├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── R ├── constants.R ├── helpers.R ├── latinr-package.R ├── latinr_article.R ├── latinr_wizard.R ├── parsers.R ├── password.R ├── print.R ├── submission.R ├── sysdata.rda ├── topics.R └── users.R ├── README.Rmd ├── README.md ├── inst ├── prism.css ├── prism.js ├── request_example.txt └── rmarkdown │ └── templates │ └── latinr_article │ ├── latinr_article.zip │ ├── resources │ ├── template_anom.tex │ ├── template_name.tex │ └── template_name_no-bottom.tex │ ├── skeleton │ ├── .Rhistory │ ├── RJournal.sty │ ├── latinr_bibliography.bib │ └── skeleton.Rmd │ └── template.yaml ├── latinr.Rproj ├── man ├── figures │ ├── logo.png │ └── wizard.png ├── latinr-package.Rd ├── latinr_article.Rd ├── latinr_checks.Rd ├── latinr_default_user.Rd ├── latinr_lists.Rd ├── latinr_password.Rd ├── latinr_submit.Rd └── latinr_wizard.Rd └── submission_conditions.yaml /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^LICENSE\.md$ 2 | ^.*\.Rproj$ 3 | ^\.Rproj\.user$ 4 | ^README\.Rmd$ 5 | ^submission_conditions\.yaml$ 6 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user/ 2 | .Rproj.user 3 | .Rhistory 4 | .RData 5 | .Ruserdata 6 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: latinr 2 | Title: Submission to LatinR 3 | Version: 0.0.0.9010 4 | Authors@R: 5 | person(given = "Elio", 6 | family = "Campitelli", 7 | role = c("aut", "cre"), 8 | email = "elio.campitelli@fcen.cima.fcen.uba.ar") 9 | Description: Facilitates creation and submissiond of abstract for the LatinR conference. 10 | License: GPL-3 11 | Encoding: UTF-8 12 | LazyData: true 13 | Depends: R (>= 2.10) 14 | Imports: 15 | rmarkdown, 16 | knitr, 17 | httr, 18 | rvest, 19 | getPass, 20 | shiny, 21 | xml2, 22 | miniUI, 23 | shinyjqui, 24 | shinyWidgets, 25 | yaml, 26 | magick, 27 | sessioninfo 28 | Suggests: 29 | keyring 30 | RoxygenNote: 7.1.1 31 | Roxygen: list(markdown = TRUE) 32 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- 1 | GNU General Public License 2 | ========================== 3 | 4 | _Version 3, 29 June 2007_ 5 | _Copyright © 2007 Free Software Foundation, Inc. <>_ 6 | 7 | Everyone is permitted to copy and distribute verbatim copies of this license 8 | document, but changing it is not allowed. 9 | 10 | ## Preamble 11 | 12 | The GNU General Public License is a free, copyleft license for software and other 13 | kinds of works. 14 | 15 | The licenses for most software and other practical works are designed to take away 16 | your freedom to share and change the works. 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However, no 510 | additional obligations are imposed on any author or copyright holder as a result of 511 | your choosing to follow a later version. 512 | 513 | ### 15. Disclaimer of Warranty 514 | 515 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. 516 | EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES 517 | PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER 518 | EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF 519 | MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE 520 | QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE 521 | DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 522 | 523 | ### 16. Limitation of Liability 524 | 525 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY 526 | COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS 527 | PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, 528 | INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE 529 | PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE 530 | OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE 531 | WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE 532 | POSSIBILITY OF SUCH DAMAGES. 533 | 534 | ### 17. Interpretation of Sections 15 and 16 535 | 536 | If the disclaimer of warranty and limitation of liability provided above cannot be 537 | given local legal effect according to their terms, reviewing courts shall apply local 538 | law that most closely approximates an absolute waiver of all civil liability in 539 | connection with the Program, unless a warranty or assumption of liability accompanies 540 | a copy of the Program in return for a fee. 541 | 542 | _END OF TERMS AND CONDITIONS_ 543 | 544 | ## How to Apply These Terms to Your New Programs 545 | 546 | If you develop a new program, and you want it to be of the greatest possible use to 547 | the public, the best way to achieve this is to make it free software which everyone 548 | can redistribute and change under these terms. 549 | 550 | To do so, attach the following notices to the program. It is safest to attach them 551 | to the start of each source file to most effectively state the exclusion of warranty; 552 | and each file should have at least the “copyright” line and a pointer to 553 | where the full notice is found. 554 | 555 | 556 | Copyright (C) 2019 Elio Campitelli 557 | 558 | This program is free software: you can redistribute it and/or modify 559 | it under the terms of the GNU General Public License as published by 560 | the Free Software Foundation, either version 3 of the License, or 561 | (at your option) any later version. 562 | 563 | This program is distributed in the hope that it will be useful, 564 | but WITHOUT ANY WARRANTY; without even the implied warranty of 565 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 566 | GNU General Public License for more details. 567 | 568 | You should have received a copy of the GNU General Public License 569 | along with this program. If not, see . 570 | 571 | Also add information on how to contact you by electronic and paper mail. 572 | 573 | If the program does terminal interaction, make it output a short notice like this 574 | when it starts in an interactive mode: 575 | 576 | latinr Copyright (C) 2019 Elio Campitelli 577 | This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. 578 | This is free software, and you are welcome to redistribute it 579 | under certain conditions; type 'show c' for details. 580 | 581 | The hypothetical commands `show w` and `show c` should show the appropriate parts of 582 | the General Public License. Of course, your program's commands might be different; 583 | for a GUI interface, you would use an “about box”. 584 | 585 | You should also get your employer (if you work as a programmer) or school, if any, to 586 | sign a “copyright disclaimer” for the program, if necessary. For more 587 | information on this, and how to apply and follow the GNU GPL, see 588 | <>. 589 | 590 | The GNU General Public License does not permit incorporating your program into 591 | proprietary programs. If your program is a subroutine library, you may consider it 592 | more useful to permit linking proprietary applications with the library. If this is 593 | what you want to do, use the GNU Lesser General Public License instead of this 594 | License. But first, please read 595 | <>. 596 | -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 1 | # Generated by roxygen2: do not edit by hand 2 | 3 | export(latinr_article) 4 | export(latinr_checks) 5 | export(latinr_countries) 6 | export(latinr_default_user_get) 7 | export(latinr_default_user_set) 8 | export(latinr_password_get) 9 | export(latinr_password_remove) 10 | export(latinr_password_set) 11 | export(latinr_submit) 12 | export(latinr_topics) 13 | export(latinr_types) 14 | export(latinr_wizard) 15 | -------------------------------------------------------------------------------- /R/constants.R: -------------------------------------------------------------------------------- 1 | 2 | latinr_service <- function() { 3 | "latinr_easychair" 4 | } 5 | 6 | .latinr_url <- function(what) { 7 | switch(what, 8 | verify = "https://easychair.org/account/verify", 9 | login = "https://easychair.org/account/signin", 10 | latinr = "https://easychair.org/conferences/?conf=latinr2021", 11 | singup = "https://easychair.org/account/signup", 12 | submit = "https://easychair.org/conferences/submission_new_z.cgi", 13 | stop("Unrecognised what") 14 | ) 15 | } 16 | 17 | .topics <- c("Aplicaciones de R en distintas disciplinas de la academia y la industria", 18 | "Uso de R en conjunto con otros lenguajes de programaci\u00F3n y plataformas", 19 | "Desarrollo de nuevos paquetes R", 20 | "Uso innovador de paquetes R existentes", 21 | "Uso de R en la ense\u00F1anza", 22 | "Iniciativas innovadoras para el aprendizaje de R", 23 | "Investigaci\u00F3n reproducible usando R", 24 | "An\u00E1lisis