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app.R
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app.R
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######################
### Be-Breeder 2.0 ###
######################
######################################################################################
######################################################################################
### ###
### Be-Breeder 2.0 is a R/Shiny application for statistical analysis and plant ###
### breeding developed by Prof. Dr. Roberto Fritsche Neto, Dr. Filipe Inacio ###
### Matias and PhD candidates Julia Silva Morosini and Fernando Garcia Espolador, ###
### who integrate the Laboratory of Allogamous Plant Breeding group - Department ###
### of Genetics, "Luiz de Queiroz"College of Agriculture, University of Sao Paulo, ###
### Brazil. ###
### ###
### This app is free for online use, just the intellectual property is reserved in ###
### periodicals by scientific citations of Be-Breeder papers. ###
### ###
### ###
### Contact: ###
### ###
### Avenida Padua Dias, 11 - Caixa Postal 83 ###
### CEP: 13418-900 - Piracicaba - Sao Paulo - Brasil ###
### Phone: 55 (19) 3429-4125 Line 45 ###
### ###
### E-mail: roberto.neto@usp.br ###
### filipematias23@usp.br ###
### julia.morosini@usp.br ###
### ###
### https://twitter.com/Alogamas_ESALQ ###
### http://www.genetica.esalq.usp.br/alogamas/index2.html ###
### ###
######################################################################################
######################################################################################
### Libraries ###
library(shiny)
library(shinydashboard)
library(Matrix)
library(lme4)
library(lmerTest)
library(agricolae)
library(rrBLUP)
library(adegenet)
library(poppr)
library(ape)
library(matrixcalc)
library(data.table)
library(cluster)
library(fpc)
library(stringr)
library(snpReady)
library(corrgram)
library(corrr)
library(tableHTML)
source("NCII.R")
source("diallels.R")
source("gardner.R")
##################
### Shiny - Ui ###
##################
# #####################################################################################################################################################################################
header <- dashboardHeader(title = "Be-Breeder 2.0",
titleWidth = 250)
# #####################################################################################################################################################################################
sidebar <- dashboardSidebar(
tags$head(tags$style(HTML('.main-header .logo {
font-family: "Georgia", Times, "Times New Roman", serif;
font-weight: bold;
font-size: 25px;
}'))),
width = 250,
sidebarUserPanel("User Menu:"),
sidebarMenu(
id = "tabs",
menuItem("Start", tabName = "start",icon = icon("cogs"), badgeLabel = "new", badgeColor = "green"),
menuItem("Learning",icon = icon("graduation-cap"),
menuSubItem("Inbreeding Effect", tabName = "Lear1", icon = icon("angle-double-right")),
menuSubItem("Qualitative x Quantitative", tabName = "Lear3", icon = icon("angle-double-right")),
menuSubItem("Progeny Size", tabName = "Lear4", icon = icon("angle-double-right")),
menuSubItem("Selection Effect (HWE)", tabName = "Lear5", icon = icon("angle-double-right")),
menuSubItem("Genetic Variance Components", tabName = "Lear6", icon = icon("angle-double-right")),
menuSubItem("Synthetic Pop. Construction", tabName = "Lear7", icon = icon("angle-double-right")),
menuItem("Recurrent Selection", icon = icon("angle-double-right"),
menuSubItem("Intrapopulation",tabName = "Lear8", icon = icon("angle-double-right")),
menuSubItem("Reciprocal",tabName = "Lear81", icon = icon("angle-double-right"))),
menuItem("Hybrids (Jenkins)",icon = icon("angle-double-right"),
menuSubItem("Hybrid Prediction", tabName = "Lear91", icon = icon("angle-double-right")),
menuSubItem("Number of Hybrids", tabName = "Lear92", icon = icon("angle-double-right"))),
menuSubItem("Genotype x Environment", tabName = "Lear10", icon = icon("angle-double-right")),
menuSubItem("Heterosis", tabName = "Lear11", icon = icon("angle-double-right")),
menuSubItem("Tester Effect", tabName = "Lear12", icon = icon("angle-double-right")),
menuSubItem("Genetic Drift", tabName = "Lear13", icon = icon("angle-double-right")),
menuSubItem("Indirect Selection", tabName = "Lear14", icon = icon("angle-double-right")),
menuSubItem("Residual Effect on Selection", tabName = "Lear15", icon = icon("angle-double-right")),
menuSubItem("Replicates vs Population size", tabName = "Lear16", icon = icon("angle-double-right")),
menuSubItem("Economics in Plant Breeding", tabName = "Lear17", icon = icon("angle-double-right")),
menuSubItem("Linkage Disequilibrium (LD)", tabName = "Lear18", icon = icon("angle-double-right")),
menuSubItem("Cycles to Reduce LD", tabName = "Lear19", icon = icon("angle-double-right"))),
menuItem("Phenotypic Breeding", icon = icon("leaf"),
menuItem("Experimental Analysis", icon = icon("angle-double-right"),
menuSubItem("", tabName = "subitem11", icon = icon("th")),
menuSubItem("Statistical Model", tabName = "subitem12")),
menuItem("Diallel Analysis", icon = icon("venus-mars"),
menuItem("Griffing Design",icon = icon("angle-double-right"),
menuSubItem("Dataset",tabName ="subitem1311"),
menuSubItem("Analysis",tabName ="subitem1312")),
menuItem("Gardner and Eberhart Design",icon = icon("angle-double-right"),
menuSubItem("Dataset",tabName ="subitem1321"),
menuSubItem("Analysis",tabName ="subitem1322")),
menuItem("Factorial Design",icon = icon("angle-double-right"),
menuSubItem("Dataset",tabName ="subitem1331"),
