{"id":16272586,"url":"https://github.com/rempsyc/pubmeddashboard","last_synced_at":"2025-03-19T23:31:10.919Z","repository":{"id":182140458,"uuid":"668007787","full_name":"rempsyc/pubmedDashboard","owner":"rempsyc","description":"Creating PubMed Data Visualization Dashboards","archived":false,"fork":false,"pushed_at":"2024-05-30T14:51:54.000Z","size":43791,"stargazers_count":4,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-17T12:21:53.410Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://rempsyc.github.io/pubmedDashboard/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/rempsyc.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":null,"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":"2023-07-18T19:58:57.000Z","updated_at":"2024-07-21T17:00:23.000Z","dependencies_parsed_at":"2023-07-18T21:49:57.745Z","dependency_job_id":"bcbc86f1-d9ce-43f3-bbc8-8eb6df1d33ec","html_url":"https://github.com/rempsyc/pubmedDashboard","commit_stats":null,"previous_names":["rempsyc/pubmeddashboard"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rempsyc%2FpubmedDashboard","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rempsyc%2FpubmedDashboard/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rempsyc%2FpubmedDashboard/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rempsyc%2FpubmedDashboard/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rempsyc","download_url":"https://codeload.github.com/rempsyc/pubmedDashboard/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244524846,"owners_count":20466512,"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":[],"created_at":"2024-10-10T18:18:22.684Z","updated_at":"2025-03-19T23:31:08.852Z","avatar_url":"https://github.com/rempsyc.png","language":"R","funding_links":["https://github.com/sponsors/rempsyc"],"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# pubmedDashboard: Creating PubMed Data Visualization Dashboards \u003cimg src='man/figures/logo.png' align=\"right\" height=\"139\" style=\"float:right; height:200px;\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![R-CMD-check](https://github.com/rempsyc/pubmedDashboard/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rempsyc/pubmedDashboard/actions)\n[![r-universe](https://rempsyc.r-universe.dev/badges/pubmedDashboard)](https://rempsyc.r-universe.dev/ui/#package:pubmedDashboard)\n[![CRAN status](https://www.r-pkg.org/badges/version/pubmedDashboard)](https://CRAN.R-project.org/package=pubmedDashboard)\n[![Last-commit](https://img.shields.io/github/last-commit/rempsyc/pubmedDashboard)](https://github.com/rempsyc/pubmedDashboard/commits/main)\n[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)\n[![sponsors](https://img.shields.io/github/sponsors/rempsyc)](https://github.com/sponsors/rempsyc)\n[![followers](https://img.shields.io/github/followers/rempsyc?style=social)](https://github.com/rempsyc?tab=followers)\n[![stars](https://img.shields.io/github/stars/rempsyc/pubmedDashboard?style=social)](https://github.com/rempsyc/pubmedDashboard/stargazers)\n\u003c!-- badges: end --\u003e\n\n**This package is now deprecated in favour of the [`pubDashboard`](https://rempsyc.github.io/pubDashboard/) package.**\n\nThe goal of `pubmedDashboard` is to facilitate the creation of pretty data visualization dashboards using the `flexdashboard` and `easyPubMed` packages.\n\n## Installation\n\nYou can install the development version of `pubmedDashboard` like so:\n\n``` r\n# If `remotes` isn't installed, use `install.packages(\"remotes\")`\nremotes::install_github(\"rempsyc/pubmedDashboard\")\n```\n\n## Basic Examples\n\n`pubmedDashboard` helps parse the address to identify department and university of affiliation, as well as country.\n\n```{r, warning=FALSE}\nlibrary(pubmedDashboard)\n\naddress \u003c- c(\n  \"Department of Psychology, Cornell University, Ithaca, New York 14853-7601.\",\n  \"Dipartimento di Psicologia Generale, Università di Padova, Italy.\",\n  \"Universität Mannheim, Federal Republic of Germany.\",\n  \"Département de psychologie, Université du Québec à Montréal, Canada.\"\n)\n\nget_affiliation(address, \"department\")\n\nget_affiliation(address, \"university\")\n\nget_country(address)\n```\n\n## Mega Function\n\nOne simple function allows to download the paper data from PubMed, convert the XLM data to a dataframe, extract affiliations, match universities to countries, identify countries and continents, and save the file to disk for later reuse.\n\n```{r example, warning=FALSE}\nsave_process_pubmed_batch(\n  pubmed_query_string = \"passion [Title/Abstract]\",\n  journal = c(\"Journal of Personality and Social Psychology\", \"Health Psychology\"),\n  year_low = 2023,\n  year_high = 2030\n)\n```\n\n## Table formatting functions\n\nVarious functions allow to prepare DT tables to display specific information, such as journal paper percentages by continent or country.\n\n```{r read_bind_all, message=FALSE}\ndata \u003c- read_bind_all_data()\n```\n\n```{r table_continent, eval = FALSE}\ntable_continent(data)\n```\n\n\n![](man/figures/table_journal_continent.png)\n\n## Figure formatting functions\n\n```{r waffle_country, warning=FALSE, message=FALSE}\nwaffle_country(data)\n```\n\n\n## Example Dashboards\n\nThe full source-code for these dashboards are available on the corresponding button at the top-right of each dashboard.\n\n### Neglected 95% Dashboard\n\n[![](man/figures/n95.png)](https://remi-theriault.com/dashboards/neglected_95)\n\n### Passion Dashboard\n\n[![](man/figures/passion.png)](https://remi-theriault.com/dashboards/passion)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frempsyc%2Fpubmeddashboard","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frempsyc%2Fpubmeddashboard","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frempsyc%2Fpubmeddashboard/lists"}