de grandes datos con R", 25 | "Aprendizaje autom\u00E1tico con R", 26 | "Visualizaci\u00F3n de datos con R", 27 | "An\u00E1lisis de redes con R", 28 | "An\u00E1lisis de datos espaciales con R", 29 | "Uso de R para an\u00E1lisis de datos abiertos") 30 | 31 | 32 | 33 | .submission_track <- "257342" 34 | 35 | .topics_number <- seq(323629, 323640) 36 | 37 | .types <- c("oral", "poster", "table", "lightning") 38 | 39 | .types_number <- c(171277, 171278, 171277, 171279) 40 | -------------------------------------------------------------------------------- /R/helpers.R: -------------------------------------------------------------------------------- 1 | check_latest_version <- function() { 2 | description <- readLines("https://raw.githubusercontent.com/LatinR/latinr/master/DESCRIPTION") 3 | latest_version <- description[grepl("Version:", description)] 4 | latest_version <- gsub("Version: ", "", latest_version) 5 | pkg_info <- sessioninfo::package_info("latinr", dependencies = FALSE) 6 | 7 | this_version_loaded <- pkg_info$loadedversion 8 | this_version_disk <- pkg_info$ondiskversion 9 | 10 | 11 | 12 | if (latest_version != this_version_disk) { 13 | stop("Your version of latinr (", this_version_disk, ") is not the most recent (", 14 | latest_version, "). Please update with `devtools::install_github(\"latinr/latinr\")`", 15 | "and restart R (In RStudio: Session -> Restart R).") 16 | } 17 | 18 | if (latest_version != this_version_loaded) { 19 | stop("Your loaded version of latinr (", this_version_loaded, ") is not the most recent (", 20 | latest_version, "). Please restart R (In RStudio: Session -> Restart R).") 21 | 22 | } 23 | } 24 | 25 | 26 | check_submissions_open <- function() { 27 | submissions <- yaml::read_yaml("https://raw.githubusercontent.com/LatinR/latinr/master/submission_conditions.yaml") 28 | if (!submissions$open) { 29 | stop("The latinr package is not ready for submissions yet.") 30 | } 31 | } 32 | -------------------------------------------------------------------------------- /R/latinr-package.R: -------------------------------------------------------------------------------- 1 | #' @section Overview: 2 | #' 3 | #' This package attempts to automate as much as possible the creation and submission process of 4 | #' abstracts for the LatinR conference. You write in RMarkdown and all submission details are 5 | #' added to the yaml header. Then, before submission, the package does some basic checks, renders 6 | #' the document using the provided LaTeX template and finally submits it. 7 | #' 8 | #' @section Creating a submission: 9 | #' 10 | #' If you use RStudio, you can fo to File -> New File -> R Markdown -> From Template and 11 | #' select "LatinR submission article". This will create a skeleton document along with other 12 | #' helper files into the selected folder. 13 | #' 14 | #' You'll see that all the important data is managed by the yaml header. You can either populate it 15 | #' manually or, a bit easier, use [latinr_wizard()] to launch a small user interface that will guide 16 | #' you and finally give you a valid yaml header that you can copy and paste into your document. 17 | #' 18 | #' 19 | #' @section Submitting and article: 20 | #' 21 | #' One you're happy with your article, it's time to submit it. First, if you haven't already, you'll 22 | #' need to create an account at https://easychair.org/account/signup and then save your 23 | #' login information using [latinr_password_set()]. The email associated with the account you are 24 | #' using to submit your article has to match the email of one of the authors. 25 | #' 26 | #' To submit your article use [latinr_submit()]. By default, it will search for .Rmd files in the 27 | #' current working directory and if it finds only one, it process it. First, you will be shown the 28 | #' submission information (such as author details, title, keywords, etc...) so you can check that 29 | #' everything is in order. Then, it will render and open the PDF so you can also check the finished 30 | #' submission. 31 | #' 32 | #' If all it's OK, the article will be submitted. Be aware that this process is still a bit 33 | #' experimental so things can fail. It's VERY IMPORTANT that at the end of the process you go to 34 | #' your account an make a final check so that you're sure that the submission information, as well as 35 | #' the article PDF have been correctly submitted. If you find any problem, correct them right there 36 | #' on the website. 37 | #' 38 | #' @keywords internal 39 | "_PACKAGE" 40 | 41 | # The following block is used by usethis to automatically manage 42 | # roxygen namespace tags. Modify with care! 43 | ## usethis namespace: start 44 | ## usethis namespace: end 45 | NULL 46 | -------------------------------------------------------------------------------- /R/latinr_article.R: -------------------------------------------------------------------------------- 1 | #' R Markdown output format for submissions to LatinR 2 | #' 3 | #' 4 | #' @inheritParams rmarkdown::pdf_document 5 | #' @param anonymise whether to anonymise the PDF 6 | #' @param author_bottom whether to add author information at the bottom of the 7 | #' page. 8 | #' 9 | #' @export 10 | latinr_article <- function( ..., keep_tex = FALSE, highlight = "default", citation_package = "default", 11 | latex_engine = "xelatex", anonymise = TRUE, author_bottom = FALSE) { 12 | pdf_document_format( 13 | "latinr_article", 14 | submission = anonymise, 15 | author_bottom = author_bottom, 16 | keep_tex = keep_tex, highlight = highlight, 17 | citation_package = citation_package, latex_engine = latex_engine, 18 | md_extensions = c("-autolink_bare_uris"),... 19 | ) 20 | } 21 | 22 | pdf_document_format <- function(format, submission = TRUE, author_bottom = TRUE, ...) { 23 | 24 | if (isTRUE(submission)) { 25 | template <- find_resource(format, 'template_anom.tex') 26 | } else { 27 | if (isTRUE(author_bottom)) { 28 | template <- find_resource(format, 'template_name.tex') 29 | } else { 30 | template <- find_resource(format, 'template_name_no-bottom.tex') 31 | } 32 | 33 | } 34 | 35 | fmt <- rmarkdown::pdf_document(..., template = template) 36 | fmt$inherits <- "pdf_document" 37 | fmt 38 | } 39 | 40 | 41 | find_resource <- function(template, file = 'template.tex') { 42 | res <- system.file( 43 | "rmarkdown", "templates", template, "resources", file, package = "latinr" 44 | ) 45 | if (res == "") stop( 46 | "Couldn't find template file ", template, "/resources/", file, call. = FALSE 47 | ) 48 | res 49 | } 50 | 51 | 52 | #' Checks that metadata is ok 53 | #' 54 | #' Does basics checks on metadata so that it adheres to submission guidelines. 55 | #' 56 | #' @param metadata yaml metadata. 57 | #' @param check_is_error whether to treat fails as errors or only warnings 58 | #' useful during development). 59 | #' 60 | #' @export 61 | latinr_checks <- function(metadata, check_is_error = TRUE) { 62 | authors <- metadata$authors 63 | required <- c("last_name", "email", "country", "affiliation") 64 | 65 | missing_fields <- lapply(seq_along(authors), function(a) { 66 | person <- authors[[a]] 67 | len <- lengths(person[names(person) %in% required]) 68 | nulls <- names(person)[names(person) %in% required][len == 0] 69 | length_0 <- nchar(person[names(person) %in% required]) == 0 70 | length_0 <- names(person)[names(person) %in% required][length_0] 71 | 72 | missing_fields <- required[ !(required %in% names(person)) ] 73 | 74 | 75 | missing_fields <- c(nulls, missing_fields, length_0) 76 | 77 | if (length(missing_fields) != 0) { 78 | paste0("Author ", a, ": missing ", knitr::combine_words(missing_fields)) 79 | } else { 80 | "" 81 | } 82 | }) 83 | 84 | errors <- unlist(missing_fields) 85 | errors <- errors[nchar(errors) != 0] 86 | 87 | 88 | 89 | n_correspondence <- Reduce("+", lapply(authors, function(a) isTRUE(a$corresponding))) 90 | 91 | if (n_correspondence == 0) { 92 | errors <- c(errors, "Missing corresponding author") 93 | } 94 | 95 | if (is.null(metadata$title)) { 96 | errors <- c(errors, "Missing title") 97 | } 98 | 99 | 100 | keywords <- metadata$keywords 101 | 102 | if (sum(lengths(keywords)) < 3) { 103 | errors <- c(errors, "At least three keywords needed") 104 | } 105 | 106 | 107 | if (!