menuSubItem("Analysis",tabName ="subitem1332"))),
menuItem("Index Selection", icon = icon("angle-double-right"),
menuSubItem("Index File",tabName ="subitem141"),
menuSubItem("Index Analysis",tabName ="subitem142")),
menuItem("Correlation Analysis",icon = icon("angle-double-right"),
menuSubItem("File Input",tabName ="subitem151"),
menuSubItem("Coefficients and graphs",tabName ="subitem152")),
menuItem("Path Analysis",icon = icon("angle-double-right"),
menuSubItem("Trait File",tabName ="subitem161"),
menuSubItem("Path Analysis",tabName ="subitem162")),
menuItem("Biplot Analysis",icon = icon("angle-double-right"),
menuSubItem("Dataset",tabName ="subitem171"),
menuSubItem("GE Biplot",tabName ="subitem172"),
menuSubItem("GE Cluster",tabName ="subitem174")),
menuItem("Experiment Designs",icon = icon("angle-double-right"),
menuSubItem("Designs",tabName ="subitem18"))),
menuItem("Molecular Breeding", icon = icon("sitemap"),
menuItem("Genotyping Data",icon = icon("wrench"),
menuItem("Quality Control", icon = icon("angle-double-right"),
menuSubItem("Sample Set",tabName = "mol121", icon = icon("angle-double-right")),
menuSubItem("HapMap",tabName = "mol1212", icon = icon("angle-double-right")),
menuSubItem("Raw Data",tabName = "mol122", icon = icon("angle-double-right"))),
menuItem("Kinship Matrix", icon = icon("angle-double-right"),
menuSubItem("Z Matrix",tabName = "mol11", icon = icon("angle-double-right")),
menuSubItem("Kinship Matrix", tabName = "mol13", icon = icon("angle-double-right")))),
menuItem("Genomic Selection (GS)",icon = icon("angle-double-right"),
menuItem("GS analysis",icon = icon("angle-double-right"),
menuSubItem("Phenotypic file", tabName = "mol21", icon = icon("angle-double-right")),
menuSubItem("Z Matrix", tabName = "mol22", icon = icon("angle-double-right")),
menuSubItem("rrBLUP", tabName = "mol23", icon = icon("angle-double-right"))),
menuItem("Prediction and Selection",icon = icon("angle-double-right"),
menuSubItem("Marker effect", tabName = "mol241", icon = icon("angle-double-right")),
menuSubItem("Z Matrix", tabName = "mol242", icon = icon("angle-double-right")),
menuSubItem("Selection", tabName = "mol243", icon = icon("angle-double-right")))),
menuItem("Genomic Association (GWAS)",icon = icon("angle-double-right"),
menuSubItem("Phenotypic file", tabName = "mol31", icon = icon("angle-double-right")),
menuSubItem("HapMap|t(Z)", tabName = "mol32", icon = icon("angle-double-right")),
menuSubItem("Scores", tabName = "mol33", icon = icon("angle-double-right")),
menuSubItem("Manhattan plot", tabName = "mol34", icon = icon("angle-double-right"))),
menuItem("Diversity Analysis",icon = icon("angle-double-right"),
menuItem("Genetic Diversity",icon = icon("angle-double-right"),
menuSubItem("Dataset",tabName = "mol41",icon = icon("angle-double-right")),
menuSubItem("Diversity Summary",tabName = "mol42",icon = icon("angle-double-right")),
menuSubItem("Graphs",tabName = "mol43",icon = icon("angle-double-right"))),
menuItem("Discriminant Analysis",icon = icon("angle-double-right"),
menuSubItem("Dataset",tabName = "mol61",icon = icon("angle-double-right")),
menuSubItem("Graphs",tabName = "mol62",icon = icon("angle-double-right"))),
menuItem("Population Genetics",icon = icon("angle-double-right"),
menuSubItem("Subpopulation Groups",tabName = "mol51",icon = icon("angle-double-right")),
menuSubItem("Z Matrix",tabName = "mol52",icon = icon("angle-double-right")),
menuSubItem("PopGen Analysis",tabName = "mol53",icon = icon("angle-double-right"))))),
menuItem("Information", icon = icon("info-circle"),
menuSubItem("About Be-Breeder 2.0", tabName = "info1", icon = icon("angle-double-right")),
menuSubItem("Please cite us", tabName = "info2", icon = icon("angle-double-right")),
menuSubItem("Team Contact", tabName = "info3", icon = icon("angle-double-right"))),
menuItem(" ",icon = icon("angle-right"), badgeLabel = "Download Manual",badgeColor = "red",href = "http://vencovsky.esalq.usp.br:3838/shiny/manual/Manual_BeBreeder.pdf"),
htmlTemplate("flagC.html",align = "center")
))
# #####################################################################################################################################################################################
body <- dashboardBody(
tabItems(
# #####################################################################################################################################################################################
tabItem("start", box(status = "primary", height = 700, width = 600, align = "center",
fluidRow(
infoBox(hr(), "Home Page",icon=icon("home"), fill = T, color = "aqua",
href = "http://www.genetica.esalq.usp.br/alogamas/index2.html"),
infoBox(hr(), "USP Page",icon=icon("users"), fill = T, color = "aqua",
href = "http://www.en.esalq.usp.br"),
infoBox(hr(), "Twitter Page",icon=icon("twitter"), fill = T, color = "aqua",
href = "https://twitter.com/Alogamas_ESALQ?ref_src=twsrc%5Etfw")),
br(),
tags$style(make_css(list('.box',
c('text-align','font-size', 'font-family', 'color'),
c('top','25px', 'arial', 'red')))),
strong("version 2.0: NEW FEATURES AVAILABLE!"),
br(),
br(),
a(id = "web_button", class = "btn action_button",
href = "http://vencovsky.esalq.usp.br:3838/shiny/manual/Manual_BeBreeder.pdf",
img(src="logobb19.jpg", height = 320, width = 950, align = "center"))
)),
# #####################################################################################################################################################################################
# Learning
# #####################################################################################################################################################################################
tabItem("Lear1",
