program_summary() finds all projects, publications,
and citations funded by the Funding Opportunity Announcements
(FOAs) in tbl, and summarizes by year the number of projects,
total award ammount, publications, citation count, and relative
citation ratio.
program_projects() returns a tibble of project
numbers and standardized contact PI name and project title.
program_publications() retrieves basic information
for all projects in the program.
Usage
program_summary(tbl, verbose = FALSE)
program_projects(tbl, by = c("foa", "project"), verbose = FALSE)
program_publications(tbl, verbose = FALSE)Arguments
- tbl
A tibble with column
opportunity_numbergiving the FOAs that define the program.- verbose
logical(1) report additional detail about progress of reporter and icite queries.
- by
character(1) indicating how program projects are summarized -- by
foaso that projects funded by more than one FOA are reported for each FOA, orprojectso that the summary is by project number across FOA.
Value
program_summary() returns a tibble ordered by fiscal year
summarizing project activity. Columns are
fiscal_year: integer() year of program.program: integer() number of active projects funded by this program.project: integer() number of projects funded by any program.program_amount: integer() award amount to active projects from this program.project_amount: integer() award amount across all programs.publications: integer() number of publications.citation_count: integer() citations to publications in year.relative_citation_ratio: numeric() sum of relative citation ratios for all publications in year.
program_projects() returns a tibble summarizing projects
funded under the FOAs. With by = "foa" (default), columns
are:
opportunity_number: character() full FOA funding the project.core_project_num: character() core project number.project_start_date: date() start date of projectproject_end_date: date() end date of project; maybe in the futurecontact_pi_name: character() name of most-recent contact PI for FOA and core project number.project_title: character() project title.fiscal_year: integer() fiscal years of funding; may differ from project duration (end date - start date.award_amount: integer() award amount through programs in the FOAs.
With by = "project", columns are the same but with
project_start_date, project_end_date, fiscal_year,
award_amount and most recent contact PI and project title
summarized over all FOAs under which a project was funded.
program_publications() returns a tibble with columns:
opportunity_number: character() full FOA funding the project.core_project_num: character() core project number.pmid: integer() PubMed identifier.year,title,authors,journal,doi: publication information.citn: integer() number of publicatons citing this publication, fromicite().rcr: relative citation ratio, as defined byicite().fcr: field citation rate, as defined byicite().
Details
program_summary() can return rows corresponding to years
before and after the years the FOAs were active. Values before
the FOA activity represent either a project funded through
other programs, or a grantee assigning credit to the FOA for a
citation published prior to the start of the FOA, or to a
project funded by FOAs not included in the input tbl but with
the same core project number as a funded project. Values after
the end of the FOA represent publications that acknowledge the
FOA after the termination of the grant.
program_projects() provides a single row for each
project. It chooses as opportunity_number the most recent FOA
under which the project was funded. It chooses as
contact_pi_name and project_title the name of the contact
PI and project title of the largest award in the most recent
year of funding.
Examples
foas <- tribble(
~opportunity_number, ~description,
"RFA-CA-19-039", "Early-Stage Development of ...",
"RFA-CA-19-038", "Development of Innovative ...",
"RFA-CA-19-040", "Advanced Development of ...",
"RFA-CA-19-041", "Sustained Support of..."
