About the Pandemic PACT Figshare repository
The Pandemic PACT data is meant to be publicly available for download from Figshare as per information from the research programme’s website (see here) and based on its open peer review paper on Wellcome Open Research describing the study protocol.
However, the link provided from the website (https://figshare.com/s/58527668245cb63f14f5) leads to a privately-shared Figshare collection. This means that the collection is only accessible to those who created it and to those who have been authorised to access it. The contents of the collection can be seen. However, the individual items cannot be viewed interactively from the browser and cannot be downloaded. This was the case as at 24 August 2024 when development of this package was initiated and continue to current date. This is contrary to what is mentioned in the research programme’s website:
“The data set can be downloaded from this website and all metadata and the dataset can be downloaded from Figshare.”
and in the study protocol under open peer review:
“Finally, the database is saved as a csv file and made available to the public on Figshare and can additionally be downloaded from the online funding tracker.”
Thinking that maybe this was just a mistake (i.e., that there is a private and public repository and the link to the private repository was the one that was mistakenly shared), a simple search was performed within Figshare using the keyword “Pandemic PACT” in the search field. This search yielded several results the most relevant of which was the following:
https://portal.sds.ox.ac.uk/pandemicpact
which is a University of Oxford-owned instance of Figshare containing the various data products (tracker data, data dictionary, scoping review data, extended data) referred to and used by the research programme. More importantly, this collection is public hence any individual, whether logged into Figshare or not, can view and download the datasets. Without further examining, it would be easy to think that this might be the publicly available data and data products being referred to by the website and the research protocol.
However, on closer inspection, the datasets within this collection were last updated in 2023 and the names of the file indicated that these were demonstration datasets.
Knowing that the research programme was indeed using Figshare to host its dataset (but not accessible) and given the existence of this demonstration dataset within the University of Oxford Figshare instance, development of Figshare-specific functions within the pactr package utilised the demonstration collection to prototype the Figshare-interface functions with the hope that if Pandemic PACT does decide to share their official dataset on Figshare publicly, the refactoring needed to get the current functions working will be minimal.
As such, the following guidance on use of the pactr Figshare interface functions should be used only for demonstration, development, and testing purposes and should not be used for production or research tasks.
Figshare interface
This package provides an application programming interface (API) to the research programme’s Figshare repository to provide programmatic access to its publicly available tracker data along with it’s other data products.
The functions for Figshare interface are wrappers to specific
functions of the {deposits}
package which provides the underlying universal interface to various
online research data deposition services including Figshare. Current
Figshare-specific functionalities available in pactr
are:
Listing of outputs/assets available from the Pandemic PACT Figshare repository (experimental);
Downloading of outputs/assets available from the Pandemic PACT Figshare repository (experimental);
Reading of dataset outputs/assets available from the Pandemic PACT Figshare repository (experimental); and,
Processing of Pandemic PACT data (experimental).
Figshare workflow
The following diagram illustrates the current steps (along with their corresponding functions) in the designed API for interfacing with the Figshare repository.
Set a Figshare client
Usage of pactr always starts with the setting up of a Figshare client. This requires creating a Figshare account and then creating a personal access token here.
Once a Figshare token is created, it needs to be stored as a local environment variable. This can be done using the following command in R:
Sys.setenv("FIGSHARE_TOKEN"="YOUR_TOKEN_HERE")Once this token has been set as described above, the following command can be run to setup a Figshare client:
pact_client <- pact_client_set()Once a Figshare client has been setup, you can now perform the functionalities provided by the pactr package.