fluidPage(
titlePanel("Inbreeding Effect"),
h4(em("In here, one can observe the fluctuation in additive and dominance genetic variances between and within populations as a function of the inbreeding coefficient
(Wright's F statistics), and visualize how the genotype frequencies change according to the level of self-generation", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
selectInput("Lear1.1", "Self-Generation:",
choices = c("F1","F2","F3","F4","F5","F6","F7","F8","F9","F.inf"),width = 150),
sliderInput("Lear1.2","Wright's inbreeding coefficient (F)",0,1,0),
tableOutput("cont.Lear.1.0"),
helpText("ABOUT:"),
helpText('The results are given using the following equations:'),
img(src='Lear1.jpg',height = 200, width = 170)),
mainPanel(plotOutput("cont.Lear.1"))))),
# ######################################################################################################################################################################################
tabItem("Lear3",
fluidPage(
titlePanel("Qualitative x Quantitative"),
h4(em("In here, one can simulate the genetic structure of a trait, choosing the number of genes with dominance, partial dominance, and additive effects. The aim is to
observe how the intra-allelic interactions influence the number of phenotypic classes and the frequency of each class in the population", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
sliderInput("Lear3.1", "Number of dominant genes",0,30,15,step =1),
sliderInput("Lear3.2", "Number of partial dominant genes",0,30,10,step =1),
sliderInput("Lear3.3", "Number of additive genes",0,30,15,step =1)),
mainPanel(plotOutput("cont.Lear.3"))))),
# ######################################################################################################################################################################################
tabItem("Lear4",
fluidPage(
titlePanel("Progeny Size"),
h4(em("In here, one can estimate the number of individuals to be evaluated in the progeny in order to obtain a genotype carrying a trait of interest controled by n genes in a
population that has undergone m inbreeding generations, with a certain probability (P)", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
numericInput("Lear4.1","Number of Genes (n)",min = 0,value = 0),
numericInput("Lear4.2","Self-Generation (m)",min = 0,value = 0),
sliderInput("Lear4.3", "Precision (P)",0,1,0.95),
helpText("ABOUT:"),
helpText("Progeny size is given by 'nº', calculated as:"),
img(src='Lear4.jpg',height = 150, width = 160)),
tableOutput("cont.Lear.4")))),
#verbatimTextOutput("cont.Lear.4")))),
# ######################################################################################################################################################################################
tabItem("Lear5",
fluidPage(
titlePanel("Selection Effect (HWE)"),
h4(em("In here, one can simulate different scenarios to understand how a locus with 2 alleles is affected by selection regarding the Hardy-Weinberg equilibrium (HWE) according to
the number of genotypes (original and selected), their correspondent phenotypic value, the inbreeding rate, and the broad-sense heritability", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
numericInput("Lear5.2","Number of AA genotype",min = 0,value = 1),
numericInput("Lear5.3","Number of Aa genotype",min = 0,value = 0),
numericInput("Lear5.4","Number of aa genotype",min = 0,value = 0),
sliderInput("Lear5.41","Rate of Inbreeding",0,1,0),
numericInput("Lear5.5","Yield of AA",min = 0,value = 0),
numericInput("Lear5.6","Yield of Aa",min = 0,value = 0),
numericInput("Lear5.7","Yield of aa",min = 0,value = 0),
sliderInput("Lear5.11", "Heritability",0,1,1),
numericInput("Lear5.8","Number of AA selected",min = 0,value = 0),
numericInput("Lear5.9","Number of Aa selected",min = 0,value = 0),
numericInput("Lear5.10","Number of aa selected",min = 0,value = 0),
helpText("ABOUT:"),
helpText("Results are calculated using the following equations:"),
img(src='Lear5.jpg',height = 160, width = 230),
helpText("DS = selection differential"),
helpText("SG = selection gain (response to selection)")),
mainPanel(
#textOutput("con.Lear.5.01"),
htmlOutput("phr1"),
tableOutput("cont.Lear.5.0"),
htmlOutput("phr2"),
tableOutput("cont.Lear.5.1"),
htmlOutput("phr3"),
tableOutput("cont.Lear.5.2"),
htmlOutput("phr4"),
tableOutput("cont.Lear.5.3"),
htmlOutput("phr5"),
tableOutput("cont.Lear.5.4"),
htmlOutput("phr6"),
tableOutput("cont.Lear.5.5"))))),
#verbatimTextOutput("cont.Lear.5")))),
# ######################################################################################################################################################################################
tabItem("Lear6",
fluidPage(
titlePanel("Genetic Variance Components"),
h4(em("In here, one can set up the additive (a) and dominance (d) effects of a locus with two alleles (p and q) in order to observe how they impact on
the magnitude and relationship among the genetic variance components", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
sliderInput("Lear6.2","Frequency of allele (p)",0,1,0.6),
sliderInput("Lear6.1","Dominance Effect (d)",0,2.5,0.5),
sliderInput("Lear6.3","Additive Effect (a)",0,1,0.3),
#verbatimTextOutput("cont.Lear.6.1")),
helpText("ABOUT:"),
helpText("Results are calculated using the following equations:"),
img(src='Lear6.1.jpg',height = 200, width = 200),
helpText("add = average degree of dominance")),
mainPanel(plotOutput("cont.Lear.6"),
tableOutput("cont.Lear.6.1"))))),
