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_number
giving 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
foa
so that projects funded by more than one FOA are reported for each FOA, orproject
so 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>