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ui.R
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executable file
·526 lines (493 loc) · 78.6 KB
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#
# This is the user-interface definition of a Shiny web application. You can
# run the application by clicking 'Run App' above.
#
# Find out more about building applications with Shiny here:
#
# http://shiny.rstudio.com/
#
library(shiny)
library(bslib)
library(ape)
library(paletteer)
library(coda)
library(corHMM)
#devtools::install_github(repo = 'https://github.com/liamrevell/phytools',force = TRUE)
library(phytools)
library(shinyjs)
library(rhandsontable)
library(shinyWidgets)
library(DDD)
library(diversitree)
theme <- bs_theme(version = 5, bootswatch = "minty", primary = "#0BB48C",secondary = "#C1D9DB",
"font-size-base" = "1.0rem", "enable-rounded" = T
) %>%
bs_add_rules(
'.navbar:not(.fixed-bottom):not(.navbar-fixed-bottom):not(.navbar-fixed-bottom) {
margin-bottom: 0px;}
.container, .container-fluid, .container-xxl, .container-xl, .container-lg, .container-md, .container-sm {
padding-left: 0.1rem;
padding-right: 0.1rem;
}
.navbar-brand { margin-left: 1rem;}
.row>* {padding-right: calc(var(--bs-gutter-x) * 0.7);
padding-left: calc(var(--bs-gutter-x) * 0.7);}
.nav-tabs .nav-link, .nav-tabs>li>a, .nav-tabs .nav-pills>li>a, .nav-tabs ul.nav.navbar-nav>li>a{
margin-left: 0.45rem;
margin-top: 0.5rem;
}
.nav-link, .nav-tabs>li>a, .nav-pills>li>a, ul.nav.navbar-nav>li>a{
color: #5a5a5a;
}
.nav-tabs .nav-link.active, .nav-tabs>li>a.active, .nav-tabs .nav-pills>li>a.active, .nav-tabs ul.nav.navbar-nav>li>a.active, .nav-tabs .nav-item.show .nav-link, .nav-tabs .nav-item.in .nav-link, .nav-tabs .nav-item.show .nav-tabs>li>a, .nav-tabs .nav-item.in .nav-tabs>li>a, .nav-tabs .nav-item.show .nav-pills>li>a, .nav-tabs .nav-item.in .nav-pills>li>a, .nav-tabs>li.show .nav-link, .nav-tabs>li.in .nav-link, .nav-tabs>li.show .nav-tabs>li>a, .nav-tabs>li.in .nav-tabs>li>a, .nav-tabs>li.show .nav-pills>li>a, .nav-tabs>li.in .nav-pills>li>a, .nav-tabs .nav-pills>li.show .nav-link, .nav-tabs .nav-pills>li.in .nav-link, .nav-tabs .nav-pills>li.show .nav-tabs>li>a, .nav-tabs .nav-pills>li.in .nav-tabs>li>a, .nav-tabs .nav-pills>li.show .nav-pills>li>a, .nav-tabs .nav-pills>li.in .nav-pills>li>a, .nav-tabs .nav-item.show ul.nav.navbar-nav>li>a, .nav-tabs .nav-item.in ul.nav.navbar-nav>li>a, .nav-tabs>li.show ul.nav.navbar-nav>li>a, .nav-tabs>li.in ul.nav.navbar-nav>li>a, .nav-tabs .nav-pills>li.show ul.nav.navbar-nav>li>a, .nav-tabs .nav-pills>li.in ul.nav.navbar-nav>li>a, .nav-tabs ul.nav.navbar-nav>li.show:not(.dropdown) .nav-link, .nav-tabs ul.nav.navbar-nav>li.in:not(.dropdown) .nav-link, .nav-tabs ul.nav.navbar-nav>li.show:not(.dropdown) .nav-tabs>li>a, .nav-tabs ul.nav.navbar-nav>li.in:not(.dropdown) .nav-tabs>li>a, .nav-tabs ul.nav.navbar-nav>li.show:not(.dropdown) .nav-pills>li>a, .nav-tabs ul.nav.navbar-nav>li.in:not(.dropdown) .nav-pills>li>a, .nav-tabs ul.nav.navbar-nav>li.show:not(.dropdown) ul.nav.navbar-nav>li>a, .nav-tabs ul.nav.navbar-nav>li.in:not(.dropdown) ul.nav.navbar-nav>li>a {
color: #0BB48C;
}