(metadata$type %in% .types)) { 108 | errors <- c(errors, paste0("Submission type mus be ", 109 | knitr::combine_words(.types, and = " or "))) 110 | } 111 | 112 | if (length(errors) != 0) { 113 | text <- paste0("\nFound the following errors:\n * ", paste(errors, collapse = "\n * ")) 114 | if (isTRUE(check_is_error)) { 115 | stop(text) 116 | } else { 117 | cat(text) 118 | } 119 | } 120 | invisible(errors) 121 | } 122 | 123 | 124 | -------------------------------------------------------------------------------- /R/latinr_wizard.R: -------------------------------------------------------------------------------- 1 | #' Opens a user interface to populate yaml fields 2 | #' 3 | #' 4 | #' @export 5 | latinr_wizard <- function() { 6 | notification_css <- shiny::HTML("#shiny-notification-panel { 7 | position:fixed; 8 | width: 70%; 9 | }") 10 | 11 | 12 | style_card <- "background-color:#fafafa;padding:15px;margin-bottom: 10px;border:1px solid gray;box-shadow: 0 4px 8px 0 rgba(0, 0, 0, 0.2), 0 6px 20px 0 rgba(0, 0, 0, 0.19);border-radius: 3px" 13 | 14 | 15 | countries <- as.character(.countries$countries) 16 | names(countries) <- rownames(.countries) 17 | 18 | topics <- seq_along(.topics) 19 | names(topics) <- .topics 20 | 21 | types <- .types 22 | names(types) <- c("Oral presentation", "Poster", "Round table", "Lightning talk") 23 | 24 | author_infoui <- function(id){ 25 | ns <- shiny::NS(id) 26 | 27 | shiny::tags$div(class = "author-panel", id = id, 28 | style = style_card, 29 | shiny::fluidRow( 30 | shiny::column(width = 6, 31 | shiny::textInput(ns("first_name"), "First Name", value = "", width = "100%") 32 | ), 33 | shiny::column(width = 6, 34 | shiny::textInput(ns("last_name"), "Last Name", value = "", width = "100%") 35 | ) 36 | ), 37 | shiny::textInput(ns("affiliation"), "Affiliation", value = "", width = "100%"), 38 | shiny::fluidRow( 39 | shiny::column(width = 8, 40 | shiny::textInput(ns("email"), "Email", value = "", width = "100%") 41 | ), 42 | shiny::column(width = 4, 43 | shinyWidgets::materialSwitch( 44 | inputId = ns("is_corresponding"), 45 | label = "Corresponding author", 46 | status = "primary", 47 | right = TRUE 48 | ) 49 | ), 50 | shiny::tags$style(type='text/css', paste0(".material-switch { margin-top: 30px;}")), 51 | # checkboxInput(ns("is_corresponding"), "Corresponding author", value = TRUE) 52 | ), 53 | shiny::textInput(ns("url"), "URL", value = "", width = "100%"), 54 | shiny::fluidRow( 55 | shiny::column(width = 12, 56 | shiny::selectInput(ns("country"), "Country", countries, selectize = TRUE, width = "100%")) 57 | ), 58 | shiny::fluidRow( 59 | shiny::column(width = 6, align = "center", offset = 3, 60 | shiny::actionButton(ns("remove"), NULL, icon = shiny::icon("minus")) 61 | ) 62 | ) 63 | ) 64 | } 65 | 66 | author_info <- function(input, output, session){ 67 | ns <- session$ns 68 | id <- substr(ns(""), 1, nchar(ns("")) - 1) 69 | shiny::observeEvent( input$remove , { 70 | 71 | shiny::removeUI(paste0("#", id)) 72 | shinyjqui::jqui_sortable('#author', operation = "destroy") 73 | shinyjqui::jqui_sortable('#author', operation = "enable") 74 | }) 75 | } 76 | 77 | 78 | ui <- miniUI::miniPage( 79 | shiny::tags$head( 80 | shiny::tags$link(rel = "stylesheet", type = "text/css", href = "inst/prism.css"), 81 | shiny::tags$style(notification_css) 82 | ), 83 | miniUI::gadgetTitleBar("LatinR2020", 84 | right = miniUI::miniTitleBarButton("save", "Save", primary = TRUE) 85 | ), 86 | miniUI::miniTabstripPanel( 87 | miniUI::miniTabPanel("Authors", icon = shiny::icon("users"), 88 | miniUI::miniContentPanel( 89 | # actionButton("inspect", "inspect"), 90 | shinyjqui::jqui_sortable( 91 | shiny::div(id = "author" 92 | ) 93 | ), 94 | shiny::fluidRow( 95 | shiny::column(width = 6, align = "center", offset = 3, 96 | shiny::actionButton("add_author", NULL, icon = shiny::icon("plus")) 97 | ) 98 | ) 99 | ) 100 | ), 101 | miniUI::miniTabPanel("Presentation", icon = shiny::icon("file"), 102 | miniUI::miniContentPanel( 103 | shiny::tags$div(class = "presentation-panel", style = style_card, 104 | shiny::fluidRow( 105 | shiny::column(width = 6, 106 | shiny::selectInput("type", "Presentation Type", types, width = "100%"), 107 | ), 108 | shiny::column(width = 6, 109 | shiny::uiOutput("presenter") 110 | ) 111 | ), 112 | shiny::selectInput("lang", "Language", c("Spanish" = "spanish", 113 | "Portuguese" = "portuguese", 114 | "English" = "english"), 115 | width = "100%"), 116 | shiny::textInput("title", "Title", value = "", width = "100%"), 117 | shiny::selectizeInput("keywords", "Keywords", c(), 118 | multiple = TRUE, options = list( 119 | 'plugins' = list('remove_button'), 120 | 'create' = TRUE, 121 | 'persist' = FALSE)), 122 | # shiny::textInput("keywords", "Keywords", "", width = "100%"), 123 | shiny::selectInput("topics", "Topics", topics, multiple = TRUE, width = "100%") 124 | ) 125 | ) 126 | ), 127 | miniUI::miniTabPanel("Header", icon = shiny::icon("stream"), 128 | miniUI::miniContentPanel( 129 | shiny::verbatimTextOutput("yaml") 130 | ) 131 | ) 132 | ) 133 | ) 134 | 135 | server <- function(input, output, session) { 136 | author_count <- shiny::reactiveVal(1) 137 | shiny::insertUI("#author", 138 | ui = author_infoui("author_1"), 139 | where = "beforeEnd") 140 | shiny::callModule(author_info, "author_1") 141 | shinyjqui::jqui_sortable('#author', operation = "destroy") 142 | shinyjqui::jqui_sortable('#author', operation = "enable") 143 | 144 | shiny::observeEvent(input$add_author , { 145 | author_count(author_count() + 1) 146 | author_id <- paste0("author_", shiny::isolate(author_count())) 147 | shiny::insertUI("#author", 148 | ui = author_infoui(author_id), 149 | where = "beforeEnd") 150 | 151 | 152 | shiny::callModule(author_info, author_id) 153 | 154 | shinyjqui::jqui_sortable('#author', operation = "destroy") 155 | shinyjqui::jqui_sortable('#author', operation = "enable") 156 | 157 | 158 | }) 159 | 160 | shiny::observeEvent( input$inspect , { 161 | browser() 162 | }) 163 | 164 | authors <- shiny::reactive({ 165 | authors <- input$author_order$id 166 | lapply(authors, function(a) { 167 | list(first_name = input[[paste0(a, "-first_name")]], 168 | last_name = input[[paste0(a, "-last_name")]], 169 | email = input[[paste0(a, "-email")]], 170 | country = input[[paste0(a, "-country")]], 171 | affiliation = input[[paste0(a, "-affiliation")]], 172 | url = input[[paste0(a, "-url")]], 173 | corresponding = input[[paste0(a, "-is_corresponding")]] 174 | ) 175 | }) 176 | }) 177 | 178 | output$presenter <- shiny::renderUI({ 179 | speaker_choices <- vapply(seq_along(authors()), function(a) { 180 | paste0("(", a, ") ", authors()[[a]]$first_name, " ", authors()[[a]]$last_name) 181 | }, "a") 182 | 183 | shiny::selectInput("presenter", "Presenter", 184 | choices = stats::setNames(seq_along(speaker_choices), speaker_choices), 185 | width = "100%") 186 | }) 187 | 188 | metadata <- shiny::reactive({ 189 | yaml_list <- list( 190 | type = input$type, 191 | language = input$lang, 192 | title = input$title, 193 | topics = as.integer(input$topics), 194 | authors = authors(), 195 | presenter = as.integer(input$presenter), 196 | keywords = as.list(input$keywords), 197 | bibliography = "latinr_bibliography.bib", 198 | `biblio-style` = "apalike-es", 199 | output = list(`latinr::latinr_article` = list( 200 | keep_tex = FALSE, 201 | submission = FALSE 202 | )), 203 | params = list( 204 | check_is_error = FALSE 205 | ) 206 | ) 207 | }) 208 | 209 | 210 | yaml <- shiny::reactive({ 211 | yaml <- yaml::as.yaml(metadata()) 212 | errors <- latinr_checks(shiny::isolate(metadata()), check_is_error = FALSE) 213 | 214 | if (length(errors) > 0) { 215 | 216 | text <- shiny::p("Found the following errors:", shiny::tags$br(), 217 | shiny::tags$ul( 218 | shiny::tagList( 219 | lapply(errors, function(x) shiny::tags$li(x)) 220 | ) 221 | ) 222 | ) 223 | 224 | shiny::showNotification(text, type = "warning") 225 | } 226 | 227 | paste0("---\n", yaml, "---") 228 | }) 229 | 230 | 231 | file <- NULL 232 | output$yaml <- shiny::renderText(yaml()) 233 | 234 | shiny::observeEvent(input$save, { 235 | file <<- file.choose(new = TRUE) 236 | 237 | extension <- tools::file_ext(file) 238 | if (nchar(extension) == 0) { 239 | file <- paste0(file, ".Rmd") 240 | } 241 | 242 | skeleton <- system.file("inst/rmarkdown/templates/latinr_article/skeleton/", 243 | "skeleton.Rmd", package = "latinr", mustWork = TRUE) 244 | bib <- system.file("inst/rmarkdown/templates/latinr_article/skeleton/", 245 | "latinr_bibliography.bib", package = "latinr", mustWork = TRUE) 246 | style <- system.file("inst/rmarkdown/templates/latinr_article/skeleton/", 247 | "RJournal.sty", package = "latinr", mustWork = TRUE) 248 | 249 | lines <- paste0(yaml(), "\n\n", 