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ui.R
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ui.R
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##################################################
#####
##### Age and Growth app - User Interface (UI)
##### Jonas Vasconcelos-Filho
##### 09/06/2019
##### v 1.0
#####
##################################################
# check.packages <- function(pkg){
# new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
# if (length(new.pkg))
# install.packages(new.pkg, dependencies = TRUE)
# sapply(pkg, require, character.only = TRUE)
# }
library("shiny")
library("devtools")
library("nlstools")
library("FSA")
library("fishmethods")
library("shinydashboard")
library("shinyWidgets")
library("ggplot2")
library("waiter")
library("shinyalert")
library("AICcmodavg")
title <- a(href="https://github.com/JonasVasconcelos",
style = "font-family: monospace; color: white;",
img(src="logo.png", width = '75'),
strong('FiShiny'))
sidebar <- {dashboardSidebar(
sidebarMenu(id = "tabs",
menuItem("Home", tabName = "home",
icon = icon("home")),
menuItem(text = "Length-Weight Relationship", tabName = "lwr",
icon = icon("chart-line"),
menuSubItem(text = "Input", tabName = "lwrinput",
icon = icon("upload")),
menuSubItem("Graph and Fit", tabName = "graphlwr",
icon = icon("bar-chart-o"))
),
menuItem(text = "Age and Growth",
tabName = "age",
icon = icon("chart-line"),
menuSubItem(text = "Input", tabName = "ageinput",
icon = icon("upload")),
menuSubItem("Graph", tabName = "graph",
icon = icon("bar-chart-o")),
menuSubItem("Models", tabName = "models",
icon = icon("fas fa-chart-line")),
menuSubItem("Kimura", tabName = "kimura",
icon = icon("question"))
)
# ,
#
# menuItem(text = "Morphometrics", tabName = "morpho",
# icon = icon("ruler-horizontal"),
# menuSubItem(text = "Input Images", tabName = "morphoinput",
# icon = icon("upload")),
# menuSubItem("Measurement", tabName = "graph",
# icon = icon("ruler-horizontal"))
# )
)
)}
Home <- {
tabItem(
tabName = "home",
p(
"Do you have trouble with growth model fits? Your problems are over there that is an easy way to fit the von Bertalanffy, Gompertz, and Logistic functions. And as a tip, you can set how many bootstraps you want for confidence intervals, use the Akaike criterion for model evaluation, and run comparisons between groups.",
style = "font-family: 'helvetica'; font-size: 12pt; text-align: justify"
)
)
}
AgeInput <- {tabItem(tabName = "ageinput",
fluidRow(
box(title = "Input sets",
status = "primary",
solidHeader = T,
collapsible = TRUE,
fileInput("agefile",
"Upload the file",
multiple = T),
helpText("Select the read.table parameters below"),
checkboxInput(inputId = "ageheader",
label = "Header",
value = T),
checkboxInput(inputId = "agestringAsFactors",
label = "stringAsFactors",
value = T),
radioButtons(inputId = "agesep",
label = "Separator",
choices = c(Semicolon = ";",
Comma = ",",
Tab = "\t",
Space = " "))
),
box(title = "Data table",
status = "primary",
solidHeader = T,
collapsible = TRUE,
uiOutput("agetb")
)
)
)}
GraphInputAge <- {tabItem(tabName = "graph",
fluidRow(
box(title = "Variables and Graphical Parameters",
status = "primary",
solidHeader = T,
collapsible = TRUE,
selectInput("agex", "1. Select x-variable",
choices = "", selected = "", multiple = F),
selectInput("agey", "2. Select y-variable",
choices = "", selected = "", multiple = F),
textInput("xlab", "3. Type the x-label."),
textInput("ylab", "4. Type the y-label."),
numericInput("agepch", "5. Choose the symbol points.",min = 1, max = 20, step = 1, value = 1),
selectInput("agecolpt", "6. Choose the color points.",
choices = c("Black" = 1,
"Red" = 2,
"Green" = 3,
"Blue" = 4,
"Cyan" = 5,
"Magenta" = 6,
"Yellow" = 7,
"Gray" = 8),
multiple = F, selected = 1),
radioButtons("downloadfile", "Select the file type:",
choices = c("tiff" = "tiff",
"jpeg" = "jpeg")),
numericInput("width", "Width (px):", value = 2400, min = 800, max = 4000),
