Website dataset workflow

Ernest Guevarra

The Pandemic PACT data is publicly available for download from its website. pactr provides an application programming interface (API) to the research programme’s dataset available from its website data download facility allowing for programmatic access to its publicly available funder tracker dataset.

Website data interface

The functions for interfacing with the data available from the Pandemic PACT website allow for downloading, reading, and processing. Current website data-specific functionalities available in pactr are:

1. Downloading of Pandemic PACT dataset available from the website (stable);

2. Reading of Pandemic PACT dataset available from the website (stable); and,

3. Processing of Pandemic PACT dataset available from the website (experimental).

Website data workflow

Download data available from website

To download the Pandemic PACT tracker dataset available from its website, the following command can be used:

## Save the dataset from website to a temporary directory ----
pact_download_website(path = tempdir())

which will return the path to the downloaded dataset:

#> [1] "/tmp/RtmpkRyT53/pandemic-pact-grants.csv"

Read the Pandemic PACT tracker dataset from the website

Instead of downloading, the Pandemic PACT dataset available from its website can be read into R directly as follows:

pact_read_website()

which results in the following:

#> # A tibble: 19,172 × 39
#>    GrantID PubMedGrantId             GrantTitleEng Abstract GrantStartYear
#>    <chr>   <chr>                     <chr>         <chr>             <int>
#>  1 C00018  unknown                   "Mathematica… "Mathem…             NA
#>  2 C00019  CCP-nCoV                  "Cohort foll… "Cohort…             NA
#>  3 C00020  THERAMAB                  "Identificat… "Identi…             NA
#>  4 C00021  None                      "Using socia… "Using …             NA
#>  5 C00022  CoV-CONTACT               "Follow-up o… "Follow…             NA
#>  6 C00023  Réplicon                  "Development… "Develo…             NA
#>  7 C00024  A Toolbox for SARS-CoV-2… "Potentiatin… "Potent…             NA
#>  8 C00025  NHP Model                 "Establishme… "Establ…             NA
#>  9 C00026  SARS-CoV2-LIPS            "Antibody pr… "Antibo…             NA
#> 10 C00027  SARS-CoV-2_EVOLSERO       "Evolution o… "Evolut…             NA
#> # ℹ 19,162 more rows
#> # ℹ 34 more variables: PublicationYearOfAward <int>, GrantEndYear <int>,
#> #   ResearchInstitutionName <chr>, GrantAmountConverted <dbl>,
#> #   StudySubject <chr>, Ethnicity <chr>, AgeGroups <chr>, Rurality <chr>,
#> #   VulnerablePopulations <chr>, OccupationalGroups <chr>,
#> #   StudyType <chr>, ClinicalTrial <chr>, Pathogen <chr>,
#> #   InfluenzaA <chr>, InfluenzaH1 <chr>, InfluenzaH2 <chr>, …

Process the Pandemic PACT tracker dataset from the website

The package includes functions that will process the Pandemic PACT tracker dataset into specific structures and aggregations that will allow for further plotting and reporting of similar outputs that are currently presented in the Pandemic PACT website.

For example, the following will process the Pandemic PACT tracker dataset into an aggregated dataset structure that can be used to create a similar plot to the one presented in the website.

pact_read_website() |>
  pact_process_website() |>
  pact_process_topic_group(topic = "Disease", group = "GrantStartYear")

which produces the following output:

#> Error in pact_process_topic_group(pact_process_website(pact_data), topic = "Disease", : could not find function "pact_process_topic_group"
#> Error: object 'tidy_df' not found