From 8b59a392e61e5e1f980aefddf002b6684eedced3 Mon Sep 17 00:00:00 2001 From: Sebastian Funk Date: Tue, 18 Jun 2024 14:56:14 +0100 Subject: [PATCH] update paper machine and papers --- .github/workflows/update-publications.yaml | 34 ++ _automation/get_new_papers.R | 58 ++- _data/papers.bib | 497 ++++++++++++--------- 3 files changed, 367 insertions(+), 222 deletions(-) diff --git a/.github/workflows/update-publications.yaml b/.github/workflows/update-publications.yaml index d26e14b..ad7de67 100644 --- a/.github/workflows/update-publications.yaml +++ b/.github/workflows/update-publications.yaml @@ -59,6 +59,40 @@ jobs: bib <- paste(c(bib_old, bib_new), collapse = "\n") write(bib, "_data/papers.bib") + + ## filter latest version + df <- bib2df("_data/papers.bib") |> + dplyr::mutate( + version = dplyr::if_else( + grepl("wellcomeopenres", DOI), + sub("^.*\\.([1-9][0-9]*)$", "\\1", DOI), + "1" + ), + base_doi = dplyr::if_else( + grepl("wellcomeopenres", DOI), + sub("\\.([1-9][0-9]*)$", "", DOI), + DOI + ) + ) |> + dplyr::group_by(base_doi) |> + dplyr::filter(version == max(version)) |> + dplyr::ungroup() |> + dplyr::select(-base_doi, -version) + + ## filter preprints + df <- df |> + dplyr::group_by(TITLE) |> + dplyr::mutate(n = dplyr::n()) |> + dplyr::mutate(id = seq_len(dplyr::n())) |> + dplyr::mutate(n_pp = sum(JOURNAL == "medRxiv")) |> + dplyr::filter( + !((n_pp < n) & (JOURNAL == "medRxiv")) + ) |> + dplyr::filter( + !(n > 1 & id < max(id)) + ) |> + dplyr::ungroup() + shell: Rscript {0} - uses: peter-evans/create-pull-request@v6 diff --git a/_automation/get_new_papers.R b/_automation/get_new_papers.R index 90e8ba4..7188a18 100644 --- a/_automation/get_new_papers.R +++ b/_automation/get_new_papers.R @@ -1,22 +1,40 @@ -`%>%` <- magrittr::`%>%` - get_new_papers_orcid <- function(orcid, from_date) { - - rcrossref::cr_works(filter = list(orcid = orcid, - from_deposit_date = from_date, - type = "journal-article")) %>% + refs <- rcrossref::cr_works(filter = list( + orcid = orcid, + from_deposit_date = from_date + )) |> purrr::pluck("data") - + + if (nrow(refs) > 0) { + refs <- refs |> + dplyr::mutate( + container.title = dplyr::if_else( + publisher == "Cold Spring Harbor Laboratory", + "medRxiv", + container.title + ), + type = dplyr::if_else( + publisher == "Cold Spring Harbor Laboratory", + "journal-article", + type + ) + ) |> + dplyr::filter(type == "journal-article") + existing_papers <- dois_from_bib("_data/papers.bib") + refs <- refs |> + dplyr::filter(!(doi %in% existing_papers)) + } + return(refs) } get_new_papers_team <- function(from_date) { - recent_papers <- fs::dir_ls("_data/team", regexp = "\\w+\\-\\w+\\.yml") %>% - purrr::map(yaml::read_yaml) %>% - purrr::keep(function(x) x[["current-member"]]) %>% - purrr::map("orcid") %>% - purrr::keep(~ !is.null(.x)) %>% - purrr::map_dfr(get_new_papers_orcid, from_date = from_date) %>% + recent_papers <- fs::dir_ls("_data/team", regexp = "\\w+\\-\\w+\\.yml") |> + purrr::map(yaml::read_yaml) |> + purrr::keep(function(x) x[["current-member"]]) |> + purrr::map("orcid") |> + purrr::keep(~ !is.null(.x)) |> + purrr::map_dfr(get_new_papers_orcid, from_date = from_date) |> dplyr::distinct() return(recent_papers) @@ -24,14 +42,14 @@ get_new_papers_team <- function(from_date) { } create_bibentries <- function(papers) { - papers %>% + papers |> dplyr::mutate( author = purrr::map(author, ~ dplyr::filter(.x, !is.na(given) &!is.na(family))), author = purrr::map(author, ~ paste(.x$given, .x$family)), author = purrr::map(author, as.person), year = format(lubridate::parse_date_time(issued, c("Y-m-d", "Y-m", "Y")), "%Y") - ) %>% - dplyr::rowwise() %>% + ) |> + dplyr::rowwise() |> dplyr::mutate( bib = list(bibentry( "Article", @@ -42,7 +60,13 @@ create_bibentries <- function(papers) { doi = doi, key = ids::adjective_animal() )) - ) %>% + ) |> dplyr::pull(bib) } + +dois_from_bib <- function(bib) { + bib |> + bibtex::read.bib() |> + purrr::map_chr(~ .x$doi) +} diff --git a/_data/papers.bib b/_data/papers.bib index a128cd7..a6b01d0 100644 --- a/_data/papers.bib +++ b/_data/papers.bib @@ -1,225 +1,312 @@ -@article{Funk_2019, - doi = {10.1371/journal.pcbi.1006785}, - year = 2019, - month = {feb}, - publisher = {Public Library of Science ({PLoS})}, - volume = {15}, - number = {2}, - pages = {e1006785}, - author = {Sebastian Funk and Anton Camacho and Adam J. Kucharski and Rachel Lowe and Rosalind M. Eggo and W. John Edmunds}, - editor = {Christian Althaus}, - title = {Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15}, - journal = {{PLOS} Computational Biology} -} -@article{Camacho_2015, - doi = {10.1371/currents.outbreaks.406ae55e83ec0b5193e30856b9235ed2}, - year = 2015, - publisher = {Public Library of Science ({PLoS})}, - author = {Anton Camacho and Adam Kucharski and Yvonne Aki-Sawyerr and Mark A. White and Stefan Flasche and Marc Baguelin and Timothy Pollington and Julia R. Carney and Rebecca Glover