250 | "```{r submission-checks, echo=FALSE, warning=TRUE}\n", 251 | "# Runs some basic checks in metadata. To disable, set check_is_error to FALSE\n", 252 | "latinr::latinr_checks(rmarkdown::metadata, params$check_is_error)\n", 253 | "```\n\n", 254 | "```{r setup, include=FALSE}\n", 255 | "knitr::opts_chunk$set(echo = TRUE)\n", 256 | "```\n") 257 | 258 | writeLines(lines, file) 259 | 260 | file.copy(bib, file.path(dirname(file), basename(bib))) 261 | file.copy(style, file.path(dirname(file), basename(style))) 262 | 263 | shiny::showModal(shiny::modalDialog(shiny::h3("All files generated!"), 264 | shiny::actionButton("open_file", "Open file"))) 265 | }) 266 | 267 | 268 | shiny::observeEvent(input$open_file, { 269 | utils::file.edit(file) 270 | }) 271 | 272 | shiny::observeEvent(input$cancel, shiny::stopApp()) 273 | 274 | } 275 | 276 | shiny::runGadget(ui, server = server, stopOnCancel = FALSE, 277 | viewer = shiny::dialogViewer("", width = 800, height = 800)) 278 | } 279 | -------------------------------------------------------------------------------- /R/parsers.R: -------------------------------------------------------------------------------- 1 | 2 | 3 | .parse_authors <- function(authors) { 4 | authors <- lapply(seq_along(authors), function(n) { 5 | author <- authors[[n]] 6 | if (isTRUE(author$corresponding)) { 7 | author$corresponding <- "on" 8 | } else { 9 | author$corresponding <- NULL 10 | } 11 | 12 | names <- names(author) 13 | names[names == "affiliation"] <- "Affiliation" 14 | author[["affiliation"]] <- paste(author[["affiliation"]], collapse = " - ") 15 | names <- paste0(names, n) 16 | names(author) <- names 17 | 18 | return(author) 19 | } 20 | ) 21 | return(unlist(authors, FALSE)) 22 | } 23 | 24 | 25 | 26 | .parse_topics <- function(topics) { 27 | topics <- .topics_number[topics] 28 | topics <- as.list(topics) 29 | names(topics) <- rep("topic", length(topics)) 30 | return(topics) 31 | } 32 | 33 | -------------------------------------------------------------------------------- /R/password.R: -------------------------------------------------------------------------------- 1 | #' Password management 2 | #' 3 | #' Functions to save, get and remove latinr passwords. 4 | #' 5 | #' @param user,password username and password. If `NULL`, they will be asked 6 | #' interactively (recommended). 7 | #' @param check_credentials whether to validate credentials before saving them 8 | #' (recommended). 9 | #' 10 | #' @details 11 | #' By default, `latinr_password_set()` will try to validate the credentials to 12 | #' so that only valid credentials are saved. However, this needs an active 13 | #' internet conection. Use `check_credentials = FALSE` if you are sure your 14 | #' credentials are correct but don't have internet. 15 | #' 16 | #' The default `NULL` value for user and password is the recommended method for 17 | #' secuirity, as otherwise your credentials will be saved in plain text in the 18 | #' command history. 19 | #' 20 | #' @name latinr_password 21 | #' @aliases latinr_password_remove latinr_password_get latinr_password_set 22 | NULL 23 | 24 | 25 | #' @describeIn latinr_password Set a new user/password combination 26 | #' @export 27 | latinr_password_set <- function(user = NULL, password = NULL, check_credentials = TRUE) { 28 | keyring_check() 29 | if (is.null(user) || is.null(password)) { 30 | user <- readline("User: ") 31 | if (is.null(user) | user == "") { 32 | stop("No user supplied.") 33 | } 34 | password <- getPass::getPass(msg = "Password: ", noblank = TRUE) 35 | if (is.null(password)) { 36 | stop("No password supplied.") 37 | } 38 | } 39 | 40 | bypass_message <- " or use `check_credentials = FALSE` to bypass login verification" 41 | ok_user <- !check_credentials 42 | if (!ok_user) { 43 | ok_user <- latinr_password_check(user, password) 44 | } 45 | 46 | if (isTRUE(ok_user[["ok"]]) | !check_credentials) { 47 | if(keyring::default_backend()$name != "env") { 48 | keyring::keyring_unlock() 49 | } 50 | keyring::key_set_with_value(service = latinr_service(), 51 | username = user, 52 | password = password) 53 | } else { 54 | stop(ok_user[["message"]], bypass_message) 55 | } 56 | return(invisible(user)) 57 | } 58 | 59 | #' @describeIn latinr_password Get password for an user. 60 | #' @export 61 | latinr_password_get <- function(user) { 62 | keyring_check() 63 | if(keyring::default_backend()$name != "env") { 64 | keyring::keyring_unlock() 65 | } 66 | keyring::key_get(service = latinr_service(), 67 | username = user) 68 | } 69 | 70 | #' @describeIn latinr_password Remove an user/password combination. 71 | #' @export 72 | latinr_password_remove <- function(user) { 73 | keyring_check() 74 | keyring::key_delete(service = latinr_service(), 75 | username = user) 76 | } 77 | 78 | 79 | latinr_password_check <- function(user, password) { 80 | url <- .latinr_url(what = "verify") 81 | response <- try(httr::POST(url, body = list(name = user, 82 | password = password)), 83 | silent = TRUE) 84 | if (inherits(response, "try-error")) { 85 | return(list(ok = FALSE, 86 | message = "Couldn't verify login information. Check your internet connection")) 87 | } 88 | response_url <- httr::parse_url(response[["url"]]) 89 | verified <- !is.null(response_url[["query"]][["info"]]) 90 | 91 | if (!verified) { 92 | return(list(ok = FALSE, 93 | message = paste0("Login verification failed for user ", 94 | user, 95 | ". Check your credentials"))) 96 | } 97 | 98 | return(list(ok = TRUE, 99 | cookie = httr::cookies(response))) 100 | } -------------------------------------------------------------------------------- /R/print.R: -------------------------------------------------------------------------------- 1 | print_form_data <- function(metadata) { 2 | 3 | cat(metadata$title, "\n") 4 | 5 | a <- switch(metadata$type, 6 | oral = cat("Oral presentation\n"), 7 | poster = cat("Poster\n"), 8 | table = cat("Round table\n")) 9 | cat("\n") 10 | 11 | 12 | a <- lapply(seq_along(metadata$authors), 13 | function(n) { 14 | author <- metadata$authors[[n]] 15 | cat("Author #", n, ":\n", sep = "") 16 | cat(" Name: ", author$first_name, author$last_name, "\n") 17 | cat(" Email: ", author$email, "\n") 18 | cat(" Affiliation: ", author$affiliation, "\n") 19 | cat(" Country: ", rownames(.countries)[.countries$countries == author$country], "\n") 20 | cat(" Corresponding:", author$corresponding, "\n\n") 21 | }) 22 | 23 | cat("Keywords:", paste0(metadata$keywords, collapse = " - "), "\n") 24 | cat("Topics:\n") 25 | cat(" * ", paste0(.topics[metadata$topics], collapse = "\n * "), sep = "") 26 | cat("\n") 27 | return(invisible(metadata)) 28 | } 29 | 30 | -------------------------------------------------------------------------------- /R/submission.R: -------------------------------------------------------------------------------- 1 | #' Submit an article to LatinR 2 | #' 3 | #' @param rmd rmarkdown source file of the submission. 4 | #' @param pdf pdf file for submission. If `NULL`, the source file will be 5 | #' rendered and used as file (recommended). 6 | #' @param user user used for submission. 7 | #' @param check whether to ask for confirmation (recommended). 8 | #' 9 | #' @details 10 | #' It is highly recommended to use the latinr template that comes with 11 | #' this package and to use `pdf = NULL` as this will ensure that the publication 12 | #' adheres to the correct format and is appropriately anonymised. 13 | #' 14 | #' It's also very important to check that your submission has gone through 15 | #' correctly. 16 | #' 17 | #' @export 18 | latinr_submit <- function(rmd = list.files(getwd(), pattern = ".Rmd"), 19 | pdf = NULL, 20 | user = latinr_default_user_get(), 21 | check = TRUE) { 22 | disclaimer <- "----- IMPORTANT!! ----- \nAutomatic submission is still experimental. \nPlease be sure to manually check your submision at the end of the process and correct it if needed!" 23 | 24 | message(disclaimer) 25 | 26 | check_latest_version() 27 | check_submissions_open() 28 | 29 | if (length(rmd) == 0) { 30 | stop("No Rmd file selected") 31 | } 32 | 33 | if (length(rmd) > 1) { 34 | stop("Multiple Rmd files selected") 35 | } 36 | 37 | metadata <- rmarkdown::yaml_front_matter(rmd) 38 | 39 | 40 | if (is.null(user)) { 41 | user <- readline("User: ") 42 | password <- getPass::getPass(msg = "Password: ", noblank = TRUE) 43 | if (is.null(password)) { 44 | stop("No password supplied.") 