# ######################################################################################################################################################################################
tabItem("Lear7",
fluidPage(
titlePanel("Constructing Synthetic Populations"),
h4(em("In here, the aim is to visualize how the number of alleles of a gene relates to genetic variability due to heterozigosity. The user provides the number of alleles
and their respective initial frequencies in the composition of the population.", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
sliderInput("Lear7.1","Number of alleles",0,10,10,step = 1),
textAreaInput("Lear7.2","Frequency of each allele (Sum = 1.0)",
value = "0.1,\n0.1,\n0.1,\n0.1,\n0.1,\n0.1,\n0.1,\n0.1,\n0.1,\n0.1",
rows = 10, width = 80)),
mainPanel(
tableOutput("cont.Lear.7"),
helpText("ABOUT:"),
helpText("Results are calculated using the following equations:"),
img(src='Lear7.jpg',height = 150, width = 250))
))),
#verbatimTextOutput("cont.Lear.7")))),
# ######################################################################################################################################################################################
tabItem("Lear8",
fluidPage(
titlePanel("Intrapopulation Recurrent Selection"),
h4(em("Considering the IRS breeding scheme, the user can simulate different selection scenarios defining the evaluation and recombination units and derived parameters to obtain
the estimates of response to selection, effective size of the population (Ne), and inbreeding coefficient (Wright'F)", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
radioButtons('Lear8.1', '| Evaluation/Recombination | c | D1 | Ne |',
c("| HS/HS | 1/4 | 0 | 4 |"='MI/MI',
"| HS/S1 | 1/2 | 0 | 1 |"='MI/S1',
"| FS/FS | 1/2 | 0 | 2 |"='IC/IC',
"| FS/S1 | 1/2 | 0 | 1 |"='IC/S1',
"| S1/S1 | 1 |1/2| 1 |"='S1/S1',
"| S2/S2 | 3/2 |5/4| 2/3 |"='S2/S2'),
'MI/MI'),
numericInput("Lear8.2","Number of Progenies Evaluated",min = 0,value = 0),
sliderInput("Lear8.3","Inbreeding Depression",0,1,0),
sliderInput("Lear8.4","Heritability",0,1,0),
sliderInput("Lear8.5","Selection Intensity",0,50,0,step = 1),
sliderInput("Lear8.6","Number of cycles",1,20,1,step = 1),
sliderInput("Lear8.7","Cycle Interval (year)",0.2,7,1,step = 0.1),
helpText("ABOUT:"),
helpText("Results are calculated using the following equation:"),
img(src='Lear8.jpg',width = 250,height = 110)),
mainPanel(tableOutput("cont.Lear.8a1"),
plotOutput("cont.Lear.8g"))))),
# ######################################################################################################################################################################################
tabItem("Lear81",
fluidPage(
titlePanel("Reciprocal Recurrent Selection"),
h4(em("Considering the RRS breeding scheme, the user can simulate different selection scenarios defining the evaluation and recombination units and derived parameters to obtain
the estimates of response to selection, effective size of the population (Ne) for each group, and inbreeding coefficient (Wright'F) for each group", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
radioButtons('Lear81.1', '| Evaluation/Recombination | c | Ne |',
c("| HS/HS | 1/8 | 4 |"='MI/MI',
"| HS/S1 | 1/4 | 1 |"='MI/S1',
"| TC/HS | 1/16| 4 |"='TC/MI',
"| FS/S1 | 1/4 | 1 |"='IC/S1'),
'MI/MI'),
numericInput("Lear81.21","Number of Progenies - Group 1",min = 0,value = 0),
numericInput("Lear81.22","Number of Progenies - Group 2",min = 0,value = 0),
sliderInput("Lear81.41","Heritability - Group 1",0,1,0),
sliderInput("Lear81.42","Heritability - Group 2",0,1,0),
sliderInput("Lear81.51","Selection Intensity (i1)",1,50,1,step = 1),
sliderInput("Lear81.52","Selection Intensity (i2)",1,50,1,step = 1),
sliderInput("Lear81.6","Number of cycles",1,20,1,step = 1),
sliderInput("Lear81.7","Cycle Interval (year)",0.2,7,1,step = 0.1),
helpText("ABOUT:"),
helpText("Results are calculated using the following equation:"),
img(src='Lear8.1.jpg',width = 250,height = 110)),
mainPanel(tableOutput("cont.Lear.8.1"),
plotOutput("cont.Lear.81g"))))),
# ######################################################################################################################################################################################
tabItem("Lear91",
fluidPage(
titlePanel("Hybrid Prediction"),
h4(em("The user can obtain the predicted value for three-way hybrids (TH) and double-cross hybrids (DH) through the input of a .txt file
containing the mean phenotypic values for the single-cross hybrids (SH)", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
fileInput('file.L9', 'Choose File:',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv',".txt")),
tags$hr(),
checkboxInput('header.L9', 'Header', FALSE),
radioButtons('sep.L9', 'Separator',
c(Comma=',',
Semicolon=';',
Tab='\t'),
','),
radioButtons('quote.L9', 'Quote',
c(None='',
'Double Quote'='"',
'Single Quote'="'"),
''),
selectInput("Lear91.out", "Look Options:",
choices = c("Table",
"Three-way Cross Hybrids Prediction",
"Double Cross Hybrids Prediction")),
checkboxInput("ex.L.9","Example", FALSE),
helpText("ABOUT:"),
helpText("Results are calculated using the following equation:"),
img(src='Lear9.1.jpg',width = 300,height = 150)),
tableOutput("cont.Lear.9.1")))),
# ######################################################################################################################################################################################
tabItem("Lear92",
fluidPage(
titlePanel("Number of Hybrids"),
h4(em("The user can obtain the potential number of single-cross hybrids (SH), three-way hybrids (TH), and double-cross hybrids (DH), given the number of lines in a
