Commit 4c796096 authored by khalid's avatar khalid
Browse files

Add Manley english corrections

parent ec76131b
......@@ -177,7 +177,7 @@ ui <- fluidPage(
sidebarPanel( width = 3,
conditionalPanel(condition="input.tabselected==2",
h5("DAFNEE Usage Index calculator :"),
h6("Athor's articles in academia-friendly journals / Author's total articles in surveyed journals"),
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", ""),
......@@ -193,7 +193,7 @@ ui <- fluidPage(
br(),
plotOutput("AuthorsWords", height = "500px" )
),
conditionalPanel(condition="input.tabselected==1", plotOutput("journalLags", height = "1000px" ))
conditionalPanel(condition="input.tabselected==1", plotOutput("journalLags", height = "1000px" ), h6("adapted from : https://quantixed.org/tag/lag-times/"))
),
mainPanel( width = 9,
......@@ -203,17 +203,17 @@ 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 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>"))),
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 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 ~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>")),
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 to the Institut des Sciences de l'Evolution de Montpellier publish.</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 with 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),
shinydashboard::infoBox("Support",HTML(paste( "Developer: Khalid Belkhir", br(), "Biblio : Christine Bibal, Laure Paradis")), icon = icon("list", lib = "glyphicon"), color = "yellow", fill = TRUE,width = 6),
shinydashboard::infoBox("Contact", "nicolas.galtier@umontpellier.fr", icon = icon("link", lib = "glyphicon"), color = "yellow", fill = TRUE, width = 6)
),
fluidRow(style = "height:400px;",
......@@ -530,7 +530,7 @@ output$journalLags <- renderPlot({
{
#adapted from : https://www.r-bloggers.com/2021/04/ten-years-vs-the-spread-ii-calculating-publication-lag-times-in-r/
theData = read.csv( file = journalData )
theData$year=as.factor(theData$year)
theData$year = as.factor(theData$year)
theData$recacc <-as.Date(theData$accdate) - as.Date(theData$recdate)
theData$recpub <-as.Date(theData$pubdate) - as.Date(theData$recdate)
theData$accpub <-as.Date(theData$pubdate) - as.Date(theData$accdate)
......
......@@ -18,31 +18,24 @@ cd $dossier/bibethique
git reset --hard
git pull
rm -rf ../bibethique80*
#start newer instances
for i in {1..30}
do
if [ $i -lt 10 ] ;then
cp -R $dossier/bibethique $dossier/bibethique800$i
sed -i "s/entete = \"DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution\"/entete = 'DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution$i'/" $dossier/bibethique800$i/app.R
#sed -i "s/entete = \"DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution\"/entete = 'DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution$i'/" $dossier/bibethique800$i/app.R
Rscript -e "setwd('$dossier/bibethique800$i');shiny::runApp('$dossier/bibethique800$i', port=800$i, host='0.0.0.0')" 1>&2 >> /usr/local/mbbshiny/bibethique_${i}.log &
else
cp -R $dossier/bibethique $dossier/bibethique80$i
sed -i "s/entete = \"DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution\"/entete = 'DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution$i'/" /$dossier/bibethique80$i/app.R
#sed -i "s/entete = \"DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution\"/entete = 'DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution$i'/" /$dossier/bibethique80$i/app.R
Rscript -e "setwd('$dossier/bibethique80$i');shiny::runApp('$dossier/bibethique80$i', port=80$i, host='0.0.0.0')" 1>&2 >> /usr/local/mbbshiny/bibethique_${i}.log &
fi
done
#check
ps aux | grep shiny | grep -v grep | grep -v mbbshiny | awk '{print $2}'
#Pour initialiser
# for i in {1..30}
# do
# if [ $i -lt 10 ] ;then
# curl 162.38.181.43:800$i
# else
# curl 162.38.181.43:80$i
# fi
# done
# on shiny.mbb.univ-montp2.fr (162.38.181.10) juste 10 instances
......@@ -55,19 +48,13 @@ git pull
for i in {0..9}
do
cp -R $dossier/bibethique $dossier/bibethique800$i
sed -i "s/entete = \"DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution\"/entete = 'DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution. .10:$i'/" $dossier/bibethique800$i/app.R
#sed -i "s/entete = \"DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution\"/entete = 'DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution. .10:$i'/" $dossier/bibethique800$i/app.R
Rscript -e "setwd('$dossier/bibethique800$i');shiny::runApp('$dossier/bibethique800$i', port=800$i, host='0.0.0.0')" 1>&2 >> $dossier/bibethiquelogs/bibethique_${i}.log &
done
#check
ps aux | grep shiny | grep -v grep | grep -v mbbshiny | awk '{print $2}'
#Pour initialiser
# for i in {0..9}
# do
# curl 162.38.181.10:800$i
# done
# on khalid (162.38.181.45) juste 10 instances
......@@ -80,18 +67,14 @@ git pull
for i in {0..9}
do
cp -R $dossier/bibethique $dossier/bibethique800$i
sed -i "s/entete = \"DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution\"/entete = 'DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution. .45:$i'/" $dossier/bibethique800$i/app.R
#sed -i "s/entete = \"DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution\"/entete = 'DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution. .45:$i'/" $dossier/bibethique800$i/app.R
Rscript -e "setwd('$dossier/bibethique800$i');shiny::runApp('$dossier/bibethique800$i', port=800$i, host='0.0.0.0')" 1>&2 >> $dossier/bibethiquelogs/bibethique_${i}.log &
done
#check
ps aux | grep shiny | grep -v grep | grep -v mbbshiny | awk '{print $2}'
#Pour initialiser
# for i in {0..9}
# do
# curl 162.38.181.45:800$i
# done
#on idcov2
Dans /etc/nginx/nginx.conf
......@@ -113,7 +96,10 @@ http {
default_type application/octet-stream;
ssl_protocols TLSv1 TLSv1.1 TLSv1.2; # Dropping SSLv3, ref: POODLE
ssl_prefer_server_ciphers on;
access_log /var/log/nginx/access.log;
log_format upstreamlog '[$time_local] $remote_addr - $remote_user - $host to: $upstream_addr: $request $status upstream_response_time $upstream_response_time msec $msec request_time $request_time';
access_log /var/log/nginx/access.log upstreamlog;
error_log /var/log/nginx/error.log;
gzip on;
map $http_upgrade $connection_upgrade {
......
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