45 | } 46 | } else { 47 | password <- latinr_password_get(user) 48 | } 49 | 50 | if (isTRUE(check)) { 51 | print_form_data(metadata) 52 | cat("Source file:", rmd, "\n\n") 53 | 54 | cat("Upload with username:", user, "\n\n") 55 | 56 | ok <- readline("Is the above information correct? (y/n) ") 57 | if (tolower(ok) != "y") { 58 | return(invisible(NULL)) 59 | } 60 | } 61 | 62 | message("Checking metadata") 63 | latinr_checks(metadata, check_is_error = TRUE) 64 | 65 | if (is.null(pdf)) { 66 | message("Rendering file") 67 | 68 | output_options <- metadata[["output"]][[1]] 69 | output_options["anonymise"] <- TRUE 70 | 71 | pdf <- rmarkdown::render(rmd, quiet = TRUE, 72 | output_format = do.call(latinr_article, output_options), 73 | params = list(check_is_error = TRUE)) 74 | } 75 | 76 | # uses magick to count number of pages because pdftools requires 77 | # installing a system library and is a pita whereas magick comes 78 | # preinstalled in most linux distros. 79 | n_pages <- length(magick::image_read(pdf)) 80 | if (n_pages > 2) { 81 | stop("The file has more than the accepted numebr of pages (2).") 82 | } 83 | 84 | 85 | if (isTRUE(check)) { 86 | pdf_open <- readline("Press (enter) to check your submission file. ") 87 | file.show(pdf) 88 | pdf_ok <- readline("Send this file? (y/n) ") 89 | 90 | if (tolower(pdf_ok) != "y") { 91 | return(invisible(NULL)) 92 | } 93 | } 94 | 95 | n_authors <- length(metadata$authors) 96 | keep <- c("title", "keywords", "abstract") 97 | # No more type? 98 | # metadata$field47997 <- .types_number[.types == metadata$type] 99 | 100 | authors <- .parse_authors(metadata$authors) 101 | metadata$keywords <- paste0(metadata$keywords, collapse = "\n") 102 | metadata <- metadata[names(metadata) %in% keep] 103 | names(metadata)[names(metadata) == "abstract"] <- "abstr" # Name on the form 104 | 105 | form_data <- c(authors, metadata) 106 | 107 | ### Submit form 108 | url <- .latinr_url("latinr") 109 | message("Logging in") 110 | session <- rvest::session(url) 111 | login_form <- rvest::html_form(session)[[1]] 112 | login_form <- rvest::html_form_set(login_form, 113 | name = user, 114 | password = password) 115 | session <- suppressMessages(rvest::session_submit(session, login_form)) 116 | 117 | 118 | 119 | # If previously submitted 120 | session_try <- try(rvest::session_follow_link(session, "author"), silent = TRUE) 121 | if (inherits(session_try, "try-error")) { 122 | session <- rvest::session_follow_link(session, "make a new submission") 123 | } else { 124 | session <- session_try 125 | menu <- rvest::html_element(session, css = "#menu1") 126 | 127 | click <- rvest::html_attr(menu, "onclick") 128 | 129 | click <- gsub("Menu.followLink\\('menu1','", "", click) 130 | click <- sub("'\\)", "", click) 131 | session <- rvest::session_jump_to(session, paste0("https://easychair.org", click)) 132 | } 133 | 134 | submit_form <- rvest::html_form(session)[[1]] 135 | 136 | message("Submitting") 137 | submit_form <- add_authors(submit_form, n_authors) 138 | form_data$form <- submit_form 139 | submit_form <- do.call(rvest::html_form_set, form_data) 140 | 141 | # Workaround because rvest doesn't do file upload correctly. 142 | submit_form <- rvest:::submission_build(submit_form, NULL) 143 | submit_form$values$upload114286 <- httr::upload_file(pdf) 144 | resp <- suppressMessages(rvest:::submission_submit(submit_form, session$config, handle = session$handle)) 145 | session <- rvest:::session_set_response(session, resp) 146 | 147 | title <- rvest::html_text(rvest::html_nodes(session, "title")[[1]]) 148 | 149 | if (substr(title, 1, 21) != "LatinR2021 Submission") { 150 | errors <- rvest::html_text(rvest::html_node(session, "div.subcontent ul")) 151 | 152 | msg <- "There was an error with your submission" 153 | 154 | if (is.null(errors)) { 155 | msg <- paste0(msg, ", but I'm still not smart enought to know which :(!\n", 156 | "Check your submission details and if you still get this error, submit manually", 157 | paste0(" at ", .latinr_url("latinr"))) 158 | } else { 159 | msg <- paste0(msg, ":\n", paste(errors, collapse = "\n")) 160 | } 161 | 162 | stop(msg) 163 | 164 | } 165 | message(title) 166 | message("Submission successful! Check your email for confirmation.") 167 | return(invisible(TRUE)) 168 | 169 | } 170 | 171 | 172 | add_authors <- function(form, n_authors) { 173 | new_form <- form 174 | if (n_authors < 4) { 175 | return(form) 176 | } 177 | 178 | fields <- c("first_name", "last_name", "email", "country", "url", "Affiliation", "corresponding") 179 | based_on <- paste0(fields, "1") 180 | # Agrega autores mayores a 3 181 | for (i in seq_len(n_authors - 3) + 3) { 182 | new_fields <- paste0(fields, i) 183 | 184 | for (f in seq_along(new_fields)) { 185 | new_form <- add_field(new_form, new_fields[f], based_on[f]) 186 | 187 | } 188 | 189 | } 190 | return(new_form) 191 | } 192 | 193 | 194 | add_field <- function(form, new_name, based_on) { 195 | new_form <- form 196 | new_form$fields[[new_name]] <- new_form$fields[[based_on]] 197 | new_form$fields[[new_name]]$name <- new_name 198 | 199 | return(new_form) 200 | } 201 | -------------------------------------------------------------------------------- /R/sysdata.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LatinR/latinr/645bac7d9461b7d440f25c9575d8fb0b9bc08296/R/sysdata.rda -------------------------------------------------------------------------------- /R/topics.R: -------------------------------------------------------------------------------- 1 | #' Latinr lists 2 | #' 3 | #' Lists of important information for filling in metadata. 4 | #' 5 | #' @name latinr_lists 6 | NULL 7 | 8 | #' @describeIn latinr_lists List of topics 9 | #' @export 10 | latinr_topics <- function() { 11 | .topics 12 | } 13 | 14 | #' @describeIn latinr_lists List of countries with country codes. 15 | #' @export 16 | latinr_countries <- function() { 17 | .countries 18 | } 19 | 20 | #' @describeIn latinr_lists List of possible types of presentation. 21 | #' @export 22 | latinr_types <- function() { 23 | .types 24 | } 25 | -------------------------------------------------------------------------------- /R/users.R: -------------------------------------------------------------------------------- 1 | #' Default users 2 | #' 3 | #' @param user user to use as the default (`NULL` means no default user). 4 | #' 5 | #' @return 6 | #' `latinr_default_user_get()` returns the default user set with `latinr_default_user_get()` 7 | #' or the user if there's only one user saved with `latinr_password_set()`. 8 | #' 9 | #' `latinr_default_user_get()` sets the default user (for the current session) 10 | #' and returns the supplied user invisibly. 11 | #' 12 | #' @aliases latinr_default_user_get latinr_default_user_set 13 | #' @name latinr_default_user 14 | NULL 15 | 16 | #' @describeIn latinr_default_user Sets the default user. 17 | #' @export 18 | latinr_default_user_set <- function(user = NULL) { 19 | options("LATINR.DEFAULT.USER" = user) 20 | return(invisible(user)) 21 | } 22 | 23 | #' @describeIn latinr_default_user Gets the default user. 24 | #' @export 25 | latinr_default_user_get <- function() { 26 | # First priotiy: global option 27 | user <- getOption("LATINR.DEFAULT.USER", default = NULL) 28 | 29 | if (is.null(user)) { 30 | # Second priority: check if only one user 31 | keyring_check() 32 | all_keys <- keyring::key_list() 33 | latinr_keys <- all_keys[all_keys[["service"]] == latinr_service(), ] 34 | 35 | if (nrow(latinr_keys) == 0) { 36 | warning("No users saved. Create an account at ", .latinr_url("latinr"), 37 | " and (optionally) use 'latinr_password_set()' to save it.") 38 | user <- NULL 39 | } else if (nrow(latinr_keys) > 1) { 40 | stop("Multiple users present in keyring. Use 'latinr_default_user_set()' ", 41 | "to set the default user manually.") 42 | } else { 43 | user <- latinr_keys[["username"]] 44 | } 45 | } 46 | 47 | return(user) 48 | } 49 | 50 | 51 | keyring_check <- function() { 52 | has_keyring <- requireNamespace("keyring", quietly = TRUE) 53 | if (!has_keyring) { 54 | stop("Credentials management needs the keyring package.\n", 55 | 'You can install it with `install.packages("keyring")`') 56 | } 57 | return(invisible(has_keyring)) 58 | } 59 | -------------------------------------------------------------------------------- /README.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | output: github_document 3 | --- 4 | 5 | 6 | 7 | ```{r, include = FALSE} 8 | knitr::opts_chunk$set( 9 | collapse = TRUE, 10 | comment = "#>", 11 | fig.path = "man/figures/README-", 12 | out.width = "100%" 13 | ) 14 | ``` 15 | # latinr 16 | 17 | 18 | 19 | 20 | latinr is a package that streamlines the submission process to the [LatinR](http://latin-r.com/) conference. 