080

yarn serve
+

# Compiles and minifies for production

yarn build
+

# Run your unit tests

Well... I have not written tests but the infrastructure is there to use jest.

yarn test:unit
+

# Pushing to the live site

Travis-CI is configured to automatically build the site with every push to master, so don't push to master until you are ready for your code to go live.

  • Travis config is in .travis.yml

# Issues

I (kn) need to fix the npm version on something older. The command is

nvm use --lts
+

Needed to install nvm to make this work. Can't remember how I did that; possibly through macports.

# Project Layout

  • /src: all TypeScript and Vue files go here
  • /src/assets: images, .csvs, etc that get packaged by webpack
  • /src/components: shared Vue components go here
  • /src/HomeIndex.vue: the front page. Add new thumbnails for pages or other content here.
  • /src/runs: Each page has its own folder under the /src/runs folder. +
    • Connect up your new pages by adding a new folder here, and also adding a new URL to /src/router.ts. Anyone who knows the URL can then see the page. When you are ready for the public to also find it, add a link to /src/components/TopBar.vue and to the homepage.
    • Each run should use a readme.md file under /src/assets so that researchers can add notes without having to learn the build system.
  • /scripts: Python scripts go here, which are used for preprocessing EpiSim results
  • /public: large .zip files, project notes, etc go in public. These files are pushed as-is by webpack; i.e. they are not packaged in any way

# Thank you!

Good luck and thanks for the help! -- Billy (opens new window)

