From d7e90d2919c8e02489bbfe00418078c457f83247 Mon Sep 17 00:00:00 2001 From: ZekeMarshall Date: Mon, 8 Jul 2024 15:49:17 +0100 Subject: [PATCH] Addressing the review comments from Mike Mahoney --- JOSS/paper.Rmd | 58 ++++----- JOSS/paper.bib | 323 ++++++++++++++++++++++++++---------------------- JOSS/paper.html | 211 +++++++++++++++++-------------- JOSS/paper.md | 60 ++++----- 4 files changed, 352 insertions(+), 300 deletions(-) diff --git a/JOSS/paper.Rmd b/JOSS/paper.Rmd index dac5cd6..dd17e32 100644 --- a/JOSS/paper.Rmd +++ b/JOSS/paper.Rmd @@ -1,5 +1,5 @@ --- -title: '`RMAVIS` v1.0: a R Shiny application for the analysis of vegetation survey data and assignment to GB NVC communities.' +title: '`RMAVIS` v1.0: a Shiny application for the analysis of vegetation survey data and assignment to GB NVC communities.' tags: - Vegetation science - NVC @@ -34,7 +34,7 @@ output: # Summary -`RMAVIS` is a R Shiny application for the assignment of vegetation sample +`RMAVIS` is a Shiny application for the assignment of vegetation sample plot data to British National Vegetation Classification (NVC) communities [@rodwell1991;@rodwell1992;@rodwell1992a;@rodwell1995;@rodwell2000]. @@ -62,7 +62,7 @@ output of the ECOFACT project [@bunce1999], with the latest version released in # Statement of need -The requirement for a new program in the form of a R Shiny [@chang2024] +The requirement for a new program in the form of a Shiny [@chang2024] application arises from several needs, namely to: 1) accommodate updates to the NVC; 2) provide a means to easily reproduce and attribute the results of the NVC @@ -147,32 +147,32 @@ and 4) Newborough Warren [@wallace2018]. Version 1.0 of `RMAVIS` was built under R 4.4.0 [@rcoreteam] and depends on the -`bookdown` [@xie2024], -`bsicons` [@sievert2023], -`bslib` [@sievert2024], -`dplyr` [@wickham2019], -`ggplot2` [@wickham2019], -`htmltools` [@cheng2024], -`htmlwidgets` [@vaidyanathan2023], -`kableExtra` [@zhu2024], -`knitr` [@xie2024], -`magrittr` [@stefan2022], -`markdown` [@xie2023], -`plotly` [@sievert2020], -`purrr` [@wickham2019], -`reactable` [@lin2024], -`readr` [@wickham2019], -`rhandsontable` [@owen2021], -`rmarkdown` [@allaire2023], -`shiny` [@chang2024], -`shinybusy` [@meyer2024], -`shinyjs` [@attali2023], -`shinyWidgets` [@perrier2024], -`stringr`[@wickham2019], -`tibble` [@wickham2019], -`tidyr` [@wickham2019], -`vegan` [@oksanen2022], and -`writexl` [@ooms2024] R packages. +`bookdown` [@xie2024b], # DONE +`bsicons` [@sievert2023a], # DONE +`bslib` [@sievert2024a], # DONE +`dplyr` [@wickham2019], # DONE +`ggplot2` [@wickham2019], # DONE +`htmltools` [@cheng2024], # DONE +`htmlwidgets` [@vaidyanathan2023], # DONE +`kableExtra` [@zhu2024a], # DONE +`knitr` [@xie2024c], # DONE +`magrittr` [@bache2022a], # DONE +`markdown` [@xie2024d], # DONE +`plotly` [@sievert2020], # DONE +`purrr` [@wickham2019], # DONE +`reactable` [@lin2023], # DONE +`readr` [@wickham2019], # DONE +`rhandsontable` [@owen2021a], # DONE +`rmarkdown` [@allaire2024], # DONE +`shiny` [@chang2024], # DONE +`shinybusy` [@meyer2024a], # DONE +`shinyjs` [@attali2021], # DONE +`shinyWidgets` [@perrier2024a], # DONE +`stringr`[@wickham2019], # DONE +`tibble` [@wickham2019], # DONE +`tidyr` [@wickham2019], # DONE +`vegan` [@oksanen2024a], and # DONE +`writexl` [@ooms2024a] R packages. # DONE # Conclusion diff --git a/JOSS/paper.bib b/JOSS/paper.bib index d180e8d..68ad64f 100644 --- a/JOSS/paper.bib +++ b/JOSS/paper.bib @@ -1,23 +1,37 @@ -@misc{allaire2023, - title = {Rmarkdown: {{Dynamic Documents}} for {{R}}}, - shorttitle = {Rmarkdown}, - author = {Allaire, {\relax JJ} and Xie, Yihui and Dervieux, Christophe and