21 | 22 | ## Installation 23 | 24 | You can install latinr from [GitHub](https://github.com/) with: 25 | 26 | ``` r 27 | # install.packages("devtools") 28 | devtools::install_github("latinr/latinr") 29 | ``` 30 | 31 | Optionally, latinr can use the keyring package to safely store your credentials. In unix-based platforms, you might need to install `libsodium` manually. You can do this by typing one of the following commands in your terminal: 32 | 33 | * `sudo apt install libsodium-dev` in Debian, Ubuntu, and derivatives. 34 | 35 | * `yum install libsodium-devel` in Fedora, EPEL. 36 | 37 | * `brew install libsodium` in OSX. 38 | 39 | And then: 40 | ```r 41 | install.packages("keyring") 42 | ``` 43 | 44 | ## Usage 45 | 46 | If you are going to submit an article to LatinR, you will need to create an user at `r latinr:::.latinr_url("latinr")`. Then, use 47 | 48 | ```r 49 | latinr:::latinr_password_set() 50 | ``` 51 | 52 | to save your credentials in your machine. 53 | 54 | To start writing your submission, in RStudio, go to File -> New File -> R Markdown -> From Template and choose "LatinR submission article". This will give you an example article that uses the correct template and has the important metadata. 55 | 56 | Alternatively, you can use the UI wizard with `latinr::latinr_wizard()`. It will open up a shiny interface to help you populate your submission and then save the result into a file. 57 | 58 | ![](man/figures/wizard.png) 59 | 60 | 61 | When you finish writing your article, use `latinr::latinr_submit()`. By default, it will check that the metadata is in order, will render your rmarkdown file with anonymisation and upload it to the confference. If everything was in order, you will receive an email. 62 | 63 | As a last step, check that your submission is in the website with the correct information. 64 | 65 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | # latinr 5 | 6 | 7 | 8 | 9 | latinr is a package that streamlines the submission process to the 10 | [LatinR](http://latin-r.com/) conference. 11 | 12 | ## Installation 13 | 14 | You can install latinr from [GitHub](https://github.com/) with: 15 | 16 | ``` r 17 | # install.packages("devtools") 18 | devtools::install_github("latinr/latinr") 19 | ``` 20 | 21 | Optionally, latinr can use the keyring package to safely store your 22 | credentials. In unix-based platforms, you might need to install 23 | `libsodium` manually. You can do this by typing one of the following 24 | commands in your terminal: 25 | 26 | - `sudo apt install libsodium-dev` in Debian, Ubuntu, and derivatives. 27 | 28 | - `yum install libsodium-devel` in Fedora, EPEL. 29 | 30 | - `brew install libsodium` in OSX. 31 | 32 | And then: 33 | 34 | ``` r 35 | install.packages("keyring") 36 | ``` 37 | 38 | ## Usage 39 | 40 | If you are going to submit an article to LatinR, you will need to create 41 | an user at . Then, 42 | use 43 | 44 | ``` r 45 | latinr:::latinr_password_set() 46 | ``` 47 | 48 | to save your credentials in your machine. 49 | 50 | To start writing your submission, in RStudio, go to File -> New File 51 | -> R Markdown -> From Template and choose “LatinR submission 52 | article”. This will give you an example article that uses the correct 53 | template and has the important metadata. 54 | 55 | Alternatively, you can use the UI wizard with `latinr::latinr_wizard()`. 56 | It will open up a shiny interface to help you populate your submission 57 | and then save the result into a file. 58 | 59 | ![](man/figures/wizard.png) 60 | 61 | When you finish writing your article, use `latinr::latinr_submit()`. By 62 | default, it will check that the metadata is in order, will render your 63 | rmarkdown file with anonymisation and upload it to the confference. If 64 | everything was in order, you will receive an email. 65 | 66 | As a last step, check that your submission is in the website with the 67 | correct information. 68 | -------------------------------------------------------------------------------- /inst/prism.css: -------------------------------------------------------------------------------- 1 | /* PrismJS 1.17.1 2 | https://prismjs.com/download.html#themes=prism-solarizedlight&languages=r */ 3 | /* 4 | Solarized Color Schemes originally by Ethan Schoonover 5 | http://ethanschoonover.com/solarized 6 | 7 | Ported for PrismJS by Hector Matos 8 | Website: https://krakendev.io 9 | Twitter Handle: https://twitter.com/allonsykraken) 10 | */ 11 | 12 | /* 13 | SOLARIZED HEX 14 | --------- ------- 15 | base03 #002b36 16 | base02 #073642 17 | base01 #586e75 18 | base00 #657b83 19 | base0 #839496 20 | base1 #93a1a1 21 | base2 #eee8d5 22 | base3 #fdf6e3 23 | yellow #b58900 24 | orange #cb4b16 25 | red #dc322f 26 | magenta #d33682 27 | violet #6c71c4 28 | blue #268bd2 29 | cyan #2aa198 30 | green #859900 31 | */ 32 | 33 | code[class*="language-"], 34 | pre[class*="language-"] { 35 | color: #657b83; 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72 | } 73 | 74 | :not(pre) > code[class*="language-"], 75 | pre[class*="language-"] { 76 | background-color: #fdf6e3; /* base3 */ 77 | } 78 | 79 | /* Inline code */ 80 | :not(pre) > code[class*="language-"] { 81 | padding: .1em; 82 | border-radius: .3em; 83 | } 84 | 85 | .token.comment, 86 | .token.prolog, 87 | .token.doctype, 88 | .token.cdata { 89 | color: #93a1a1; /* base1 */ 90 | } 91 | 92 | .token.punctuation { 93 | color: #586e75; /* base01 */ 94 | } 95 | 96 | .namespace { 97 | opacity: .7; 98 | } 99 | 100 | .token.property, 101 | .token.tag, 102 | .token.boolean, 103 | .token.number, 104 | .token.constant, 105 | .token.symbol, 106 | .token.deleted { 107 | color: #268bd2; /* blue */ 108 | } 109 | 110 | .token.selector, 111 | .token.attr-name, 112 | .token.string, 113 | .token.char, 114 | .token.builtin, 115 | .token.url, 116 | .token.inserted { 117 | color: #2aa198; /* cyan */ 118 | } 119 | 120 | .token.entity { 121 | color: #657b83; /* base00 */ 122 | background: #eee8d5; /* base2 */ 123 | } 124 | 125 | .token.atrule, 126 | .token.attr-value, 127 | .token.keyword { 128 | color: #859900; 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4 | Prism.languages.r={comment:/#.*/,string:{pattern:/(['"])(?:\\.|(?!\1)[^\\\r\n])*\1/,greedy:!0},"percent-operator":{pattern:/%[^%\s]*%/,alias:"operator"},boolean:/\b(?:TRUE|FALSE)\b/,ellipsis:/\.\.(?:\.|\d+)/,number:[/\b(?:NaN|Inf)\b/,/(?:\b0x[\dA-Fa-f]+(?:\.\d*)?|\b\d+\.?\d*|\B\.\d+)(?:[EePp][+-]?\d+)?[iL]?/],keyword:/\b(?:if|else|repeat|while|function|for|in|next|break|NULL|NA|NA_integer_|NA_real_|NA_complex_|NA_character_)\b/,operator:/->?>?|<(?:=|=!]=?|::?|&&?|\|\|?|[+*\/^$@~]/,punctuation:/[(){}\[\],;]/}; 5 | -------------------------------------------------------------------------------- /inst/request_example.txt: -------------------------------------------------------------------------------- 1 | -----------------------------15446075827322774522002851 2 | Content-Disposition: form-data; name="track" 3 | 4 | 240492 5 | -----------------------------15446075827322774522002851 6 | Content-Disposition: form-data; name="a" 7 | 8 | 21838528 9 | -----------------------------15446075827322774522002851 10 | Content-Disposition: form-data; name="first_name1" 11 | 12 | Elio 13 | -----------------------------15446075827322774522002851 14 | Content-Disposition: form-data; name="last_name1" 15 | 16 | Camp 17 | -----------------------------15446075827322774522002851 18 | Content-Disposition: form-data; name="email1" 19 | 20 | 21 | -----------------------------15446075827322774522002851 22 | Content-Disposition: form-data; name="country1" 23 | 24 | 25 | -----------------------------15446075827322774522002851 26 | Content-Disposition: form-data; name="Affiliation1" 27 | 28 | 29 | -----------------------------15446075827322774522002851 30 | Content-Disposition: form-data; name="url1" 31 | 32 | 33 | -----------------------------15446075827322774522002851 34 | Content-Disposition: form-data; name="corresponding1" 35 | 36 | on 37 | -----------------------------15446075827322774522002851 38 | Content-Disposition: form-data; name="speaker" 39 | 40 | 1 41 | -----------------------------15446075827322774522002851 42 | Content-Disposition: form-data; name="first_name2" 43 | 44 | 45 | -----------------------------15446075827322774522002851 46 | Content-Disposition: