Commit e5a6e9c7 authored by khalid's avatar khalid
Browse files

Change DAFNEE labels

parent a7bb2100
......@@ -176,8 +176,8 @@ ui <- fluidPage(
sidebarLayout(position ='right',
sidebarPanel( width = 3,
conditionalPanel(condition="input.tabselected==2",
h5("DAFNEE Usage Index calculator :"),
h6("Author's papers listed In DAFNEE / papers in the inspected list of journals (journals where ISEM authors publisher since 2014)"),
h5("DAFNEE Usage Index calculator :"),
h6("Athor's articles in academia-friendly journals / total articles in surveyed journals"),
#radioButtons("IndexMethod", label = h3("Calculate index as"),
#choices = list("Author's papers listed In DAFNEE / Total papers" = 1, "Author's papers listed In DAFNEE / papers in curated ISEM list of journals since 2014" = 2), selected = 1),
textInput("nom", "Author last name", ""),
......@@ -203,14 +203,14 @@ ui <- fluidPage(
tabPanel( "About", value=3,
fluidRow(
shinydashboard::infoBox(HTML("<h3><strong>Motivations</strong></h3>"), icon = icon("heart-empty", lib = "glyphicon"), color = "yellow", fill =TRUE,width=12, HTML("
<p>The scientific publishing market is widely recognized to be dysfunctional [1]. The average price of publishing is an order of magnitude higher than the real cost [2,3]. This anomaly essentially results from the \"publish or perish\" situation in which individual scientists are placed, and the power of large publishing groups with high profit margins [4].
Not all scientific journals, however, are economically equivalent. Some are run by non-profit organizations. Some are associated to learned societies, so that publication fees are partly reinvested in academia. Some are supported at moderate cost by scholarly institutions. Scientists are not always well informed about the complexity of journals' business models, and rarely include this criterion when deciding to interact with a journal as an author, reviewer or editor. Yet, to support academia-friendly journals is a way to contribute to a fairer scientific publishing system.</p>"))),
<p>The scientific publishing market is widely recognized to be dysfunctional [1]. The average price of publishing is an order of magnitude higher than the real cost [2,3]. This anomaly essentially results from the 'publish or perish' situation in which individual scientists are placed, and the power of large publishing groups with high profit margins [4].
Not all scientific journals, however, are economically equivalent. Some are run by non-profit organizations. Some are associated to learned societies, so that publication fees are partly reinvested in academia. Some are supported at moderate cost by scholarly institutions. Scientists are not always well informed about the complexity of journals' business models, and rarely include this criterion when deciding to interact with a journal as an author, reviewer or editor. Yet, to support academia-friendly journals is a way to contribute to a fairer scientific publishing system.</p>"))),
shinydashboard::infoBox(HTML("<h3><strong>Content</strong></h3>"), icon = icon("folder-open", lib = "glyphicon"), color = "yellow", fill =TRUE,width=12,
HTML("<p>The DAFNEE database offers a list of ~250 non-profit, learned society, museum or university-associated journals relevant to the field of ecology and evolutionary biology. The database includes generalist journals (e.g. eLife, PLoS Biol, PNAS, Science), flagship society journals (e.g. Am Nat, Ecology, JEB, Proc B, MBE, Syst Biol), Open Science initiatives (e.g. Peer Communiy In, MorphoMuseuM), and many high-quality journals in palaeo-archaeobiology, systematics, genetics, theoretical biology, organismal biology, environmental and health sciences. Journals can be queried by topic, business model, academic partnership, publication fees, and impact factor. In addition, an interactive tool gives every scientist the opportunity to evaluate and compare his/her own percentage of academia-friendly journal usage.</p>")),