McPherson, Jonathan and Luraschi, Javier and Ushey, Kevin and Atkins, Aron and Wickham, Hadley and Cheng, Joe and Chang, Winston and Iannone, Richard}, - year = {2023}, - abstract = {Dynamic Documents for R}, - copyright = {GPL-3.0}, - url = {https://github.com/rstudio/rmarkdown} +@misc{allaire2024, + title = {{rmarkdown}: {{Dynamic Documents}} for {{R}}}, + author = {Allaire, J. J. and Xie, Yihui and Dervieux, Christophe and McPherson, Jonathan and Luraschi, Javier and Ushey, Kevin and Atkins, Aron and Wickham, Hadley and Cheng, Joe and Chang, Winston and Iannone, Richard and Dunning, Andrew and Yasumoto, Atsushi and Schloerke, Barret and Sievert, Carson and Ryan, Devon and Aust, Frederik and Allen, Jeff and Seo, JooYoung and Barrett, Malcolm and Hyndman, Rob and Lesur, Romain and Storey, Roy and Arslan, Ruben and Oller, Sergio and PBC, Posit and Otto, Mark and Thornton, Jacob and Farkas, Alexander and Jehl, Scott and Sagalaev, Ivan and Franko, Greg and MacFarlane, John and Raggett, Dave and Gandy, Dave and Sperry, Ben and Drifty and Lister, Aidan and Jonsson, Benct Philip and Krewinkel, Albert}, + year = {2024}, + month = may, + urldate = {2024-07-08}, + abstract = {Convert R Markdown documents into a variety of formats.}, + copyright = {GPL-3}, + doi = {10.32614/CRAN.package.rmarkdown} } -@misc{attali2023, - title = {Shinyjs: {{Easily Improve}} the {{User Experience}} of {{Your Shiny Apps}} in {{Seconds}}}, - author = {Attali, Dean}, - year = {2023}, - url = {https://deanattali.com/shinyjs/} +@misc{attali2021, + title = {{shinyjs}: {{Easily Improve}} the {{User Experience}} of {{Your Shiny Apps}} in {{Seconds}}}, + author = {Attali, Dean}, + year = {2021}, + month = dec, + urldate = {2024-07-08}, + copyright = {MIT + file LICENSE}, + doi = {10.32614/CRAN.package.shinyjs} +} + +@misc{bache2022a, + title = {{magrittr}: {{A Forward-Pipe Operator}} for {{R}}}, + author = {Bache, Stefan Milton and Wickham, Hadley and Henry, Lionel and PBC, Posit}, + year = {2022}, + month = mar, + urldate = {2024-07-08}, + copyright = {MIT + file LICENSE}, + doi = {10.32614/CRAN.package.magrittr} } @misc{bsbi2017ellenbergF, author = {BSBI}, - title = {Ellenberg indicator F (moisture)}, + title = {Ellenberg indicator {F} (moisture)}, day = {15}, month = {10}, year = {2017}, @@ -26,7 +40,7 @@ @misc{bsbi2017ellenbergF @misc{bsbi2017ellenbergL, author = {BSBI}, - title = {Ellenberg indicator L (light)}, + title = {Ellenberg indicator {L} (light)}, day = {15}, month = {10}, year = {2017}, @@ -35,7 +49,7 @@ @misc{bsbi2017ellenbergL @misc{bsbi2017ellenbergN, author = {BSBI}, - title = {Ellenberg indicator N (nitrogen)}, + title = {Ellenberg indicator {N} (nitrogen)}, day = {9}, month = {10}, year = {2017}, @@ -44,7 +58,7 @@ @misc{bsbi2017ellenbergN @misc{bsbi2017ellenbergR, author = {BSBI}, - title = {Ellenberg indicator R (reaction)}, + title = {Ellenberg indicator {R} (reaction)}, day = {26}, month = {4}, year = {2017}, @@ -53,7 +67,7 @@ @misc{bsbi2017ellenbergR @misc{bsbi2017ellenbergS, author = {BSBI}, - title = {Ellenberg indicator S (salt tolerance)}, + title = {Ellenberg indicator {S} (salt tolerance)}, day = {26}, month = {4}, year = {2017}, @@ -89,22 +103,24 @@ @misc{butcher2020 publisher = {Stockport: UKHab Ltd} } -@manual{chang2024, - title = {shiny: Web Application Framework for R}, - author = {Winston Chang and Joe Cheng and JJ Allaire and Carson Sievert and Barret Schloerke and Yihui Xie and Jeff Allen and Jonathan McPherson and Alan Dipert and Barbara Borges}, - year = {2024}, - note = {R package version 1.8.0.9000, - https://github.com/rstudio/shiny}, - url = {https://shiny.posit.co/} +@misc{chang2024, + title = {{Shiny}: {{Web Application Framework}} for {{R}}}, + author = {Chang, Winston and Cheng, Joe and Allaire, J. J. and Sievert, Carson and Schloerke, Barret and Xie, Yihui and Allen, Jeff and McPherson, Jonathan and Dipert, Alan and Borges, Barbara and PBC, Posit and Otto, Mark and Thornton, Jacob and Khan, Prem Nawaz and Tsaran, Victor and Lembree, Dennis and Chakravarthula, Srinivasu and O'Connor, Cathy and Petre, Stefan and Rowls, Andrew and Reavis, Brian and Bejaoui, Salmen and Ineshin, Denis and Samhuri, Sami and Fraser, John and Gruber, John and Sagalaev, Ivan and R. Core Team}, + year = {2024}, + month = apr, + urldate = {2024-07-08}, + copyright = {GPL-3 {\textbar} file LICENSE}, + keywords = {WebTechnologies}, + doi = {10.32614/CRAN.package.shiny} } @misc{cheng2024, - title = {Htmltools: {{Tools}} for {{HTML}}}, - shorttitle = {Htmltools}, - author = {Cheng, Joe and Sievert, Carson and Schloerke, Barret and Chang, Winston and Xie, Yihui and Allen, Jeff and Software, Posit and PBC}, - year = {2024}, - month = apr, - copyright = {GPL-2 {\textbar} GPL-3 [expanded from: GPL ({$\geq$} 2)]} + title = {{htmltools}: {{Tools}} for {{HTML}}}, + author = {Cheng, Joe and Sievert, Carson and Schloerke, Barret and Chang, Winston and Xie, Yihui and Allen, Jeff and PBC, Posit}, + year = {2024}, + month = apr, + copyright = {GPL-2 {\textbar} GPL-3 [expanded from: GPL ({$\geq$} 2)]}, + doi = {10.32614/CRAN.package.htmltools} } @misc{cieem2022, @@ -160,24 +176,26 @@ @manual{jncc2008 } @article{kass2023, - title = {Wallace 2: A Shiny App for Modeling Species Niches and Distributions Redesigned to Facilitate Expansion via Module Contributions}, - shorttitle = {Wallace 2}, - author = {Kass, Jamie M. and {Pinilla-Buitrago}, Gonzalo E. and Paz, Andrea and Johnson, Bethany A. and {Grisales-Betancur}, Valentina and Meenan, Sarah I. and Attali, Dean and Broennimann, Olivier and Galante, Peter J. and Maitner, Brian S. and Owens, Hannah L. and Varela, Sara and {Aiello-Lammens}, Matthew E. and Merow, Cory and Blair, Mary E. and Anderson, Robert P.}, - year = {2023}, - journal = {Ecography}, - volume = {2023}, - number = {3}, - pages = {e06547}, - issn = {1600-0587}, - doi = {10.1111/ecog.06547}, - urldate = {2024-02-20} + title = {{wallace} 2: A Shiny App for Modeling Species Niches and Distributions Redesigned to Facilitate Expansion via Module Contributions}, + author = {Kass, Jamie M. and {Pinilla-Buitrago}, Gonzalo E. and Paz, Andrea and Johnson, Bethany A. and {Grisales-Betancur}, Valentina and Meenan, Sarah I. and Attali, Dean and Broennimann, Olivier and Galante, Peter J. and Maitner, Brian S. and Owens, Hannah L. and Varela, Sara and {Aiello-Lammens}, Matthew E. and Merow, Cory and Blair, Mary E. and Anderson, Robert P.}, + year = {2023}, + journal = {Ecography}, + volume = {2023}, + number = {3}, + pages = {e06547}, + issn = {1600-0587}, + doi = {10.1111/ecog.06547}, + urldate = {2024-02-20} } -@misc{lin2024, - title = {Reactable: {{Interactive Data Tables}} for {{R}}}, - author = {Lin, Greg}, - year = {2024}, - url = {https://glin.github.io/reactable/} +@misc{lin2023, + title = {{reactable}: {{Interactive Data Tables}} for {{R}}}, + author = {Lin, Greg and Linsley, Tanner and Russell, Kent and Vaidyanathan, Ramnath and Cheng, Joe and Allaire, {\relax JJ} and Xie, Yihui and Russell, Kenton and Aboukhadijeh, Feross and Shtylman, Roman and Halliday, James and PBC, Posit}, + year = {2023}, + month = mar, + urldate = {2024-07-08}, + copyright = {MIT + file LICENSE}, + doi = {10.32614/CRAN.package.reactable} } @article{maciejewski2020, @@ -211,24 +229,28 @@ @misc{marrs2019 url = {https://www.ceh.ac.uk/sites/default/files/Tablefit-Aug2016.zip} } -@misc{meyer2024, - title = {Shinybusy: {{Busy Indicators}} and {{Notifications}} for '{{Shiny}}' {{Applications}}}, - author = {Meyer, Fanny and Perrier, Victor}, - year = {2024}, - url = {https://github.com/dreamRs/shinybusy} +@misc{meyer2024a, + title = {{shinybusy}: {{Busy Indicators}} and {{Notifications}} for '{{Shiny}}' {{Applications}}}, + author = {Meyer, Fanny and Perrier, Victor and Silex Technologies}, + year = {2024}, + month = mar, + urldate = {2024-07-08}, + abstract = {Add indicators (spinner, progress bar, gif) in your 'shiny' applications to show the user that the server is busy. And other tools to let your users know something is happening (send notifications, reports, ...).}, + copyright = {GPL-3}, + doi = {10.32614/CRAN.package.shinybusy} } @article{mucina2016a, - title = {Vegetation of {{Europe}}: Hierarchical Floristic Classification System of Vascular Plant, Bryophyte, Lichen, and Algal Communities}, + title = {Vegetation of {{Europe}}: Hierarchical Floristic Classification System of Vascular Plant, Bryophyte, Lichen, and Algal Communities}, shorttitle = {Vegetation of {{Europe}}}, - author = {Mucina, Ladislav and B{\"u}ltmann, Helga and Dier{\ss}en, Klaus and Theurillat, Jean-Paul and Raus, Thomas and {\v C}arni, Andra{\v z} and {\v S}umberov{\'a}, Kate{\v r}ina and Willner, Wolfgang and Dengler, J{\"u}rgen and Garc{\'i}a, Rosario Gavil{\'a}n and Chytr{\'y}, Milan and H{\'a}jek, Michal and Di Pietro, Romeo and Iakushenko, Dmytro and Pallas, Jens and Dani{\"e}ls, Fred J.A. and Bergmeier, Erwin and Santos Guerra, Arnoldo and Ermakov, Nikolai and Valachovi{\v c}, Milan and Schamin{\'e}e, Joop H.J. and Lysenko, Tatiana and Didukh, Yakiv P. and Pignatti, Sandro and Rodwell, John S. and Capelo, Jorge and Weber, Heinrich E. and Solomeshch, Ayzik and Dimopoulos, Panayotis and Aguiar, Carlos and Hennekens, Stephan M. and Tich{\'y}, Lubom{\'i}r}, - year = {2016}, - journal = {Applied Vegetation Science}, - volume = {19}, - number = {S1}, - pages = {3--264}, - issn = {1654-109X}, - doi = {10.1111/avsc.12257} + author = {Mucina, Ladislav and B{\"u}ltmann, Helga and Dier{\ss}en, Klaus and Theurillat, Jean-Paul and Raus, Thomas and {\v C}arni, Andra{\v z} and {\v S}umberov{\'a}, Kate{\v r}ina and Willner, Wolfgang and Dengler, J{\"u}rgen and Garc{\'i}a, Rosario Gavil{\'a}n and Chytr{\'y}, Milan and H{\'a}jek, Michal and Di Pietro, Romeo and Iakushenko, Dmytro and Pallas, Jens and Dani{\"e}ls, Fred J.A. and Bergmeier, Erwin and Santos Guerra, Arnoldo and Ermakov, Nikolai and Valachovi{\v c}, Milan and Schamin{\'e}e, Joop H.J. and Lysenko, Tatiana and Didukh, Yakiv P. and Pignatti, Sandro and Rodwell, John S. and Capelo, Jorge and Weber, Heinrich E. and Solomeshch, Ayzik and Dimopoulos, Panayotis and Aguiar, Carlos and Hennekens, Stephan M. and Tich{\'y}, Lubom{\'i}r}, + year = {2016}, + journal = {Applied Vegetation Science}, + volume = {19}, + number = {S1}, + pages = {3--264}, + issn = {1654-109X}, + doi = {10.1111/avsc.12257} } @misc{nbn2024Anthocerotophyta, @@ -271,36 +293,46 @@ @misc{nbn2024Tracheophyta urldate = {2024-04-28} } -@misc{oksanen2022, - title = {Vegan: {{Community Ecology Package}}}, - shorttitle = {Vegandevs/Vegan}, - author = {Oksanen, Jari and Simpson, Gavin and Solymos, Peter and Lahti, Leo and Hannigan, Geoffrey and Weedon, James and Sz{\"o}cs, Eduard and McGlinn, Dan and Legendre, Pierre and Zhilong and Bolker, Ben and Chirico, Michael and Friendly, Michael and Stier, Adrian and Borcard, Daniel and van Dunn{\'e}, Frans and Bengtsson, Henrik and Andersen, Kasper Skytte and Barbour, Matt and Minchin, Peter and FitzJohn, Rich and Laviron, Xavier