form-data; name="last_name2" 47 | 48 | 49 | -----------------------------15446075827322774522002851 50 | Content-Disposition: form-data; name="email2" 51 | 52 | 53 | -----------------------------15446075827322774522002851 54 | Content-Disposition: form-data; name="country2" 55 | 56 | 57 | -----------------------------15446075827322774522002851 58 | Content-Disposition: form-data; name="Affiliation2" 59 | 60 | 61 | -----------------------------15446075827322774522002851 62 | Content-Disposition: form-data; name="url2" 63 | 64 | 65 | -----------------------------15446075827322774522002851 66 | Content-Disposition: form-data; name="corresponding2" 67 | 68 | on 69 | -----------------------------15446075827322774522002851 70 | Content-Disposition: form-data; name="first_name3" 71 | 72 | 73 | -----------------------------15446075827322774522002851 74 | Content-Disposition: form-data; name="last_name3" 75 | 76 | 77 | -----------------------------15446075827322774522002851 78 | Content-Disposition: form-data; name="email3" 79 | 80 | 81 | -----------------------------15446075827322774522002851 82 | Content-Disposition: form-data; name="country3" 83 | 84 | 85 | -----------------------------15446075827322774522002851 86 | Content-Disposition: form-data; name="Affiliation3" 87 | 88 | 89 | -----------------------------15446075827322774522002851 90 | Content-Disposition: form-data; name="url3" 91 | 92 | 93 | -----------------------------15446075827322774522002851 94 | Content-Disposition: form-data; name="corresponding3" 95 | 96 | on 97 | -----------------------------15446075827322774522002851 98 | Content-Disposition: form-data; name="first_name4" 99 | 100 | 101 | -----------------------------15446075827322774522002851 102 | Content-Disposition: form-data; name="last_name4" 103 | 104 | 105 | -----------------------------15446075827322774522002851 106 | Content-Disposition: form-data; name="email4" 107 | 108 | 109 | -----------------------------15446075827322774522002851 110 | Content-Disposition: form-data; name="country4" 111 | 112 | 113 | -----------------------------15446075827322774522002851 114 | Content-Disposition: form-data; name="Affiliation4" 115 | 116 | 117 | -----------------------------15446075827322774522002851 118 | Content-Disposition: form-data; name="url4" 119 | 120 | 121 | -----------------------------15446075827322774522002851 122 | Content-Disposition: form-data; name="corresponding4" 123 | 124 | on 125 | -----------------------------15446075827322774522002851 126 | Content-Disposition: form-data; name="title" 127 | 128 | asasd 129 | -----------------------------15446075827322774522002851 130 | Content-Disposition: form-data; name="keywords" 131 | 132 | asdasd 133 | asdasd 134 | asdasfds 135 | -----------------------------15446075827322774522002851 136 | Content-Disposition: form-data; name="topic" 137 | 138 | 281909 139 | -----------------------------15446075827322774522002851 140 | Content-Disposition: form-data; name="topic" 141 | 142 | 281910 143 | -----------------------------15446075827322774522002851 144 | Content-Disposition: form-data; name="topic" 145 | 146 | 281911 147 | -----------------------------15446075827322774522002851 148 | Content-Disposition: form-data; name="topic" 149 | 150 | 281912 151 | -----------------------------15446075827322774522002851 152 | Content-Disposition: form-data; name="topic" 153 | 154 | 281913 155 | -----------------------------15446075827322774522002851 156 | Content-Disposition: form-data; name="topic" 157 | 158 | 281914 159 | -----------------------------15446075827322774522002851 160 | Content-Disposition: form-data; name="topic" 161 | 162 | 281915 163 | -----------------------------15446075827322774522002851 164 | Content-Disposition: form-data; name="topic" 165 | 166 | 281916 167 | -----------------------------15446075827322774522002851 168 | Content-Disposition: form-data; name="topic" 169 | 170 | 281917 171 | -----------------------------15446075827322774522002851 172 | Content-Disposition: form-data; name="topic" 173 | 174 | 281918 175 | -----------------------------15446075827322774522002851 176 | Content-Disposition: form-data; name="topic" 177 | 178 | 281919 179 | -----------------------------15446075827322774522002851 180 | Content-Disposition: form-data; name="topic" 181 | 182 | 281920 183 | -----------------------------15446075827322774522002851 184 | Content-Disposition: form-data; name="field44396" 185 | 186 | 162533 187 | -----------------------------15446075827322774522002851 188 | Content-Disposition: form-data; name="upload90642"; filename="metamer.pdf" 189 | Content-Type: application/pdf 190 | 191 | %PDF-1.5 192 | %äðíø 193 | 15 0 obj 194 | <> 195 | stream 196 | xÚ­ْܶñ=_Á¼q«f‚Ȳ¼rÙe+¶µyÊäÁִyŒxl¼þúô3\%®JIµ@£»Ñã}ò”Â?åéþ‡^Ùx_. 52 | 53 | When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this: 54 | 55 | ```{r cars} 56 | summary(cars) 57 | ``` 58 | 59 | ## Including Plots 60 | 61 | You can also embed plots, for example: 62 | 63 | ```{r pressure, echo=FALSE} 64 | plot(pressure) 65 | ``` 66 | 67 | Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.[@Nuncio2011] 68 | -------------------------------------------------------------------------------- /inst/rmarkdown/templates/latinr_article/template.yaml: -------------------------------------------------------------------------------- 1 | name: LatinR submission article 2 | description: > 3 | Template for creating an article for submission to LatinR. 4 | create_dir: false 5 | 6 | -------------------------------------------------------------------------------- /latinr.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: Sweave 13 | LaTeX: pdfLaTeX 14 | 15 | BuildType: Package 16 | PackageUseDevtools: Yes 17 | PackageInstallArgs: --no-multiarch --with-keep.source 18 | PackageRoxygenize: rd,collate,namespace 19 | -------------------------------------------------------------------------------- /man/figures/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LatinR/latinr/645bac7d9461b7d440f25c9575d8fb0b9bc08296/man/figures/logo.png -------------------------------------------------------------------------------- /man/figures/wizard.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LatinR/latinr/645bac7d9461b7d440f25c9575d8fb0b9bc08296/man/figures/wizard.png -------------------------------------------------------------------------------- /man/latinr-package.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/latinr-package.R 3 | \docType{package} 4 | \name{latinr-package} 5 | \alias{latinr} 6 | \alias{latinr-package} 7 | \title{latinr: Submission to LatinR} 8 | \description{ 9 | \if{html}{\figure{logo.png}{options: align='right' alt='logo' width='120'}} 10 | 11 | Facilitates creation and submissiond of abstract for the LatinR conference. 12 | } 13 | \section{Overview}{ 14 | 15 | 16 | This package attempts to automate as much as possible the creation and submission process of 17 | abstracts for the LatinR conference. You write in RMarkdown and all submission details are 18 | added to the yaml header. Then, before submission, the package does some basic checks, renders 19 | the document using the provided LaTeX template and finally submits it. 20 | } 21 | 22 | \section{Creating a submission}{ 23 | 24 | 25 | If you use RStudio, you can fo to File -> New File -> R Markdown -> From Template and 26 | select "LatinR submission article". This will create a skeleton document along with other 27 | helper files into the selected folder. 28 | 29 | You'll see that all the important data is managed by the yaml header. You can either populate it 30 | manually or, a bit easier, use \code{\link[=latinr_wizard]{latinr_wizard()}} to launch a small user interface that will guide 31 | you and finally give you a valid yaml header that you can copy and paste into your document. 32 | } 33 | 34 | \section{Submitting and article}{ 35 | 36 | 37 | One you're happy with your article, it's time to submit it. First, if you haven't already, you'll 38 | need to create an account at https://easychair.org/account/signup and then save your 39 | login information using \code{\link[=latinr_password_set]{latinr_password_set()}}. The email associated with the account you are 40 | using to submit your article has to match the email of one of the authors. 