ui.R
In Como-DTC-Collaboration/comomodels-explore: A shiny app accompanied with the package comomodels
#
# The user-interface definition of a shiny app object.
#
# packages required by comomodels
library(tidyverse) # tidyselect >1.1.1
library(deSolve)
library(ggplot2)
library(reshape2)
library(magrittr)
# packages for drawing model diagram
library(DiagrammeR)
# packages for building interactive plots
library(plotly)
# packages for building shiny app
library(shiny)
library(miniUI)
library(shinydashboard)
library(shinyjs)
# core package
library(comomodels)
# load ancestral SARS-CoV-2 transmission as default transmission parameters
parameters <- covid_transmission_parameters()
beta_default <- (parameters$mu + parameters$gamma) * parameters$R0
jscode <- "
shinyjs.collapse = function(boxid) {
$('#' + boxid).closest('.box').find('[data-widget=collapse]').click();
}
"
css <- "
.irs-from, .irs-to { color: black; background: transparent }
"
# define several aesthetics
format.sidebar.box.params.main <- list(width = "100%", collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE)
format.sidebar.box.params.sub <- c()
header = dashboardHeader(title = "CoMo Models")
# Interactive params (transmission params)
sidebar = dashboardSidebar(
## ====================== SEIRD ======================= ##
conditionalPanel(condition="input.simulation == 'SEIRD_params'",
box(title = "Transmission parameters",
width= "100%", background = "black",
# beta
box(title = withMathJax("$$\\beta$$"),
id = "seird.params.beta",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "beta", label = withMathJax("$$\\beta$$"),
min = 0.000, max = 1.000, step = 0.0001, value = beta_default)
),
# kappa
box(title = withMathJax("$$\\kappa$$"),
id = "seird.params.kappa",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "kappa", label = withMathJax("$$\\kappa$$"),
min = 0.000, max = 1.000, step = 0.0001, value = parameters$kappa)
),
# gamma
box(title = withMathJax("$$\\gamma$$"),
id = "seird.params.gamma",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "gamma", label = withMathJax("$$\\gamma$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$gamma)
),
# mu
box(title = withMathJax("$$\\mu$$"),
id = "seird.params.mu",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "mu", label = withMathJax("$$\\mu$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$mu)
)
)
),
## =================== SEIaImIsRD ===================== ##
conditionalPanel(condition="input.simulation == 'SEIaImIsRD_params'",
box(title = "Transmission parameters",
width= "100%", background = "black",
# beta
box(title = withMathJax("$$\\beta$$"),
id = "sc.params.beta",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "sc.beta.ia", label = withMathJax("$$\\beta_{I_a}$$"),
min = 0.000, max = 1.500, step = 0.0001, value = 0.800),
sliderInput(inputId = "sc.beta.im", label = withMathJax("$$\\beta_{I_m}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.900),
sliderInput(inputId = "sc.beta.is", label = withMathJax("$$\\beta_{I_s}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 1.000)
),
# kappa
box(title = withMathJax("$$\\kappa$$"),
id = "sc.params.kappa",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "sc.kappa", label = withMathJax("$$\\kappa$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.1000)
),
# omega (REMOVED)
#box(title = withMathJax("$$\\omega$$"),
# id = "sc.params.omega",
# width = "100%", background = "black",
# collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
# sliderInput(inputId = "sc.omega", label = withMathJax("$$\\omega$$"),
# min = 0.000, max = 1.000, step = 0.0001, value = 0.500)
#),
# p_symptom
box(title = withMathJax("$$\\eta$$"),
id = "sc.params.p_symptom",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "sc.p_symptom.im", label = withMathJax("$$\\eta_{E->I_m}$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = 0.1400),
sliderInput(inputId = "sc.p_symptom.is", label = withMathJax("$$\\eta_{E->I_s}$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = 0.0500)
),
# gamma
box(title = withMathJax("$$\\gamma$$"),
id = "sc.params.gamma",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "sc.gamma.ia", label = withMathJax("$$\\gamma_{I_a}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.9000),
sliderInput(inputId = "sc.gamma.im", label = withMathJax("$$\\gamma_{I_m}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.5000),
sliderInput(inputId = "sc.gamma.is", label = withMathJax("$$\\gamma_{I_s}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.0100)
),
# mu
box(title = withMathJax("$$\\mu$$"),
