{ "_id": "6a1f3794b401979e73428c9e", "Package": "pubmedDashboard", "Title": "Creating PubMed Data Visualization Dashboards", "Version": "0.0.3", "Authors@R": "person(\"Rémi\", \"Thériault\", , \"remi.theriault@mail.mcgill.ca\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-4315-6788\"))", "Description": "Package to facilitate the creation of data visualization\ndashboards through the flexdashboard and easyPubMed packages.\nThis package is now deprecated in favour of the pubDashboard\npackage.", "License": "GPL (>= 3)", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.1", "LazyData": "true", "URL": "https://github.com/rempsyc/pubmedDashboard,\nhttps://rempsyc.github.io/pubmedDashboard/", "BugReports": "https://github.com/rempsyc/pubmedDashboard/issues", "Remotes": [ "jimjam-slam/ggflags", "hrbrmstr/waffle" ], "Config/pak/sysreqs": "libgdal-dev gdal-bin libgeos-dev make libicu-dev\nlibjpeg-dev libxml2-dev libssl-dev libproj-dev libsqlite3-dev\nlibx11-dev", "Repository": "https://rempsyc.r-universe.dev", "Date/Publication": "2024-05-30 14:46:59 UTC", "RemoteUrl": "https://github.com/rempsyc/pubmedDashboard", "RemoteRef": "HEAD", "RemoteSha": "823f2fb5ed2f606350181d914909155011340376", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-15 05:44:07 UTC", "User": "root" }, "Author": "Rémi Thériault [aut, cre] (ORCID:\n)", "Maintainer": "Rémi Thériault ", "MD5sum": "79c439e887b4dfca180ec9e5b2196f5e", "_user": "rempsyc", "_type": "src", "_file": "pubmedDashboard_0.0.3.tar.gz", "_fileid": "91513739970563e6fca29e144d33956ba92214e063cb0413d0f1cf7e17993f0c", "_filesize": 8573992, "_sha256": "91513739970563e6fca29e144d33956ba92214e063cb0413d0f1cf7e17993f0c", "_created": "2026-05-15T05:44:07.000Z", "_published": "2026-06-02T20:05:40.304Z", "_distro": "noble", "_jobs": [ { "job": 79161169155, "time": 177, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7010903059" 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"https://github.com/r-universe/rempsyc/actions/runs/25902357445", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/rempsyc/pubmedDashboard", "_commit": { "id": "823f2fb5ed2f606350181d914909155011340376", "author": "Rémi Thériault <13123390+rempsyc@users.noreply.github.com>", "committer": "Rémi Thériault <13123390+rempsyc@users.noreply.github.com>", "message": "deprecation message\n", "time": 1717080419 }, "_maintainer": { "name": "Rémi Thériault", "email": "remi.theriault@mail.mcgill.ca", "login": "rempsyc", "mastodon": "@rempsyc@mastodon.world", "bluesky": "@remi-theriault.com", "linkedin": "in/rempsyc", "orcid": "0000-0003-4315-6788", "twitter": "@rempsyc", "uuid": 13123390 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "easyPubMed", "role": "Imports" }, { "package": "rempsyc", "role": "Imports" }, { "package": "insight", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "stringi", "role": "Imports" }, { "package": "countrycode", "role": "Imports" }, { "package": "Ecfun", "role": "Imports" }, { "package": "lubridate", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "waffle", "version": ">= 1.0.1", "role": "Suggests" }, { "package": "ggflags", "version": ">= 0.0.3", "role": "Suggests" }, { "package": "plotly", "role": "Suggests" }, { "package": "ggtext", "role": "Suggests" }, { "package": "dygraphs", "role": "Suggests" }, { "package": "xts", "role": "Suggests" }, { "package": "rstudioapi", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "rempsyc", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 4, "_contributors": [ { "user": "rempsyc", "count": 104, "uuid": 13123390 } ], "_userbio": { "uuid": 13123390, "type": "user", "name": "Rémi Thériault", "description": "Postdoc @centerconflictcooperation" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/pubmedDashboard" }, "_devurl": "https://github.com/rempsyc/pubmeddashboard", "_pkgdown": "https://rempsyc.github.io/pubmedDashboard/", "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/pubmedDashboard.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "add_affiliation", "add_region", "all_articles_to_df", "article_to_df2", "batch_pubmed_download2", "check_pubmed_api_token", "clean_journals_continents", "convert_hex_to_char", "detect_missing_journals", "dygraph_year", "extract_split_address", "get_affiliation", "get_country", "match_university", "partial_vlookup", "read_bind_all_data", "render_dashboard", "save_process_pubmed_batch", "scatter_continent_year", "scatter_country_year", "scatter_figure1", "table_continent", "table_continent_journal", "table_continent_year", "table_country", "table_country_journal", "table_country_year", "table_journal_count", "table_missing_country", "waffle_continent", "waffle_continent_journal", "waffle_country", "waffle_country_journal" ], "_datasets": [ { "name": "countries", "title": "List of countries taken from the package 'countrycode'", "object": "countries", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "journal_field", "title": "List of academic journals and corresponding fields", "object": "journal_field", "class": [ "data.frame" ], "fields": [ "journal", "journal_short", "field", "original_journal" ], "rows": 57, "table": true, "tojson": true }, { "name": "universities", "title": "A data frame of university and corresponding country", "object": "universities", "class": [ "data.frame" ], "fields": [ "country_code", "university" ], "rows": 9420, "table": true, "tojson": true }, { "name": "us_states", "title": "List of US states taken from the package 'countrycode'", "object": "us_states", "class": [ "data.frame" ], "fields": [ "state.name", "state.abb", "state.regex" ], "rows": 50, "table": true, "tojson": true }, { "name": "world_capitals", "title": "List of world capitals taken from the package 'maps'", "object": "world_capitals", "class": [ "data.frame" ], "fields": [ "name", "country.etc", "pop", "lat", "long", "capital" ], "rows": 259, "table": true, "tojson": true } ], "_help": [ { "page": "add_affiliation", "title": "Add affiliations to pubmedDashboard dataframe", "topics": [ "add_affiliation" ] }, { "page": "add_region", "title": "Add regions to pubmedDashboard dataframe", "topics": [ "add_region" ] }, { "page": "all_articles_to_df", "title": "Convert list of PubMed XLM files to dataframe", "topics": [ "all_articles_to_df" ] }, { "page": "article_to_df2", "title": "Convert PubMed XLM files to dataframe", "topics": [ "article_to_df2" ] }, { "page": "batch_pubmed_download2", "title": "Download PubMed data with query string", "topics": [ "batch_pubmed_download2" ] }, { "page": "check_pubmed_api_token", "title": "Check whether the PubMed API token is of the correct length and valid", "topics": [ "check_pubmed_api_token" ] }, { "page": "clean_journals_continents", "title": "Clean dataframe, for names of journals and continents", "topics": [ "clean_journals_continents" ] }, { "page": "convert_hex_to_char", "title": "Convert a Hex string to regular text", "topics": [ "convert_hex_to_char" ] }, { "page": "countries", "title": "List of countries taken from the package 'countrycode'", "topics": [ "countries" ] }, { "page": "detect_missing_journals", "title": "Detect missing journals", "topics": [ "detect_missing_journals" ] }, { "page": "dygraph_year", "title": "Generate a dygraph of journal paper percentages, by country and year", "topics": [ "dygraph_year" ] }, { "page": "extract_split_address", "title": "Extracts correct component from a splitted affiliation address", "topics": [ "extract_split_address" ] }, { "page": "get_affiliation", "title": "Get affiliations", "topics": [ "get_affiliation" ] }, { "page": "get_country", "title": "Get country", "topics": [ "get_country" ] }, { "page": "journal_field", "title": "List of academic journals and corresponding fields", "topics": [ "journal_field" ] }, { "page": "match_university", "title": "Match list of universities to countries in a dataframe", "topics": [ "match_university" ] }, { "page": "partial_vlookup", "title": "Like Excel vlookup/grep, both both ways", "topics": [ "partial_vlookup" ] }, { "page": "read_bind_all_data", "title": "Read local pubmedDashboard data files and bind them in a single dataframe", "topics": [ "read_bind_all_data" ] }, { "page": "render_dashboard", "title": "Render complete pubmedDashboard dashboard", "topics": [ "render_dashboard" ] }, { "page": "save_process_pubmed_batch", "title": "Mega function to process and save PubMed data", "topics": [ "save_process_pubmed_batch" ] }, { "page": "scatter_continent_year", "title": "Generate table of journal paper percentages, by continent and year", "topics": [ "scatter_continent_year" ] }, { "page": "scatter_country_year", "title": "Generate table of journal paper percentages, by continent and year", "topics": [ "scatter_country_year" ] }, { "page": "scatter_figure1", "title": "Generate table of journal paper percentages, by continent and year", "topics": [ "scatter_figure1" ] }, { "page": "table_continent", "title": "Generate table of journal paper percentages, by continent", "topics": [ "table_continent" ] }, { "page": "table_continent_journal", "title": "Generate table of journal paper percentages, by continent and journals", "topics": [ "table_continent_journal" ] }, { "page": "table_continent_year", "title": "Generate table of journal paper percentages, by continent and year", "topics": [ "table_continent_year" ] }, { "page": "table_country", "title": "Generate table of journal paper percentages, by country", "topics": [ "table_country" ] }, { "page": "table_country_journal", "title": "Generate table of journal paper percentages, by continent and year", "topics": [ "table_country_journal" ] }, { "page": "table_country_year", "title": "Generate table of journal paper percentages, by country and year", "topics": [ "table_country_year" ] }, { "page": "table_journal_count", "title": "Count number of papers per journal, with year range", "topics": [ "table_journal_count" ] }, { "page": "table_missing_country", "title": "Generate table of journal paper percentages, by country", "topics": [ "table_missing_country" ] }, { "page": "universities", "title": "A data frame of university and corresponding 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