From 09466bbaa9ca92873ea17233e5ec01a3007894d2 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 15 Jul 2025 11:03:34 +0100 Subject: [PATCH 1/3] Add file with key citations for DataSHIELD --- inst/CITATION | 131 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 131 insertions(+) create mode 100644 inst/CITATION diff --git a/inst/CITATION b/inst/CITATION new file mode 100644 index 00000000..2be63039 --- /dev/null +++ b/inst/CITATION @@ -0,0 +1,131 @@ +bibentry( + bibtype = "Article", + title = "{DataSHIELD: taking the analysis to the data, not the data to the analysis}", + author = c( + person("Amadou", "Gaye"), + person("Yannick", "Marcon"), + person("Julia", "Isaeva"), + person("Philippe", "{LaFlamme}"), + person("Andrew", "Turner"), + person("Elinor M", "Jones"), + person("Joel", "Minion"), + person("Andrew W", "Boyd"), + person("Christopher J", "Newby"), + person("Marja-Liisa", "Nuotio"), + person("Rebecca", "Wilson"), + person("Oliver", "Butters"), + person("Barnaby", "Murtagh"), + person("Ipek", "Demir"), + person("Dany", "Doiron"), + person("Lisette", "Giepmans"), + person("Susan E", "Wallace"), + person("Isabelle", "Budin-Lj{\\o}sne"), + person("Carsten", "{Oliver Schmidt}"), + person("Paolo", "Boffetta"), + person("Mathieu", "Boniol"), + person("Maria", "Bota"), + person("Kim W", "Carter"), + person("Nick", "{deKlerk}"), + person("Chris", "Dibben"), + person("Richard W", "Francis"), + person("Tero", "Hiekkalinna"), + person("Kristian", "Hveem"), + person("Kirsti", "Kval{\\o}y"), + person("Sean", "Millar"), + person("Ivan J", "Perry"), + person("Annette", "Peters"), + person("Catherine M", "Phillips"), + person("Frank", "Popham"), + person("Gillian", "Raab"), + person("Eva", "Reischl"), + person("Nuala", "Sheehan"), + person("Melanie", "Waldenberger"), + person("Markus", "Perola"), + person("Edwin", "{van den Heuvel}"), + person("John", "Macleod"), + person("Bartha M", "Knoppers"), + person("Ronald P", "Stolk"), + person("Isabel", "Fortier"), + person("Jennifer R", "Harris"), + person("Bruce H R", "Woffenbuttel"), + person("Madeleine J", "Murtagh"), + person("Vincent", "Ferretti"), + person("Paul R", "Burton") + ), + journal = "International Journal of Epidemiology", + year = "2014", + volume = "43", + number = "6", + pages = "1929--1944", + doi = "10.1093/ije/dyu188", +) + +bibentry( + bibtype = "Article", + title = "{DataSHIELD – New Directions and Dimensions}", + author = c( + person("Rebecca C.", "Wilson"), + person("Oliver", "W. Butters"), + person("Demetris", "Avraam"), + person("James", "Baker"), + person("Jonathan A.", "Tedds"), + person("Andrew", "Turner"), + person("Madeleine", "Murtagh"), + person("Paul", "R. Burton") + ), + journal = "Data Science Journal", + year = "2017", + volume = "16", + number = "21", + pages = "1--21", + doi = "10.5334/dsj-2017-021" +) + +bibentry( + bibtype = "Article", + title = "{DataSHIELD: mitigating disclosure risk in a multi-site federated analysis platform}", + author = c( + person("Demetris", "Avraam"), + person("Rebecca C", "Wilson"), + person("Noemi", "{Aguirre Chan}"), + person("Soumya", "Banerjee"), + person("Tom R P", "Bishop"), + person("Olly", "Butters"), + person("Tim", "Cadman"), + person("Luise", "Cederkvist"), + person("Liesbeth", "Duijts"), + person("Xavier", "{Escrib{\\a`a} Montagut}"), + person("Hugh", "Garner"), + person("Gon{\\c c}alo", "Gon{\\c c}alves"), + person("Juan R", "Gonz{\\a'a}lez"), + person("Sido", "Haakma"), + person("Mette", "Hartlev"), + person("Jan", "Hasenauer"), + person("Manuel", "Huth"), + person("Eleanor", "Hyde"), + person("Vincent W V", "Jaddoe"), + person("Yannick", "Marcon"), + person("Michaela Th", "Mayrhofer"), + person("Fruzsina", "Molnar-Gabor"), + person("Andrei Scott", "Morgan"), + person("Madeleine", "Murtagh"), + person("Marc", "Nestor"), + person("Anne-Marie", "{Nybo Andersen}"), + person("Simon", "Parker"), + person("Angela", "{Pinot de Moira}"), + person("Florian", "Schwarz"), + person("Katrine", "Strandberg-Larsen"), + person("Morris AvSwertz"), + person("Marieke", "Welten"), + person("Stuart", "Wheater"), + person("Paul", "Burton") + ), + journal = "Bioinformatics Advances", + year = "2024", + volume = "5", + number = "1", + pages = "1--21", + doi = "10.1093/bioadv/vbaf046", + editor = person("Thomas", "Lengauer"), + publisher = "Oxford University Press (OUP)" +) From 654e914f77112294477e2122cd8ce20b159f664f Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 15 Jul 2025 12:24:41 +0100 Subject: [PATCH 2/3] Update DESCRIPTION to include reference to the citations --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3943a07f..1c5c6270 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -4,7 +4,7 @@ Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have been designed to only share non disclosive summary statistics, with built in automated output checking based on statistical disclosure control. With data sites setting the threshold values for - the automated output checks. + the automated output checks. For more details, see 'citation("dsBase")'. Version: 6.3.3 Authors@R: c(person(given = "Paul", family = "Burton", From 89f9256bdaa781fe577b068c5707851b742a93bc Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 16 Jul 2025 13:18:29 +0100 Subject: [PATCH 3/3] Add missing bibentry to auto-link the R package citation --- inst/CITATION | 3 +++ 1 file changed, 3 insertions(+) diff --git a/inst/CITATION b/inst/CITATION index 2be63039..0d81fdd6 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,3 +1,6 @@ +bibentry("Manual", + other = unlist(citation(auto = meta), recursive = FALSE)) + bibentry( bibtype = "Article", title = "{DataSHIELD: taking the analysis to the data, not the data to the analysis}",