Case study: specific projects • grantpubcite

Compiled: 2023-12-12

This article illustrates how one might explore specific project numbers. Start by attaching our package and others we will use.

library(grantpubcite)
library(DT)

Projects

Suppose one is interested in specific projects, and the grant project numbers are known. Define and search for them.

project_nums <- c("U01CA190234", "U24CA194354")

Query the NIH Reporter for the projects of interest. The use of project_nums= for the argument required some reflection on the API schema provided at the end of the API projects endpoint.

projects <- reporter_projects(project_nums = project_nums)

Explore the data, for instance finding the Funding Opportunity Announcement the grants were reward under, and the fiscal years in which they were active.

projects |>
    group_by(core_project_num) |>
    summarize(
        foa = unique(opportunity_number),
        first_year = min(fiscal_year),
        last_year = max(fiscal_year),
        project_title = unique(project_title)
    ) |>
    gpc_datatable()

Publications

Use the core project numbers to retrieve known publications

core_project_nums <-
    pull(projects, "core_project_num") |>
    unique()
publications <- reporter_publications(core_project_nums = core_project_nums)

The number of publications associated with each grant are as follows:

publications |>
    count(coreproject) |>
    gpc_datatable()

Many publications were attributed to both grants

publications |>
    count(pmid, name = "cited_by") |>
    count(cited_by) |>
    gpc_datatable()

Citations

Obtain citation information (including information about the orginal publication) using the publications tibble

citations <- icite(publications)

There are 67 citation records, one for each publication. Explore these interactively

citations |>
    select(pmid, citation_count, relative_citation_ratio, year, title) |>
    gpc_datatable()

Use a ‘join’ between tables to associate publications and citations

left_join(publications, citations) |>
    group_by(coreproject, year) |>
    summarize(
        n_publications = n(),
        total_citations = sum(citation_count)
    ) |>
    gpc_datatable()
#> Joining with `by = join_by(pmid)`
#> `summarise()` has grouped output by 'coreproject'. You can override using the
#> `.groups` argument.

Session information

sessionInfo()
#> R version 4.3.2 (2023-10-31)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.3 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> time zone: UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] DT_0.31            grantpubcite_0.0.3 dplyr_1.1.4       
#> 
#> loaded via a namespace (and not attached):
#>  [1] sass_0.4.8        utf8_1.2.4        generics_0.1.3    stringi_1.8.2    
#>  [5] hms_1.1.3         digest_0.6.33     magrittr_2.0.3    evaluate_0.23    
#>  [9] fastmap_1.1.1     jsonlite_1.8.8    httr_1.4.7        purrr_1.0.2      
#> [13] fansi_1.0.6       crosstalk_1.2.1   textshaping_0.3.7 jquerylib_0.1.4  
#> [17] cli_3.6.1         rlang_1.1.2       crayon_1.5.2      ellipsis_0.3.2   
#> [21] bit64_4.0.5       withr_2.5.2       cachem_1.0.8      yaml_2.3.7       
#> [25] parallel_4.3.2    tools_4.3.2       tzdb_0.4.0        memoise_2.0.1    
#> [29] curl_5.2.0        vctrs_0.6.5       rjsoncons_1.0.1   R6_2.5.1         
#> [33] lifecycle_1.0.4   stringr_1.5.1     fs_1.6.3          htmlwidgets_1.6.4
#> [37] bit_4.0.5         vroom_1.6.5       ragg_1.2.6        pkgconfig_2.0.3  
#> [41] desc_1.4.3        pkgdown_2.0.7     pillar_1.9.0      bslib_0.6.1      
#> [45] glue_1.6.2        systemfonts_1.0.5 xfun_0.41         tibble_3.2.1     
#> [49] tidyselect_1.2.0  knitr_1.45        htmltools_0.5.7   rmarkdown_2.25   
#> [53] readr_2.1.4       compiler_4.3.2