and {brendanf}}, - year = {2022}, - month = oct, - doi = {10.5281/zenodo.7185692}, - howpublished = {Zenodo} -} - -@misc{ooms2024, - title = {Writexl: {{Export Data Frames}} to {{Excel}} 'xlsx' {{Format}}}, - author = {Ooms, Jeroen}, - year = {2024}, - url = {https://ropensci.r-universe.dev/writexl https://docs.ropensci.org/writexl/} -} - -@misc{owen2021, - title = {Rhandsontable}, - author = {Owen, Jonathan}, - year = {2021}, - abstract = {A htmlwidgets implementation of Handsontable.js}, - url = {https://github.com/jrowen/rhandsontable} +@misc{oksanen2024a, + title = {{vegan}: {{Community Ecology Package}}}, + author = {Oksanen, Jari and Simpson, Gavin L. and Blanchet, F. Guillaume and Kindt, Roeland and Legendre, Pierre and Minchin, Peter R. and O'Hara, R. B. and Solymos, Peter and Stevens, M. Henry H. and Szoecs, Eduard and Wagner, Helene and Barbour, Matt and Bedward, Michael and Bolker, Ben and Borcard, Daniel and Carvalho, Gustavo and Chirico, Michael and Caceres, Miquel De and Durand, Sebastien and Evangelista, Heloisa Beatriz Antoniazi and FitzJohn, Rich and Friendly, Michael and Furneaux, Brendan and Hannigan, Geoffrey and Hill, Mark O. and Lahti, Leo and McGlinn, Dan and Ouellette, Marie-Helene and Cunha, Eduardo Ribeiro and Smith, Tyler and Stier, Adrian and Braak, Cajo J. F. Ter and Weedon, James}, + year = {2024}, + month = may, + urldate = {2024-07-08}, + copyright = {GPL-2}, + keywords = {Environmetrics,Phylogenetics,Psychometrics,Spatial}, + doi = {10.32614/CRAN.package.vegan} } -@misc{perrier2024, - title = {{{shinyWidgets}}: {{Custom Inputs Widgets}} for {{Shiny}}}, - author = {Perrier, Victor and Meyer, Fanny and Granjon, David}, - year = {2024}, - url = {https://github.com/dreamRs/shinyWidgets} +@misc{ooms2024a, + title = {{writexl}: {{Export Data Frames}} to {{Excel}} 'xlsx' {{Format}}}, + author = {Ooms, Jeroen and McNamara, John}, + year = {2024}, + month = feb, + urldate = {2024-07-08}, + copyright = {BSD\_2\_clause + file LICENSE}, + doi = {10.32614/CRAN.package.writexl} +} + +@misc{owen2021a, + title = {{rhandsontable}: {{Interface}} to the '{{Handsontable}}.Js' {{Library}}}, + author = {Owen, Jonathan and Allen, Jeff and Xie, Yihui and Martoglio, Enzo and Ger, Inberg and Marcin, Warpechowski and Gregor, Aisch and Adam, Draper and Tim, Wood and Iskren, Chernev and David, Bushell and Kent, Russell and Jon, Rohan and James, Greene and Dillon, Hammill}, + year = {2021}, + month = may, + urldate = {2024-07-08}, + copyright = {MIT + file LICENSE}, + doi = {10.32614/CRAN.package.rhandsontable} +} + +@misc{perrier2024a, + title = {{{shinyWidgets}}: {{Custom Inputs Widgets}} for {{Shiny}}}, + shorttitle = {{{shinyWidgets}}}, + author = {Perrier, Victor and Meyer, Fanny and Granjon, David and Fellows, Ian and Davis, Wil and Matthews, Spencer}, + year = {2024}, + month = apr, + urldate = {2024-07-08}, + copyright = {GPL-3}, + doi = {10.32614/CRAN.package.shinyWidgets} } @article{perrin2018, @@ -479,20 +511,24 @@ @book{sievert2020 isbn = {978-0-429-44727-3} } -@misc{sievert2023, - title = {Bsicons: {{Easily Work}} with '{{Bootstrap}}' {{Icons}}}, - shorttitle = {Bsicons}, - author = {Sievert, Carson and Posit Software PBC and Otto, Mark}, - year = {2023}, - month = nov, - copyright = {MIT + file LICENSE} +@misc{sievert2023a, + title = {{bsicons}: {{Easily Work}} with '{{Bootstrap}}' {{Icons}}}, + author = {Sievert, Carson and PBC, Posit and Otto, Mark}, + year = {2023}, + month = nov, + urldate = {2024-07-08}, + copyright = {MIT + file LICENSE}, + doi = {10.32614/CRAN.package.bsicons} } -@misc{sievert2024, - title = {Bslib: {{Custom}} '{{Bootstrap}}' '{{Sass}}' {{Themes}} for 'Shiny' and 