.navbar-light .navbar-nav .show>.nav-link, .navbar-light .navbar-nav .in>.nav-link, .navbar-light .navbar-nav .nav-tabs>li.show>a, .navbar-light .navbar-nav .nav-tabs>li.in>a, .navbar-light .navbar-nav .nav-pills>li.show>a, .navbar-light .navbar-nav .nav-pills>li.in>a, .navbar.navbar-default .navbar-nav .show>.nav-link, .navbar.navbar-default .navbar-nav .in>.nav-link, .navbar.navbar-default .navbar-nav .nav-tabs>li.show>a, .navbar.navbar-default .navbar-nav .nav-tabs>li.in>a, .navbar.navbar-default .navbar-nav .nav-pills>li.show>a, .navbar.navbar-default .navbar-nav .nav-pills>li.in>a, .navbar-light ul.nav.navbar-nav>li.show>a, .navbar-light ul.nav.navbar-nav>li.in>a, .navbar.navbar-default ul.nav.navbar-nav>li.show>a, .navbar.navbar-default ul.nav.navbar-nav>li.in>a, .navbar-light .navbar-nav .nav-link.active, .navbar-light .navbar-nav .nav-tabs>li>a.active, .navbar-light .navbar-nav .nav-pills>li>a.active, .navbar.navbar-default .navbar-nav .nav-link.active, .navbar.navbar-default .navbar-nav .nav-tabs>li>a.active, .navbar.navbar-default .navbar-nav .nav-pills>li>a.active, .navbar-light ul.nav.navbar-nav>li>a.active, .navbar.navbar-default ul.nav.navbar-nav>li>a.active {
color: #0BB48C;
}
.navbar-brand{
font-size: 1.2rem;
font-weight: 500;
}
.navbar-light .navbar-brand, .navbar.navbar-default .navbar-brand {
color: #67847d;}
'
)
shinyUI(
navbarPage(title = "Guane", theme = theme,
tabPanel("Home",
includeHTML("www/home.html"),
),
navbarMenu("Methods",
tabPanel("Independent Contrats", imageOutput("home_img")
),
tabPanel("Ancestral character estimation",
fluidPage(theme = theme,
tabsetPanel(type = "tabs",
tabPanel("Data",
fluidRow(
column(3,wellPanel(selectInput("tree", "Load tree",c("Select" = "select","Example" = "examp","Import tree" = "treeFile")),
conditionalPanel(condition = "input.tree=='treeFile'",
# selectInput("format", "Tree format",c("Select" = "select","Nexus" = "Nexus","Newick" = "Newick")),
fileInput("fileTree", "Load file")),
actionButton("importTree", "Import tree"), hr(),
selectInput("csvData", "Load csv", c("Select" = "select", "Example" = "exampCSV", "Import data" = "DataFile")),
conditionalPanel(condition = "input.csvData == 'DataFile'",
fileInput("fileCSV", "Load file")),
actionButton("importCSV", "Import csv"), hr(),
checkboxInput("checknames", "Check tree & data names"),
selectInput('dataVar','Select a character',choices = 'Select', selected = NULL),
selectInput('typeChar', 'Confirm character type', choices = c('Select','Discrete','Continuous'), selected = 'Select'), hr(),
numericInput(inputId = "seed", label = "Set seed",value = 999, min = 1, max = 1000000)
)
),
column(9,fluidRow(column(9,plotOutput(outputId = 'PhyloPlot', inline = T)),
column(3,wellPanel(checkboxInput("tipLabels", "Tip labels"),
conditionalPanel(condition = "input.tipLabels==1",
sliderInput("tipSize", "Tip label size",step = 0.1,min = 0, max = 3, value = 0.5)),
checkboxInput("branchLength", "Edge length"),
sliderInput("PlotWidthDt", "Tree width (px)",step = 100,min = 100, max = 1000, value = 400),
sliderInput("PlotHeightDt", "Tree height (px)",step = 100,min = 100, max = 1000, value = 800),
selectInput("plotType", "Tree type",
c("Phylogram" = "phylogram", "Cladogram" = "cladogram", "Fan" = "fan", "Unrooted" = "unrooted", "Radial" = "radial", "tidy" = "Tidy" ), selected = "phylogram")
)
)
),hr(),
fluidRow(column(12,verbatimTextOutput("objects")))
)
)
),
tabPanel("Analysis",
conditionalPanel(condition = "input.typeChar == 'Continuous'",
tabsetPanel(id = "ContinuousCharacter",
tabPanel(title = "Maximum Likelihood", useShinyjs(),
div(id = 'ResetConCharML',
fluidRow(column(3,wellPanel(radioButtons("transform1", "Data transformation",