id = "sc.params.mu",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "sc.mu.ia", label = withMathJax("$$\\mu_{I_a}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.0050),
sliderInput(inputId = "sc.mu.im", label = withMathJax("$$\\mu_{I_m}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.0500),
sliderInput(inputId = "sc.mu.is", label = withMathJax("$$\\mu_{I_s}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.3000)
)
)
),
## =================== SEIRD_Age ====================== ##
conditionalPanel(condition="input.simulation == 'SEIRDAge_params'",
# input contact matrices
fileInput(inputId = "age.contact.files", label = "Load contact matrices and population (.rda format)",
accept = ".rda", multiple = TRUE, placeholder = "Please select files all at once"),
# select country from the contact matrix info (allow one only)
selectInput(inputId = "age.country", label = "Select country",
choices = NULL, multiple = FALSE),
# transmission params
box(title = "Transmission parameters",
width= "100%", background = "black",
# beta
box(title = withMathJax("$$\\beta$$"),
id = "age.params.beta",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "age.beta", label = withMathJax("$$\\beta$$"),
min = 0.000, max = 1.500, step = 0.0001, value = beta_default)
),
# kappa
box(title = withMathJax("$$\\kappa$$"),
id = "age.params.kappa",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "age.kappa", label = withMathJax("$$\\kappa$$"),
min = 0.000, max = 1.000, step = 0.0001, value = parameters$kappa)
),
# gamma
box(title = withMathJax("$$\\gamma$$"),
id = "age.params.gamma",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "age.gamma", label = withMathJax("$$\\gamma$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$gamma)
),
# mu
box(title = withMathJax("$$\\mu$$"),
id = "age.params.mu",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "age.mu", label = withMathJax("$$\\mu$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$mu)
)
)
),
## ===================== SEIRDV ======================= ##
conditionalPanel(condition="input.simulation == 'SEIRDV_params'",
# transmission params
box(title = "Transmission parameters",
width= "100%", background = "black",
# beta
box(title = withMathJax("$$\\beta$$"),
id = "vac.params.beta",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.beta", label = withMathJax("$$\\beta$$"),
min = 0.0000, max = 1.5000, step = 0.0001, value = beta_default)
),
# kappa
box(title = withMathJax("$$\\kappa$$"),
id = "vac.params.kappa",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.kappa", label = withMathJax("$$\\kappa$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$kappa)
),
# gamma
box(title = withMathJax("$$\\gamma$$"),
id = "vac.params.gamma",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.gamma", label = withMathJax("$$\\gamma$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$gamma)
),
# mu
box(title = withMathJax("$$\\mu$$"),
id = "vac.params.mu",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.mu", label = withMathJax("$$\\mu$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$mu)
),
# nu (vac rate)
box(title = withMathJax("$$\\nu$$"),
id = "vac.params.nu",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.nu", label = withMathJax("$$\\nu$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = 0.4000)
),
# delta (rate of immunity loss)
box(title = withMathJax("$$\\delta_V$$"),
id = "vac.params.delta.v",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.delta.v", label = withMathJax("$$\\delta_V$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = 0.1000)
),
box(title = withMathJax("$$\\delta_R$$"),
id = "vac.params.delta.r",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.delta.r", label = withMathJax("$$\\delta_R$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = 0.0500)
),
box(title = withMathJax("$$\\delta_{VR}$$"),
id = "vac.params.delta.vr",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.delta.vr", label = withMathJax("$$\\delta_{VR}$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = 0.0200)
)
)
),
## =================== SEIRD_RU ===================== ##
conditionalPanel(condition="input.simulation == 'SEIRD_RU_params'",
# input contact matrices
fileInput(inputId = "ru.contact.files", label = "Load contact matrices and demographic data (.rda format)",
accept = ".rda", multiple = TRUE, placeholder = "Please select files all at once"),
# select country from the contact matrix info (allow one only)
selectInput(inputId = "ru.country", label = "Select country",
choices = NULL, multiple = FALSE),