numericInput("height", "Height (px):", value = 1800, min = 600, max = 3000),
numericInput("res", "Resolution (dpi):", value = 300, min = 72, max = 300)
),
box(title = "Plot",
status = "primary",
solidHeader = T,
collapsible = TRUE,
plotOutput("plot")
)
)
)}
ModelGraphsAge <- {tabItem(tabName = "models",
fluidRow(
tabBox(
title = "Input",
tabPanel(
title = "Models",
status = "primary",
solidHeader = T,
collapsible = TRUE,
checkboxInput("modelsvbgf","von Bertalanffy", F),
checkboxInput("modelsgomp","Gompertz", F),
checkboxInput("modelslog","Logistic", F),
checkboxInput("boot","Bootstrap", F),
numericInput("nboot", "How many bootstrap do you want?",
value = 999),
plotOutput("plot2", brush = "plot_brush")
),
tabPanel(
title = "von Bertalanffy",
status = "primary",
solidHeader = T,
collapsible = TRUE,
shinyjs::useShinyjs(),
sliderInput("vbgfL", "Linf/Winf", min = 0, max = 1000, value = 50, step = 1),
sliderInput("vbgfK", "K", min = 0, max = 5, value = 1, step = 0.01),
sliderInput("vbgft0", "t0", min = -2.5, max = 2.5, value = 0, step = 0.01),
plotOutput("plot3", brush = "plot_brush")
),
tabPanel(
title = "Gompertz",
status = "primary",
sliderInput("gompL", "Linf/Winf", min = 0, max = 1000, value = 50, step = 1),
sliderInput("gompgi", "gi", min = 0.001, max = 10, value = 5, step = 0.01),
sliderInput("gompti", "ti", min = -5, max = 5, value = 0, step = 0.01),
plotOutput("plot4", brush = "plot_brush")
),
tabPanel(
title = "Logistic",
status = "primary",
sliderInput("logL", "Linf/Winf", min = 0, max = 1000, value = 50, step = 1),
sliderInput("logginf", "gninf", min = 0.001, max = 5, value = 2.5, step = 0.01),
sliderInput("logti", "ti", min = -5, max = 5, value = 0, step = 0.01),
plotOutput("plot5", brush = "plot_brush")
)
),
tabBox(
title = "Fit",
tabPanel(
title = "von Bertalanffy",
status = "primary",
solidHeader = T,
collapsible = TRUE,
plotOutput("vbgfBoot2"),
downloadButton("downVBGF",
"Download the plot"),
verbatimTextOutput("modVBGF2"),
downloadButton("downloadDataVBGF",
"Download stats")
),
tabPanel(
title = "Gompertz",
status = "primary",
solidHeader = T,
collapsible = TRUE,
plotOutput("gomBoot"),
downloadButton("downGomp",
"Download the plot"),
verbatimTextOutput("modGom2"),
downloadButton("downloadDataGomp",
"Download stats")
),
tabPanel(
title = "Logistic",
status = "primary",
solidHeader = T,
collapsible = TRUE,
plotOutput("logBoot2"),
downloadButton("downLog",
"Download the plot"),
verbatimTextOutput("modLog2"),
downloadButton("downloadDataLog",
"Download stats")
),
tabPanel(
title = "All model",
status = "primary",
solidHeader = T,
collapsible = TRUE,
plotOutput("todos"),
downloadButton("downAll",
"Download the plot"),
tableOutput("AICprint"),
downloadButton("downloadAIC",
"Download the AIC table")
)
)
)
)}
KimuraAge <- {tabItem(tabName = "kimura",
fluidRow(
box(
title = "Kimura",
status = "primary",
solidHeader = T,
collapsible = TRUE,
selectInput("kimurafactor", "Which group?",
choices = "", selected = "", multiple = F),
radioButtons(inputId = "kimuramodel",
label = "Model",
choices = c("von Bertalanffy" = 1,
"Gompertz" = 2,
"Logistic" = 3))),
box(
title = "Stats",
status = "primary",
solidHeader = T,
collapsible = TRUE,
downloadButton("downloadKimura",
"Download stats"),
verbatimTextOutput("kimuraTab")
)
)
)}
LWRInput <- {tabItem(tabName = "lwrinput",
fluidRow(
box(title = "Input sets",
status = "primary",
solidHeader = T,
collapsible = TRUE,
fileInput("lwrfile",
"Upload the file",
multiple = T),
helpText("Select the read.table parameters below"),
checkboxInput(inputId = "lwrheader",
label = "Header",
value = T),
checkboxInput(inputId = "lwrstringAsFactors",
label = "stringAsFactors",
value = T),
radioButtons(inputId = "lwrsep",
label = "Separator",
choices = c(Semicolon = ";",
Comma = ",",
Tab = "\t",
Space = " "))
),
box(title = "Data table",
status = "primary",
solidHeader = T,
collapsible = TRUE,
uiOutput("lwrtb")
)
)
)}
GraphInputLWR <- {tabItem(tabName = "graphlwr",
fluidRow(
tabBox(
title = "Input",
tabPanel(
