Get COVID-19 resource metadata

getResourcesData(
  query = NULL,
  types = NULL,
  size = 10,
  fetchAll = FALSE,
  fields = NULL,
  sort = NULL,
  facets = NULL,
  facet_size = 10
)

Arguments

query: (optional) constructs a query over ALL fields, or a fielded query searching within specific fields. Fielded query terms should be separated by ` AND ` or ` OR `. See Elasticserach query strings for more info.
types: (optional) vector of resource type to return. The most frequent types include: "Publication", "ClinicalTrial", "Dataset", "Protocol", "SoftwareSourceCode", "Analysis".
size: (optional) number of records to return (default = 10)
fetchAll: (optional) Boolean whether to return all results for the query
fields: (optional) vector specifying which fields to return. Returns all by default. See the outbreak schema for possible fields.
sort: (optional) field to sort by. Add `-` to sort in descending order
facets: (optional) field by which to aggregate (count) their frequency
facet_size: (optional) how many facet groups to include in the facet total (default = 10, max = 1000)

Value

Examples

library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
# Get the date latest date for every resource (newest of dateModified, dateCreated, datePublished)
resources_by_date = getResourcesData(query = "date:[2020-01-01 TO *]", fields = "date")

# Get all metadata on remdesivir
remdesivir = getResourcesData(query = "remdesivir", fetchAll = TRUE, fields = c("@type", "name", "curatedBy"))
remdesivir %>% count(`@type`) %>% arrange(desc(n))
#> # A tibble: 11 × 2
#>    `@type`                         n
#>    <chr>                       <int>
#>  1 Publication                  3108
#>  2 ClinicalTrial                 460
#>  3 Dataset                        62
#>  4 ImageObject                    14
#>  5 Protocol                       14
#>  6 ScholarlyArticle               13
#>  7 Report                          3
#>  8 MediaObject                     2
#>  9 Book                            1
#> 10 Chapter                         1
#> 11 PresentationDigitalDocument     1

# Get all metadata for remdesivir Clinical Trials or Datasets
remdesivir_trials_data = getResourcesData(query = "remdesivir", types = c("ClinicalTrial", "Dataset"), fetchAll = TRUE, fields = c("@type", "name", "curatedBy"))
remdesivir_trials_data %>% count(`@type`) %>% arrange(desc(n))
#> # A tibble: 2 × 2
#>   `@type`           n
#>   <chr>         <int>
#> 1 ClinicalTrial   460
#> 2 Dataset          62