c("Raw data" = "NoTrans","Natural logarithm" = "ln","Log base 10" = "log10",
"Square Root" = "squareRoot","Cube Root" = "cubeRoot",
"Reciprocal" = "reciprocal","Exponential" = "exp1"),selected = "NoTrans"),
checkboxInput("AncPIC", "Phylogenetic independent contrast estimation"),hr(),
selectInput("ModelContinuous", "Fit model",c("BM" = "BM","OU" = "OU","EB" = "EB"),multiple = TRUE,selected = NULL),
conditionalPanel(condition = "input.ModelContinuous.indexOf('BM') > -1",
textInput('maxitBM', 'Max iter BM', value = '2000')),
conditionalPanel(condition = "input.ModelContinuous.indexOf('EB') > -1",
textInput('maxitEB', 'Max iter EB', value = '200')),
conditionalPanel(condition = "input.ModelContinuous.indexOf('OU') > -1",
textInput('maxitOU', 'Max iter OU', value = '20')),
actionButton("runAncML", "run"),hr(),
checkboxInput("MLModAIC", "Model selection - AIC"),hr(),
radioButtons("exportMLanc", "Export output",c("R object (RDS)" = "MLancRDS","TXT" = "MLancTXT")),
downloadButton("downloadAnc", "Download"),hr(),
actionButton("ResetConMl", "Reset Panel")
)
),
column(9,fluidRow(column(6,
fluidRow(column(12,plotOutput(outputId = 'PhyloPlot2', inline = T)))),
column(6,
fluidRow(column(12,plotOutput(outputId = 'histo1'))),
fluidRow(column(12,plotOutput(outputId = 'QQ1'))))
),
wellPanel(fluidRow(column(4,selectInput('mapModelMl','Plot model',choices = NULL, selected = NULL),
sliderInput("tipSizeContMl", "Tip label size",step = 0.1,min = 0, max = 3, value = 0.7)),
column(4, sliderInput("PlotWidthContMl", "Tree width (px)",step = 100,min = 100, max = 1000, value = 400),
sliderInput("PlotHeightContMl", "Tree height (px)",step = 100,min = 100, max = 1000, value = 800)
),
column(4,checkboxInput('phenogramML', 'Phenogram'),
conditionalPanel('input.phenogramML == 1',
checkboxInput('NormalScaleConML', 'Normal scale')),
actionButton('PlotEditorML', 'Plot Editor'))
)
),hr(),
fluidRow(column(12,verbatimTextOutput("infoPanelContinuousML"))))
)
)
),
tabPanel("Bayesian MCMC",fluidRow(column(3,wellPanel(selectInput("parametersBI", "Set parameters",
c("Select" = "select","By default" = "defaultBI","Costumize" = "costumizeBI")),
conditionalPanel(condition = "input.parametersBI == 'costumizeBI'",
textInput('sig2BI','Sig2: Brownian Motion rate'),
textInput('aBI','a: Root node state'),
textInput('sampleBI','Sample')
),
textInput('ngenBI','Number of generations',200000),
textInput('BurninBI','Burn-in',0.2),
actionButton("runAncBI", "Run"),hr(),
radioButtons("exportAncBI", "Export output",
c("R object (RDS)" = "BIancRDS","TXT" = "BIancTXT")),
downloadButton("downloadAncBI", "Download")
)
),
column(9,fluidRow(column(6,
fluidRow(column(12,plotOutput(outputId = 'PhyloPlot4',inline = T,click = "plot_click")))
),
column(6,
fluidRow(column(12,plotOutput(outputId = 'trace1'))),
fluidRow(column(12,plotOutput(outputId = 'desnsity1'))))
),
wellPanel(fluidRow(column(4,selectInput('plotNodesBI','Plot posterior prob. by node',choices = NULL, selected = NULL,multiple = TRUE),
sliderInput("tipSizeContBI", "Tip label size",step = 0.1,min = 0, max = 3, value = 0.7)),
column(4, sliderInput("PlotWidthContBI", "Tree width (px)",step = 100,min = 100, max = 1000, value = 400),
sliderInput("PlotHeightContBI", "Tree height (px)",step = 100,min = 100, max = 1000, value = 800)),
column(4,checkboxInput('phenogramBI', 'Tree phenogram'),
actionButton('PlotEditorBI', 'Tree Editor'))
)
),hr(),
fluidRow(column(12,verbatimTextOutput("infoPanelContinuousBI")))
)
)
)
)
