Commit fada1c03 authored by khalid's avatar khalid
Browse files

More journals and change lags position

parent f15b5f4c
......@@ -16,7 +16,7 @@ require(ggridges)
require(gridExtra)
library(bslib)
library(shinyjs)
aca_synonymous <- read.table("./journals/acad_journal_synonyms.tsv", header=F, quote="", sep="\t", stringsAsFactors=F)
nonaca_synonymous <- read.table("./journals/nonacad_journal_synonyms.tsv", header=F, quote="", sep="\t", stringsAsFactors=F)
......@@ -28,6 +28,7 @@ AnnotatedJournals <- read.table("./journals/annotated_journals.tsv", header=F, s
AnnotatedJournals = rbind(AnnotatedJournals, nonaca_synonymous,aca_synonymous )
ethicals <- read.table("./journals/ethical_journals.csv", header=T, sep="\t",quote = '""', stringsAsFactors=F)
CurrentDAFNNEjournals = dim(ethicals)[1]
ethicals = ethicals[, - which(colnames(ethicals) == "curator")] #d'ont show curators
ethicals = ethicals[, - which(colnames(ethicals) == "curator_notes")] #d'ont show curators_notes
......@@ -152,6 +153,7 @@ getPubmedPapiers<- function(nom, prenom, maxPapers = 30, fic)
ui <- fluidPage(
useShinyjs(),
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "style.css"),
#tags$style("div.dataTables_scrollHead span {color: black;}"),
......@@ -174,9 +176,35 @@ ui <- fluidPage(
add_busy_spinner(spin = "cube-grid", margins = c(500, 500)), #position='full-page'),
titlePanel(h2(entete , align = "center"), windowTitle=entete ),
sidebarLayout(position ='right',
sidebarPanel( width = 3,
sidebarPanel( width = 1,id="sidebar",
conditionalPanel(condition="input.tabselected==2",
h5("DAFNEE Usage Index calculator :"),
# h5("DAFNEE Usage Index calculator :"),
# h6("Author's articles in academia-friendly journals / Author's 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", ""),
# textInput("prenom", "Author first name", ""),
# actionButton("NewPubmedAuthor", "Get pubmed records", icon("download")),
# #actionButton("NewGoogleAuthor", "Get Google Scholar records", icon("download")),
# actionButton("ExtractISEMAuthor", "Get ISEM records", icon("download")),
# #actionButton("add_btn", "Add a Ref"),
# #actionButton("delete_btn", "Delete Selected Ref"),
# br(), br(),
# plotOutput("AbstractWords", height = "500px" ),
# br(),
# plotOutput("AuthorsWords", height = "500px" )
)
),
mainPanel( width = 11,
tabsetPanel(type = "tabs",id = "tabselected",
tabPanel("Browse DAFNEE", value=1, h4(paste0(CurrentDAFNNEjournals, " non-profit, learned society, or university-associated journals relevant to the field of ecology and evolutionary biology"), style="text-align: center;font-family: 'Times New Roman', Times, serif;"), br(), DT::dataTableOutput("EthicJournals"),conditionalPanel(condition="input.tabselected==1", plotOutput("journalLags", height = "300px" ), h6("adapted from : https://quantixed.org/tag/lag-times/"))),
tabPanel("Author usage index", value=2,
fluidRow(
column(8,plotOutput("ethicalityPlot", height="350px"), DTOutput("shiny_table")),
column(4,h5("DAFNEE Usage Index calculator :"),
h6("Author's articles in academia-friendly journals / Author's 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),
......@@ -191,23 +219,30 @@ ui <- fluidPage(
br(), br(),
plotOutput("AbstractWords", height = "500px" ),
br(),
plotOutput("AuthorsWords", height = "500px" )
),
conditionalPanel(condition="input.tabselected==1", plotOutput("journalLags", height = "1000px" ), h6("adapted from : https://quantixed.org/tag/lag-times/"))
),
mainPanel( width = 9,
tabsetPanel(type = "tabs",id = "tabselected",
tabPanel("Browse DAFNEE", value=1, h4("250 non-profit, learned society, or university-associated journals relevant to the field of ecology and evolutionary biology", style="text-align: center;font-family: 'Times New Roman', Times, serif;"), br(), DT::dataTableOutput("EthicJournals")),
tabPanel("Author usage index", value=2, plotOutput("ethicalityPlot", height="350px"), DTOutput("shiny_table")),
plotOutput("AuthorsWords", height = "500px" ) )
)
),
tabPanel( "About", value=3,
fluidRow(
fluidRow( width=12,
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 known to be dysfunctional [1]. The average publishing price is an order of magnitude above the real cost [2,3]. This anomaly essentially results from the 'publish or perish' pressure placed on individual scientists, and the power of large publishing groups with high profit margins [4].