title = "Variables",
status = "primary",
solidHeader = T,
collapsible = TRUE,
helpText("Choose the variables below"),
selectInput("lwrx", "1. Select x-variable:",
choices = "", selected = "", multiple = F),
selectInput("lwry", "2. Select y-variable:",
choices = "", selected = "", multiple = F),
selectInput("lwrfactor", "3. Select factor-variable:",
choices = "", selected = "None", multiple = F),
radioButtons("lwrmodel", "4. Select the model:",
choices = c("Non-Linear" = 1,
"Linear" = 0)),
checkboxInput("lwrIC", "Confidence Interval", F),
sliderInput("lwrICalpha", "Level", min = 0, max = 1,
value = 0.95, step = 0.01),
shinyjs::useShinyjs(),
helpText("Set the seed parameters values below"),
sliderInput("lwrA", "Intercept (a)", min = -2, max = 2,
value = 0.01, step = 0.01),
sliderInput("lwrB", "Slope (b)", min = 0, max = 5,
value = 3, step = 0.1),
),
tabPanel(
title = "Graphical Parameters",
status = "primary",
solidHeader = T,
collapsible = TRUE,
helpText("Set the graphical parameters below (Optional)"),
textInput("xlablwr", "3. Type the x-label."),
textInput("ylablwr", "4. Type the y-label."),
numericInput("lwrpch", "5. Choose the symbol points.",
min = 1, max = 20, step = 1, value = 1),
selectInput("lwrcolpt", "6. Choose the color points.",
choices = c("Black" = 1,
"Red" = 2,
"Green" = 3,
"Blue" = 4,
"Cyan" = 5,
"Magenta" = 6,
"Yellow" = 7,
"Gray" = 8),
multiple = F, selected = 1),
sliderInput("lwrptsize", "7. Point size:",
min = 0.1, max = 3, value = 1, step = 0.1),
sliderInput("lwrptalpha", "8. Point opacity:",
min = 0, max = 1, value = 1, step = 0.01),
radioButtons("downloadfilelwr", "Select the file type:",
choices = c("tiff" = "tiff",
"jpeg" = "jpeg")),
numericInput("widthlwr", "Width (px):", value = 2400, min = 800, max = 4000),
numericInput("heightlwr", "Height (px):", value = 1800, min = 600, max = 3000),
numericInput("reslwr", "Resolution (dpi):", value = 300, min = 72, max = 300)
)
),
tabBox(
title = "Output",
tabPanel(
title = "Plot",
status = "primary",
solidHeader = T,
collapsible = TRUE,
plotOutput("plotlwr"),
downloadButton("downLWRplot",
"Download the plot"),
verbatimTextOutput("plotlwrstat"),
downloadButton("downLWRstat",
"Download stats")
)
# ,
# tabPanel(
# title = "ANOVA/ANCOVA",
# status = "primary",
# solidHeader = T,
# collapsible = TRUE,
#
# verbatimTextOutput("plotlwrstat"),
# downloadButton("downLWRstat",
# "Download stats")
# ),
# tabPanel(
# title = "Stats",
# status = "primary",
# solidHeader = T,
# collapsible = TRUE
# )
)
)
)}
shinyUI(
dashboardPage(
dashboardHeader( title = title),
dashboardSidebar(sidebar),
dashboardBody(
shinyjs::useShinyjs(),
autoWaiter(html = spin_loaders(id = 15,
color = rgb(0.25, 0.25, 0.25, 0.5)),
color = rgb(0.1, 0.1, 0.1, 0),
fadeout = T),
tags$style(type="text/css",
".shiny-output-error { visibility: hidden; }",
".shiny-output-error:before { visibility: hidden; }"),
tabItems(Home,
LWRInput,
GraphInputLWR,
AgeInput,
GraphInputAge,
ModelGraphsAge,
KimuraAge
),
)
)
)
# ,
#
# tabItem(
# tabName = "models",
# plotOutput("plot"),
# hr(),
#
# fluidRow(
# column(3,
#
#
# column(4,
# strong("Parameters"),
#
# shinyjs::useShinyjs(),
# "von Bertalanffy",
# sliderInput("vbgfL", "Linf/Winf", min = 0, max = 1000, value = 50, step = 1),
# sliderInput("vbgfK", "K", min = 0, max = 10, value = 5, step = 0.01),
# sliderInput("vbgft0", "t0", min = -5, max = 5, value = 0, step = 0.01),
#
# "Gompertz",
# sliderInput("gompL", "Linf", min = 0, max = 1000, value = 50, step = 1),
# sliderInput("gompgi", "gi", min = 0, max = 10, value = 5, step = 0.01),
# sliderInput("gompti", "ti", min = -5, max = 5, value = 0, step = 0.01),
#
# "Logistic",
# sliderInput("logL", "Linf", min = 0, max = 1000, value = 50, step = 1),
# sliderInput("logginf", "gninf", min = 0, max = 10, value = 5, step = 0.01),
# sliderInput("logti", "ti", min = -5, max = 5, value = 0, step = 0.01)
#
#
# # "Models:",
# # c("von Bertalanffy" = "vbgf",
# # "Gompertz" = "gomp",
# # "Logistic" = "log"))
# )
#)
#)