and Elizabeth Smout and Amanda Tiffany and W. John Edmunds and Sebastian Funk}, - title = {Temporal Changes in Ebola Transmission in Sierra Leone and Implications for Control Requirements: a Real-time Modelling Study}, - journal = {{PLoS} Currents} -} -@article{Finger_2019, - doi = {10.1186/s12916-019-1288-7}, - year = 2019, - month = {mar}, - publisher = {Springer Science and Business Media {LLC}}, - volume = {17}, - number = {1}, - author = {Flavio Finger and Sebastian Funk and Kate White and M. Ruby Siddiqui and W. John Edmunds and Adam J. Kucharski}, - title = {Real-time analysis of the diphtheria outbreak in forcibly displaced Myanmar nationals in Bangladesh}, - journal = {{BMC} Medicine} -} -@article{Hellewell_2020, - doi = {10.1016/s2214-109x(20)30074-7}, - year = 2020, - month = {apr}, - publisher = {Elsevier {BV}}, - volume = {8}, - number = {4}, - pages = {e488--e496}, - author = {Joel Hellewell and Sam Abbott and Amy Gimma and Nikos I Bosse and Christopher I Jarvis and Timothy W Russell and James D Munday and Adam J Kucharski and W John Edmunds and Sebastian Funk and Rosalind M Eggo and Fiona Sun and Stefan Flasche and Billy J Quilty and Nicholas Davies and Yang Liu and Samuel Clifford and Petra Klepac and Mark Jit and Charlie Diamond and Hamish Gibbs and Kevin {van Zandvoort}}, - title = {Feasibility of controlling {COVID}-19 outbreaks by isolation of cases and contacts}, - journal = {The Lancet Global Health} -} -@article{Abbott_2020, - doi = {10.12688/wellcomeopenres.16006.2}, - year = 2020, - month = {dec}, - publisher = {F1000 Research Ltd}, - volume = {5}, - pages = {112}, - author = {Sam Abbott and Joel Hellewell and Robin N. Thompson and Katharine Sherratt and Hamish P. Gibbs and Nikos I. Bosse and James D. Munday and Sophie Meakin and Emma L. Doughty and June Young Chun and Yung-Wai Desmond Chan and Flavio Finger and Paul Campbell and Akira Endo and Carl A. B. Pearson and Amy Gimma and Tim Russell and Stefan Flasche and Adam J. Kucharski and Rosalind M. Eggo and Sebastian Funk}, - title = {Estimating the time-varying reproduction number of {SARS}-{CoV}-2 using national and subnational case counts}, - journal = {Wellcome Open Research} -} -@article{Abbott_2020, - doi = {10.12688/wellcomeopenres.15718.1}, - year = 2020, - month = {feb}, - publisher = {F1000 Research Ltd}, - volume = {5}, - pages = {17}, - author = {Sam Abbott and Joel Hellewell and James Munday and Sebastian Funk}, - title = {The transmissibility of novel Coronavirus in the early stages of the 2019-20 outbreak in Wuhan: Exploring initial point-source exposure sizes and durations using scenario analysis}, - journal = {Wellcome Open Research} -} -@article{Munday_2021, - doi = {10.1038/s41467-021-22213-0}, - year = 2021, - month = {mar}, - publisher = {Springer Science and Business Media {LLC}}, - volume = {12}, - number = {1}, - author = {James D. Munday and Katharine Sherratt and Sophie Meakin and Akira Endo and Carl A. B. Pearson and Joel Hellewell and Sam Abbott and Nikos I. Bosse and Katherine E. Atkins and Jacco Wallinga and W. John Edmunds and Albert Jan {van Hoek} and Sebastian Funk}, - title = {Implications of the school-household network structure on {SARS}-{CoV}-2 transmission under school reopening strategies in England}, - journal = {Nature Communications} -} -@article{Sherratt_2021, - doi = {10.1098/rstb.2020.0283}, - year = 2021, - month = {may}, - publisher = {The Royal Society}, - volume = {376}, - number = {1829}, - author = {Katharine Sherratt and Sam Abbott and Sophie R. Meakin and Joel Hellewell and James D. Munday and Nikos Bosse and Mark Jit and Sebastian Funk}, - title = {Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of {COVID}-19 in England}, - journal = {Philosophical Transactions of the Royal Society B: Biological Sciences} -} -@article{Endo_2020, - doi = {10.12688/wellcomeopenres.15842.3}, - year = 2020, - month = {jul}, - publisher = {F1000 Research Ltd}, - volume = {5}, - pages = {67}, - author = {Akira Endo and Sam Abbott and Adam J. Kucharski and Sebastian Funk}, - title = {Estimating the overdispersion in {COVID}-19 transmission using outbreak sizes outside China}, - journal = {Wellcome Open Research} -} -@article{Endo_2021, - doi = {10.12688/wellcomeopenres.16344.3}, - year = 2021, - month = {mar}, - publisher = {F1000 Research Ltd}, - volume = {5}, - pages = {239}, - author = {Akira Endo and Quentin J. Leclerc and Gwenan M. Knight and Graham F. Medley and Katherine E. Atkins and Sebastian Funk and Adam J. Kucharski}, - title = {Implication of backward contact tracing in the presence of overdispersed transmission in {COVID}-19 outbreaks}, - journal = {Wellcome Open Research} -} -@article{Bracher2021, - title = {A Pre-Registered Short-Term Forecasting Study of {{COVID-19}} in {{Germany}} and {{Poland}} during the Second Wave}, - author = {Bracher, J. and Wolffram, D. and Deuschel, J. and G{\"o}rgen, K. and