# transmission params
box(title = "Transmission parameters",
width= "100%", background = "black",
# beta
box(title = withMathJax("$$\\beta$$"),
id = "ru.params.beta",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "ru.beta", label = withMathJax("$$\\beta$$"),
min = 0.0000, max = 1.5000, step = 0.0001, value = beta_default)
),
# kappa
box(title = withMathJax("$$\\kappa$$"),
id = "ru.params.kappa",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "ru.kappa", label = withMathJax("$$\\kappa$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$kappa)
),
# gamma
box(title = withMathJax("$$\\gamma$$"),
id = "ru.params.gamma",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "ru.gamma", label = withMathJax("$$\\gamma$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$gamma)
),
# mu
box(title = withMathJax("$$\\mu$$"),
id = "ru.params.mu",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "ru.mu", label = withMathJax("$$\\mu$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$mu)
),
# C (connectedness)
box(title = withMathJax("Connectedness"),
id = "ru.params.c",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "ru.c", label = withMathJax("Connectedness"),
min = 0.0000, max = 1.0000, step = 0.0001, value = 0.1000)
)
)
)
)
body = dashboardBody(
shinyjs::useShinyjs(),
# extendShinyjs(text = jscode, functions = c("winprint")),
tabsetPanel(
id = "simulation",
## ==================== SEIRD ======================== ##
tabPanel(title="SEIRD", value='SEIRD_params',
div(class = "col-sm-12 col-md-12 col-lg-10",
fluidRow(
box(width = 6,
title="Model",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
# actionButton(inputId = "control.params.beta", label = withMathJax("$\\beta$")),
box(width = "100%",
title = "Diagram",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
h5("Please click on the transmission parameters you want to modify on the diagram below:"),
grVizOutput(outputId = "model_flowchart"),
verbatimTextOutput(outputId = "SEIRD.param.desc")
),
box(width = "100%",
title = "SEIRD ODE system",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
fluidPage(
uiOutput(outputId = 'dS'),
uiOutput(outputId = 'dE'),
uiOutput(outputId = 'dI'),
uiOutput(outputId = 'dR'),
uiOutput(outputId = 'dD')
)
),
box(width = "100%",
title = "Basic Reproduction Number",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
verbatimTextOutput(outputId = "R0")
)
),
# actionButton("slider.hide.beta", "hide beta"),
box(width = 6,
title="Simulation",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "Download simulation results",
collapsible = FALSE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
downloadButton("download.SEIRD", "Download"),
#downloadButton("download.SEIRD.changes", "Changes")
),
box(width = "100%",
title = "States",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRD.states")
),
box(width = "100%",
title = "Daily Incidence and Deaths",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRD.changes")
)
)
)
)
),
## ====================== SEIaImIsRD ============================== ##
tabPanel(title="SEIaImIsRD", value='SEIaImIsRD_params',
div(class = "col-sm-12 col-md-12 col-lg-10",
fluidRow(
box(width = 6,
title="Model",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "Diagram",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
h5("Please click on the transmission parameters you want to modify on the diagram below:"),
grVizOutput(outputId = "sc_model_flowchart"),
verbatimTextOutput(outputId = "SEIaImIsRD.param.desc")
),
box(width = "100%",
title = "SEIaImIsRD ODE system",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
fluidPage(uiOutput(outputId = 'sc.dS'),
uiOutput(outputId = 'sc.dE'),
uiOutput(outputId = 'sc.dI'),
uiOutput(outputId = 'sc.dR'),
uiOutput(outputId = 'sc.dD')
)
),
box(width = "100%",
title = "Basic Reproduction Number",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
verbatimTextOutput(outputId = "sc.R0")
)
),
box(width = 6,
title="Simulation",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "States",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIaImIsRD.states")
),
box(width = "100%",
title = "Daily Incidence and Deaths",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIaImIsRD.changes")
)
)
)
)
),
## ====================== SEIRDAge ============================ ##
tabPanel(title="SEIRDAge", value='SEIRDAge_params',
div(class = "col-sm-12 col-md-12 col-lg-10", # row-sm-12 row-md-6 row-lg-auo",
fluidRow(
box(width = 6,
title="Model",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "Diagram",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