'Rmarkdown'}, - author = {Sievert, Carson and Cheng, Joe and {Aden-Buie}, Garrick}, - year = {2024}, - url = {https://rstudio.github.io/bslib/} +@misc{sievert2024a, + title = {{bslib}: {{Custom}} '{{Bootstrap}}' '{{Sass}}' {{Themes}} for 'Shiny' and 'Rmarkdown'}, + author = {Sievert, Carson and Cheng, Joe and {Aden-Buie}, Garrick and PBC, Posit and Aguilar, Javi and Park, Thomas}, + year = {2024}, + month = mar, + urldate = {2024-07-08}, + copyright = {MIT + file LICENSE}, + doi = {10.32614/CRAN.package.bslib} } @article{smart2000, @@ -531,15 +567,6 @@ @misc{smart2024 year = {2024} } -@misc{stefan2022, - title = {Magrittr: {{A Forward-Pipe Operator}} for {{R}}}, - shorttitle = {Magrittr}, - author = {Stefan, Stefan Milton and Wickham, Hadley and Henry, Lionel and RStudio}, - year = {2022}, - month = mar, - copyright = {MIT + file LICENSE} -} - @article{sturbois2023, title = {Ecological Quality Assessment: {{A}} Framework to Report Ecosystems Quality and Their Dynamics from Reference Conditions}, shorttitle = {Ecological Quality Assessment}, @@ -553,13 +580,14 @@ @article{sturbois2023 doi = {10.1002/ecs2.4726} } + @misc{vaidyanathan2023, - title = {Htmlwidgets: {{HTML Widgets}} for {{R}}}, - shorttitle = {Htmlwidgets}, - author = {Vaidyanathan, Ramnath and Xie, Yihui and Allaire, J. J. and Cheng, Joe and Sievert, Carson and Russell, Kenton and Hughes, Ellis and Software, Posit and PBC}, - year = {2023}, - month = dec, - copyright = {MIT + file LICENSE} + title = {{htmlwidgets}: {{HTML Widgets}} for {{R}}}, + author = {Vaidyanathan, Ramnath and Xie, Yihui and Allaire, J. J. and Cheng, Joe and Sievert, Carson and Russell, Kenton and Hughes, Ellis and PBC, Posit}, + year = {2023}, + month = dec, + copyright = {MIT + file LICENSE}, + doi = {10.32614/CRAN.package.htmlwidgets} } @unpublished{wallace2017, @@ -590,7 +618,6 @@ @article{wallace2023 url = {https://www.britishwildlife.com/article/article-volume-35-number-3-page-193-200/} } - @article{wickham2019, title = {Welcome to the {{Tidyverse}}}, author = {Wickham, Hadley and Averick, Mara and Bryan, Jennifer and Chang, Winston and McGowan, Lucy D'Agostino and Fran{\c c}ois, Romain and Grolemund, Garrett and Hayes, Alex and Henry, Lionel and Hester, Jim and Kuhn, Max and Pedersen, Thomas Lin and Miller, Evan and Bache, Stephan Milton and M{\"u}ller, Kirill and Ooms, Jeroen and Robinson, David and Seidel, Dana Paige and Spinu, Vitalie and Takahashi, Kohske and Vaughan, Davis and Wilke, Claus and Woo, Kara and Yutani, Hiroaki}, @@ -604,6 +631,7 @@ @article{wickham2019 doi = {10.21105/joss.01686} } + @article{wood2015, title = {Woodland Survey of Great Britain 1971-2001}, volume = {7}, @@ -619,42 +647,47 @@ @article{wood2015 pages = {203-214} } -@misc{xie2023, - title = {Markdown: {{Render Markdown}} with 'Commonmark'}, - shorttitle = {Markdown}, - author = {Xie, Yihui}, - year = {2023}, - month = dec, - url = {https://cran.r-project.org/web/packages/markdown/index.html} +@misc{xie2024b, + title = {{bookdown}: {{Authoring Books}} and {{Technical Documents}} with {{R Markdown}}}, + author = {Xie, Yihui and Dervieux, Christophe and Allaire, J. J. and Kim, Albert and {Samuel-Rosa}, Alessandro and Oles, Andrzej and Yasumoto, Atsushi and Frederik, Aust and Quast, Bastiaan and Marwick, Ben and Ismay, Chester and Franklund, Clifton and Emaasit, Daniel and Shuman, David and Attali, Dean and Tyre, Drew and Valentiner, Ellis and van Dunne, Frans and Wickham, Hadley and Allen, Jeff and Bryan, Jennifer and McPhers, Jonathan and Seo, JooYoung and Robbins, Joyce and Huang, Junwen and Cheung, Kevin and Ushey, Kevin and Seonghyun, Kim and Muller, Kirill and Selzer, Luciano and Lincoln, Matthew and Held, Maximilian and Sachs, Michael and Bojanowski, Michal and Werth, Nathan and Ross, Noam and Hickey, Peter and Marinho, Pedro Rafael D. and Lesur, Romain and Bhatnagar, Sahir and Dekel, Shir and Simpson, Steve and Onkelinx, Thierry and Fulco, Vincent and Qiu, Yixuan and Dong, Zhuoer and Szopka, Bartek and Rocha, Zeno}, + year = {2024}, + month = jul, + urldate = {2024-07-08}, + abstract = {Output formats and utilities for authoring books and technical documents with R Markdown.