41 | 42 | To submit your article use \code{\link[=latinr_submit]{latinr_submit()}}. By default, it will search for .Rmd files in the 43 | current working directory and if it finds only one, it process it. First, you will be shown the 44 | submission information (such as author details, title, keywords, etc...) so you can check that 45 | everything is in order. Then, it will render and open the PDF so you can also check the finished 46 | submission. 47 | 48 | If all it's OK, the article will be submitted. Be aware that this process is still a bit 49 | experimental so things can fail. It's VERY IMPORTANT that at the end of the process you go to 50 | your account an make a final check so that you're sure that the submission information, as well as 51 | the article PDF have been correctly submitted. If you find any problem, correct them right there 52 | on the website. 53 | } 54 | 55 | \author{ 56 | \strong{Maintainer}: Elio Campitelli \email{elio.campitelli@fcen.cima.fcen.uba.ar} 57 | 58 | } 59 | \keyword{internal} 60 | -------------------------------------------------------------------------------- /man/latinr_article.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/latinr_article.R 3 | \name{latinr_article} 4 | \alias{latinr_article} 5 | \title{R Markdown output format for submissions to LatinR} 6 | \usage{ 7 | latinr_article( 8 | ..., 9 | keep_tex = FALSE, 10 | highlight = "default", 11 | citation_package = "default", 12 | latex_engine = "xelatex", 13 | anonymise = TRUE, 14 | author_bottom = FALSE 15 | ) 16 | } 17 | \arguments{ 18 | \item{...}{Arguments passed to \code{pdf_document()}.} 19 | 20 | \item{keep_tex}{Keep the intermediate tex file used in the conversion to PDF} 21 | 22 | \item{highlight}{Syntax highlighting style. Supported styles include 23 | "default", "tango", "pygments", "kate", "monochrome", "espresso", 24 | "zenburn", and "haddock". Pass \code{NULL} to prevent syntax highlighting.} 25 | 26 | \item{citation_package}{The LaTeX package to process citations, \code{natbib} 27 | or \code{biblatex}. Use \code{default} if neither package is to be used, 28 | which means citations will be processed via the command 29 | \command{pandoc-citeproc}.} 30 | 31 | \item{latex_engine}{LaTeX engine for producing PDF output. Options are 32 | "pdflatex", "lualatex", "xelatex" and "tectonic".} 33 | 34 | \item{anonymise}{whether to anonymise the PDF} 35 | 36 | \item{author_bottom}{whether to add author information at the bottom of the 37 | page.} 38 | } 39 | \description{ 40 | R Markdown output format for submissions to LatinR 41 | } 42 | -------------------------------------------------------------------------------- /man/latinr_checks.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/latinr_article.R 3 | \name{latinr_checks} 4 | \alias{latinr_checks} 5 | \title{Checks that metadata is ok} 6 | \usage{ 7 | latinr_checks(metadata, check_is_error = TRUE) 8 | } 9 | \arguments{ 10 | \item{metadata}{yaml metadata.} 11 | 12 | \item{check_is_error}{whether to treat fails as errors or only warnings 13 | useful during development).} 14 | } 15 | \description{ 16 | Does basics checks on metadata so that it adheres to submission guidelines. 17 | } 18 | -------------------------------------------------------------------------------- /man/latinr_default_user.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/users.R 3 | \name{latinr_default_user} 4 | \alias{latinr_default_user} 5 | \alias{latinr_default_user_get} 6 | \alias{latinr_default_user_set} 7 | \title{Default users} 8 | \usage{ 9 | latinr_default_user_set(user = NULL) 10 | 11 | latinr_default_user_get() 12 | } 13 | \arguments{ 14 | \item{user}{user to use as the default (\code{NULL} means no default user).} 15 | } 16 | \value{ 17 | \code{latinr_default_user_get()} returns the default user set with \code{latinr_default_user_get()} 18 | or the user if there's only one user saved with \code{latinr_password_set()}. 19 | 20 | \code{latinr_default_user_get()} sets the default user (for the current session) 21 | and returns the supplied user invisibly. 22 | } 23 | \description{ 24 | Default users 25 | } 26 | \section{Functions}{ 27 | \itemize{ 28 | \item \code{latinr_default_user_set}: Sets the default user. 29 | 30 | \item \code{latinr_default_user_get}: Gets the default user. 31 | }} 32 | 33 | -------------------------------------------------------------------------------- /man/latinr_lists.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/topics.R 3 | \name{latinr_lists} 4 | \alias{latinr_lists} 5 | \alias{latinr_topics} 6 | \alias{latinr_countries} 7 | \alias{latinr_types} 8 | \title{Latinr lists} 9 | \usage{ 10 | latinr_topics() 11 | 12 | latinr_countries() 13 | 14 | latinr_types() 15 | } 16 | \description{ 17 | Lists of important information for filling in metadata. 18 | } 19 | \section{Functions}{ 20 | \itemize{ 21 | \item \code{latinr_topics}: List of topics 22 | 23 | \item \code{latinr_countries}: List of countries with country codes. 24 | 25 | \item \code{latinr_types}: List of possible types of presentation. 26 | }} 27 | 28 | -------------------------------------------------------------------------------- /man/latinr_password.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/password.R 3 | \name{latinr_password} 4 | \alias{latinr_password} 5 | \alias{latinr_password_remove} 6 | \alias{latinr_password_get} 7 | \alias{latinr_password_set} 8 | \title{Password management} 9 | \usage{ 10 | latinr_password_set(user = NULL, password = NULL, check_credentials = TRUE) 11 | 12 | latinr_password_get(user) 13 | 14 | latinr_password_remove(user) 15 | } 16 | \arguments{ 17 | \item{user, password}{username and password. If \code{NULL}, they will be asked 18 | interactively (recommended).} 19 | 20 | \item{check_credentials}{whether to validate credentials before saving them 21 | (recommended).} 22 | } 23 | \description{ 24 | Functions to save, get and remove latinr passwords. 25 | } 26 | \details{ 27 | By default, \code{latinr_password_set()} will try to validate the credentials to 28 | so that only valid credentials are saved. However, this needs an active 29 | internet conection. Use \code{check_credentials = FALSE} if you are sure your 30 | credentials are correct but don't have internet. 31 | 32 | The default \code{NULL} value for user and password is the recommended method for 33 | secuirity, as otherwise your credentials will be saved in plain text in the 34 | command history. 35 | } 36 | \section{Functions}{ 37 | \itemize{ 38 | \item \code{latinr_password_set}: Set a new user/password combination 39 | 40 | \item \code{latinr_password_get}: Get password for an user. 41 | 42 | \item \code{latinr_password_remove}: Remove an user/password combination. 43 | }} 44 | 45 | -------------------------------------------------------------------------------- /man/latinr_submit.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/submission.R 3 | \name{latinr_submit} 4 | \alias{latinr_submit} 5 | \title{Submit an article to LatinR} 6 | \usage{ 7 | latinr_submit( 8 | rmd = list.files(getwd(), pattern = ".Rmd"), 9 | pdf = NULL, 10 | user = latinr_default_user_get(), 11 | check = TRUE 12 | ) 13 | } 14 | \arguments{ 15 | \item{rmd}{rmarkdown source file of the submission.} 16 | 17 | \item{pdf}{pdf file for submission. If \code{NULL}, the source file will be 18 | rendered and used as file (recommended).} 19 | 20 | \item{user}{user used for submission.} 21 | 22 | \item{check}{whether to ask for confirmation (recommended).} 23 | } 24 | \description{ 25 | Submit an article to LatinR 26 | } 27 | \details{ 28 | It is highly recommended to use the latinr template that comes with 29 | this package and to use \code{pdf = NULL} as this will ensure that the publication 30 | adheres to the correct format and is appropriately anonymised. 31 | 32 | It's also very important to check that your submission has gone through 33 | correctly. 34 | } 35 | -------------------------------------------------------------------------------- /man/latinr_wizard.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/latinr_wizard.R 3 | \name{latinr_wizard} 4 | \alias{latinr_wizard} 5 | \title{Opens a user interface to populate yaml fields} 6 | \usage{ 7 | latinr_wizard() 8 | } 9 | \description{ 10 | Opens a user interface to populate yaml fields 11 | } 12 | -------------------------------------------------------------------------------- /submission_conditions.yaml: -------------------------------------------------------------------------------- 1 | open: TRUE 2 | date_start: "2022-04-30" 3 | date_end: "2022-06-30" 4 | --------------------------------------------------------------------------------