List outputs/assets
To list available outputs/assets from the Pandemic PACT Figshare repository, issue the following command:
pact_list(pact_client)The output is a data.frame containing metadata regarding
contents of the Figshare Pandemic PACT group. The information within the
metadata are those provided by Figshare’s application programming
interface (API) and are either set by the Pandemic PACT data team or
by Figshare. The data.frame would look as follows:
#> # A tibble: 10 × 20
#> project_id id title doi handle url published_date thumb defined_type
#> <int> <int> <chr> <chr> <chr> <chr> <chr> <chr> <int>
#> 1 189177 26937448 PandemicPACT Data… 10.2… "" http… 2026-06-15T15… "" 3
#> 2 189177 32572314 Pandemic PACT (Cl… 10.2… "" http… 2026-06-05T12… "" 3
#> 3 189177 30084583 Ebola in the DRC … 10.2… "" http… 2026-06-02T08… "htt… 6
#> 4 NA 32261511 Hantavirus - Summ… 10.2… "" http… 2026-05-13T08… "htt… 6
#> 5 267506 31325617 RRNA Visualisatio… 10.2… "" http… 2026-03-05T15… "htt… 3
#> 6 NA 31390030 Pandemic Intellig… 10.2… "" http… 2026-02-23T14… "" 3
#> 7 189177 25412518 Direct data provi… 10.2… "" http… 2026-02-12T00… "htt… 3
#> 8 189177 25374430 PACT Grant Eligib… 10.2… "" http… 2026-02-12T00… "htt… 1
#> 9 189177 31096339 <b>Mapping the ex… 10.2… "" http… 2026-01-20T13… "" 3
#> 10 NA 30933185 Marburg Virus Dis… 10.2… "" http… 2025-12-22T13… "htt… 6
#> # ℹ 11 more variables: defined_type_name <chr>, group_id <int>, url_private_api <chr>,
#> # url_public_api <chr>, url_private_html <chr>, url_public_html <chr>, timeline <df[,2]>,
#> # resource_title <chr>, resource_doi <chr>, created_date <chr>, modified_date <chr>This function is useful in getting an overview of what is currently available in the Pandemic PACT Figshare repository.
Download outputs/assets
To download a specific output/asset - say the scoping review data - from the Pandemic PACT Figshare repository, issue the following commands:
## Get the unique identifier for the scoping review data from Figshare ----
file_id <- pact_list(pact_client) |>
subset(title == "Scoping Review Data", select = id) |>
unlist()
pact_download_figshare(pact_client, id = file_id, path = ".")This will download the file Scoping_Review-Data.xlsx
from the Pandemic PACT Figshare repository into the current working
directory.
Read the Pandemic PACT tracker dataset and data dictionary
To read the Pandemic PACT tracker dataset into R, issue the following command:
pact_read_figshare(pact_client)which outputs a data.frame of the available Pandemic
PACT funding tracker dataset that has been labelled.
pact_read_figshare(pact_client)This function reads the labelled tracker dataset by default. If the raw dataset is required, then issue the following command:
pact_read_figshare(pact_client, tracker_type = "raw")which outputs a data.frame of the available raw Pandemic
PACT funding tracker dataset.
pact_read_figshare(pact_client, tracker_type = "raw")
#> pactid grant_number grant_title_original grant_title_eng award_amount_converted
#> 1 SDS001 unknown Dummy record Dummy record 1234567
#> abstract laysummary oda_funding_used grant_type
#> 1 A dummy record to simulate a version update N/A -77 -77
#> grant_start_year study_subject___1 study_subject___2 study_subject___3 study_subject___4
#> 1 2020 0 0 1 0
#> study_subject___5 study_subject___6 study_subject____88 study_subject____99
#> 1 0 0 0 0
#> study_subject____9999 study_subject_other ethnicity___1 ethnicity___2 ethnicity___3
#> 1 0 0 0 0
#> ethnicity___4 ethnicity____88 ethnicity____99 ethnicity____9999 ethnicity_other
#> 1 0 0 1 0
#> age_groups___1 age_groups___2 age_groups___5 age_groups___6 age_groups___7 age_groups___3
#> 1 0 0 0 0 0 0
#> age_groups____88 age_groups____99 age_groups____9999 agegroups_other rurality___1
