pakillo / grateful Goto Github PK

cite_packages(out.format = "md". out.path = "docs")

pkgs = c(
  "grateful",
  "sf",
  "osmdata",
  "dodgr",
  "stplanr",
  "dplyr",
  "piggyback",
  "tidygraph",
  "sfnetworks",
  "purrr",
  "devtools"
  )
to_install = !pkgs %in% installed.packages()
if(any(to_install)) {
  install.packages(pkgs[to_install])
}
devtools::install_github("Pakillo/grateful")
#> Skipping install of 'grateful' from a github remote, the SHA1 (5fc74648) has not changed since last install.
#>   Use `force = TRUE` to force installation
purrr::map_lgl(pkgs, require, character.only = TRUE)
#> Loading required package: grateful
#> Loading required package: sf
#> Linking to GEOS 3.7.0, GDAL 2.3.2, PROJ 5.2.0
#> Loading required package: osmdata
#> Data (c) OpenStreetMap contributors, ODbL 1.0. http://www.openstreetmap.org/copyright
#> Loading required package: dodgr
#> Loading required package: stplanr
#> Warning in fun(libname, pkgname): rgeos: versions of GEOS runtime 3.7.0-CAPI-1.11.0
#> and GEOS at installation 3.6.2-CAPI-1.10.2differ
#> Loading required package: dplyr
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
#> Loading required package: piggyback
#> Loading required package: tidygraph
#> 
#> Attaching package: 'tidygraph'
#> The following object is masked from 'package:stats':
#> 
#>     filter
#> Loading required package: sfnetworks
#> Loading required package: purrr
#> Loading required package: devtools
#>  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

cites = grateful::get_citations(pkgs)
#> Warning in FUN(X[[i]], ...): no date field in DESCRIPTION file of package
#> 'dplyr'
#> Warning in FUN(X[[i]], ...): no date field in DESCRIPTION file of package
#> 'sfnetworks'
lapply(cites, write, file = "pkg.bib", append = TRUE)
#> $grateful
#> NULL
#> 
#> $sf
#> NULL
#> 
#> $osmdata
#> NULL
#> 
#> $dodgr
#> NULL
#> 
#> $stplanr
#> NULL
#> 
#> $dplyr
#> NULL
#> 
#> $piggyback
#> NULL
#> 
#> $tidygraph
#> NULL
#> 
#> $sfnetworks
#> NULL
#> 
#> $purrr
#> NULL
#> 
#> $devtools
#> NULL

# Read a CITATION.cff file
f <- system.file("examples/reprozip.cff", package = "cffr")
library(cffr)

# cffr has its own class cff
cff_s3_class <-cff_read(f)
class(cff_s3_class)
#> [1] "cff"

# You can parse it to bibentries

tobib <- cff_to_bibtex(cff_s3_class, what = "preferred")
class(tobib)
#> [1] "bibentry"

tobib
#> Anonymous (ed.) (2016). _ReproZip: Computational Reproducibility With
#> Ease_, series SIGMOD '16. doi:10.1145/2882903.2899401
#> <https://doi.org/10.1145/2882903.2899401>.

# Use with grateful
library(grateful)
citekeys <- get_citations(c("knitr", "renv"), out.dir = tempdir())

# Read to bibtex file created
fgrateful <- file.path(tempdir(), "grateful-refs.bib")

readLines(fgrateful)
#>  [1] "@Manual{knitr2023,"                                                              
#>  [2] "title = {{knitr}: A General-Purpose Package for Dynamic Report Generation in R},"
#>  [3] "  author = {Yihui Xie},"                                                         
#>  [4] "  year = {2023},"                                                                
#>  [5] "  note = {R package version 1.42},"                                              
#>  [6] "  url = {https://yihui.org/knitr/},"                                             
#>  [7] "}"                                                                               
#>  [8] ""                                                                                
#>  [9] "@Book{knitr2015,"                                                                
#> [10] "  title = {Dynamic Documents with {R} and knitr},"                               
#> [11] "  author = {Yihui Xie},"                                                         
#> [12] "  publisher = {Chapman and Hall/CRC},"                                           
#> [13] "  address = {Boca Raton, Florida},"                                              
#> [14] "  year = {2015},"                                                                
#> [15] "  edition = {2nd},"                                                              
#> [16] "  note = {ISBN 978-1498716963},"                                                 
#> [17] "  url = {https://yihui.org/knitr/},"                                             
#> [18] "}"                                                                               
#> [19] ""                                                                                
#> [20] "@InCollection{knitr2014,"                                                        
#> [21] "  booktitle = {Implementing Reproducible Computational Research},"               
#> [22] "  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},"           
#> [23] "title = {{knitr}: A Comprehensive Tool for Reproducible Research in {R}},"       
#> [24] "  author = {Yihui Xie},"                                                         
#> [25] "  publisher = {Chapman and Hall/CRC},"                                           
#> [26] "  year = {2014},"                                                                
#> [27] "  note = {ISBN 978-1466561595},"                                                 
#> [28] "}"                                                                               
#> [29] "@Manual{renv,"                                                                   
#> [30] "title = {{renv}: Project Environments},"                                         
#> [31] "  author = {Kevin Ushey},"                                                       
#> [32] "  year = {2023},"                                                                
#> [33] "  note = {R package version 0.17.3},"                                            
#> [34] "  url = {https://rstudio.github.io/renv/},"                                      
#> [35] "}"

bibtex::read.bib(fgrateful)
#> Xie Y (2023). _knitr: A General-Purpose Package for Dynamic Report
#> Generation in R_. R package version 1.42, <https://yihui.org/knitr/>.
#> 
#> Xie Y (2015). _Dynamic Documents with R and knitr_, 2nd edition.
#> Chapman and Hall/CRC, Boca Raton, Florida. ISBN 978-1498716963,
#> <https://yihui.org/knitr/>.
#> 
#> Xie Y (2014). "knitr: A Comprehensive Tool for Reproducible Research in
#> R." In Stodden V, Leisch F, Peng RD (eds.), _Implementing Reproducible
#> Computational Research_. Chapman and Hall/CRC. ISBN 978-1466561595.
#> 
#> Ushey K (2023). _renv: Project Environments_. R package version 0.17.3,
#> <https://rstudio.github.io/renv/>.