),
conditionalPanel(condition = "input.typeChar == 'Discrete'",
tabsetPanel(id = 'DiscreteCharacter',
tabPanel("Maximum Likelihood",
fluidRow(column(3, wellPanel(selectInput("typeDisML", "Estimation",choices = c('Joint' = 'joint', 'Marginal' = 'marginal'),selected = 'marginal'),
selectInput("ModelsDisML", "Set models",choices = NULL,multiple = TRUE),
uiOutput("addModel3States"),
conditionalPanel("input.AddModelDisML == 1",
br(), rHandsontableOutput("w1"), br(),
actionButton('SubmAddModel','Submit')),br(),
actionButton('RunAnalyDisML','Run'), hr(),
checkboxInput("DisMLModAIC", "Model selection - AIC"),
conditionalPanel("input.DisMLModAIC == 1",
checkboxInput("ModAverDisML", "Model averaging") ),
conditionalPanel("input.ModAverDisML == 1 & input.DisMLModAIC == 1",
selectInput("SetModAverDisML", "Set models",choices = NULL, selected = NULL, multiple = TRUE),
actionButton('RunModAverDisML','Run')), hr(),
radioButtons("exportDisMLanc", "Export output",c("R object (RDS)" = "MLancRDS","TXT" = "MLancTXT")),
selectInput("disCharOutputs", "Choose output",choices = c("Select" = "Select", "Fitted models" = "FittedModels", "AIC matrix" = "AICmatrix", "Model averaging" = "ModelAverage")),
downloadButton("downloadDisML", "Download")
)
),
column(9, fluidRow(column(6,fluidRow(plotOutput(outputId = 'PhyloPlot8',inline = T))),
column(6,fluidRow(plotOutput(outputId = 'PhyloPlot9')))
),
wellPanel(fluidRow(column(4,selectInput('plotModelDisML','Plot model',choices = NULL),
sliderInput("tipSizeDisML", "Tip label size",step = 0.1,min = 0, max = 3, value = 0.7)),
column(4,sliderInput("PlotWidthDisML", "Tree width (px)",step = 100,min = 100, max = 1000, value = 400),
sliderInput("PlotHeightDisML", "Tree height (px)",step = 100,min = 100, max = 1000, value = 800)),
column(4,checkboxInput('bestState', 'The most likely state'),
actionButton('PlotEditorDisML', 'Plot Editor'))
)
),hr(),
fluidRow(column(12,verbatimTextOutput("infoPanelDiscreteML")
)
)
)
)
),
tabPanel("Bayesian MCMC",
fluidRow(column(3,wellPanel(selectInput("QmatrixBI", "Q matrix: rates",choices = c('Select' = 'select', 'Empirical' = 'empirical', 'MCMC' = 'mcmc','Costumize' = 'costumQmDiscBI')),
conditionalPanel("input.QmatrixBI == 'costumQmDiscBI'",
br(),rHandsontableOutput(outputId = "putitamatrix"), br(),
actionButton('SubmQmatBI','Submit matrix')), br(),
conditionalPanel("input.QmatrixBI == 'empirical' | input.QmatrixBI == 'mcmc'",
selectInput("ModelsDisBI", "Set model",choices = NULL,multiple = F),
conditionalPanel("input.ModelsDisBI == 'Costumize'",
br(), rHandsontableOutput("costuModelBI"),br(),
actionButton('SubmAddModelBI','Submit model')),br()),
conditionalPanel("input.QmatrixBI == 'mcmc'",
selectInput("mcmcParDisBI", "Set mcmc parameters", choices = c('By default' = 'bydefaultmcmcDisBI','Costumize' = 'costummcmcDisBI')),
conditionalPanel("input.mcmcParDisBI == 'costummcmcDisBI'",
selectInput("priorDisBI", "Prior: Gamma parameters", choices = c('Select' = 'select','Use empirical' = 'useEmpirical','No use empirical' = 'noUseEmpirical')),
conditionalPanel("input.priorDisBI == 'useEmpirical'",
radioButtons("betavaluesDisBI", "Beta values",
c("Fix one value per rate" = "oneBeta", "Assign a value per rate" = "betaPerRate"), selected = character(0)),
conditionalPanel("input.betavaluesDisBI == 'oneBeta'",
rHandsontableOutput("matBetaValDisBI"), br(),
actionButton('SubmBetaValDisBI','Submit beta')
),
conditionalPanel("input.betavaluesDisBI == 'betaPerRate'",