)
program_summary(foas)
#> # A tibble: 6 × 8
#> fiscal_year program project program_amount project_amount publication
#> <int> <int> <int> <int> <int> <int>
#> 1 2018 NA NA NA NA 3
#> 2 2019 NA NA NA NA 7
#> 3 2020 17 18 9688464 9870795 31
#> 4 2021 14 16 8376100 8532608 81
#> 5 2022 13 16 7924287 8427808 70
#> 6 2023 8 8 5809339 5809339 70
#> # ℹ 2 more variables: citation_count <int>, relative_citation_ratio <dbl>
program_projects(foas)
#> # A tibble: 17 × 9
#> opportunity_number core_project_num project_start_date project_end_date
#> <chr> <chr> <date> <date>
#> 1 RFA-CA-19-038 R21CA248118 2020-08-01 2022-11-17
#> 2 RFA-CA-19-038 R21CA248122 2020-05-15 2023-04-30
#> 3 RFA-CA-19-038 R21CA253408 2020-09-01 2024-08-31
#> 4 RFA-CA-19-038 R21CA253498 2020-09-01 2024-08-31
#> 5 RFA-CA-19-039 U01CA247760 2020-09-01 2024-05-31
#> 6 RFA-CA-19-039 U01CA248226 2020-07-01 2024-06-30
#> 7 RFA-CA-19-039 U01CA248235 2020-08-01 2024-07-31
#> 8 RFA-CA-19-039 U01CA253403 2020-09-01 2024-08-31
#> 9 RFA-CA-19-039 U01CA253511 2020-08-15 2023-07-31
#> 10 RFA-CA-19-040 U24CA248010 2020-09-24 2025-08-31
#> 11 RFA-CA-19-040 U24CA248265 2020-07-01 2025-06-30
#> 12 RFA-CA-19-040 U24CA248453 2020-09-24 2025-08-31
#> 13 RFA-CA-19-040 U24CA248454 2020-07-15 2025-06-30
#> 14 RFA-CA-19-040 U24CA248455 2020-09-03 2025-08-31
#> 15 RFA-CA-19-040 U24CA253531 2020-09-01 2025-08-31
#> 16 RFA-CA-19-040 U24CA253539 2020-09-10 2025-08-31
#> 17 RFA-CA-19-041 U24CA248457 2020-06-01 2025-05-31
#> # ℹ 5 more variables: contact_pi_name <chr>, project_title <chr>,
#> # fiscal_year <int>, award_amount <int>, project_amount <int>
pubs <- program_publications(foas)
## note that individual publications can be represented by more
## than one project
pubs
#> # A tibble: 262 × 11
#> opportunity_number core_project_num pmid year title authors journal doi
#> <chr> <chr> <int> <int> <chr> <chr> <chr> <chr>
#> 1 RFA-CA-19-040 U24CA253539 3.64e7 2023 PDCM… Zinaid… Nuclei… 10.1…
#> 2 RFA-CA-19-040 U24CA253531 3.68e7 2023 Eval… Dariya… Tomogr… 10.3…
#> 3 RFA-CA-19-040 U24CA253531 3.72e7 2023 Co-C… Stephe… Tomogr… 10.3…
#> 4 RFA-CA-19-040 U24CA253531 3.70e7 2023 Anim… Donna … Tomogr… 10.3…
#> 5 RFA-CA-19-040 U24CA253531 3.44e7 2021 Deep… Kaushi… Cancer… 10.3…
#> 6 RFA-CA-19-040 U24CA253531 3.43e7 2022 Co-c… Sudipt… Eur J … 10.1…
#> 7 RFA-CA-19-040 U24CA253531 3.71e7 2023 An O… Seth T… Tomogr… 10.3…
#> 8 RFA-CA-19-041 U24CA248457 3.13e7 2019 Metf… Xingyu… Cancer… 10.1…
#> 9 RFA-CA-19-041 U24CA248457 3.19e7 2020 STRI… Jong W… Elife 10.7…
#> 10 RFA-CA-19-041 U24CA248457 3.21e7 2020 TEAD… Jingti… J Inve… 10.1…
#> # ℹ 252 more rows
#> # ℹ 3 more variables: citation_count <int>, relative_citation_ratio <dbl>,
#> # field_citation_rate <dbl>
## unique publications
unique_pubs <-
pubs |>
select(-c("opportunity_number", "core_project_num")) |>
distinct()
unique_pubs
#> # A tibble: 262 × 9
#> pmid year title authors journal doi citation_count
#> <int> <int> <chr> <chr> <chr> <chr> <int>
#> 1 36399494 2023 PDCM Finder: an open glo… Zinaid… Nuclei… 10.1… 3