HTML("<p>The DAFNEE database offers a list of ~250 non-profit, learned society, museum or university-associated journals relevant to the field of ecology and evolutionary biology. The database includes generalist journals (e.g. eLife, PLoS Biol, PNAS, Science), flagship society journals (e.g. Am Nat, Ecology, JEB, Proc B, MBE, Syst Biol), Open Science initiatives (e.g. Peer Communiy In, MorphoMuseuM), and many high-quality journals in palaeo-archaeobiology, systematics, genetics, theoretical biology, organismal biology, environmental and health sciences. Journals can be queried by topic, business model, academic partnership, publication fees, and impact factor. In addition, an interactive tool gives every scientist the opportunity to evaluate and compare his/her own DAFNEE usage index, defined as the ratio of PubMed articles in academia-friendly journals to PubMed articles in surveyed journals.</p>")),
shinydashboard::infoBox(HTML("<h3><strong>Curation</strong></h3>"), icon = icon("wrench", lib = "glyphicon"), color = "yellow", fill =TRUE,width=12,
HTML("<p>The content of the database is updated every 6 months via the inspection of journal websites by a group of curators. New journals are added whenever they, for the first time, publish an article by researchers affiliated to the Institut des Sciences de l'Evolution de Montpellier, or if identified by a curator.</p>")),
HTML("<p>The content of the database is updated every 6 months via the inspection of journal websites by a group of curators. Curators primarily survey the journals in which scientists affiliated to the Institut des Sciences de l'Evolution de Montpellier publish.</p>")),
fluidRow(
shinydashboard::infoBox("Curators", "Pierre-Olivier Antoine, Christophe Boëte, Frédéric Delsuc, Nicolas Galtier, Elise Huchard, Céline Scornavacca, Carole Smadja", icon = icon("list", lib = "glyphicon"), color = "yellow", fill =TRUE,width = 12),
shinydashboard::infoBox("Support", "Khalid Belkhir, Christine Bibal, Laure Paradis", icon = icon("list", lib = "glyphicon"), color = "yellow", fill = TRUE,width = 6),
......@@ -235,7 +235,7 @@ ui <- fluidPage(
server <- function(input, output){
#bslib::bs_themer()
empty_table = setNames(data.frame(matrix(ncol = 7, nrow = 0)), c('title' ,'year' , 'authors', 'journal' , 'doi' , 'abstract',"IN DAFNEE" ) )
empty_table = setNames(data.frame(matrix(ncol = 7, nrow = 0)), c('title' ,'year' , 'authors', 'journal' , 'doi' , 'abstract',"DAFNEE" ) )
this_table <- reactiveValues(table=empty_table, origine="ISEM")
......@@ -250,17 +250,17 @@ observeEvent(input$NewPubmedAuthor,{
return(NULL)
}
# par défaut tous les journaux sont tagués not inspected
# par défaut tous les journaux sont tagués not surveyed
# s'ils sont dans la liste des journaux de l'ISEM depuis 2014 ils sont tagués no (qu'ils soient DAFNEE ou non)
# s'ils sont dans DAFNEE ou sysnonymes ils seront tagués ok
t = getPubmedPapiers(nom, prenom, maxPapers=100, "Bel-Kh.csv")
Ethical = rep("not inspected", dim(t)[1])
Ethical = rep("not surveyed", dim(t)[1])
inAnnotatedJournals = toupper(trimws(t$journal)) %in% toupper(trimws(AnnotatedJournals[,1]))
Ethical[inAnnotatedJournals] = "no"
indafnee = toupper(trimws(t$journal)) %in% DAFNEE
Ethical[indafnee] = "ok"
t = cbind( t, "IN DAFNEE"=Ethical)
t = cbind( t, "DAFNEE"=Ethical)
this_table$table = t
this_table$origine = "pubmed"
})
......@@ -277,16 +277,16 @@ observeEvent(input$ExtractISEMAuthor,{