rHandsontableOutput("matBetaValuePerRateDisBI"), br(),
actionButton('SubmBetaValuePerRateDisBI','Submit betas'))
),br(),
conditionalPanel("input.priorDisBI == 'noUseEmpirical'",
radioButtons("alphaBetaValDisBI", "Alpha and Beta values",
c("Fix equal values per rate" = "oneAlphaBeta","Alpha and beta value per rate " = "alphaBetaPerRate"), character(0)),
conditionalPanel("input.alphaBetaValDisBI == 'oneAlphaBeta'",
rHandsontableOutput("matOneAlphaBetaValDisBI"),br(),
actionButton('SubmOneAlphaBetaValDisBI','Submit (a,b)')),
conditionalPanel("input.alphaBetaValDisBI == 'alphaBetaPerRate'",
rHandsontableOutput("matAlphaBetaPerRateDisBI"),br(),
actionButton('SubmAlphaBetaPerRateDisBI','Submit (a,b)*rate'))
),br(),
selectInput("vQDisBI", "vQ: variance per rate", choices = c('Select' = 'select','Equal' = 'equalvQDisBI', 'Variances' = 'vQValPerRatesDisBI')),
conditionalPanel("input.vQDisBI == 'equalvQDisBI'",
rHandsontableOutput("matequalvQValDisBI"),br(),
actionButton('SubmequalvQValDisBI','Submit vQ')
),
conditionalPanel("input.vQDisBI == 'vQValPerRatesDisBI'",
rHandsontableOutput("matvQValPerRatesDisBI"),br(),
actionButton('SubmbvQValPerRatesDisBI','Submit vQ*rates'))
), br(),
textInput('samfreqDisBI','Sample frequency',value = 10),
textInput('burninDisBI','Burn-in',value = 0.2)
),
selectInput("piBI", "Pi: prior prob. in root",choices = c('Select' = 'select', 'Fitzjohn' = 'fitzjohn', 'Stationary' = 'estimated', 'Equal' = 'equal', 'Costumize' = 'costumPiDiscBI')),
conditionalPanel("input.piBI == 'costumPiDiscBI'",
rHandsontableOutput("matPiBI"),br(),
actionButton('SubmPiBI','Submit')),br(),
textInput('nsimDisBI','nsim',value = 100),
actionButton('RunAnalyDisBI','Run'), hr()
)),
column(9,fluidRow(column(6,fluidRow(plotOutput(outputId = 'PhyloPlot10',height="800px"))),
column(6,fluidRow(plotOutput(outputId = 'PhyloPlot11')),
fluidRow(plotOutput(outputId = 'PhyloPlot12')))
),
wellPanel(fluidRow(column(4,selectInput('plotModelDisBI','Plot outcome',choices = NULL),
selectInput('ploHPDDisBI','Plot transitions',choices = NULL)),
column(4,sliderInput("PlotWidthDisBI", "Tree width (px)",step = 100,min = 100, max = 1000, value = 400),
sliderInput("PlotHeightDisBI", "Tree height (px)",step = 100,min = 100, max = 1000, value = 800)),
column(4,sliderInput("tipSizeDisBI", "Tip label size",step = 0.1,min = 0, max = 3, value = 0.7),
actionButton('PlotEditorDisBI', 'Plot Editor'))
)
),hr(),
fluidRow(column(12,verbatimTextOutput("infoPanelDiscreteBI")
)
)))),
tabPanel("Parsimony")
)
)
)
)
)
),
tabPanel("Basic Diversification Analysis",
fluidPage(theme = theme,
tabsetPanel(type = "tabs",
tabPanel("Data",
fluidRow(column(3,wellPanel(selectInput("treeDiver", "Load tree",c("Select" = "select","Example (Ultrametric)" = "exampDiverUltra", "Example (non-ultrametric)" = "exampDivernonUltra","Import tree" = "treeFileDiver")),
conditionalPanel(condition = "input.treeDiver =='treeFileDiver'",
fileInput("fileTreeDiver", "Load file")),
actionButton("importTreeDiver", "Import tree"), hr(),
checkboxInput("ultrametricDiverDT1", "Is ultrametric?"),
uiOutput("forceultrDiverDT"),
conditionalPanel(condition = "input.frcUltButtDiverDT == 'chronosDiverDt'",
checkboxInput(inputId = 'timeTaxaDiverDT', label = 'Insert time by tips'),
conditionalPanel(condition = "input.timeTaxaDiverDT == 1",
rHandsontableOutput("ageTaxaDiverDT"),
actionButton(inputId = 'addageTaxaDiverDT', label = 'add')
),
