{"id":21534522,"url":"https://github.com/teebusch/drugx","last_synced_at":"2025-03-17T20:14:46.738Z","repository":{"id":138745393,"uuid":"257406883","full_name":"Teebusch/drugx","owner":"Teebusch","description":"Webapp built with R, Shiny, and golem to show data from a mock clinical study","archived":false,"fork":false,"pushed_at":"2020-04-21T07:35:04.000Z","size":696,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-24T07:11:28.448Z","etag":null,"topics":["r","shiny"],"latest_commit_sha":null,"homepage":"","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Teebusch.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-04-20T21:22:27.000Z","updated_at":"2022-04-21T11:53:35.000Z","dependencies_parsed_at":null,"dependency_job_id":"ba37edcc-013b-4ee0-9eb8-b1c4f103eba7","html_url":"https://github.com/Teebusch/drugx","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Teebusch%2Fdrugx","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Teebusch%2Fdrugx/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Teebusch%2Fdrugx/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Teebusch%2Fdrugx/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Teebusch","download_url":"https://codeload.github.com/Teebusch/drugx/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244102855,"owners_count":20398386,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["r","shiny"],"created_at":"2024-11-24T03:11:05.163Z","updated_at":"2025-03-17T20:14:46.713Z","avatar_url":"https://github.com/Teebusch.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# Drug X Clinical Trial\n\n\u003c!-- badges: start --\u003e\n[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)\n\u003c!-- badges: end --\u003e\n\nThis is a Shiny app using some (simulated) clinical data to visualize the results of a clinical trial for the fictive drug \"Drug X\".\n\n## Installation and Use\n\nAn online demo of the app can be found at https://teebusch.shinyapps.io/drugx/\n\nYou can install and run the app locally from [Github](https://github.com/teebusch/drugx) with:\n\n``` r\n# Install devtools if needed\nif(!require(devtools)) install.packages(\"devtools\")\ndevtools::install_github(\"Teebusch/drugx\")\nlibrary(drugx)\ndrugx::run_app()\n```\n\n## Drug X Clinical Trial \n\n### Study Design\n\n- One study, 9492 observations\n- 3 arms (A = drug, B = placebo, C = combination)\n- ~150 patients in each arm\n- 7 Repeated measures: screening, baseline, 5 weekly follow-ups (day 8-36)\n- consistent, complete data (except some \"undifferentiated\" / \"other\" patient info)\n\n#### Measurements\n\n##### Patient Info\n\n- Age\n- Sex\n- Race\n\n##### Measured once at baseline:\n\n- **Biomarker 1** (numerical; Mean around 6, range 0.3-22.4)\n- **Biomarker 2** (categorical; low, medium, high)\n\n##### Measured at each visit:\n\n- **ALT** is increased with liver damage and is used to screen for and/or monitor liver disease\n- **CRP** is a blood test marker for inflammation in the body (e.g., chronic inflammatory diseases such as lupus, vasculitis, or rheumatoid arthritis (RA)\n- **IGA** high levels might be caused by allergies, chronic infections, autoimmune disorders such as RA\n\n\n### Research questions (assumed)\n\n##### Effect of Drug X on Lab values...\n\n- change compared to baseline\n- difference between drug X / placebo / combination (group difference between arms)\n\n##### controlling for / as a function of / correlation with...\n\n- Age\n- Sex\n- 2 Biomarkers\n- Screening / Baseline values\n\n## Requirements for the Shiny App \n\n### Deliverable\n\n- Shiny application to explore the properties of the data sources.\n- minimum of 2 different visualization plots\n- use of a version control \n- formated as a RStudio project, or gzip R Package.\n- delivered within 8 days of receiving these instructions.\n- 4-5 hours of work\n\n### High level goals\n\n- help explore associations between background variables and treatment\n- filter data to visualize subgroups\n- allow high level overview as well as investigating subgroups and individuals\n- comparing data in different study arms\n\n### Necessary\n\n- [x] sanity checks / cleaning of supplied data\n- [x] graphs of background variables (for all data and by study arm)\n- [x] allow to filter data by age, race, sex, biomarkers 1 and 2, performance at baseline\nsubjects\n- [x] graph that shows development of ALT, CRP, IGA for individuals \n- [x] graph that shows development of ALT, CRP, IGA by study arm (summary)\n- [x] deliver as R package\n\n## ToDo / Possible next steps\n\n- [ ] allow data to filter by performance of screening, individual patient\n- [ ] complete function documentation\n- [ ] optimize loading times by refactoring data transforms and filtering\n- [ ] comprehensive test suite \n- [ ] statistical models with significance tests\n- [ ] interactive plotly plots with hover functionality\n- [ ] tables with summary statistics\n\n\n## Open Questions\n\n- What is being done in the \"combination\" condition?\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fteebusch%2Fdrugx","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fteebusch%2Fdrugx","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fteebusch%2Fdrugx/lists"}