#> 2 36828382 2023 Evaluation of Apparent D… Dariya… Tomogr… 10.3… 3
#> 3 37218941 2023 Co-Clinical Imaging Meta… Stephe… Tomogr… 10.3… 2
#> 4 36961012 2023 Animal Models and Their … Donna … Tomogr… 10.3… 2
#> 5 34359696 2021 Deep Learning Segmentati… Kaushi… Cancer… 10.3… 17
#> 6 34328530 2022 Co-clinical FDG-PET radi… Sudipt… Eur J … 10.1… 31
#> 7 37104131 2023 An Online Repository for… Seth T… Tomogr… 10.3… 2
#> 8 31292160 2019 Metformin Inhibits Progr… Xingyu… Cancer… 10.1… 27
#> 9 31913126 2020 STRIPAK directs PP2A act… Jong W… Elife 10.7… 32
#> 10 32142794 2020 TEAD1 and TEAD3 Play Red… Jingti… J Inve… 10.1… 12
#> # ℹ 252 more rows
#> # ℹ 2 more variables: relative_citation_ratio <dbl>, field_citation_rate <dbl>
## publications per project
pubs |>
count(core_project_num, sort = TRUE) |>
left_join(program_projects(foas, by = "project"), by = "core_project_num")
#> # A tibble: 16 × 10
#> core_project_num n opportunity_number project_start_date project_end_date
#> <chr> <int> <chr> <date> <date>
#> 1 U01CA248226 74 RFA-CA-19-039 2020-07-01 2024-06-30
#> 2 U24CA248457 35 RFA-CA-19-041 2020-06-01 2025-05-31
#> 3 U01CA253403 24 RFA-CA-19-039 2020-09-01 2024-08-31
#> 4 U24CA248265 18 RFA-CA-19-040 2020-07-01 2025-06-30
#> 5 R21CA253498 16 RFA-CA-19-038 2020-09-01 2024-08-31
#> 6 U24CA248454 15 RFA-CA-19-040 2020-07-15 2025-06-30
#> 7 U24CA248453 14 RFA-CA-19-040 2020-09-24 2025-08-31
#> 8 R21CA253408 12 RFA-CA-19-038 2020-09-01 2024-08-31
#> 9 U01CA248235 12 RFA-CA-19-039 2020-08-01 2024-07-31
#> 10 U01CA247760 10 RFA-CA-19-039 2020-09-01 2024-05-31
#> 11 R21CA248122 9 RFA-CA-19-038 2020-05-15 2023-04-30
#> 12 R21CA248118 6 RFA-CA-19-038 2020-08-01 2022-11-17
#> 13 U24CA253531 6 RFA-CA-19-040 2020-09-01 2025-08-31
#> 14 U01CA253511 5 RFA-CA-19-039 2020-08-15 2023-07-31
#> 15 U24CA248010 5 RFA-CA-19-040 2020-09-24 2025-08-31
#> 16 U24CA253539 1 RFA-CA-19-040 2020-09-10 2025-08-31
#> # ℹ 5 more variables: contact_pi_name <chr>, project_title <chr>,
#> # fiscal_year <int>, award_amount <int>, project_amount <int>
## collaborations; see `?copublication`, `?cocitation`
pubs |>
count(pmid, sort = TRUE, name = "n_collab") |>
left_join(unique_pubs, by = "pmid")
#> # A tibble: 262 × 10
#> pmid n_collab year title authors journal doi citation_count
#> <int> <int> <int> <chr> <chr> <chr> <chr> <int>
#> 1 29985391 1 2018 Assembly and ac… Daniel… Nat Co… 10.1… 101
#> 2 30563849 1 2019 A Curated Resou… Karste… Mol Ce… 10.1… 127
#> 3 30583461 1 2018 Comprehensive G… Natali… Cancer… 10.3… 20
#> 4 30723579 1 2018 APOBEC-related … Amélie… Oncoim… 10.1… 48
#> 5 30773340 1 2019 A Platform of S… Xiaodo… Cancer… 10.1… 134
#> 6 31171722 1 2019 Illuminating th… Victor… J Biol… 10.1… 109
#> 7 31292160 1 2019 Metformin Inhib… Xingyu… Cancer… 10.1… 27
#> 8 31395609 1 2019 Use of Natural … Guerga… Cancer… 10.1… 54
#> 9 31513970 1 2019 Cyclin E Overex… Servan… iScien… 10.1… 3
#> 10 31695841 1 2019 The multikinase… Sean M… Oncota… 10.1… 8
#> # ℹ 252 more rows
#> # ℹ 2 more variables: relative_citation_ratio <dbl>, field_citation_rate <dbl>