Function reference • pubmedDashboard

All functions

add_affiliation(): Add affiliations to pubmedDashboard dataframe

add_region(): Add regions to pubmedDashboard dataframe

all_articles_to_df(): Convert list of PubMed XLM files to dataframe

article_to_df2(): Convert PubMed XLM files to dataframe

batch_pubmed_download2(): Download PubMed data with query string

check_pubmed_api_token(): Check whether the PubMed API token is of the correct length and valid

clean_journals_continents(): Clean dataframe, for names of journals and continents

convert_hex_to_char(): Convert a Hex string to regular text

countries: List of countries taken from the package countrycode

detect_missing_journals(): Detect missing journals

dygraph_year(): Generate a dygraph of journal paper percentages, by country and year

extract_split_address(): Extracts correct component from a splitted affiliation address

get_affiliation(): Get affiliations

get_country(): Get country

journal_field: List of academic journals and corresponding fields

match_university(): Match list of universities to countries in a dataframe

partial_vlookup(): Like Excel vlookup/grep, both both ways

read_bind_all_data(): Read local pubmedDashboard data files and bind them in a single dataframe

render_dashboard(): Render complete pubmedDashboard dashboard

save_process_pubmed_batch(): Mega function to process and save PubMed data

scatter_continent_year(): Generate table of journal paper percentages, by continent and year

scatter_country_year(): Generate table of journal paper percentages, by continent and year

scatter_figure1(): Generate table of journal paper percentages, by continent and year

table_continent(): Generate table of journal paper percentages, by continent

table_continent_journal(): Generate table of journal paper percentages, by continent and journals

table_continent_year(): Generate table of journal paper percentages, by continent and year

table_country(): Generate table of journal paper percentages, by country

table_country_journal(): Generate table of journal paper percentages, by continent and year

table_country_year(): Generate table of journal paper percentages, by country and year

table_journal_count(): Count number of papers per journal, with year range

table_missing_country(): Generate table of journal paper percentages, by country

universities: A data frame of university and corresponding country

us_states: List of US states taken from the package countrycode

waffle_continent(): Generate a waffle chart of journal paper percentages, by continent (each square = 1% of data)

waffle_continent_journal(): Generate a waffle chart of journal paper percentages, by continent (each square = 1% of data)

waffle_country(): Generate a waffle plot made of country flags

waffle_country_journal(): Generate a waffle chart of journal paper percentages, by continent (each square = 1% of data)

world_capitals: List of world capitals taken from the package maps