Ketterer, J. L. and Ullrich, A. and Abbott, S. and Barbarossa, M. V. and Bertsimas, D. and Bhatia, S. and Bodych, M. and Bosse, N. I. and Burgard, J. P. and Castro, L. and Fairchild, G. and Fuhrmann, J. and Funk, S. and Gogolewski, K. and Gu, Q. and Heyder, S. and Hotz, T. and Kheifetz, Y. and Kirsten, H. and Krueger, T. and Krymova, E. and Li, M. L. and Meinke, J. H. and Michaud, I. J. and Niedzielewski, K. and O{\.z}a{\'n}ski, T. and Rakowski, F. and Scholz, M. and Soni, S. and Srivastava, A. and Zieli{\'n}ski, J. and Zou, D. and Gneiting, T. and Schienle, M. and Li, Michael Lingzhi and Bertsimas, Dimitris and Bouardi, Hamza Tazi and Lami, Omar Skali and Soni, Saksham and Abbott, Sam and Bosse, Nikos I. and Funk, Sebastian and Barbarossa, Maria Vittoria and Fuhrmann, Jan and Meinke, Jan H. and Bracher, Johannes and Deuschel, Jannik and Gneiting, Tilmann and G{\"o}rgen, Konstantin and Ketterer, Jakob and Schienle, Melanie and Ullrich, Alexander and Wolffram, Daniel and G{\'o}rski, {\L}ukasz and {Gruziel-S{\l}omka}, Magdalena and Kaczorek, Artur and Moszy{\'n}ski, Antoni and Niedzielewski, Karol and Nowosielski, Jedrzej and Radwan, Maciej and Rakowski, Franciszek and Semeniuk, Marcin and Zieli{\'n}ski, Jakub and Bartczuk, Rafa{\l} and Kisielewski, Jan and Bhatia, Sangeeta and Biecek, Przemyslaw and Bezborodov, Viktor and Bodych, Marcin and Krueger, Tyll and Burgard, Jan Pablo and Heyder, Stefan and Hotz, Thomas and Osthus, Dave A. and Michaud, Isaac J. and Castro, Lauren and Fairchild, Geoffrey and Kheifetz, Yuri and Kirsten, Holger and Scholz, Markus and Gambin, Anna and Gogolewski, Krzysztof and Miasojedow, B{\l}a{\.z}ej and Szczurek, Ewa and Rabczenko, Daniel and Rosi{\'n}ska, Magdalena and Bawiec, Marek and Bodych, Marcin and O{\.z}a{\'n}ski, Tomasz and Pabjan, Barbara and Rafaj{\l}lowicz, Ewaryst and {Skubalska-Rafaj{\l}owicz}, Ewa and Rafaj{\l}owicz, Wojciech and Migalska, Agata and Szczurek, Ewa and Flahault, Antoine and Manetti, Elisa and Choirat, Christine and Haro, Benjamin Bejar and Krymova, Ekaterina and Lee, Gavin and Obozinski, Guillaume and Sun, Tao and Thanou, Dorina and Gu, Quanquan and Xu, Pan and Chen, Jinghui and Wang, Lingxiao and Zou, Difan and Zhang, Weitong and Srivastava, Ajitesh and Prasanna, Viktor K. and Xu, Frost Tianjian and {List of Contributors by Team} and {CovidAnalytics-DELPHI} and {epiforecasts-EpiExpert and epiforecasts-EpiNow2} and {FIAS FZJ-Epi1Ger} and {German and Polish Forecast Hub Coordination Team} and {ICM-agentModel} and {Imperial-ensemble2} and {ITWW-county repro} and {LANL-GrowthRate} and {LeipzigIMISE-SECIR} and {MIMUW-StochSEIR} and {MOCOS-agent1} and {SDSC ISG-TrendModel} and {UCLA-SuEIR} and {USC-SIkJalpha}}, - year = {2021}, - month = aug, - journal = {Nature Communications}, - volume = {12}, - number = {1}, - pages = {5173}, - issn = {2041-1723}, - doi = {10.1038/s41467-021-25207-0} -} -@article{Pavelka_2021, - doi = {10.1126/science.abf9648}, - year = 2021, - month = {may}, - publisher = {American Association for the Advancement of Science ({AAAS})}, - volume = {372}, - number = {6542}, - pages = {635--641}, - author = {Martin Pavelka and Kevin Van-Zandvoort and Sam Abbott and Katharine Sherratt and Marek Majdan and Pavol Jar{\v{c}}u{\v{s}}ka and Marek Kraj{\v{c}}{\'{\i}} and Stefan Flasche and Sebastian Funk}, - title = {The impact of population-wide rapid antigen testing on {SARS}-{CoV}-2 prevalence in Slovakia}, - journal = {Science} +@Article{Funk_2019, + AUTHOR = {Sebastian Funk and Anton Camacho and Adam J. Kucharski and Rachel Lowe and Rosalind M. Eggo and W. John Edmunds}, + EDITOR = {Christian Althaus}, + JOURNAL = {{PLOS} Computational Biology}, + MONTH = {feb}, + NUMBER = {2}, + PAGES = {e1006785}, + PUBLISHER = {Public Library of Science ({PLoS})}, + TITLE = {Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15}, + VOLUME = {15}, + YEAR = {2019}, + DOI = {10.1371/journal.pcbi.1006785}, + N = {1}, + N_PP = {0}, + ID = {1} } + + +@Article{Camacho_2015, + AUTHOR = {Anton Camacho and Adam Kucharski and Yvonne Aki-Sawyerr and Mark A. White and Stefan Flasche and Marc Baguelin and Timothy Pollington and Julia R. Carney and Rebecca Glover and Elizabeth Smout and Amanda Tiffany and W. John Edmunds and Sebastian Funk}, + JOURNAL = {{PLoS} Currents}, + PUBLISHER = {Public Library of Science ({PLoS})}, + TITLE = {Temporal Changes in Ebola Transmission in Sierra Leone and Implications for Control Requirements: a Real-time Modelling Study}, + YEAR = {2015}, + DOI = {10.1371/currents.outbreaks.406ae55e83ec0b5193e30856b9235ed2}, + N = {1}, + N_PP = {0}, + ID = {1} +} + + +@Article{Finger_2019, + AUTHOR = {Flavio Finger and Sebastian Funk and Kate White and M. Ruby Siddiqui and W. John Edmunds and Adam J. Kucharski}, + JOURNAL = {{BMC} Medicine}, + MONTH = {mar}, + NUMBER = {1}, + PUBLISHER = {Springer Science and Business Media {LLC}}, + TITLE = {Real-time analysis of the