#> 1 0 1 0 0
#> rurality___2 rurality___3 rurality____88 rurality____99 rurality____9999 rurality_other
#> 1 0 0 0 1 0
#> vulnerable_population___1 vulnerable_population___2 vulnerable_population___3
#> 1 0 0 0
#> vulnerable_population___4 vulnerable_population___5 vulnerable_population___6
#> 1 0 0 0
#> vulnerable_population___7 vulnerable_population___8 vulnerable_population___9
#> 1 0 0 0
#> vulnerable_population___10 vulnerable_population___13 vulnerable_population___11
#> 1 0 0 0
#> vulnerable_population___12 vulnerable_population____88 vulnerable_population____99
#> 1 0 0 1
#> vulnerable_population____9999 vulnerable_population_other occupational_groups___1
#> 1 0 0
#> occupational_groups___2 occupational_groups___3 occupational_groups___4
#> 1 0 0 0
#> occupational_groups___5 occupational_groups___6 occupational_groups___7
#> 1 0 0 0
#> occupational_groups___8 occupational_groups___9 occupational_groups___10
#> 1 0 0 0
#> occupational_groups___11 occupational_groups___12 occupational_groups____88
#> 1 0 0 0
#> occupational_groups____99 occupational_groups____9999 occupationalgroups_other
#> 1 1 0
#> study_type___1 study_type___2 study_type___3 study_type___4 study_type___5 study_type___6
#> 1 0 0 0 0 0 0
#> study_type___7 study_type___8 study_type___9 study_type___10 study_type___11
#> 1 0 0 0 0 0
#> study_type___12 study_type___13 study_type___14 study_type___15 study_type___16
#> 1 0 0 0 0 0
#> study_type___17 study_type____88 study_type____99 study_type____9999 study_type_main___5
#> 1 0 0 1 0 0
#> study_type_main___6 study_type_main____88 study_type_main____99 study_type_main____9999
#> 1 1 0 0 0
#> clinical_trial___1 clinical_trial___2 clinical_trial___3 clinical_trial___4
#> 1 0 0 0 0
#> clinical_trial___5 clinical_trial___6 clinical_trial___7 clinical_trial___8
#> 1 0 0 0 0
#> clinical_trial___9 clinical_trial____99 clinical_trial____9999
#> 1 0 0 0
#> report_or_literature_based_research study_type_other pathogen___243624009
#> 1 0 NA 0
#> pathogen___243615000 pathogen___243607003 pathogen___407325004 pathogen___243602009
#> 1 0 0 1 0
#> pathogen___407486001 pathogen___407479009 pathogen___np001 pathogen____99
#> 1 1 0 0 0
#> coronavirus___1263733001 coronavirus___1263732006 coronavirus___840533007
#> 1 0 0 0
#> coronavirus___12637330001 coronavirus___697932005 coronavirus____88 coronavirus____99
#> 1 0 0 0 0
#> coronavirus____9999 bunyaviridae filoviridae arenaviridae henipavirus flaviviridae
#> 1 0 NA 424206003 NA -99 NA
#> influenza_a disease___840539006 disease___43489008 disease___37109004 disease___77503002
#> 1 NA 0 1 1 0
#> disease___19065005 disease___651000146102 disease___398447004 disease___406597005
#> 1 1 1 1 0
#> disease___402917003 disease___3928002 disease___762725007 disease___359814004
#> 1 0 1 0 0
#> disease___58750007 disease___6142004 disease___dx001 disease____88 disease____9999
#> 1 0 1 0 0 0
#> disease_other mesh_terms grant_complete funder_name___395 funder_name___290
#> 1 2 0 0
#> funder_name___46 funder_name___216 funder_name___152 funder_name___139 funder_name___174
#> 1 0 0 0 0 0
#> funder_name___102 funder_name___231 funder_name___95 funder_name___339 funder_name___262
#> 1 0 0 0 0 0
#> funder_name___209 funder_name___250 funder_name___229 funder_name___220 funder_name___223
#> 1 0 0 0 0 0
#> funder_name___242 funder_name___158 funder_name___107 funder_name___29 funder_name___21
#> 1 0 0 0 0 0
#> funder_name___8 funder_name___143 funder_name___259 funder_name___337 funder_name___265
#> 1 0 0 0 0 0
#> funder_name___110 funder_name___230 funder_name___99 funder_name___203 funder_name___133
#> 1 0 0 0 0 0
#> funder_name___380 funder_name___356 funder_name___396 funder_name___272 funder_name___15
#> 1 0 0 0 0 0