}, + copyright = {GPL-3}, + doi = {10.32614/CRAN.package.bookdown} } -@misc{xie2024, - title = {Knitr: {{A General-Purpose Package}} for {{Dynamic Report Generation}} in {{R}}}, - shorttitle = {Knitr}, - author = {Xie [aut, Yihui and {cre} and Sarma, Abhraneel and Vogt, Adam and Andrew, Alastair and Zvoleff, Alex and {Al-Zubaidi}, Amar and package {http://www.andre-simon.de)}, Andre Simon (the CSS files under inst/themes/ were derived from the Highlight and Atkins, Aron and Wolen, Aaron and Manton, Ashley and Yasumoto, Atsushi and Baumer, Ben and Diggs, Brian and Zhang, Brian and Yapparov, Bulat and Pereira, Cassio and Dervieux, Christophe and Hall, David and {Hugh-Jones}, David and Robinson, David and Hemken, Doug and Murdoch, Duncan and Campitelli, Elio and Hughes, Ellis and Riederer, Emily and Hirschmann, Fabian and Simeon, Fitch and Fang, Forest and package at {inst/misc/Sweavel.sty)}, Frank E. Harrell Jr (the Sweavel and {Aden-Buie}, Garrick and Detrez, Gregoire and Wickham, Hadley and Zhu, Hao and Jeon, Heewon and Bengtsson, Henrik and Yutani, Hiroaki and Lyttle, Ian and Daniel, Hodges and Bien, Jacob and Burkhead, Jake and Manton, James and Lander, Jared and Punyon, Jason and Luraschi, Javier and Arnold, Jeff and Bryan, Jenny and file at {inst/misc/docco-classic.css)}, Jeremy Ashkenas (the CSS and Stephens, Jeremy and Hester, Jim and Cheng, Joe and Ranke, Johannes and Honaker, John and Muschelli, John and Keane, Jonathan and Allaire, J. J. and Toloe, Johan and Sidi, Jonathan and Larmarange, Joseph and Barnier, Julien and Zhong, Kaiyin and Slowikowski, Kamil and Forner, Karl and Smith, Kevin K. and Mueller, Kirill and Takahashi, Kohske and Walthert, Lorenz and Gallindo, Lucas and Hofert, Marius and Modr{\'a}k, Martin and Chirico, Michael and Friendly, Michael and Bojanowski, Michal and Kuhlmann, Michel and Patrick, Miller and Caballero, Nacho and Salkowski, Nick and Hansen, Niels Richard and Ross, Noam and Mahdi, Obada and Krivitsky, Pavel N. and Faria, Pedro and Li, Qiang and Vaidyanathan, Ramnath and Cotton, Richard and Krzyzanowski, Robert and Copetti, Rodrigo and Francois, Romain and Williamson, Ruaridh and Mati, Sagiru and Kostyshak, Scott and Meyer, Sebastian and Brouwer, Sietse and de Bernard, Simon and Rousseau, Sylvain and Wei, Taiyun and Assus, Thibaut and Lamadon, Thibaut and Leeper, Thomas and Mastny, Tim and {Torsney-Weir}, Tom and Davis, Trevor and Veitas, Viktoras and Zhu, Weicheng and Wu, Wush and Foster, Zachary and Kamvar, Zhian N. and Software, Posit and PBC}, - year = {2024}, - month = may, - copyright = {GPL-2 {\textbar} GPL-3 [expanded from: GPL]} +@misc{xie2024c, + title = {{knitr}: {{A General-Purpose Package}} for {{Dynamic Report Generation}} in {{R}}}, + author = {Xie, Yihui and Sarma, Abhraneel and Vogt, Adam and Andrew, Alastair and Zvoleff, Alex and {Al-Zubaidi}, Amar and Simon, Andre and Atkins, Aron and Wolen, Aaron and Manton, Ashley and Yasumoto, Atsushi and Baumer, Ben and Diggs, Brian and Zhang, Brian and Yapparov, Bulat and Pereira, Cassio and Dervieux, Christophe and Hall, David and {Hugh-Jones}, David and Robinson, David and Hemken, Doug and Murdoch, Duncan