# With cffr you can add references to that

cffr::write_bib(tobib, file = fgrateful, append = TRUE)
#> ℹ Creating a backup of '/tmp/RtmpuhBdXk/grateful-refs.bib' in '/tmp/RtmpuhBdXk/grateful-refs.bib.bk1'
#> ℹ Writing 1 BibTeX entry ...
#> ✔ Results written to '/tmp/RtmpuhBdXk/grateful-refs.bib'

# And now we have added a citation from a CITATION.cff file

readLines(fgrateful)
#>  [1] "@Manual{knitr2023,"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
#>  [2] "title = {{knitr}: A General-Purpose Package for Dynamic Report Generation in R},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#>  [3] "  author = {Yihui Xie},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
#>  [4] "  year = {2023},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#>  [5] "  note = {R package version 1.42},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
#>  [6] "  url = {https://yihui.org/knitr/},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
#>  [7] "}"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
#>  [8] ""                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#>  [9] "@Book{knitr2015,"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#> [10] "  title = {Dynamic Documents with {R} and knitr},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
#> [11] "  author = {Yihui Xie},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
#> [12] "  publisher = {Chapman and Hall/CRC},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
#> [13] "  address = {Boca Raton, Florida},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
#> [14] "  year = {2015},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#> [15] "  edition = {2nd},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
#> [16] "  note = {ISBN 978-1498716963},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
#> [17] "  url = {https://yihui.org/knitr/},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
#> [18] "}"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
#> [19] ""                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#> [20] "@InCollection{knitr2014,"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
#> [21] "  booktitle = {Implementing Reproducible Computational Research},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
#> [22] "  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
#> [23] "title = {{knitr}: A Comprehensive Tool for Reproducible Research in {R}},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
#> [24] "  author = {Yihui Xie},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
#> [25] "  publisher = {Chapman and Hall/CRC},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
#> [26] "  year = {2014},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#> [27] "  note = {ISBN 978-1466561595},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
#> [28] "}"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
#> [29] "@Manual{renv,"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
#> [30] "title = {{renv}: Project Environments},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
#> [31] "  author = {Kevin Ushey},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
#> [32] "  year = {2023},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#> [33] "  note = {R package version 0.17.3},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
#> [34] "  url = {https://rstudio.github.io/renv/},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
#> [35] "}"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
#> [36] "@Proceedings{rampinfreire:2016,"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
#> [37] "  title = {ReproZip: Computational Reproducibility With Ease},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
#> [38] "  author = {Remi Rampin and Juliana Freire and Fernando Chirigati and Dennis Shasha},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
#> [39] "  year = {2016},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#> [40] "  month = {jun},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#> [41] "  address = {San Francisco, US},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
#> [42] "  series = {SIGMOD '16},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
#> [43] "  doi = {10.1145/2882903.2899401},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
#> [44] "  abstract = {We present ReproZip, the recommended packaging tool for the SIGMOD Reproducibility Review. ReproZip was designed to simplify the process of making an existing computational experiment reproducible across platforms, even when the experiment was put together without reproducibility in mind. The tool creates a self-contained package for an experiment by automatically tracking and identifying all its required dependencies. The researcher can share the package with others, who can then use ReproZip to unpack the experiment, reproduce the findings on their favorite operating system, as well as modify the original experiment for reuse in new research, all with little effort. The demo will consist of examples of non-trivial experiments, showing how these can be packed in a Linux machine and reproduced on different machines and operating systems. Demo visitors will also be able to pack and reproduce their own experiments.},"
#> [45] "  date = {2016-06-26},"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
#> [46] "}"
bibtex::read.bib(fgrateful)
#> Xie Y (2023). _knitr: A General-Purpose Package for Dynamic Report
#> Generation in R_. R package version 1.42, <https://yihui.org/knitr/>.
#> 
#> Xie Y (2015). _Dynamic Documents with R and knitr_, 2nd edition.
#> Chapman and Hall/CRC, Boca Raton, Florida. ISBN 978-1498716963,
#> <https://yihui.org/knitr/>.
#> 
#> Xie Y (2014). "knitr: A Comprehensive Tool for Reproducible Research in
#> R." In Stodden V, Leisch F, Peng RD (eds.), _Implementing Reproducible
#> Computational Research_. Chapman and Hall/CRC. ISBN 978-1466561595.
#> 
#> Ushey K (2023). _renv: Project Environments_. R package version 0.17.3,
#> <https://rstudio.github.io/renv/>.
#> 
#> Anonymous (ed.) (2016). _ReproZip: Computational Reproducibility With
#> Ease_, series SIGMOD '16. doi:10.1145/2882903.2899401
#> <https://doi.org/10.1145/2882903.2899401>.