#> funder_name___252 funder_name___111 funder_name___347 funder_name___84 funder_name___291
#> 1 0 0 0 0 0
#> funder_name___312 funder_name___160 funder_name___35 funder_name___188 funder_name___100
#> 1 0 0 0 0 0
#> funder_name___293 funder_name___361 funder_name___349 funder_name___243 funder_name___166
#> 1 0 0 0 0 0
#> funder_name___384 funder_name___115 funder_name___313 funder_name___155 funder_name___281
#> 1 0 0 0 0 0
#> funder_name___397 funder_name___246 funder_name___198 funder_name___68 funder_name___377
#> 1 0 0 0 0 0
#> funder_name___388 funder_name___106 funder_name___74 funder_name___236 funder_name___298
#> 1 0 0 0 0 0
#> funder_name___297 funder_name___3 funder_name___168 funder_name___49 funder_name___193
#> 1 0 0 0 0 0
#> funder_name___16 funder_name___210 funder_name___44 funder_name___228 funder_name___136
#> 1 0 0 0 0 0
#> funder_name___131 funder_name___391 funder_name___141 funder_name___277 funder_name___28
#> 1 0 0 0 0 0
#> funder_name___18 funder_name___53 funder_name___394 funder_name___134 funder_name___92
#> 1 0 0 0 0 0
#> funder_name___128 funder_name___249 funder_name___248 funder_name___266 funder_name___199
#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 1 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 1 0 0 0
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#> 1 0 0 0 0 0
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#> 1 0 0 0 0
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#> 1 0 0 0 0
#> funder_country___175 funder_country___484 funder_country___583 funder_country___498
#> 1 0 0 0 0
#> funder_country___492 funder_country___496 funder_country___499 funder_country___500
#> 1 0 0 0 0
#> funder_country___504 funder_country___508 funder_country___104 funder_country___516
#> 1 0 0 0 0
#> funder_country___520 funder_country___524 funder_country___528 funder_country___540
#> 1 0 0 0 0
#> funder_country___554 funder_country___558 funder_country___562 funder_country___566
#> 1 0 0 0 0
#> funder_country___570 funder_country___574 funder_country___408 funder_country___580
#> 1 0 0 0 0
#> funder_country___578 funder_country___512 funder_country___586 funder_country___585
#> 1 0 0 0 0
#> funder_country___275 funder_country___591 funder_country___598 funder_country___600
#> 1 0 0 0 0
#> funder_country___604 funder_country___608 funder_country___612 funder_country___616
#> 1 0 0 0 0
#> funder_country___620 funder_country___630 funder_country___634 funder_country___807
#> 1 0 0 0 0
#> funder_country___638 funder_country___642 funder_country___643 funder_country___646
#> 1 0 0 0 0
#> funder_country___652 funder_country___654 funder_country___659 funder_country___662
#> 1 0 0 0 0
#> funder_country___663 funder_country___666 funder_country___670 funder_country___882
#> 1 0 0 0 0
#> funder_country___674 funder_country___678 funder_country___682 funder_country___686
#> 1 0 0 0 0
#> funder_country___688 funder_country___690 funder_country___694 funder_country___702
#> 1 0 0 0 0
#> funder_country___534 funder_country___703 funder_country___705 funder_country___90
#> 1 0 0 0 0
#> funder_country___706 funder_country___710 funder_country___239 funder_country___410
#> 1 0 0 0 0
#> funder_country___728 funder_country___724 funder_country___144 funder_country___729
#> 1 0 0 0 0
#> funder_country___740 funder_country___744 funder_country___752 funder_country___756
#> 1 0 0 0 0
#> funder_country___760 funder_country___158 funder_country___762 funder_country___834
#> 1 0 0 0 0
#> funder_country___764 funder_country___626 funder_country___768 funder_country___772
#> 1 0 0 0 0
#> funder_country___776 funder_country___780 funder_country___788 funder_country___792
#> 1 0 0 0 0
#> funder_country___795 funder_country___796 funder_country___798 funder_country___800
#> 1 0 0 0 0