checkboxInput(inputId = 'timeMRCADiverDT', label = 'Insert time by MRCA'),
conditionalPanel(condition = "input.timeMRCADiverDT == 1",
rHandsontableOutput("ageMRCADiverDT"),
actionButton(inputId = 'addageMRCADiverDT', label = 'add')
),
checkboxInput(inputId = 'timeNnodeDiverDT', label = 'Insert time by Nnode'),
conditionalPanel(condition = "input.timeNnodeDiverDT == 1",
rHandsontableOutput("ageNnodeDiverDT"),
actionButton(inputId = 'addageNnodeDiverDT', label = 'add')
),
checkboxInput(inputId = 'timePhyloDiverDT', label = 'Insert time clicking over phylogeny'),
conditionalPanel(condition = "input.timePhyloDiverDT == 1",
rHandsontableOutput("agePhyloDiverDT"),
actionButton(inputId = 'addPhyloDiverDT', label = 'add')
),
checkboxInput(inputId = 'timeCSVDiverDT', label = 'Insert time by loading a .csv'),
conditionalPanel(condition = "input.timeCSVDiverDT == 1",
fileInput("fileageDiverDT", "Load file"),
actionButton("importAgeCSV", "Import .csv")
),
textInput(inputId = 'lambdaChronosDiverDT',label = 'Lambda',value = '1'),
),
uiOutput("RunUltrDiverDT"), hr(),
checkboxInput("BinaryDiverDT", "Is binary?"),
uiOutput("PoliDiverDT"),
uiOutput("ButtonPoliDiverDT"),
hr(),
radioButtons("exportDiverDT", "Export output",c("R object (RDS)" = "RDSdiverDT","TXT" = "TXTdiverDT")),
downloadButton("downloadDiverDT", "Download"),hr(),
numericInput(inputId = "seedDiverDT", label = "Set seed",value = 999, min = 1, max = 1000000)
)
),
column(9,fluidRow(column(9,plotOutput(outputId = 'PhyloPlotDiver1', inline = T, click = 'plot_clickDiverDT') ),
column(3, wellPanel(checkboxInput("tipLabelsDiverDT", "Tip labels"),
conditionalPanel(condition = "input.tipLabelsDiverDT == 1",
sliderInput("tipSizeDiverDT", "Tip label size",step = 0.1,min = 0, max = 3, value = 0.5)),
checkboxInput("branchLengthDiverDT", "Edge length"),
sliderInput("PlotWidthDiverDT", "Tree width (px)",step = 100,min = 100, max = 1000, value = 500),
sliderInput("PlotHeightDiverDT", "Tree height (px)",step = 100,min = 100, max = 1000, value = 800),
selectInput("plotTypeDiverDT", "Tree type",
c("Phylogram" = "phylogram", "Cladogram" = "cladogram", "Fan" = "fan", "Unrooted" = "unrooted", "Radial" = "radial", "tidy" = "Tidy" ), selected = "phylogram")
)
)
), hr(),
fluidRow(column(12,verbatimTextOutput("infoPanelDiverData")))
)
)
),
tabPanel("Analysis",
tabsetPanel(id = 'BasicDiverification',
tabPanel("Lineage Throught of Time",
fluidRow(
column(3, wellPanel(p('Ltt plot'),
checkboxInput('dropExtinct', 'Drop extinct tips from the tree',FALSE ),
checkboxInput('logLineages', 'plot on log-linear', FALSE ),
checkboxInput('GammaPybus', 'compute γ from Pybus & Harvey (2000;Proc.Roy.Soc.B)', FALSE ),
actionButton("runDiverLtt", "Run"),hr(),
p('MCCR test'),
textInput(inputId = 'RhoMCCRdiverLtt', 'Rho: Sampling fraction', '0.9'),
textInput(inputId = 'nsimMCCRdiverLtt', 'nsim', '1000'),
actionButton("runMCCRDiverLtt", "Run")
)
),
column(9,fluidRow(column(6,fluidRow(plotOutput(outputId = 'PhyloPlotDiver2', inline = T))),
column(6,fluidRow(plotOutput(outputId = 'PhyloPlotDiver3')),
fluidRow(plotOutput(outputId = 'PhyloPlotDiver4')))
),
wellPanel(fluidRow(column(4,selectInput('plotLttTree','Plot LTT over tree',choices = NULL),
selectInput('ploLttTreeLog','Plot log-lineage',choices = NULL)),
column(4,sliderInput("PlotWidthDiverLtt", "Tree width (px)",step = 100,min = 100, max = 1000, value = 400),
sliderInput("PlotHeightDiverLtt", "Tree height (px)",step = 100,min = 100, max = 1000, value = 800)),
