Package: pubmedDashboard 0.0.3

pubmedDashboard: Creating PubMed Data Visualization Dashboards

Package to facilitate the creation of data visualization dashboards through the flexdashboard and easyPubMed packages. This package is now deprecated in favour of the pubDashboard package.

Authors:Rémi Thériault [aut, cre]

pubmedDashboard_0.0.3.tar.gz
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pubmedDashboard.pdf |pubmedDashboard.html✨
pubmedDashboard/json (API)

# Install 'pubmedDashboard' in R:
install.packages('pubmedDashboard', repos = c('https://rempsyc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rempsyc/pubmeddashboard/issues

Pkgdown site:https://rempsyc.github.io

Datasets:
  • countries - List of countries taken from the package 'countrycode'
  • journal_field - List of academic journals and corresponding fields
  • universities - A data frame of university and corresponding country
  • us_states - List of US states taken from the package 'countrycode'
  • world_capitals - List of world capitals taken from the package 'maps'

On CRAN:

Conda:

2.90 score 4 stars 6 scripts 33 exports 100 dependencies

Last updated 10 months agofrom:823f2fb5ed. Checks:4 OK, 5 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 26 2025
R-4.5-winOKMar 26 2025
R-4.5-macOKMar 26 2025
R-4.5-linuxOKMar 26 2025
R-4.4-winNOTEMar 26 2025
R-4.4-macNOTEMar 26 2025
R-4.4-linuxNOTEMar 26 2025
R-4.3-winNOTEMar 26 2025
R-4.3-macNOTEMar 26 2025

Exports:add_affiliationadd_regionall_articles_to_dfarticle_to_df2batch_pubmed_download2check_pubmed_api_tokenclean_journals_continentsconvert_hex_to_chardetect_missing_journalsdygraph_yearextract_split_addressget_affiliationget_countrymatch_universitypartial_vlookupread_bind_all_datarender_dashboardsave_process_pubmed_batchscatter_continent_yearscatter_country_yearscatter_figure1table_continenttable_continent_journaltable_continent_yeartable_countrytable_country_journaltable_country_yeartable_journal_counttable_missing_countrywaffle_continentwaffle_continent_journalwaffle_countrywaffle_country_journal

Dependencies:ashaskpassbitbit64bitopsBMAclicliprclustercolorspacecountrycodecpp11crayoncurlDEoptimRdeSolvedotCall64dplyreasyPubMedEcfunfansifarverfdafdsfieldsFNNgenericsggplot2gluegtablehdrcdehmshttrinlineinsightisobandjpegjsonlitekernlabKernSmoothkslabelinglatticeleapslifecyclelocfitlubridatemagrittrmapsMASSMatrixmclustmgcvmimemulticoolmunsellmvtnormnlmeopensslpcaPPpillarpkgconfigpracmaprettyunitsprogresspurrrR6rainbowrasterRColorBrewerRcppRCurlreadrrempsycrlangrobustbaserrcovrvestrworldmapscalesselectrspspamstringistringrsurvivalsysterratibbletidyrtidyselecttimechangetistzdbutf8vctrsviridisLitevroomwithrxml2

Readme and manuals

Help Manual

Help pageTopics
Add affiliations to pubmedDashboard dataframeadd_affiliation
Add regions to pubmedDashboard dataframeadd_region
Convert list of PubMed XLM files to dataframeall_articles_to_df
Convert PubMed XLM files to dataframearticle_to_df2
Download PubMed data with query stringbatch_pubmed_download2
Check whether the PubMed API token is of the correct length and validcheck_pubmed_api_token
Clean dataframe, for names of journals and continentsclean_journals_continents
Convert a Hex string to regular textconvert_hex_to_char
List of countries taken from the package 'countrycode'countries
Detect missing journalsdetect_missing_journals
Generate a dygraph of journal paper percentages, by country and yeardygraph_year
Extracts correct component from a splitted affiliation addressextract_split_address
Get affiliationsget_affiliation
Get countryget_country
List of academic journals and corresponding fieldsjournal_field
Match list of universities to countries in a dataframematch_university
Like Excel vlookup/grep, both both wayspartial_vlookup
Read local pubmedDashboard data files and bind them in a single dataframeread_bind_all_data
Render complete pubmedDashboard dashboardrender_dashboard
Mega function to process and save PubMed datasave_process_pubmed_batch
Generate table of journal paper percentages, by continent and yearscatter_continent_year
Generate table of journal paper percentages, by continent and yearscatter_country_year
Generate table of journal paper percentages, by continent and yearscatter_figure1
Generate table of journal paper percentages, by continenttable_continent
Generate table of journal paper percentages, by continent and journalstable_continent_journal
Generate table of journal paper percentages, by continent and yeartable_continent_year
Generate table of journal paper percentages, by countrytable_country
Generate table of journal paper percentages, by continent and yeartable_country_journal
Generate table of journal paper percentages, by country and yeartable_country_year
Count number of papers per journal, with year rangetable_journal_count
Generate table of journal paper percentages, by countrytable_missing_country
A data frame of university and corresponding countryuniversities
List of US states taken from the package 'countrycode'us_states
Generate a waffle chart of journal paper percentages, by continent (each square = 1% of data)waffle_continent
Generate a waffle chart of journal paper percentages, by continent (each square = 1% of data)waffle_continent_journal
Generate a waffle plot made of country flagswaffle_country
Generate a waffle chart of journal paper percentages, by continent (each square = 1% of data)waffle_country_journal
List of world capitals taken from the package 'maps'world_capitals