#> funder_country___804 funder_country___784 funder_country___826 funder_country___581
#> 1 0 0 1 0
#> funder_country___840 funder_country___858 funder_country___860 funder_country___548
#> 1 0 0 0 0
#> funder_country___862 funder_country___704 funder_country___92 funder_country___850
#> 1 0 0 0 0
#> funder_country___876 funder_country___732 funder_country___887 funder_country___894
#> 1 0 0 0 0
#> funder_country___716 funder_country___9999 funder_country___99999 funder_country___999999
#> 1 0 0 0 0
#> funder_country___9999999 funder_region___1 funder_region___2 funder_region___5
#> 1 0 0 0 0
#> funder_region___99999 funder_region___9999 funder_region___999999 funder_region___9999999
#> 1 1 0 0 0
#> funder_region____99 funder_complete rorid research_institition_name
#> 1 0 0 grid.4280.e National University of Singapore
#> research_institution_country research_institution_country_iso
#> 1 Singapore 702
#> research_institution_region___1 research_institution_region___2
#> 1 0 0
#> research_institution_region___5 research_institution_region___99999
#> 1 0 0
#> research_institution_region___9999 research_institution_region___999999
#> 1 0 0
#> research_institution_region___9999999 research_institution_region____99
#> 1 1 0
#> research_location_country research_location_country_iso research_location_region___1
#> 1 Singapore, Hong Kong, Thailand 702, 344, 764 0
#> research_location_region___2 research_location_region___5 research_location_region___99999
#> 1 0 0 0
#> research_location_region___9999 research_location_region___999999
#> 1 0 1
#> research_location_region___9999999 research_location_region____99
#> 1 1 0
#> researchinstitution_complete tags___1 tags___2 tags___3 tags___4
#> 1 0 0 0 0 0
#> main_research_priority_area_number_new main_research_sub_priority_number_new
#> 1 3 3a, 3b
#> secondary_research_priority_area_number_new secondary_research_sub_priority_number_new
#> 1
#> researchcategory_complete
#> 1 2
#> [ reached 'max' / getOption("max.print") -- omitted 4637 rows ]Process the Pandemic PACT tracker dataset
To process the Pandemic PACT tracker dataset downloaded from Figshare, use the following commands:
pact_read_figshare(pact_client) |>
pact_process_figshare()which outputs a data.frame of the processed Pandemic
PACT funding tracker dataset:
pact_read_figshare(pact_client) |>
pact_process_figshare()
#> # A tibble: 4,637 × 37
#> PactID Grant.Number Grant.Title.Original Grant.Title.Eng Award.Amount.Converted
#> <chr> <chr> <chr> <chr> <dbl>
#> 1 C00153 unknown Serological studies to quantify… "Serological s… 1043108.
#> 2 C00154 unknown African COVID-19 Preparedness (… "African COVID… 2462448.
#> 3 C00155 unknown COVID-19 Intervention Modelling… "COVID-19 Inte… 1699974.
#> 4 C00156 unknown The African coaLition for Epide… "The African c… 1742202.
#> 5 C00157 unknown Characterization of SARS-CoV-2 … "Characterizat… 2484600
#> 6 C00158 unknown Investigation of pre-existing i… "Investigation… 1551892.
#> 7 C00159 unknown A comprehensive study of immuno… "" 1106601.
#> 8 C00160 MC_PC_19012 Centre for Global Infectious Di… "Centre for Gl… 660260
#> 9 C00161 MC_PC_19025 ISARIC - Coronavirus Clinical C… "ISARIC - Coro… 98958.
#> 10 C00162 MC_PC_19026 MRC Centre for Virus Research (… "MRC Centre fo… 660260
#> # ℹ 4,627 more rows
#> # ℹ 32 more variables: Abstract.Eng <chr>, Laysummary <chr>, ODA.funding.used <chr>,
#> # Grant.Type <chr>, Grant.Start.Year <int>, Study.Subject <list>, Ethnicity <list>,
#> # Age.Groups <list>, Rurality <list>, Vulnerable.Population <list>,
#> # Occupational.Groups <list>, Study.Type <list>, Clinical.Trial <list>, report <chr>,
#> # Pathogen <list>, Pathogen.Specific <list>, Disease <list>, mesh_terms <chr>,
#> # complete_section1 <chr>, Funder.Name <list>, Funder.Country <list>, …