diphtheria outbreak in forcibly displaced Myanmar nationals in Bangladesh}, + VOLUME = {17}, + YEAR = {2019}, + DOI = {10.1186/s12916-019-1288-7}, + N = {1}, + N_PP = {0}, + ID = {1} +} + + +@Article{Hellewell_2020, + AUTHOR = {Joel Hellewell and Sam Abbott and Amy Gimma and Nikos I Bosse and Christopher I Jarvis and Timothy W Russell and James D Munday and Adam J Kucharski and W John Edmunds and Sebastian Funk and Rosalind M Eggo and Fiona Sun and Stefan Flasche and Billy J Quilty and Nicholas Davies and Yang Liu and Samuel Clifford and Petra Klepac and Mark Jit and Charlie Diamond and Hamish Gibbs and Kevin {van Zandvoort}}, + JOURNAL = {The Lancet Global Health}, + MONTH = {apr}, + NUMBER = {4}, + PAGES = {e488--e496}, + PUBLISHER = {Elsevier {BV}}, + TITLE = {Feasibility of controlling {COVID}-19 outbreaks by isolation of cases and contacts}, + VOLUME = {8}, + YEAR = {2020}, + DOI = {10.1016/s2214-109x(20)30074-7}, + N = {1}, + N_PP = {0}, + ID = {1} +} + + +@Article{Abbott_2020, + AUTHOR = {Sam Abbott and Joel Hellewell and Robin N. Thompson and Katharine Sherratt and Hamish P. Gibbs and Nikos I. Bosse and James D. Munday and Sophie Meakin and Emma L. Doughty and June Young Chun and Yung-Wai Desmond Chan and Flavio Finger and Paul Campbell and Akira Endo and Carl A. B. Pearson and Amy Gimma and Tim Russell and Stefan Flasche and Adam J. Kucharski and Rosalind M. Eggo and Sebastian Funk}, + JOURNAL = {Wellcome Open Research}, + MONTH = {dec}, + PAGES = {112}, + PUBLISHER = {F1000 Research Ltd}, + TITLE = {Estimating the time-varying reproduction number of {SARS}-{CoV}-2 using national and subnational case counts}, + VOLUME = {5}, + YEAR = {2020}, + DOI = {10.12688/wellcomeopenres.16006.2}, + N = {1}, + N_PP = {0}, + ID = {1} +} + + +@Article{Abbott_2020, + AUTHOR = {Sam Abbott and Joel Hellewell and James Munday and Sebastian Funk}, + JOURNAL = {Wellcome Open Research}, + MONTH = {feb}, + PAGES = {17}, + PUBLISHER = {F1000 Research Ltd}, + TITLE = {The transmissibility of novel Coronavirus in the early stages of the 2019-20 outbreak in Wuhan: Exploring initial point-source exposure sizes and durations using scenario analysis}, + VOLUME = {5}, + YEAR = {2020}, + DOI = {10.12688/wellcomeopenres.15718.1}, + N = {1}, + N_PP = {0}, + ID = {1} +} + + +@Article{Munday_2021, + AUTHOR = {James D. Munday and Katharine Sherratt and Sophie Meakin and Akira Endo and Carl A. B. Pearson and Joel Hellewell and Sam Abbott and Nikos I. Bosse and Katherine E. Atkins and Jacco Wallinga and W. John Edmunds and Albert Jan {van Hoek} and Sebastian Funk}, + JOURNAL = {Nature Communications}, + MONTH = {mar}, + NUMBER = {1}, + PUBLISHER = {Springer Science and Business Media {LLC}}, + TITLE = {Implications of the school-household network structure on {SARS}-{CoV}-2 transmission under school reopening strategies in England}, + VOLUME = {12}, + YEAR = {2021}, + DOI = {10.1038/s41467-021-22213-0}, + N = {1}, + N_PP = {0}, + ID = {1} +} + + +@Article{Sherratt_2021, + AUTHOR = {Katharine Sherratt and Sam Abbott and Sophie R. Meakin and Joel Hellewell and James D. Munday and Nikos Bosse and Mark Jit and Sebastian Funk}, + JOURNAL = {Philosophical Transactions of the Royal Society B: Biological Sciences}, + MONTH = {may}, + NUMBER = {1829}, + PUBLISHER = {The Royal Society}, + TITLE = {Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of {COVID}-19 in England}, + VOLUME = {376}, + YEAR = {2021}, + DOI = {10.1098/rstb.2020.0283}, + N = {1}, + N_PP = {0}, + ID = {1} +} + + +@Article{Endo_2020, + AUTHOR = {Akira Endo and Sam Abbott and Adam J. Kucharski and Sebastian Funk}, + JOURNAL = {Wellcome Open Research}, + MONTH = {jul}, + PAGES = {67}, + PUBLISHER = {F1000 Research Ltd}, + TITLE = {Estimating the overdispersion in {COVID}-19 transmission using outbreak sizes outside China}, + VOLUME = {5}, + YEAR = {2020}, + DOI = {10.12688/wellcomeopenres.15842.3}, + N = {1}, + N_PP = {0}, + ID = {1} +} + + +@Article{Endo_2021, + AUTHOR = {Akira Endo and Quentin J. Leclerc and Gwenan M. Knight and Graham F. Medley and Katherine E. Atkins and Sebastian Funk and Adam J. Kucharski}, + JOURNAL = {Wellcome Open Research}, + MONTH = {mar}, + PAGES = {239}, + PUBLISHER = {F1000 Research Ltd}, + TITLE = {Implication of backward contact tracing in the presence of overdispersed transmission in {COVID}-19 outbreaks}, + VOLUME = {5}, + YEAR = {2021}, + DOI = {10.12688/wellcomeopenres.16344.3}, + N = {1}, + N_PP = {0}, + ID = {1} +} + + +@Article{Bracher2021, + AUTHOR = {Bracher, J. and Wolffram, D. and Deuschel, J. and G{\"o}rgen, K. and Ketterer, J. L. and Ullrich, A. and Abbott, S. and Barbarossa, M. V. and Bertsimas, D. and Bhatia, S. and Bodych, M. and Bosse, N. I. and Burgard, J. P. and Castro, L. and Fairchild, G. and Fuhrmann, J. and Funk, S. and Gogolewski, K. and Gu, Q. and Heyder, S. and Hotz, T. and Kheifetz, Y. and Kirsten, H. and Krueger, T. and Krymova, E. and