h5("Please click on the transmission parameters you want to modify on the diagram below:"),
grVizOutput(outputId = "age_model_flowchart"),
verbatimTextOutput(outputId = "SEIRDAge.param.desc")
),
box(width = "100%",
title = "SEIRDAge ODE system",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
fluidPage(uiOutput(outputId = 'age.dS'),
uiOutput(outputId = 'age.dE'),
uiOutput(outputId = 'age.dI'),
uiOutput(outputId = 'age.dR'),
uiOutput(outputId = 'age.dD')
)
),
box(width = "100%",
title="Files loaded ",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
verbatimTextOutput(outputId = "age.contact.names")
)
),
box(width = 6,
title="Simulation",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title="Result by compartment groups",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "States",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRDAge.states.by.compartment")
),
box(width = "100%",
title = "Daily Incidence and Deaths",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRDAge.changes.by.compartment")
)
),
box(width = "100%",
title="Result by age groups",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
selectInput(inputId = "age_range.select", label = "Selected age range",
choices = NULL),
box(width = "100%",
title = "States",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRDAge.states.by.age")
),
box(width = "100%",
title = "Daily Incidence and Deaths",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRDAge.changes.by.age")
)
)
)
)
)
),
## ====================== SEIRDV ============================ ##
tabPanel(title="SEIRDV", value='SEIRDV_params',
div(class = "col-sm-12 col-md-12 col-lg-10",
fluidRow(
box(width = 6,
title="Model",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "Diagram",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
h5("Please click on the transmission parameters you want to modify on the diagram below:"),
grVizOutput(outputId = "vac_model_flowchart"),
verbatimTextOutput(outputId = "SEIRDV.param.desc")
),
box(width = "100%",
title = "SEIRDV ODE system",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
fluidPage(uiOutput(outputId = 'vac.dS'),
uiOutput(outputId = 'vac.dE'),
uiOutput(outputId = 'vac.dI'),
uiOutput(outputId = 'vac.dR'),
uiOutput(outputId = 'vac.dV'),
uiOutput(outputId = 'vac.dVR'),
uiOutput(outputId = 'vac.dD')
)
)
),
box(width = 6,
title="Simulation",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "States",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRDV.states")
),
box(width = "100%",
title = "Daily Incidence and Deaths",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRDV.changes")
)
)
)
)
),
## ====================== SEIRD_RU =========================== ##
tabPanel(title="SEIRD_RU", value='SEIRD_RU_params',
div(class = "col-sm-12 col-md-12 col-lg-10",
fluidRow(
box(width = 6,
title="Model",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "Diagram",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
h5("Please click on the transmission parameters you want to modify on the diagram below:"),
grVizOutput(outputId = "ru_model_flowchart"),
verbatimTextOutput(outputId = "SEIRD_RU.param.desc")
),
box(width = "100%",
title = "SEIRD_RU ODE system",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
fluidPage(uiOutput(outputId = 'ru.dS'),
#uiOutput(outputId = 'ru.dS_Y'),
uiOutput(outputId = 'ru.dE'),
#uiOutput(outputId = 'ru.dE_Y'),
uiOutput(outputId = 'ru.dI'),
#uiOutput(outputId = 'ru.dI_Y'),
uiOutput(outputId = 'ru.dR'),
#uiOutput(outputId = 'ru.dR_Y'),
#uiOutput(outputId = 'ru.dC_U'),
#uiOutput(outputId = 'ru.dC_Y'),
uiOutput(outputId = 'ru.dD'),
#uiOutput(outputId = 'ru.dD_Y')
)
),
box(width = "100%",
title = "Basic Reproduction Number",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
verbatimTextOutput(outputId = "ru.R0")
),
box(width = "100%",
title="Files loaded ",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
verbatimTextOutput(outputId = "ru.contact.names")
)
),
box(width = 6,
title="Simulation",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "States",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRD_RU.states")
),
box(width = "100%",
title = "Daily Incidence and Deaths",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRD_RU.changes")
)
)
)
)
)
)
)
# create ui
ui <- dashboardPage(
title = "CoMo Models",
header = dashboardHeader(title = "CoMo Models"),
sidebar = sidebar,
body = body
)
Como-DTC-Collaboration/comomodels-explore documentation built on Jan. 20, 2022, 4:49 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#