breeding population (either for one or two heterotic groups)", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
selectInput("Lear9.2.1", "Population Structure",
choices = c("One Heterotic Group",
"Two Heterotic Groups")),
# uiOutput("res3.lear92"),
numericInput("Lear9.2.2","Number of Lines", min = 0,value = 0),
numericInput("Lear9.2.3","Number of Lines in Group 1", min = 0,value = 0),
numericInput("Lear9.2.4","Number of Lines in Group 2", min = 0,value = 0),
helpText("ABOUT:"),
helpText("Results are calculated using the following equations:"),
img(src='Lear9.2.jpg',height = 300, width = 220)),
tableOutput("cont.Lear.9.2")))),
# ######################################################################################################################################################################################
tabItem("Lear10",
fluidPage(
titlePanel("Genotype x Environment"),
h4(em("In here, one can simulate different degrees of interaction considering three genotypes and two environments in order to verify how the GxE interaction influences the variances
and the broad-sense heritability", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
sliderInput("Lear10.7","Coefficient of Variation (CV)",5,20,5),
sliderInput("Lear10.8","Number of Repetitions (r)",1,4,1,step = 1),
sliderInput("Lear10.1","Yield of Genotype 1 in Environment 1",0,5,0),
sliderInput("Lear10.2","Yield of Genotype 1 in Environment 2",0,5,0),
sliderInput("Lear10.3","Yield of Genotype 2 in Environment 1",0,5,0),
sliderInput("Lear10.4","Yield of Genotype 2 in Environment 2",0,5,0),
sliderInput("Lear10.5","Yield of Genotype 3 in Environment 1",0,5,0),
sliderInput("Lear10.6","Yield of Genotype 3 in Environment 2",0,5,0),
helpText("ABOUT:"),
helpText("Equations for this tab are detailed on GitHub:", a(href="https://github.com/filipematias23/Be-Breeder/", "https://github.com/filipematias23/Be-Breeder/", target="_blank"))),
mainPanel(htmlOutput("phr10.1"),
tableOutput("cont.Lear.10a.1"),
htmlOutput("phr10.2"),
tableOutput("cont.Lear.10a.2"),
htmlOutput("phr10.3"),
tableOutput("cont.Lear.10a.3"),
plotOutput("cont.Lear.10.2"))))),
# ######################################################################################################################################################################################
tabItem("Lear11",
fluidPage(
titlePanel("Heterosis"),
h4(em("The aim in here is to understand how the heterosis fluctuates according to the number of genes, the dominance deviation, and the genetic divergence between
the parents (lines) for the simulated hybrids", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
sliderInput("Lear11.1","Number of Genes",0,100,0, step = 10),
sliderInput("Lear11.2","Dominance Deviation (d)",0,1,0, step = 0.1),
sliderInput("Lear11.3","Genetic Divergence",0,1,0, step = 0.1),
helpText("ABOUT:"),
helpText("Results are calculated using the following equations:"),
img(src='Lear11.jpg',height = 200, width = 150)),
tableOutput("cont.Lear.11")))),
# #####################################################################################################################################################################################
tabItem("Lear12",
fluidPage(
titlePanel("Tester Effect"),
h4(em("In here, the user can determine the effect of testers in a experimental condition in order to verify their impacts on the genetic variability", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
sliderInput("Lear12.1","Frequency of allele (p)",0,1,0),
sliderInput("Lear12.2","r",0,1,0),
sliderInput("Lear12.3","Additive Effect (a)",0,1,0),
sliderInput("Lear12.4","Dominance Effect (d)",0,2,0, step = 0.1),
sliderInput("Lear12.5","Inbreeding coefficient (F)",0,1,0),
verbatimTextOutput("cont.Lear.12.1"),
helpText("ABOUT:"),
helpText("Equations for this tab are detailed on GitHub:", a(href="https://github.com/filipematias23/Be-Breeder/", "https://github.com/filipematias23/Be-Breeder/", target="_blank"))),
mainPanel(plotOutput("cont.Lear.12"))))),
# mainPanel(tableOutput("cont.Lear.12.1"),
# plotOutput("cont.Lear.12"))))),
# #####################################################################################################################################################################################
tabItem("Lear13",
fluidPage(
titlePanel("Genetic Drift"),
h4(em("In here, one can understand how the occurence of genetic drift is influenced by the frequency of the allele 'a' (q) and the selection intensity adopted. From that,
is is possible to estimate how many generations are needed to eliminate this allele", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
sliderInput("Lear13.1","Frequency of allele 'a' (q)",0,1,0),
sliderInput("Lear13.2","Selection Intensity",0,1,0.1),
verbatimTextOutput("cont.Lear.13.1"),
helpText("ABOUT:"),
helpText("Equations for this tab are detailed on GitHub:", a(href="https://github.com/filipematias23/Be-Breeder/", "https://github.com/filipematias23/Be-Breeder/", target="_blank"))),
mainPanel(plotOutput("cont.Lear.13"))))),
# #####################################################################################################################################################################################
tabItem("Lear14",
fluidPage(
titlePanel("Indirect Selection"),
h4(em("In here, the user can verify the possibility of selecting a trait based on another, which is called Indirect selection. Providing the values for the parameters
requested, it is possible to calculate the response to the indirect selection", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