Li, M. L. and Meinke, J. H. and Michaud, I. J. and Niedzielewski, K. and O{\.z}a{\'n}ski, T. and Rakowski, F. and Scholz, M. and Soni, S. and Srivastava, A. and Zieli{\'n}ski, J. and Zou, D. and Gneiting, T. and Schienle, M. and Li, Michael Lingzhi and Bertsimas, Dimitris and Bouardi, Hamza Tazi and Lami, Omar Skali and Soni, Saksham and Abbott, Sam and Bosse, Nikos I. and Funk, Sebastian and Barbarossa, Maria Vittoria and Fuhrmann, Jan and Meinke, Jan H. and Bracher, Johannes and Deuschel, Jannik and Gneiting, Tilmann and G{\"o}rgen, Konstantin and Ketterer, Jakob and Schienle, Melanie and Ullrich, Alexander and Wolffram, Daniel and G{\'o}rski, {\L}ukasz and {Gruziel-S{\l}omka}, Magdalena and Kaczorek, Artur and Moszy{\'n}ski, Antoni and Niedzielewski, Karol and Nowosielski, Jedrzej and Radwan, Maciej and Rakowski, Franciszek and Semeniuk, Marcin and Zieli{\'n}ski, Jakub and Bartczuk, Rafa{\l} and Kisielewski, Jan and Bhatia, Sangeeta and Biecek, Przemyslaw and Bezborodov, Viktor and Bodych, Marcin and Krueger, Tyll and Burgard, Jan Pablo and Heyder, Stefan and Hotz, Thomas and Osthus, Dave A. and Michaud, Isaac J. and Castro, Lauren and Fairchild, Geoffrey and Kheifetz, Yuri and Kirsten, Holger and Scholz, Markus and Gambin, Anna and Gogolewski, Krzysztof and Miasojedow, B{\l}a{\.z}ej and Szczurek, Ewa and Rabczenko, Daniel and Rosi{\'n}ska, Magdalena and Bawiec, Marek and Bodych, Marcin and O{\.z}a{\'n}ski, Tomasz and Pabjan, Barbara and Rafaj{\l}lowicz, Ewaryst and {Skubalska-Rafaj{\l}owicz}, Ewa and Rafaj{\l}owicz, Wojciech and Migalska, Agata and Szczurek, Ewa and Flahault, Antoine and Manetti, Elisa and Choirat, Christine and Haro, Benjamin Bejar and Krymova, Ekaterina and Lee, Gavin and Obozinski, Guillaume and Sun, Tao and Thanou, Dorina and Gu, Quanquan and Xu, Pan and Chen, Jinghui and Wang, Lingxiao and Zou, Difan and Zhang, Weitong and Srivastava, Ajitesh and Prasanna, Viktor K. and Xu, Frost Tianjian and {List of Contributors by Team} and {CovidAnalytics-DELPHI} and {epiforecasts-EpiExpert and epiforecasts-EpiNow2} and {FIAS FZJ-Epi1Ger} and {German and Polish Forecast Hub Coordination Team} and {ICM-agentModel} and {Imperial-ensemble2} and {ITWW-county repro} and {LANL-GrowthRate} and {LeipzigIMISE-SECIR} and {MIMUW-StochSEIR} and {MOCOS-agent1} and {SDSC ISG-TrendModel} and {UCLA-SuEIR} and {USC-SIkJalpha}}, + JOURNAL = {Nature Communications}, + MONTH = {}, + NUMBER = {1}, + PAGES = {5173}, + TITLE = {A Pre-Registered Short-Term Forecasting Study of {{COVID-19}} in {{Germany}} and {{Poland}} during the Second Wave}, + VOLUME = {12}, + YEAR = {2021}, + DOI = {10.1038/s41467-021-25207-0}, + ISSN = {2041-1723}, + N = {1}, + N_PP = {0}, + ID = {1} +} + + +@Article{Pavelka_2021, + AUTHOR = {Martin Pavelka and Kevin Van-Zandvoort and Sam Abbott and Katharine Sherratt and Marek Majdan and Pavol Jar{\v{c}}u{\v{s}}ka and Marek Kraj{\v{c}}{\'{\i}} and Stefan Flasche and Sebastian Funk}, + JOURNAL = {Science}, + MONTH = {may}, + NUMBER = {6542}, + PAGES = {635--641}, + PUBLISHER = {American Association for the Advancement of Science ({AAAS})}, + TITLE = {The impact of population-wide rapid antigen testing on {SARS}-{CoV}-2 prevalence in Slovakia}, + VOLUME = {372}, + YEAR = {2021}, + DOI = {10.1126/science.abf9648}, + N = {1}, + N_PP = {0}, + ID = {1} +} + + @Article{Hart_2022, - title = {Inference of the SARS-CoV-2 generation time using UK household data}, - journal = {eLife}, - author = {William Stephen Hart and Sam Abbott and Akira Endo and Joel Hellewell and Elizabeth Miller and Nick Andrews and Philip K Maini and Sebastian Funk and Robin N Thompson}, - year = {2022}, - doi = {10.7554/elife.70767}, + AUTHOR = {William Stephen Hart and Sam Abbott and Akira Endo and Joel Hellewell and Elizabeth Miller and Nick Andrews and Philip K Maini and Sebastian Funk and Robin N Thompson}, + JOURNAL = {eLife}, + TITLE = {Inference of the SARS-CoV-2 generation time using UK household data}, + YEAR = {2022}, + DOI = {10.7554/elife.70767}, + N = {1}, + N_PP = {0}, + ID = {1} } + + @Article{Meakin_2022, - title = {Comparative assessment of methods for short-term forecasts of COVID-19 hospital admissions in England at the local level}, - journal = {BMC Medicine}, - author = {Sophie Meakin and Sam Abbott and Nikos Bosse and James Munday and Hugo Gruson and Joel Hellewell and Katharine Sherratt and Lloyd A. C. Chapman and Kiesha Prem and Petra Klepac and Thibaut Jombart and Gwenan M. Knight and Yalda Jafari and Stefan Flasche and William Waites and Mark Jit and Rosalind M. Eggo and C. Julian Villabona-Arenas and Timothy W. Russell and Graham Medley and W. John Edmunds and Nicholas G. Davies and Yang Liu and Stéphane Hué and Oliver Brady and Rachael Pung and Kaja Abbas and Amy Gimma and Paul Mee and Akira Endo and Samuel Clifford and Fiona Yueqian Sun and Ciara V. McCarthy and Billy J. Quilty and Alicia Rosello and Frank G. Sandmann and