column(4,sliderInput("tipSizeDiverLtt", "Tip label size",step = 0.1,min = 0, max = 3, value = 0.7),
actionButton('PlotEditorDiverLtt', 'Plot Editor'))
)
),hr(),
fluidRow(column(12,verbatimTextOutput("infoPanelDiverLtt")
)
)
)
)
),
tabPanel("Diversification models: ML",
fluidRow(
column(3, wellPanel( p('Set optimization method'),
selectInput(inputId = 'optModML',label = 'Method',choices = c('subplex', 'nminb', 'nlm','optim','minqa'),br()),
conditionalPanel('input.optModML == "optim"',
selectInput(inputId = 'optimModML',label = 'Algorithm',choices = c('Nelder-Mead', 'BFGS', 'CG', 'L-BFGS-B'))),
conditionalPanel('input.optModML == "minqa"',
selectInput(inputId = 'minqaModML',label = 'Algorithm',choices = c('newuoa', 'bobyqa', 'uobyqa'))),hr(),
p('Set models'),
checkboxInput(inputId = 'yuleModML',label = 'Pure Birth'),
conditionalPanel(condition = 'input.yuleModML == 1',
textInput(inputId = 'fractYuleModML',label = 'Rho',value = '1.0'),
textInput(inputId = 'BrateYuleModML',label = 'Speciation Rate',value = '0.1'),
checkboxInput(inputId = 'unresolYuModML', label = 'Unresolve tips?'),
actionButton(inputId = 'addYuleModML', label = 'add')),
checkboxInput(inputId = 'BDContModML',label = 'Birth-Death constant'),
conditionalPanel(condition = 'input.BDContModML == 1',
textInput(inputId = 'fractBDContModML',label = 'Rho',value = '0.9'),
p('Speciation & Extinction rates'),
rHandsontableOutput("BDrateModML"),
checkboxInput(inputId = 'unresolBDContModML', label = 'Unresolve tips?'),
actionButton(inputId = 'addBDContModML', label = 'add'), br()),
checkboxInput(inputId = 'BDvarSpeModML',label = 'Birth-Death variable: speciation'),
conditionalPanel(condition = 'input.BDvarSpeModML == 1',
textInput(inputId = 'fractBDvarSpeModML',label = 'Rho',value = '0.9'),
selectInput(inputId = 'distBDvarSpeModML',label = 'Distribution: Speciation rate',choices = c('Select' = 'select', 'linear.t' = 'linear.t', 'stepf.t' = 'stepf.t', 'spline.t' = 'spline.t', 'exp.t' = 'exp.t', 'sigmoid.t' = 'sigmoid.t' ), selected = NULL),
conditionalPanel("input.distBDvarSpeModML != 'select'",
rHandsontableOutput(outputId = "RateBDvarSpeModML")),
conditionalPanel("input.distBDvarSpeModML == 'spline.t'", fileInput("fileCSVSpeModML", "Load file ")),
checkboxInput(inputId = 'unresolBDvarSpeModML', label = 'Unresolve tips?'),
actionButton(inputId = 'addBDvarSpeModML', label = 'add'), br()),
checkboxInput(inputId = 'BDvarExtModML',label = 'Birth-Death variable: extinction'),
conditionalPanel(condition = 'input.BDvarExtModML == 1',
textInput(inputId = 'fractBDvarExtModML',label = 'Rho',value = '0.9'),
selectInput(inputId = 'distBDvarExtModML',label = 'Distribution: Extinction rate',choices = c('Select' = 'select', 'linear.t' = 'linear.t', 'stepf.t' = 'stepf.t', 'spline.t' = 'spline.t', 'exp.t' = 'exp.t', 'sigmoid.t' = 'sigmoid.t' ), selected = NULL),
conditionalPanel("input.distBDvarExtModML != 'select'",
rHandsontableOutput(outputId = "RateBDvarExtModML")),
conditionalPanel("input.distBDvarExtModML == 'spline.t'", fileInput("fileCSVExtModML", "Load file ")),
checkboxInput(inputId = 'unresolBDvarExtModML', label = 'Unresolve tips?'),
actionButton(inputId = 'addBDvarExtModML', label = 'add'), br()),
checkboxInput(inputId = 'BDvarSpeExtModML',label = 'Birth-Death variable: Spec. & Exti.'),
conditionalPanel(condition = 'input.BDvarSpeExtModML == 1',
textInput(inputId = 'fractBDvarSpeExtModML',label = 'Rho',value = '0.9'),