Last Updated: 2/27/2023, 1:14:20 PM

+ ← + + Plots + + → +

+ + + diff --git a/public/docs/index.html b/public/docs/index.html new file mode 100644 index 00000000..d4c46acc --- /dev/null +++ b/public/docs/index.html @@ -0,0 +1,29 @@ + + + + + + COVID-SIM Documentation + + + + + + + + + + + + + + + diff --git a/scripts/build-site.sh b/scripts/build-site.sh index a6684cb0..febc203f 100644 --- a/scripts/build-site.sh +++ b/scripts/build-site.sh @@ -11,9 +11,18 @@ IFS=$'\n\t' echo BUILD: Getting RKI_FILE -RKI_FILE=https://www.arcgis.com/sharing/rest/content/items/f10774f1c63e40168479a1feb6c7ca74/data +RKI_FILE=https://media.githubusercontent.com/media/robert-koch-institut/SARS-CoV-2-Infektionen_in_Deutschland/main/Aktuell_Deutschland_SarsCov2_Infektionen.csv wget -nv -O rki.csv $RKI_FILE +ls -al rki.csv +head rki.csv + +echo "FILTER the RKI csv file ---" +# NOTE: cut doesn't handle commas inside quotes! So the columns are off-by-one +# The "NeuGenesen" column in the cut output is ACTUALLY the RefDatum. +# cut -d "," -f3,4,7,9,15,16 < rki-all.csv > rki.csv +# head rki.csv +# ls -al rki.csv # fetch the RKI hospitalization data from Github, data is in: # https://github.com/robert-koch-institut/COVID-19-Hospitalisierungen_in_Deutschland @@ -23,6 +32,7 @@ cp -f COVID-Hospitalization/Archiv/`ls COVID-Hospitalization/Archiv | tail -1` s echo BUILD: Create [city]-cases.csv files # create the [city]-cases.csv files +python3 --version python3 scripts/rki-update.py rki.csv echo BUILD: Check out SVN and move *.csv files @@ -69,6 +79,14 @@ svn commit --username $SVN_USER --password $SVN_PASSWORD --no-auth-cache -m "Au # Back to root folder cd ../.. +export NODE_OPTIONS="--openssl-legacy-provider" + +# Build docs first +cd docs +yarn +yarn build +cd .. + # DONE WITH PREP! Build the site. echo BUILD: Finally lets build the site yarn install diff --git a/scripts/rki-update.py b/scripts/rki-update.py index 234ed91c..4f212d26 100644 --- a/scripts/rki-update.py +++ b/scripts/rki-update.py @@ -1,13 +1,12 @@ -#!/usr/bin/env python3.7 # -*- coding: utf-8 -*- # # RKI Data Parser # -# Requires Python 3.7, pandas and dfply +# Requires Python 3.7+, pandas and dfply # You can install pandas and dfply with one command: # pip install pandas dfply # -# Usage: python rki-update.py [RKI-filename.csv] +# Usage: python3 rki-update.py [RKI-filename.csv] print("RKI Updater script") @@ -41,15 +40,15 @@ sep=[4, 5, 7, 8, 10], convert=True, remove=False, -) >> select(X.Bundesland, X.Landkreis, X.AnzahlFall, X.year, X.month, X.day, X.myear, X.mmonth, X.mday) +) >> select(X.IdLandkreis, X.AnzahlFall, X.year, X.month, X.day, X.myear, X.mmonth, X.mday) # Berlin fname = "berlin-cases.csv" print(fname) berlin = ( csv - >> filter_by(X.Bundesland == "Berlin") - >> group_by(X.Bundesland, X.year, X.month, X.day) + >> filter_by(X.IdLandkreis >= 11001, X.IdLandkreis <= 11012) + >> group_by(X.IdLandkreis, X.year, X.month, X.day) >> summarize(cases=X.AnzahlFall.sum()) >> arrange(X.year, X.month, X.day) ) @@ -61,8 +60,8 @@ print(fname) mberlin = ( csv - >> filter_by(X.Bundesland == "Berlin") - >> group_by(X.Bundesland, X.myear, X.mmonth, X.mday) + >> filter_by(X.IdLandkreis >= 11001, X.IdLandkreis <= 11012) + >> group_by(X.IdLandkreis, X.myear, X.mmonth, X.mday) >> summarize(cases=X.AnzahlFall.sum()) >> arrange(X.myear, X.mmonth, X.mday) >> rename(year=X.myear, month=X.mmonth, day=X.mday) @@ -73,98 +72,83 @@ # Koeln fname = "cologne-cases.csv" print(fname) -berlin = ( +cologne = ( csv - >> filter_by(X.Bundesland == "Berlin") - >> group_by(X.Bundesland, X.year, X.month, X.day) + >> filter_by(X.IdLandkreis == 5315) + >> group_by(X.IdLandkreis, X.year, X.month, X.day) >> summarize(cases=X.AnzahlFall.sum()) >> arrange(X.year, X.month, X.day) ) -berlin.to_csv(fname, index=False, columns=["year", "month", "day", "cases"]) +cologne.to_csv(fname, index=False, columns=["year", "month", "day", "cases"]) # Koeln - Meldedatum fname = "cologne-cases-meldedatum.csv" print(fname) -mberlin = ( +mcologne = ( csv - >> filter_by(X.Bundesland == "Berlin") - >> group_by(X.Bundesland, X.myear, X.mmonth, X.mday) + >> filter_by(X.IdLandkreis == 5315) + >> group_by(X.IdLandkreis, X.myear, X.mmonth, X.mday) >> summarize(cases=X.AnzahlFall.sum()) >> arrange(X.myear, X.mmonth, X.mday) >> rename(year=X.myear, month=X.mmonth, day=X.mday) ) -mberlin.to_csv(fname, index=False, columns=["year", "month", "day", "cases"]) - +mcologne.to_csv(fname, index=False, columns=["year", "month", "day", "cases"]) # München fname = "munich-cases.csv" print(fname) munich = ( csv - >> filter_by(X.Landkreis == "SK München") - >> group_by(X.Landkreis, X.year, X.month, X.day) + >> filter_by(X.IdLandkreis == 9162) + >> group_by(X.IdLandkreis, X.year, X.month, X.day) >> summarize(cases=X.AnzahlFall.sum()) >> arrange(X.year, X.month, X.day) ) munich.to_csv(fname, index=False, columns=["year", "month", "day", "cases"]) -# Köln -fname = "cologne-cases.csv" -print(fname) -cologne = ( - csv - >> filter_by(X.Landkreis == "SK Köln") - >> group_by(X.Landkreis, X.year, X.month, X.day) - >> summarize(cases=X.AnzahlFall.sum()) - >> arrange(X.year, X.month, X.day) -) - -cologne.to_csv(fname, index=False, columns=["year", "month", "day", "cases"]) - - # Heinsberg -fname = "heinsberg-cases.csv" -print(fname) -heinsberg = ( - csv - >> filter_by(X.Landkreis == "LK Heinsberg") - >> group_by(X.Landkreis, X.year, X.month, X.day) - >> summarize(cases=X.AnzahlFall.sum()) - >> arrange(X.year, X.month, X.day) -) - -heinsberg.to_csv(fname, index=False, columns=["year", "month", "day", "cases"]) +# fname = "heinsberg-cases.csv" +# print(fname) +# heinsberg = ( +# csv +# >> filter_by(X.IdLandkreis == 5370016) +# >> group_by(X.IdLandkreis, X.year, X.month, X.day) +# >> summarize(cases=X.AnzahlFall.sum()) +# >> arrange(X.year, X.month, X.day) +# ) + +# heinsberg.to_csv(fname, index=False, columns=["year", "month", "day", "cases"]) ### same by reporting date (Meldedatum): # needs to be re-read because the original file is garbled (could be fixed) -csv = pd.read_csv(sys.argv[1], parse_dates=True) +# csv = pd.read_csv('https://media.githubusercontent.com/media/robert-koch-institut/SARS-CoV-2-Infektionen_in_Deutschland/main/Aktuell_Deutschland_SarsCov2_Infektionen.csv', parse_dates=True) + +# sys.argv[1] # split out dates -csv >>= separate( - X.Meldedatum, - ["year", "dash1", "month", "dash2", "day"], - sep=[4, 5, 7, 8, 10], - convert=True, - remove=False, -) >> select(X.Bundesland, X.Landkreis, X.AnzahlFall, X.year, X.month, X.day) +# csv >>= separate( +# X.Meldedatum, +# ["year", "dash1", "month", "dash2", "day"], +# sep=[4, 5, 7, 8, 10], +# convert=True, +# remove=False, +# ) >> select(X.IdLandkreis, X.AnzahlFall, X.year, X.month, X.day) # Berlin -fname = "berlin-cases-by-reporting-date.csv" -print(fname) -berlin = ( - csv - >> filter_by(X.Bundesland == "Berlin") - >> group_by(X.Bundesland, X.year, X.month, X.day) - >> summarize(cases=X.AnzahlFall.sum()) - >> arrange(X.year, X.month, X.day) -) - -berlin.to_csv(fname, index=False, columns=["year", "month", "day", "cases"]) - - +# fname = "berlin-cases-by-reporting-date.csv" +# print(fname) +# berlin = ( +# csv +# >> filter_by(X.IdLandkreis >= 11001, X.IdLandkreis <= 11012) +# >> group_by(X.IdLandkreis, X.year, X.month, X.day) +# >> summarize(cases=X.AnzahlFall.sum()) +# >> arrange(X.year, X.month, X.day) +# ) + +# berlin.to_csv(fname, index=False, columns=["year", "month", "day", "cases"]) print("--Done!") diff --git a/src/assets/berlin-cases-meldedatum.csv b/src/assets/berlin-cases-meldedatum.csv index 676d90b5..cfadbc3a 100644 --- a/src/assets/berlin-cases-meldedatum.csv +++ b/src/assets/berlin-cases-meldedatum.csv @@ -640,4 +640,4 @@ year,month,day,cases 2021,12,3,2087 2021,12,4,610 2021,12,5,275 -2021,12,6,1912 +2021,12,6,1912 \ No newline at end of file diff --git a/src/assets/berlin-cases.csv b/src/assets/berlin-cases.csv index e93ae957..34cd1033 100644 --- a/src/assets/berlin-cases.csv +++ b/src/assets/berlin-cases.csv @@ -659,4 +659,4 @@ year,month,day,cases 2021,12,3,1849 2021,12,4,581 2021,12,5,253 -2021,12,6,1818 +2021,12,6,1818 \ No newline at end of file diff --git a/src/assets/cologne-cases-meldedatum.csv b/src/assets/cologne-cases-meldedatum.csv index 676d90b5..cfadbc3a 100644 --- a/src/assets/cologne-cases-meldedatum.csv +++ b/src/assets/cologne-cases-meldedatum.csv @@ -640,4 +640,4 @@ year,month,day,cases 2021,12,3,2087 2021,12,4,610 2021,12,5,275 -2021,12,6,1912 +2021,12,6,1912 \ No newline at end of file diff --git a/src/assets/cologne-cases.csv b/src/assets/cologne-cases.csv index c1d9f55a..6ccb1711 100755 --- a/src/assets/cologne-cases.csv +++ b/src/assets/cologne-cases.csv @@ -662,4 +662,4 @@ year,month,day,cases 2021,12,3,691 2021,12,4,402 2021,12,5,499 -2021,12,6,582 +2021,12,6,582 \ No newline at end of file diff --git a/src/assets/heinsberg-cases.csv b/src/assets/heinsberg-cases.csv index c14c2fa3..c7075520 100755 --- a/src/assets/heinsberg-cases.csv +++ b/src/assets/heinsberg-cases.csv @@ -614,4 +614,4 @@ year,month,day,cases 2021,12,1,156 2021,12,2,191 2021,12,3,73 -2021,12,6,185 +2021,12,6,185 \ No newline at end of file diff --git a/src/assets/munich-cases.csv b/src/assets/munich-cases.csv index 89d96293..687fdd42 100755 --- a/src/assets/munich-cases.csv +++ b/src/assets/munich-cases.csv @@ -656,4 +656,4 @@ year,month,day,cases 2021,12,3,879 2021,12,4,516 2021,12,5,540 -2021,12,6,157 +2021,12,6,157 \ No newline at end of file diff --git a/src/assets/reports.ts b/src/assets/reports.ts index 0157f9c1..cbf6cff1 100644 --- a/src/assets/reports.ts +++ b/src/assets/reports.ts @@ -8,7 +8,7 @@ const reports: { md: string; title: string; url: string; html: string }[] = [ { md: '/reports/report-2023-02-27.md', title: '27 February 2023', - url: 'https://doi.org/10.14279/depositonce-17034', + url: 'https://doi.org/10.14279/depositonce-17034.2', html: '', }, { diff --git a/src/assets/rki-deutschland-hospitalization.csv b/src/assets/rki-deutschland-hospitalization.csv index 4b95670c..84f53a9c 100644 --- a/src/assets/rki-deutschland-hospitalization.csv +++ b/src/assets/rki-deutschland-hospitalization.csv @@ -10147,4 +10147,4 @@ Datum,Bundesland,Bundesland_Id,Altersgruppe,fixierte_7T_Hospitalisierung_Faelle, 2021-03-12,Thüringen,16,00+,157,261,261,261,261,2120237,7.4,12.31,12.31,12.31,12.31 2021-03-11,Thüringen,16,00+,168,252,252,252,252,2120237,7.92,11.89,11.89,11.89,11.89 2021-03-10,Thüringen,16,00+,173,251,251,251,251,2120237,8.16,11.84,11.84,11.84,11.84 -2021-03-09,Thüringen,16,00+,154,237,237,237,237,2120237,7.26,11.18,11.18,11.18,11.18 +2021-03-09,Thüringen,16,00+,154,237,237,237,237,2120237,7.26,11.18,11.18,11.18,11.18 \ No newline at end of file diff --git a/src/components/TopNavBar.vue b/src/components/TopNavBar.vue index 6d9dc0dc..d88e9ab7 100644 --- a/src/components/TopNavBar.vue +++ b/src/components/TopNavBar.vue @@ -20,10 +20,9 @@ @click='clickedBurger') .navbar-start .navbar-item.has-dropdown.is-hoverable(:class="{'is-active': isDropdownActive}") - a.navbar-link 2023.02.27 - .navbar-dropdown - a.navbar-item(:href="'/cologne/2023-02-15/2-firstWave'") Report February 27 - + a.navbar-link 2023.02.27 + .navbar-dropdown + a.navbar-item(:href="'/cologne/2023-02-15/2-firstWave'") Report February 27 .navbar-item.has-dropdown.is-hoverable(:class="{'is-active': isDropdownActive}") a.navbar-link 2022.12.02 .navbar-dropdown diff --git a/src/views/v2/MutationsPlot.vue b/src/views/v2/MutationsPlot.vue index 717fad45..b417a3c8 100644 --- a/src/views/v2/MutationsPlot.vue +++ b/src/views/v2/MutationsPlot.vue @@ -1,10 +1,10 @@ + .mutations-plots(v-if="!isResizing") + vue-plotly.plot1(:data="dataLines" :layout="layout" :options="options" @relayout="handleRelayout") + vue-plotly.plot2(:data="dataLines2" :layout="layout2" :options="options" @relayout="handleRelayout") + vue-plotly.plot3(:data="dataLines3" :layout="layout3" :options="options" @relayout="handleRelayout") + +