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# library(shiny); library("embryogrowth"); runApp("/Users/marcgirondot/Documents/Espace_de_travail_R/_shiny/tsd/")
# library(shiny); runApp("http://max3.ese.u-psud.fr:3838/phenology/")
library(shiny)
package.embryogrowth <- require('embryogrowth')
# Define UI for application that draws a histogram
shinyUI(fluidPage(
# Application title
wellPanel(
wellPanel(
HTML("<small><i><font color='#006699'>The Virtual Data initiative, run by LABEX P2IO and supported by Université Paris-Sud, is thanked for providing computing resources on its cloud infrastructure.</font></i></small>")
),
h1("Temperature-dependent sex determination", align = "center")
, h2("at constant temperature", align = "center")
, p(em("Temperature-dependent sex determination (TSD) is a type of environmental
sex determination in which the temperatures experienced during embryonic
development determine the sex of the offspring. It is present in all crocodilians,
many turtles and squamates."))
, p(strong("The embryogrowth R package is a set of tools used
to model embryo growth and sexual phenotype linked to
temperature."))
, p("This web server version v. 4.1 is a simplified version of the complete tools available ",
a("here."
, href="https://cran.r-project.org/package=embryogrowth"
, target="_blank"))
, p(paste0("Embryogrowth package ", packageVersion("embryogrowth"), " is developped by ")
, a("Marc Girondot"
, href="https://hebergement.universite-paris-saclay.fr/marcgirondot/"
, target="_blank"))
, p(paste0("Database version ", as.character(DatabaseTSD$Version[1])))
)
, wellPanel(
p(" The methods have been published in:")
, p(a(
img(src="PDF.png", height=35, width=35),
"Girondot, M. 1999 Statistical description of temperature-dependent
sex determination using maximum likelihood. Evolutionary Ecology Research
1, 479-486.",
href="https://www.researchgate.net/publication/242076781_Statistical_description_of_temperature-dependent_sex_determination_using_maximum_likelihood",
target="_blank"))
, p(a(
img(src="PDF.png", height=35, width=35),
"Godfrey, M.H., Delmas, V. & Girondot, M. 2003 Assessment of
patterns of temperature-dependent sex determination using maximum likelihood
model selection. Ecoscience 10, 265-272.",
href="https://www.researchgate.net/profile/Marc_Girondot/publications?sorting=newest&page=5",
target="_blank"))
, p(a(
img(src="PDF.png", height=35, width=35),
"Hulin, V., Delmas, V., Girondot, M., Godfrey, M.H. & Guillon, J.-M. 2009
Temperature-dependent sex determination and global change: Are some species at
greater risk? Oecologia 160, 493-506.",
href="https://www.researchgate.net/publication/24192820_Temperature-dependent_sex_determination_and_global_change_are_some_species_at_greater_risk",
target="_blank"))
, p(a(
img(src="PDF.png", height=35, width=35),
"Abreu-Grobois FA, Morales-Mérida BA, Hart CE, Guillon J-M, Godfrey MH,
Navarro E, Girondot M: Recent advances on the estimation of the thermal reaction norm
for sex ratios. PeerJ 2020, 8:e8451.",
href="https://www.researchgate.net/publication/339687789_Distributed_under_Creative_Commons_CC-BY_40_OPEN_ACCESS_Recent_advances_on_the_estimation_of_the_thermal_reaction_norm_for_sex_ratios",
target="_blank"))
, helpText(strong("These methods MUST not be used for incubation data at non-constant temperatures, both
for temperature versus sex ratio and incubation duration versus sex ratio."))
)
# Sidebar with a slider input for the number of bins
, sidebarLayout(
sidebarPanel(
wellPanel(
h4("Load dataset from litterature")
, selectInput("Species", "Species"
, choices=as.list(levels(as.factor(embryogrowth::DatabaseTSD$Species)))
, selected = NULL, multiple = FALSE,
selectize = TRUE, width = NULL, size = NULL)
# , selectInput("RMU", "RMU"
# , choices=as.list(c("All", levels(as.factor(embryogrowth::DatabaseTSD$RMU))[-1]))
# , selected = NULL, multiple = TRUE,
# selectize = TRUE, width = NULL, size = NULL)
, uiOutput("RMUControls")
, helpText("RMU are the Regional Managment Units defined for marine turles in ",
a("Wallace B.P., et al. (2023) Marine turtle regional management units 2.0:
an updated framework for conservation and research of wide-ranging megafauna
species. Endangered Species Research, 52, 209-223.",
href="https://www.int-res.com/articles/esr2023/52/n052p209.pdf",
target="_blank"))
, actionButton("goButton", "Go!")
)
, wellPanel(h4("Options to evaluate TSD")
, radioButtons("Male", "Should the data presented as male or female relative frequency?", list(Male=1, Female=2), selected=1, inline = TRUE)
, radioButtons("Temperature", "Analyze sex ratio against temperature or incubation duration ?", list(Temperature=1, Duration=2), selected=1, inline = TRUE)
, selectInput("Equation", "What equation should be used?"
, choices=list("GSD", "Logistic", "Hill", "Richards", "Double-Richards", "Hulin", "flexit")
, selected = "Logistic", multiple = FALSE,
selectize = TRUE, width = NULL, size = NULL)
, radioButtons("Intersexes", "How to count intersexes?", list(Discard=1, Males=2), selected=1, inline = TRUE)
, h4("Initial values for fit")
, numericInput("P", "P value", "", width = "50%")
, numericInput("S", "S value", "", width = "50%")
, helpText("In most of the cases, you can let these boxes empty.")
)
, wellPanel(h4("Prediction")
, textInput("Prediction", "Values for which sex ratio should be predicted:", "30")
, helpText("Values can be separated with space or commas.")
, actionButton("predictButton", "Predict")
)
)
,
# Show a plot of the generated distribution
mainPanel(
plotOutput("distPlot")
, h4("Synthesis for TSD model")
, verbatimTextOutput(outputId="resultsInfo")
, h4("Data used for the fit")
, tableOutput(outputId="Data")
# , verbatimTextOutput(outputId="Data")
, h4("References")
, verbatimTextOutput(outputId="references")
, h4("Prediction")
, tableOutput(outputId="Prediction")
# , verbatimTextOutput(outputId="Prediction")
# , verbatimTextOutput(outputId="p")
)
)
))
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