sliderInput("Lear14.1","Heritability of trait 'x'",0,1,0),
sliderInput("Lear14.2","Correlation between 'x' and 'y'",0,1,0),
numericInput("Lear14.3","Number of individuals evaluated",min = 0,value = 10),
numericInput("Lear14.4","Number of individuals selected",min = 0,value = 0),
helpText("ABOUT:"),
helpText("Equations for this tab are detailed on GitHub:", a(href="https://github.com/filipematias23/Be-Breeder/", "https://github.com/filipematias23/Be-Breeder/", target="_blank"))),
mainPanel(tableOutput("cont.Lear.14.1"),
plotOutput("cont.Lear.14"))))),
# #####################################################################################################################################################################################
tabItem("Lear15",
fluidPage(
titlePanel("Residual Effect on Selection"),
h4(em("The aim in this tab is to analyze if the selection process in a breeding population is being reliable and capturing the best breeding values. Among other variables,
it is displayed the genetic variability (GV) for each scenario", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
numericInput("Lear15.1","Number of individuals evaluated",min = 0,value = 10),
sliderInput("Lear15.2","Selection Intensity (%)",0,20,0),
sliderInput("Lear15.3","Heritability",0,1,0),
helpText("ABOUT:"),
helpText("Equations for this tab are detailed on GitHub:", a(href="https://github.com/filipematias23/Be-Breeder/", "https://github.com/filipematias23/Be-Breeder/", target="_blank"))),
tableOutput("cont.Lear.15")))),
# #####################################################################################################################################################################################
tabItem("Lear16",
fluidPage(
titlePanel("Replicates vs Population size"),
h4(em("In here, the user here may infer what the impact of the number of replicates on the population size is, and especially, what is the increment of that
on the response to selection (RS), simulating different scenarios in function of the parameters above", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
sliderInput("Lear16.1","Number of replicates",1,5,1),
numericInput("Lear16.2","Number of plots available",min = 0,value = 0),
numericInput("Lear16.3","Number of genotypes selected",min = 0,value = 0),
sliderInput("Lear16.4","Trait Heritability",0,1,0),
verbatimTextOutput("cont.Lear.16.1"),
helpText("ABOUT:"),
helpText("Equations for this tab are detailed on GitHub:", a(href="https://github.com/filipematias23/Be-Breeder/", "https://github.com/filipematias23/Be-Breeder/", target="_blank"))),
mainPanel(plotOutput("cont.Lear.16"))))),
# #####################################################################################################################################################################################
tabItem("Lear17",
fluidPage(
titlePanel("Economics in Plant Breeding"),
h4(em("In here, the aim is to provide a broader framework of a breeding process, considering the cost spent per plot, the viability, and the expected genetic gain. By that,
the user can observe the influence of the nature of the trait and the experimental size on the total costs", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
numericInput("Lear17.1","Number of genotypes evaluated",min = 0,value = 10),
numericInput("Lear17.2","Number of genotypes selected",min = 0,value = 0),
sliderInput("Lear17.3","Trait Heritability",0,1,0),
sliderInput("Lear17.4","Number of replicates",1,5,1),
sliderInput("Lear17.5","Time (year/cycle)",0.2,7,0.2),
numericInput("Lear17.6","Cost to evaluate one plot (U$)",min = 0,value = 10),
verbatimTextOutput("cont.Lear.17.1"),
helpText("ABOUT:"),
helpText("Equations for this tab are detailed on GitHub:", a(href="https://github.com/filipematias23/Be-Breeder/", "https://github.com/filipematias23/Be-Breeder/", target="_blank"))),
mainPanel(plotOutput("cont.Lear.17"))))),
# ######################################################################################################################################################################################
tabItem("Lear18",
fluidPage(
titlePanel("Linkage Disequilibrium (LD)"),
h4(em("In here, one can simulate different conditions informing the frequencies of the haplotypes AB, Ab, aB, and ab, and the rates of the alleles A, a, B,
and b. The application will then estimate whether the loci are independent", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
sliderInput("Lear18.1","Frequency of haplotype AB",0,1,0),
sliderInput("Lear18.2","Frequency of haplotype Ab",0,1,0),
sliderInput("Lear18.3","Frequency of haplotype aB",0,1,0),
uiOutput('ui.lear18.1'),
sliderInput("Lear18.5","Frequency of A",0,1,0),
uiOutput('ui.lear18.2'),
sliderInput("Lear18.7","Frequency of B",0,1,0),
uiOutput('ui.lear18.3')),
mainPanel(tableOutput("cont.Lear.18"),
helpText("ABOUT:"),
helpText("Equations for this tab are detailed on GitHub:", a(href="https://github.com/filipematias23/Be-Breeder/", "https://github.com/filipematias23/Be-Breeder/", target="_blank")))))),
# ######################################################################################################################################################################################
tabItem("Lear19",
fluidPage(
titlePanel("Cycles to Reduce LD"),
h4(em("In here, combining the loss of linkage disequilibrium (LD) aimed to the recombination ratio between loci in a population, it is possible to compute how many cycles are
needed to dissipate the LD", style = "color:gray")),
br(),
sidebarLayout(
sidebarPanel(
sliderInput("Lear19.1","Loss of LD (%)",0,100,5),