t = ISEMpub[(stringi::stri_trans_general(toupper(trimws(ISEMpub$nom)), "Latin-ASCII") == nom & stringi::stri_trans_general(toupper(trimws(ISEMpub$prenom)), "Latin-ASCII")==prenom) , c(-1,-2,-3)]
# par défaut tous les journaux sont tagués not inspected
# par défaut tous les journaux sont tagués not surveyed
# s'ils sont dans la liste des journaux de l'ISEM depuis 2014 ils sont d'abord tagués no (qu'ils soient DAFNEE ou non)
# s'ils sont dans DAFNEE ou sysnonymes ils seront tagués ok
Ethical = rep("not inspected", dim(t)[1])
Ethical = rep("not surveyed", dim(t)[1])
inAnnotatedJournals = toupper(trimws(t$journal)) %in% toupper(trimws(AnnotatedJournals[,1]))
Ethical[inAnnotatedJournals] = "no"
indafnee = toupper(trimws(t$journal)) %in% DAFNEE
Ethical[indafnee] = "ok"
t = cbind( t, "IN DAFNEE"=Ethical)
t = cbind( t, "DAFNEE"=Ethical)
this_table$table = t
this_table$origine = "ISEM"
})
......@@ -297,7 +297,7 @@ output$EthicJournals <- DT::renderDataTable({
datatable(ethicals, style = "bootstrap4", class = 'table-bordered table-condensed',
colnames = c("Journal", "Field", "Publisher", "Business model", "Institution", "Institution type", "Website","APC €uros", "Impact Factor", "PCI partnership"),
caption = htmltools::tags$caption( style = 'caption-side: top; text-align: center;',
htmltools::HTML("Click on a journal name to get its publications lag times from pubmed data (if available) since 2005 to present")
htmltools::HTML("Click on a journal name to get its publications lag times from pubmed data (if available) since 2005")
),
options = list( pageLength = 15,
dom = "Bfrtip",
......@@ -418,7 +418,7 @@ output$shiny_table <- DT::renderDataTable({
datatable(this_table$table, style= "bootstrap4",class = 'table-bordered table-condensed',
caption = htmltools::tags$caption( style = 'caption-side: top; text-align: center;',
htmltools::HTML('DAFNEE academia-friendly Journals : <span style="color:forestgreen; font-size:18px"><i class="glyphicon glyphicon-thumbs-up"></i></span>&nbsp;&nbsp;&nbsp; not in DAFNEE academia-friendly Journals : <span style="color:red; font-size:18px"><i class="glyphicon glyphicon-thumbs-down"></i></span>&nbsp;&nbsp;&nbsp; Journals not inspected : <span style="color:grey; font-size:18px"><i class="glyphicon glyphicon-eye-close"></i></span>' )
htmltools::HTML('Journal in DAFNEE : <span style="color:forestgreen; font-size:18px"><i class="glyphicon glyphicon-thumbs-up"></i></span>&nbsp;&nbsp;&nbsp; not in DAFNEE : <span style="color:red; font-size:18px"><i class="glyphicon glyphicon-thumbs-down"></i></span>&nbsp;&nbsp;&nbsp; not surveyed : <span style="color:grey; font-size:18px"><i class="glyphicon glyphicon-eye-close"></i></span>' )
),
options = list( pageLength = 15,
dom = "Bfrtip",
......@@ -465,11 +465,11 @@ output$shiny_table <- DT::renderDataTable({
output$ethicalityPlot <- renderPlot({
#here we will ignore journals not listed in AnnotatedJournals since 2014
nbDAFNEE = sum(this_table$table$`IN DAFNEE`=="ok")
nbISEMnotDAFNEE = sum(this_table$table$`IN DAFNEE`=="no")
nbDAFNEE = sum(this_table$table$`DAFNEE`=="ok")
nbISEMnotDAFNEE = sum(this_table$table$`DAFNEE`=="no")
# if (input$IndexMethod == 1) # all papers
# {
# PercentEthical = (nbDAFNEE * 100) / length(this_table$table$`IN DAFNEE`)
# PercentEthical = (nbDAFNEE * 100) / length(this_table$table$`DAFNEE`)
# ISEMethicIndex = ISEMdistrib$nbethics*100 / ISEMdistrib$totpubs
# subtitle = "% of DAFNEE Journals among author's refs "
# }
......
......@@ -11,7 +11,7 @@ lancer shinyloadtest depuis 3 machines différentes avec un nombre de user de 10
#kill running shiny apps
sudo kill -9 $(ps aux | grep shiny | grep -v grep | grep -v mbbshiny | awk '{print $2}')
dossier =
dossier="/opt/shiny"
cd $dossier/bibethique
#get latest version
......
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