and Campitelli, Elio and Hughes, Ellis and Riederer, Emily and Hirschmann, Fabian and Simeon, Fitch and Fang, Forest and Harrell Jr, Frank E. and {Aden-Buie}, Garrick and Detrez, Gregoire and Wickham, Hadley and Zhu, Hao and Jeon, Heewon and Bengtsson, Henrik and Yutani, Hiroaki and Lyttle, Ian and Daniel, Hodges and Bien, Jacob and Burkhead, Jake and Manton, James and Lander, Jared and Punyon, Jason and Luraschi, Javier and Arnold, Jeff and Bryan, Jenny and Ashkenas, Jeremy and Stephens, Jeremy and Hester, Jim and Cheng, Joe and Ranke, Johannes and Honaker, John and Muschelli, John and Keane, Jonathan and Allaire, J. J. and Toloe, Johan and Sidi, Jonathan and Larmarange, Joseph and Barnier, Julien and Zhong, Kaiyin and Slowikowski, Kamil and Forner, Karl and Smith, Kevin K. and Mueller, Kirill and Takahashi, Kohske and Walthert, Lorenz and Gallindo, Lucas and Hofert, Marius and Modr{\'a}k, Martin and Chirico, Michael and Friendly, Michael and Bojanowski, Michal and Kuhlmann, Michel and Patrick, Miller and Caballero, Nacho and Salkowski, Nick and Hansen, Niels Richard and Ross, Noam and Mahdi, Obada and Krivitsky, Pavel N. and Faria, Pedro and Li, Qiang and Vaidyanathan, Ramnath and Cotton, Richard and Krzyzanowski, Robert and Copetti, Rodrigo and Francois, Romain and Williamson, Ruaridh and Mati, Sagiru and Kostyshak, Scott and Meyer, Sebastian and Brouwer, Sietse and de Bernard, Simon and Rousseau, Sylvain and Wei, Taiyun and Assus, Thibaut and Lamadon, Thibaut and Leeper, Thomas and Mastny, Tim and {Torsney-Weir}, Tom and Davis, Trevor and Veitas, Viktoras and Zhu, Weicheng and Wu, Wush and Foster, Zachary and Kamvar, Zhian N. and PBC, Posit}, + year = {2024}, + month = jul, + urldate = {2024-07-08}, + copyright = {GPL-2 {\textbar} GPL-3 [expanded from: GPL]}, + doi = {10.32614/CRAN.package.knitr} } -@misc{xie2024, - title = {Bookdown: {{Authoring Books}} and {{Technical Documents}} with {{R Markdown}}}, - author = {Xie, Yihui}, +@misc{xie2024d, + title = {{markdown}: {{Render Markdown}} with 'Commonmark'}, + author = {Xie, Yihui and Allaire, J. J. and Horner, Jeffrey and Bengtsson, Henrik and Hester, Jim and Qiu, Yixuan and Takahashi, Kohske and November, Adam and Caballero, Nacho and Ooms, Jeroen and Leeper, Thomas and Cheng, Joe and Oles, Andrzej and PBC, Posit}, year = {2024}, - copyright = {GPL-3.0}, - url = {https://github.com/rstudio/bookdown} + month = jun, + urldate = {2024-07-08}, + copyright = {MIT + file LICENSE}, + keywords = {ReproducibleResearch}, + doi = {10.32614/CRAN.package.markdown} } -@misc{zhu2024, - title = {{{kableExtra}}}, - author = {Zhu, Hao}, - year = {2024}, - abstract = {Construct Complex Table with knitr::kable() + pipe.}, - url = {https://github.com/haozhu233/kableExtra} +@misc{zhu2024a, + title = {{{kableExtra}}: {{Construct Complex Table}} with 'kable' and {{Pipe Syntax}}}, + shorttitle = {{{kableExtra}}}, + author = {Zhu, Hao and Travison, Thomas and Tsai, Timothy and Beasley, Will and Xie, Yihui and Yu, GuangChuang and Laurent, St{\'e}phane and Shepherd, Rob and Sidi, Yoni and Salzer, Brian and Gui, George and Fan, Yeliang and Murdoch, Duncan and {Arel-Bundock}, Vincent and Evans, Bill}, + year = {2024}, + month = jan, + urldate = {2024-07-08}, + doi = {10.32614/CRAN.package.kableExtra} } - - - diff --git a/JOSS/paper.html b/JOSS/paper.html index 4c38c51..9b50d17 100644 --- a/JOSS/paper.html +++ b/JOSS/paper.html @@ -10,9 +10,9 @@ - + -RMAVIS v1.0: a R Shiny application for the analysis of vegetation survey data and assignment to GB NVC communities. +RMAVIS v1.0: a Shiny application for the analysis of vegetation survey data and assignment to GB NVC communities.