selectInput(inputId = 'distBDvarSpeExtModMLsp',label = 'Distribution: speciation rate',choices = c('Select' = 'select', 'linear.t' = 'linear.t', 'stepf.t' = 'stepf.t', 'spline.t' = 'spline.t', 'exp.t' = 'exp.t', 'sigmoid.t' = 'sigmoid.t' ), selected = NULL),
conditionalPanel("input.distBDvarSpeExtModMLsp != 'select'",
rHandsontableOutput(outputId = "RateBDvarSpeExtModMLsp")),
conditionalPanel("input.distBDvarSpeExtModMLsp == 'spline.t'", fileInput("fileCSVSpeExtModMLsp", "Load file ")),
selectInput(inputId = 'distBDvarSpeExtModMLex',label = 'Distribution: speciation rate',choices = c('Select' = 'select', 'linear.t' = 'linear.t', 'stepf.t' = 'stepf.t', 'spline.t' = 'spline.t', 'exp.t' = 'exp.t', 'sigmoid.t' = 'sigmoid.t' ), selected = NULL),
conditionalPanel("input.distBDvarSpeExtModMLex != 'select'",
rHandsontableOutput(outputId = "RateBDvarSpeExtModMLex")),
conditionalPanel("input.distBDvarSpeExtModMLex == 'spline.t'", fileInput("fileCSVSpeExtModMLsp", "Load file ")),
checkboxInput(inputId = 'unresolBDvarSpeExtModML', label = 'Unresolve tips?'),
actionButton(inputId = 'addBDvarSpeExtModML', label = 'add'), br()),
checkboxInput(inputId = 'CladoDepenModML',label = 'Clado-dependent model'),
checkboxInput(inputId = 'DiverDepentModML',label = 'Diversity-dependent model'),
conditionalPanel(condition = 'input.DiverDepentModML == 1',
selectInput(inputId = 'optModMLDDD',label = 'Optimization method',choices = c('subplex', 'simplex'),br()),
textInput(inputId = 'missnumDiverModML',label = 'Missing species',value = '1'),
selectInput(inputId = 'modelDiverModML', label = 'model of diversity-dependence', choices =
c('Linear: birth rate & K parameter' = '1',
'Linear: bith rate & K\' parameter' = '1.3',
'Positive: bith rate & K\' parameter + lambda' = '1.4',
'Negative & Positive: birth rate & K\' parameter + lambda' = '1.5',
'Exponential: birth rate & K parameter' = '2',
'Variant exponential: birth rate & offset at infinity' = '2.1',
'1/n: birth rate' = '2.2',
'Exponential birth rate & X parameter' = '2.3',
'Linear: death rate' = '3',
'Exponential: death rate' = '4',
'Variant exponential: death rate & offset at infinity' = '4.1',
'1/n: death rate & offset at infinity' = '4.2',
'Linear: birth & death rate' = '5'
)
),
actionButton(inputId = 'addDiverDepentModML', label = 'add'), br(),
),
selectInput(inputId = 'modelsFitModML', label = 'Models', choices = NULL, selected = NULL, multiple = T), hr(),
actionButton(inputId = 'ModelRunModML', label = 'RUN'), hr(),
checkboxInput(inputId = 'AICModML',label = 'AIC'), hr(),
radioButtons("exportModML", "Export output",c("R object (RDS)" = "RDSModML","TXT" = "TXTModML")),
downloadButton("downloadModML", "Download")
)
),
column(9,fluidRow(column(6, fluidRow(plotOutput(outputId = 'PhyloPlotDiver5', inline = T))),
column(6, fluidRow(plotOutput(outputId = 'PhyloPlotDiver6')))),
wellPanel(fluidRow(column(6,sliderInput("PlotWidthDiverModML", "Tree width (px)",step = 100,min = 100, max = 1000, value = 400),
sliderInput("PlotHeightDiverModML", "Tree height (px)",step = 100,min = 100, max = 1000, value = 800)),
column(6,sliderInput("tipSizeDiverModML", "Tip label size",step = 0.1,min = 0, max = 3, value = 0.7),
actionButton('PlotEditorDiverModML', 'Plot Editor'))),hr(),
fluidRow(column(12,verbatimTextOutput("infoPanelDiverModML")))))
)
)
)
)
))),
tabPanel("SSE Models")
),
tabPanel("Plot Edition"),
tabPanel("R code", verbatimTextOutput("Rcode")
)
)
)