sliderInput("Lear19.2","Recombination fraction between loci",0,0.5,0.05),
verbatimTextOutput("cont.Lear.19.1"),
helpText("ABOUT:"),
helpText("Equations for this tab are detailed on GitHub:", a(href="https://github.com/filipematias23/Be-Breeder/", "https://github.com/filipematias23/Be-Breeder/", target="_blank"))),
mainPanel(plotOutput("cont.Lear.19"))))),
# ######################################################################################################################################################################################
# Phenotypic Breeding
# ######################################################################################################################################################################################
tabItem("subitem11",
fluidPage(
titlePanel("Uploading Files"),
sidebarLayout(
sidebarPanel(
fileInput('file1', 'Choose File:',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv',".txt")),
tags$hr(),
checkboxInput('header', 'Header', FALSE),
radioButtons('sep', 'Separator',
c(Comma=',',
Semicolon=';',
Tab='\t'),
','),
radioButtons('quote', 'Quote',
c(None='',
'Double Quote'='"',
'Single Quote'="'"),
''),
selectInput("table.1", "Look Options:",
choices = c("Table","Data Structure","Names"),width = 150),
checkboxInput("info.11",strong(code("HELP")), FALSE),
checkboxInput("ex.11","Example", FALSE)),
verbatimTextOutput("contents11")))),
# #####################################################################################################################################################################################
tabItem("subitem12",
fluidPage(
titlePanel("Statistical Model"),
sidebarLayout(
sidebarPanel(
checkboxInput('res.12.name', 'Sources of Variation', FALSE),
textInput("model","Type the Statistical Model", width = 700,
value = "y~Block+Site+(1|Genotype)+(1|Genotype:Site)"),
checkboxInput('ml', 'ML(Default = REML)', FALSE),
checkboxInput('res.12.fix', 'Genotype as Fixed (Default = Random)', FALSE),
actionButton("res.12.run","run",icon = icon("hand-o-up")),
selectInput("res.12.1", "Choose Results:",
choices = c("Mean",
"Summary",
"ANOVA",
"Analysis of Deviance",
"BLUE","Adjusted Means",
"BLUP","Predicted Means"),width = 200),
sliderInput("res.12.2", "Selection Intensity",0,100,100),
textInput("name.txt.12","Type the File Name"),
downloadButton('downloadData12', 'Download'),
checkboxInput("info.12",strong(code("HELP")), FALSE)),
verbatimTextOutput("contents12")))),
# #####################################################################################################################################################################################
tabItem("subitem1311",
fluidPage(
titlePanel("Uploading Files"),
sidebarLayout(
sidebarPanel(
fileInput('file1311', 'Choose File.txt',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv',".txt")),
tags$hr(),
checkboxInput('header1311', 'Header', FALSE),
radioButtons('sep1311', 'Separator',
c(Comma=',',
Semicolon=';',
Tab='\t'),
','),
radioButtons('quote1311', 'Quote',
c(None='',
'Double Quote'='"',
'Single Quote'="'"),
''),
checkboxInput("info.1311",strong(code("HELP")), FALSE),
checkboxInput("ex.1311","Example", FALSE)),
verbatimTextOutput("contents1311")))),
# #####################################################################################################################################################################################
tabItem("subitem1321",
fluidPage(
titlePanel("Uploading Files"),
sidebarLayout(
sidebarPanel(
fileInput('file1321', 'Choose File.txt',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv',".txt")),
tags$hr(),
checkboxInput('header1321', 'Header', FALSE),
radioButtons('sep1321', 'Separator',
c(Comma=',',
Semicolon=';',
Tab='\t'),
','),
radioButtons('quote1321', 'Quote',
c(None='',
'Double Quote'='"',
'Single Quote'="'"),
''),
checkboxInput("info.1321",strong(code("HELP")), FALSE),
checkboxInput("ex.1321","Example", FALSE)),
verbatimTextOutput("contents1321")))),
# #####################################################################################################################################################################################
tabItem("subitem1331",
fluidPage(
titlePanel("Uploading Files"),
sidebarLayout(
sidebarPanel(
fileInput('file1331', 'Choose File.txt',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv',".txt")),
tags$hr(),
checkboxInput('header1331', 'Header', FALSE),
radioButtons('sep1331', 'Separator',
c(Comma=',',
Semicolon=';',
Tab='\t'),
','),
radioButtons('quote1331', 'Quote',
c(None='',
'Double Quote'='"',
'Single Quote'="'"),
''),
checkboxInput("info.1331",strong(code("HELP")), FALSE),
checkboxInput("ex.1331","Example", FALSE)),
verbatimTextOutput("contents1331")))),
# #####################################################################################################################################################################################
tabItem("subitem1312",
fluidPage(
titlePanel("Griffing Design"),
sidebarLayout(
sidebarPanel(
selectInput("res.1312", "Choose Results:",
choices = c("Output")),
textInput("name.txt.1312","Type the Name File"),
downloadButton('downloadData1312', 'Download'),
checkboxInput("info.1312",strong(code("HELP")), FALSE)),
verbatimTextOutput("contents1312")))),
# #####################################################################################################################################################################################
tabItem("subitem1322",
fluidPage(
titlePanel("Gardner and Eberhart Design"),
sidebarLayout(
sidebarPanel(
selectInput("res.1322", "Choose Results:",
choices = c("Output")),