Yet not all scientific journals are economically equivalent. Some are run by non-profit organizations. Some are associated with learned societies, so the 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 take this criterion into account when deciding to interact with a journal as an author, reviewer or editor. Supporting academia-friendly journals, though, is a way to contribute to a fairer scientific publishing system.</p>"))),
Yet not all scientific journals are economically equivalent. Some are run by non-profit organizations. Some are associated with learned societies, so the 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 journal business models, and rarely take this criterion into account when deciding to interact with a journal as an author, reviewer or editor. Supporting academia-friendly journals, though, 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 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 specialized 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. An interactive tool gives scientists an opportunity to evaluate and compare his/her DAFNEE usage index, defined as the ratio of PubMed articles in academia-friendly journals to PubMed articles in surveyed journals.</p>")),
HTML("<p>The DAFNEE database offers a list of ~280 non-profit, learned society, museum or university-associated journals relevant to ecology and evolutionary biology. The database includes generalist journals (e.g. eLife, PLoS Biol, PNAS, Science), flagship society journals (e.g. Am Nat, Heredity, JEB, Proc B, MBE, Syst Biol), Open Science initiatives (e.g. Peer Communiy In, MorphoMuseuM), and many high-quality journals specialized in palaeo-archaeobiology, systematics, genetics, theoretical biology, organismal biology, environmental and health sciences. Journals can be queried/sorted by topic, business model, academic partnership, publication fees, and impact factor.</p>")),
shinydashboard::infoBox(HTML("<h3><strong>Attributes</strong></h3>"), icon = icon("barcode", lib = "glyphicon"), color = "yellow", fill =TRUE,width=12,
HTML("<ol> <li>Journal [Journal name] </li>
<li>Field [an arbitrary thematic classification of journals intended to ease DAFNEE browsing] </li>
<li>Publisher Business model [subscription, reader pays; OA: Open Acce, author pays; diamond_OA: free Open Access, neither reader nor author pays; hybrid: author choses OA or not] </li>
<li>Institution [non profit/governmental/university/society (co-)owning/associated with the journal] </li>
<li>Institution type [Society: learned society; Uni/Gov: university or governmental research institution; Museum: museum/botanical garden; Non-profit: not-for-profit organisation]</li>
<li>Web site [journal Web site]</li>
<li>APC [Article Processing Charges; what authors have to pay for Open Access; there might be publication charges in the non-OA model (not provided); APC are in euros]</li>
<li>Impact Factor [or equivalent measures of journal average citation rate]</li>
<li>PCI partnership [relationship with the Peer Community In initiative]</li></ol>")),
shinydashboard::infoBox(HTML("<h3><strong>DAFNEE usage Index</strong></h3>"), icon = icon("signal", lib = "glyphicon"), color = "yellow", fill =TRUE,width=12,
HTML("<p>An interactive tool gives scientists an opportunity to evaluate and compare his/her DAFNEE usage index. This is defined as the ratio of the author's PubMed articles in academia-friendly journals to PubMed articles in journals surveyed by DAFNEE.</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. Curators primarily survey the journals in which scientists affiliated with the Institut des Sciences de l'Evolution de Montpellier publish.</p>")),
......@@ -234,10 +269,23 @@ Yet not all scientific journals are economically equivalent. Some are run by non
server <- function(input, output){
#bslib::bs_themer()
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")
observeEvent(input[["tabselected"]], {
print(input[["tabselected"]])
if(input[["tabselected"]] == "5"){ #5 n'existe pas donc hide tout le temps
showElement(selector = "#sidebar")
removeCssClass("main", "col-sm-12")
addCssClass("main", "col-sm-9")
}else{
hideElement(selector = "#sidebar")
removeCssClass("main", "col-sm-9")
addCssClass("main", "col-sm-12")
}
})
observeEvent(input$NewPubmedAuthor,{
if (isolate(input$nom) != "" & isolate(input$prenom) != "")
......@@ -554,7 +602,7 @@ output$journalLags <- renderPlot({
labs(x = "Publication date", y = "Received-Accepted (days)") +
theme(axis.text=element_text(size=20), axis.title=element_text(size=20,face="bold"))
grid.arrange(p1, p2, p3, p4, nrow = 4, top=paste0("Publications lag times for ",journal))
grid.arrange(p1, p2, p3, p4, nrow = 1, top=paste0("Publications lag times for ",journal))
}
}
......
......@@ -281,4 +281,4 @@
"Zoologia" "evolution/systematics" "PenSoft" "OA" "Sociedade Brasileira de Zoologia" "Society" "https://zoologia.pensoft.net/" "none" 450 "0.743" "Frederic_Delsuc"
"Zoologica Scripta" "evolution/systematics" "Wiley" "hybrid" "Norwegian Academy of Science and Letters; Royal Swedish Academy of Sciences" "Uni/Gouv" "https://onlinelibrary.wiley.com/journal/14636409" "none" 2500 "2.603" "Frederic_Delsuc"
"Zoological Journal of the Linnean Society" "evolution/systematics" "Oxford University Press" "hybrid" "Linnean Society" "Society" "https://academic.oup.com/zoolinnean" "none" 2812 "2.824" "Frederic_Delsuc"
"Zoosystema" "evolution/systematics" "BioOne" "diamond_OA" "Museum National d'Histoire Naturelle" "Museum" "https://sciencepress.mnhn.fr/fr/periodiques/zoosystema" "none" 0 "0.434" "Frederic_Delsuc"
"Zoosystema" "evolution/systematics" "BioOne" "diamond_OA" "Museum National d'Histoire Naturelle" "Museum" "https://sciencepress.mnhn.fr/fr/periodiques/zoosystema" "none" 0 "0.434" "Frederic_Delsuc"
......@@ -43,6 +43,12 @@ sudo kill -9 $(ps aux | grep shiny | grep -v grep | grep -v mbbshiny | awk '{pri
dossier="/usr/local/maintenance"
#cd $dossier
# git clone https://gitlab.mbb.univ-montp2.fr/khalid/bibethique.git
# cd $dossier/bibethique
# scp -r khalid@162.38.181.45:/disk1/projets/workspace/bibethique/Output .
# mkdir $dossier/bibethiquelogs/
cd $dossier/bibethique
#get latest version
git reset --hard
......
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