Rosanna C. Barnard and Adam J. Kucharski and Simon R. Procter and Christopher I. Jarvis and Hamish P. Gibbs and David Hodgson and Rachel Lowe and Katherine E. Atkins and Mihaly Koltai and Carl A. B. Pearson and Emilie Finch and Kerry L. M. Wong and Matthew Quaife and Kathleen O’Reilly and Damien C. Tully and Sebastian Funk}, - year = {2022}, - doi = {10.1186/s12916-022-02271-x}, + AUTHOR = {Sophie Meakin and Sam Abbott and Nikos Bosse and James Munday and Hugo Gruson and Joel Hellewell and Katharine Sherratt and Lloyd A. C. Chapman and Kiesha Prem and Petra Klepac and Thibaut Jombart and Gwenan M. Knight and Yalda Jafari and Stefan Flasche and William Waites and Mark Jit and Rosalind M. Eggo and C. Julian Villabona-Arenas and Timothy W. Russell and Graham Medley and W. John Edmunds and Nicholas G. Davies and Yang Liu and Stéphane Hué and Oliver Brady and Rachael Pung and Kaja Abbas and Amy Gimma and Paul Mee and Akira Endo and Samuel Clifford and Fiona Yueqian Sun and Ciara V. McCarthy and Billy J. Quilty and Alicia Rosello and Frank G. Sandmann and Rosanna C. Barnard and Adam J. Kucharski and Simon R. Procter and Christopher I. Jarvis and Hamish P. Gibbs and David Hodgson and Rachel Lowe and Katherine E. Atkins and Mihaly Koltai and Carl A. B. Pearson and Emilie Finch and Kerry L. M. Wong and Matthew Quaife and Kathleen O’Reilly and Damien C. Tully and Sebastian Funk}, + JOURNAL = {BMC Medicine}, + TITLE = {Comparative assessment of methods for short-term forecasts of COVID-19 hospital admissions in England at the local level}, + YEAR = {2022}, + DOI = {10.1186/s12916-022-02271-x}, + N = {1}, + N_PP = {0}, + ID = {1} } + + @Article{pure_pipit, - title = {Heavy-tailed sexual contact networks and monkeypox epidemiology in the global outbreak, 2022}, - journal = {Science}, - author = {Akira Endo and Hiroaki Murayama and Sam Abbott and Ruwan Ratnayake and Carl A. B. Pearson and W. John Edmunds and Elizabeth Fearon and Sebastian Funk}, - year = {2022}, - doi = {10.1126/science.add4507}, + AUTHOR = {Akira Endo and Hiroaki Murayama and Sam Abbott and Ruwan Ratnayake and Carl A. B. Pearson and W. John Edmunds and Elizabeth Fearon and Sebastian Funk}, + JOURNAL = {Science}, + TITLE = {Heavy-tailed sexual contact networks and monkeypox epidemiology in the global outbreak, 2022}, + YEAR = {2022}, + DOI = {10.1126/science.add4507}, + N = {1}, + N_PP = {0}, + ID = {1} } + + @Article{gangly_boubou, - title = {Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools}, - journal = {Proceedings of the National Academy of Sciences}, - author = {Akira Endo and Mitsuo Uchida and Yang Liu and Katherine E. Atkins and Adam J. Kucharski and Sebastian Funk and Kaja Abbas and Kevin {van Zandvoort} and Nikos I Bosse and Naomi R Waterlow and Damien C Tully and Sophie R Meakin and Matthew Quaife and Timothy W Russell and Mark Jit and Anna M Foss and Alicia Rosello and Billy J Quilty and Kiesha Prem and Gwenan M Knight and Sam Abbott and Petra Klepac and Oliver Brady and Carl A B Pearson and Graham Medley and Samuel Clifford and Christopher I Jarvis and James D Munday and Frank G Sandmann and Fiona Yueqian Sun and Thibaut Jombart and Joel Hellewell and Hamish P Gibbs and Rosanna C Barnard and Rosalind M Eggo and Amy Gimma and Jack Williams and Nicholas G. Davies and Emily S Nightingale and Simon R Procter and W John Edmunds and Alicia Showering and Rachel Lowe and Katharine Sherratt and C Julian Villabona-Arenas and David Simons and Yung-Wai Desmond Chan and Stefan Flasche}, - year = {2022}, - doi = {10.1073/pnas.2203019119}, + AUTHOR = {Akira Endo and Mitsuo Uchida and Yang Liu and Katherine E. Atkins and Adam J. Kucharski and Sebastian Funk and Kaja Abbas and Kevin {van Zandvoort} and Nikos I Bosse and Naomi R Waterlow and Damien C Tully and Sophie R Meakin and Matthew Quaife and Timothy W Russell and Mark Jit and Anna M Foss and Alicia Rosello and Billy J Quilty and Kiesha Prem and Gwenan M Knight and Sam Abbott and Petra Klepac and Oliver Brady and Carl A B Pearson and Graham Medley and Samuel Clifford and Christopher I Jarvis and James D Munday and Frank G Sandmann and Fiona Yueqian Sun and Thibaut Jombart and Joel Hellewell and Hamish P Gibbs and Rosanna C Barnard and Rosalind M Eggo and Amy Gimma and Jack Williams and Nicholas G. Davies and Emily S Nightingale and Simon R Procter and W John Edmunds and Alicia Showering and Rachel Lowe and Katharine Sherratt and C Julian Villabona-Arenas and David Simons and Yung-Wai Desmond Chan and Stefan Flasche}, + JOURNAL = {Proceedings of the National Academy of Sciences}, + TITLE = {Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools}, + YEAR = {2022}, + DOI = {10.1073/pnas.2203019119}, + N = {1}, + N_PP = {0}, + ID = {1} } + + @Article{pharmaceutical_phoebe, - title = {Comparing human and model-based forecasts of COVID-19 in Germany and Poland}, - journal = {PLOS Computational Biology}, - author = {Nikos I. Bosse and Sam Abbott and Johannes Bracher and Habakuk Hain and Billy J. Quilty and Mark Jit and Edwin {van Leeuwen} and Anne Cori and Sebastian Funk}, - year = {2022}, - doi = {10.1371/journal.pcbi.1010405}, + AUTHOR = {Nikos I. Bosse and Sam Abbott and Johannes Bracher and Habakuk Hain and Billy J. Quilty and Mark Jit and Edwin {van Leeuwen} and Anne Cori and Sebastian Funk}, + JOURNAL = {PLOS Computational Biology}, + TITLE = {Comparing human and model-based forecasts of COVID-19 in Germany and Poland}, + YEAR = {2022}, + DOI = {10.1371/journal.pcbi.1010405}, + N = {1}, + N_PP = {0}, + ID = {1} } + + @Article{irrationalistic_myotis, - title = {Sebastian Funk, Sam Abbott and Johannes Bracher's discussion contribution to the papers in Session 2 of the Royal Statistical Society's Special Topic Meeting on Covid‐19 Transmission: 11 June 2021}, - journal = {Journal of the Royal Statistical Society: Series A (Statistics in Society)}, - author = {Sebastian Funk and Sam Abbott and Johannes Bracher}, - year = {2022}, - doi = {10.1111/rssa.12974}, + AUTHOR = {Sebastian Funk and Sam Abbott and Johannes Bracher}, + JOURNAL = {Journal of the Royal Statistical Society: Series A (Statistics in Society)}, + TITLE = {Sebastian Funk, Sam Abbott and Johannes Bracher's discussion contribution to the papers in Session 2 of the Royal Statistical Society's Special Topic Meeting on Covid‐19 Transmission: 11 June 2021}, + YEAR = {2022}, + DOI = {10.1111/rssa.12974}, + N = {1}, + N_PP = {0}, + ID = {1} } + + @Article{cleansable_armednylonshrimp, - title = {Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations}, - journal = {eLife}, - author = {Katharine Sherratt and Hugo Gruson and Rok Grah and Helen Johnson and Rene Niehus and Bastian Prasse and Frank Sandmann and Jannik Deuschel and Daniel Wolffram and Sam Abbott and Alexander Ullrich and Graham Gibson and Evan L Ray and Nicholas G Reich and Daniel Sheldon and Yijin Wang and Nutcha Wattanachit and Lijing Wang and Jan Trnka and Guillaume Obozinski and Tao Sun and Dorina Thanou and Loic Pottier and Ekaterina Krymova and Jan H Meinke and Maria Vittoria Barbarossa and Neele Leithauser and Jan Mohring and Johanna Schneider and Jaroslaw Wlazlo and Jan Fuhrmann and Berit Lange and Isti Rodiah and Prasith Baccam and Heidi Gurung and Steven Stage and Bradley Suchoski and Jozef Budzinski and Robert Walraven and Inmaculada Villanueva and Vit Tucek and Martin Smid and Milan Zajicek and Cesar Perez Alvarez and Borja Reina and Nikos I Bosse and Sophie R Meakin and Lauren Castro and Geoffrey Fairchild and Isaac Michaud and Dave Osthus and Pierfrancesco Alaimo Di Loro and Antonello Maruotti and Veronika Eclerova and Andrea Kraus and David Kraus and Lenka Pribylova and Bertsimas Dimitris and Michael Lingzhi Li and Soni Saksham and Jonas Dehning and Sebastian Mohr and Viola Priesemann and Grzegorz Redlarski and Benjamin Bejar and Giovanni Ardenghi and Nicola Parolini and Giovanni Ziarelli and Wolfgang Bock and Stefan Heyder and Thomas Hotz and David E Singh and Miguel Guzman-Merino and Jose L Aznarte and David Morina and Sergio Alonso and Enric Alvarez and Daniel Lopez and Clara Prats and Jan Pablo Burgard and Arne Rodloff and Tom Zimmermann and Alexander Kuhlmann and Janez Zibert and Fulvia Pennoni and Fabio Divino and Marti Catala and Gianfranco Lovison and Paolo Giudici and Barbara Tarantino and Francesco Bartolucci and Giovanna Jona Lasinio and Marco Mingione and Alessio Farcomeni and Ajitesh Srivastava and Pablo Montero-Manso and Aniruddha Adiga and Benjamin Hurt and Bryan Lewis and Madhav Marathe and Przemyslaw Porebski and Srinivasan Venkatramanan and Rafal P Bartczuk and Filip Dreger and Anna Gambin and Krzysztof Gogolewski and Magdalena Gruziel-Slomka and Bartosz Krupa and Antoni Moszyński and Karol Niedzielewski and Jedrzej Nowosielski and Maciej Radwan and Franciszek Rakowski and Marcin Semeniuk and Ewa Szczurek and Jakub Zielinski and Jan Kisielewski and Barbara Pabjan and Kirsten Holger and Yuri Kheifetz and Markus Scholz and Biecek Przemyslaw and Marcin Bodych and Maciej Filinski and Radoslaw Idzikowski and Tyll Krueger and Tomasz Ozanski and Johannes Bracher and Sebastian Funk}, - year = {2023}, - doi = {10.7554/elife.81916}, + AUTHOR = {Katharine Sherratt and Hugo Gruson and Rok Grah and Helen Johnson and Rene Niehus and Bastian Prasse and Frank Sandmann and Jannik Deuschel and Daniel Wolffram and Sam Abbott and Alexander Ullrich and Graham Gibson and Evan L Ray and Nicholas G Reich and Daniel Sheldon and Yijin Wang and Nutcha Wattanachit and Lijing Wang and Jan Trnka and Guillaume Obozinski and Tao Sun and Dorina Thanou and Loic Pottier and Ekaterina Krymova and Jan H Meinke and Maria Vittoria Barbarossa and Neele Leithauser and Jan Mohring and Johanna Schneider and Jaroslaw Wlazlo and Jan Fuhrmann and Berit Lange and Isti Rodiah and Prasith Baccam and Heidi Gurung and Steven Stage and