textInput("name.txt.1322","Type the Name File"),
downloadButton('downloadData1322', 'Download'),
checkboxInput("info.1322",strong(code("HELP")), FALSE)),
verbatimTextOutput("contents1322")))),
# #####################################################################################################################################################################################
tabItem("subitem1332",
fluidPage(
titlePanel("Factorial Design"),
sidebarLayout(
sidebarPanel(
selectInput("res.1332", "Choose Results:",
choices = c("Output")),
textInput("name.txt.1332","Type the Name File"),
downloadButton('downloadData1332', 'Download'),
checkboxInput("info.1332",strong(code("HELP")), FALSE)),
verbatimTextOutput("contents1332")))),
# #####################################################################################################################################################################################
tabItem("subitem141",
fluidPage(
titlePanel("Index Selection"),
sidebarLayout(
sidebarPanel(
fileInput('file14', 'Choose File',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv',".txt")),
tags$hr(),
checkboxInput('header.14', 'Header', FALSE),
radioButtons('sep.14', 'Separator',
c(Comma=',',
Semicolon=';',
Tab='\t'),
','),
radioButtons('quote.14', 'Quote',
c(None='',
'Double Quote'='"',
'Single Quote'="'"),
''),
checkboxInput("info.141",strong(code("HELP")), FALSE),
checkboxInput("ex.14","Example", FALSE)),
verbatimTextOutput("contents14.1")))),
# #####################################################################################################################################################################################
tabItem("subitem142",
fluidPage(
titlePanel("Index Analysis"),
sidebarLayout(
sidebarPanel(
checkboxInput('res.14.name', 'Trait Names', FALSE),
textInput("vec.14", "Type a vector with weights (comma delimited)", "0.3,-0.5,0.1,-0.1"),
sliderInput("res.14", "Selection Intensity",0,100,100),
textInput("name.txt.14","Type the File Name"),
downloadButton('downloadData14', 'Download'),
checkboxInput("info.142",strong(code("HELP")), FALSE)),
verbatimTextOutput("contents14.2")))),
# #####################################################################################################################################################################################
tabItem("subitem151",
fluidPage(
titlePanel("Uploading Files"),
sidebarLayout(
sidebarPanel(
fileInput('file15', 'Choose File.txt',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv',".txt")),
tags$hr(),
checkboxInput('header15', 'Header', FALSE),
radioButtons('sep15', 'Separator',
c(Comma=',',
Semicolon=';',
Tab='\t'),
','),
radioButtons('quote15', 'Quote',
c(None='',
'Double Quote'='"',
'Single Quote'="'"),
''),
checkboxInput("info.151",strong(code("HELP")), FALSE),
checkboxInput("ex.15.0","Example", FALSE)),
verbatimTextOutput("contents151")))),
# #####################################################################################################################################################################################
tabItem("subitem152",
fluidPage(
titlePanel("Correlation Analysis"),
sidebarLayout(
sidebarPanel(
selectInput("res.15.2", "Choose Results:",
choices = c("Genotype Correlation",
"pValue")),
numericInput("res.15.3","Minimum Value of Correlation",min = c(-1),max = 1,value = 0.1,step = 0.01),
textInput("name.txt.15","Type the File Name"),
downloadButton('downloadData15', 'Download'),
checkboxInput("info.152",strong(code("HELP")), FALSE)),
mainPanel(verbatimTextOutput("contents15.2"),
plotOutput("contents15.1"),
plotOutput("contents15.3"))))),
# #####################################################################################################################################################################################
tabItem("subitem161",
fluidPage(
titlePanel("Uploading Files"),
sidebarLayout(
sidebarPanel(
fileInput('file16', 'Choose File.txt',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv',".txt")),
tags$hr(),
checkboxInput('header16', 'Header', FALSE),
radioButtons('sep16', 'Separator',
c(Comma=',',
Semicolon=';',
Tab='\t'),
','),
radioButtons('quote16', 'Quote',
c(None='',
'Double Quote'='"',
'Single Quote'="'"),
''),
checkboxInput("info.161",strong(code("HELP")), FALSE),
checkboxInput("ex.16","Example", FALSE)),
verbatimTextOutput("contents161")))),
# #####################################################################################################################################################################################
tabItem("subitem162",
fluidPage(
titlePanel("Path Analysis"),
sidebarLayout(
sidebarPanel(
checkboxInput('res.16.name', 'Trait Names', FALSE),
textInput("name.16", "Main Trait", "trait1"),
selectInput("res.16.2", "Choose Results:",
choices = c("Path Analysis",
"Traits Correlation")),
textInput("name.txt.16","Type the File Name"),
downloadButton('downloadData16', 'Download'),
checkboxInput("info.162",strong(code("HELP")), FALSE)),
verbatimTextOutput("contents16.2")))),
# #####################################################################################################################################################################################
tabItem("subitem171",
fluidPage(
titlePanel("Uploading Files"),
sidebarLayout(
sidebarPanel(
fileInput('file17', 'Choose File.txt',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv',".txt")),
tags$hr(),
checkboxInput('header17', 'Header', FALSE),
radioButtons('sep17', 'Separator',
c(Comma=',',
Semicolon=';',
Tab='\t'),
','),
radioButtons('quote17', 'Quote',
c(None='',
'Double Quote'='"',
'Single Quote'="'"),
''),