Bradley Suchoski and Jozef Budzinski and Robert Walraven and Inmaculada Villanueva and Vit Tucek and Martin Smid and Milan Zajicek and Cesar Perez Alvarez and Borja Reina and Nikos I Bosse and Sophie R Meakin and Lauren Castro and Geoffrey Fairchild and Isaac Michaud and Dave Osthus and Pierfrancesco Alaimo Di Loro and Antonello Maruotti and Veronika Eclerova and Andrea Kraus and David Kraus and Lenka Pribylova and Bertsimas Dimitris and Michael Lingzhi Li and Soni Saksham and Jonas Dehning and Sebastian Mohr and Viola Priesemann and Grzegorz Redlarski and Benjamin Bejar and Giovanni Ardenghi and Nicola Parolini and Giovanni Ziarelli and Wolfgang Bock and Stefan Heyder and Thomas Hotz and David E Singh and Miguel Guzman-Merino and Jose L Aznarte and David Morina and Sergio Alonso and Enric Alvarez and Daniel Lopez and Clara Prats and Jan Pablo Burgard and Arne Rodloff and Tom Zimmermann and Alexander Kuhlmann and Janez Zibert and Fulvia Pennoni and Fabio Divino and Marti Catala and Gianfranco Lovison and Paolo Giudici and Barbara Tarantino and Francesco Bartolucci and Giovanna Jona Lasinio and Marco Mingione and Alessio Farcomeni and Ajitesh Srivastava and Pablo Montero-Manso and Aniruddha Adiga and Benjamin Hurt and Bryan Lewis and Madhav Marathe and Przemyslaw Porebski and Srinivasan Venkatramanan and Rafal P Bartczuk and Filip Dreger and Anna Gambin and Krzysztof Gogolewski and Magdalena Gruziel-Slomka and Bartosz Krupa and Antoni Moszyński and Karol Niedzielewski and Jedrzej Nowosielski and Maciej Radwan and Franciszek Rakowski and Marcin Semeniuk and Ewa Szczurek and Jakub Zielinski and Jan Kisielewski and Barbara Pabjan and Kirsten Holger and Yuri Kheifetz and Markus Scholz and Biecek Przemyslaw and Marcin Bodych and Maciej Filinski and Radoslaw Idzikowski and Tyll Krueger and Tomasz Ozanski and Johannes Bracher and Sebastian Funk}, + JOURNAL = {eLife}, + TITLE = {Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations}, + YEAR = {2023}, + DOI = {10.7554/elife.81916}, + N = {1}, + N_PP = {0}, + ID = {1} } + + @Article{semiparalysis_olingo, - title = {Scoring epidemiological forecasts on transformed scales}, - journal = {PLOS Computational Biology}, - author = {Nikos I. Bosse and Sam Abbott and Anne Cori and Edwin {van Leeuwen} and Johannes Bracher and Sebastian Funk}, - year = {2023}, - doi = {10.1371/journal.pcbi.1011393}, -} -@Article{manipulative_redheadedwoodpecker, - title = {Human judgement forecasting of COVID-19 in the UK}, - journal = {Wellcome Open Research}, - author = {Nikos I. Bosse and Sam Abbott and Johannes Bracher and Edwin {van Leeuwen} and Anne Cori and Sebastian Funk}, - year = {2023}, - doi = {10.12688/wellcomeopenres.19380.1}, + AUTHOR = {Nikos I. Bosse and Sam Abbott and Anne Cori and Edwin {van Leeuwen} and Johannes Bracher and Sebastian Funk}, + JOURNAL = {PLOS Computational Biology}, + TITLE = {Scoring epidemiological forecasts on transformed scales}, + YEAR = {2023}, + DOI = {10.1371/journal.pcbi.1011393}, + N = {1}, + N_PP = {0}, + ID = {1} } + + @Article{malevolent_babirusa, - title = {Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England}, - journal = {PLOS Computational Biology}, - author = {James D. Munday and Sam Abbott and Sophie Meakin and Sebastian Funk}, - year = {2023}, - doi = {10.1371/journal.pcbi.1011453}, + AUTHOR = {James D. Munday and Sam Abbott and Sophie Meakin and Sebastian Funk}, + JOURNAL = {PLOS Computational Biology}, + TITLE = {Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England}, + YEAR = {2023}, + DOI = {10.1371/journal.pcbi.1011453}, + N = {1}, + N_PP = {0}, + ID = {1} } -@Article{semiparalysis_olingo, - title = {Scoring epidemiological forecasts on transformed scales}, - journal = {PLOS Computational Biology}, - author = {Nikos I. Bosse and Sam Abbott and Anne Cori and Edwin {van Leeuwen} and Johannes Bracher and Sebastian Funk}, - year = {2023}, - doi = {10.1371/journal.pcbi.1011393}, -} -@Article{manipulative_redheadedwoodpecker, - title = {Human judgement forecasting of COVID-19 in the UK}, - journal = {Wellcome Open Research}, - author = {Nikos I. Bosse and Sam Abbott and Johannes Bracher and Edwin {van Leeuwen} and Anne Cori and Sebastian Funk}, - year = {2023}, - doi = {10.12688/wellcomeopenres.19380.1}, -} -@Article{malevolent_babirusa, - title = {Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England}, - journal = {PLOS Computational Biology}, - author = {James D. Munday and Sam Abbott and Sophie Meakin and Sebastian Funk}, - year = {2023}, - doi = {10.1371/journal.pcbi.1011453}, + + +@Article{gentlewomanly_bandicoot, + AUTHOR = {Nikos I. Bosse and Sam Abbott and Johannes Bracher and Edwin {van Leeuwen} and Anne Cori and Sebastian Funk}, + JOURNAL = {Wellcome Open Research}, + TITLE = {Human judgement forecasting of COVID-19 in the UK}, + YEAR = {2024}, + DOI = {10.12688/wellcomeopenres.19380.2}, + N = {2}, + N_PP = {0}, + ID = {2} }