# The user-interface definition of a shiny app object.
#
# packages required by comomodels
library(tidyverse) # tidyselect >1.1.1
library(deSolve)
library(ggplot2)
library(reshape2)
library(magrittr)
# packages for drawing model diagram
library(DiagrammeR)
# packages for building interactive plots
library(plotly)
# packages for building shiny app
library(shiny)
library(miniUI)
library(shinydashboard)
library(shinyjs)
# core package
library(comomodels)
# load ancestral SARS-CoV-2 transmission as default transmission parameters
parameters <- covid_transmission_parameters()
beta_default <- (parameters$mu + parameters$gamma) * parameters$R0
jscode <- "
shinyjs.collapse = function(boxid) {
$('#' + boxid).closest('.box').find('[data-widget=collapse]').click();
}
"
css <- "
.irs-from, .irs-to { color: black; background: transparent }
"
# define several aesthetics
format.sidebar.box.params.main <- list(width = "100%", collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE)
format.sidebar.box.params.sub <- c()
header = dashboardHeader(title = "CoMo Models")
# Interactive params (transmission params)
sidebar = dashboardSidebar(
## ====================== SEIRD ======================= ##
conditionalPanel(condition="input.simulation == 'SEIRD_params'",
box(title = "Transmission parameters",
width= "100%", background = "black",
# beta
box(title = withMathJax("$$\\beta$$"),
id = "seird.params.beta",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "beta", label = withMathJax("$$\\beta$$"),
min = 0.000, max = 1.000, step = 0.0001, value = beta_default)
),
# kappa
box(title = withMathJax("$$\\kappa$$"),
id = "seird.params.kappa",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "kappa", label = withMathJax("$$\\kappa$$"),
min = 0.000, max = 1.000, step = 0.0001, value = parameters$kappa)
),
# gamma
box(title = withMathJax("$$\\gamma$$"),
id = "seird.params.gamma",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "gamma", label = withMathJax("$$\\gamma$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$gamma)
),
# mu
box(title = withMathJax("$$\\mu$$"),
id = "seird.params.mu",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "mu", label = withMathJax("$$\\mu$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$mu)
)
)
),
## =================== SEIaImIsRD ===================== ##
conditionalPanel(condition="input.simulation == 'SEIaImIsRD_params'",
box(title = "Transmission parameters",
width= "100%", background = "black",
# beta
box(title = withMathJax("$$\\beta$$"),
id = "sc.params.beta",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "sc.beta.ia", label = withMathJax("$$\\beta_{I_a}$$"),
min = 0.000, max = 1.500, step = 0.0001, value = 0.800),
sliderInput(inputId = "sc.beta.im", label = withMathJax("$$\\beta_{I_m}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.900),
sliderInput(inputId = "sc.beta.is", label = withMathJax("$$\\beta_{I_s}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 1.000)
),
# kappa
box(title = withMathJax("$$\\kappa$$"),
id = "sc.params.kappa",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "sc.kappa", label = withMathJax("$$\\kappa$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.1000)
),
# omega (REMOVED)
#box(title = withMathJax("$$\\omega$$"),
# id = "sc.params.omega",
# width = "100%", background = "black",
# collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
# sliderInput(inputId = "sc.omega", label = withMathJax("$$\\omega$$"),
# min = 0.000, max = 1.000, step = 0.0001, value = 0.500)
#),
# p_symptom
box(title = withMathJax("$$\\eta$$"),
id = "sc.params.p_symptom",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "sc.p_symptom.im", label = withMathJax("$$\\eta_{E->I_m}$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = 0.1400),
sliderInput(inputId = "sc.p_symptom.is", label = withMathJax("$$\\eta_{E->I_s}$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = 0.0500)
),
# gamma
box(title = withMathJax("$$\\gamma$$"),
id = "sc.params.gamma",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "sc.gamma.ia", label = withMathJax("$$\\gamma_{I_a}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.9000),
sliderInput(inputId = "sc.gamma.im", label = withMathJax("$$\\gamma_{I_m}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.5000),
sliderInput(inputId = "sc.gamma.is", label = withMathJax("$$\\gamma_{I_s}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.0100)
),
# mu
box(title = withMathJax("$$\\mu$$"),
id = "sc.params.mu",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "sc.mu.ia", label = withMathJax("$$\\mu_{I_a}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.0050),
sliderInput(inputId = "sc.mu.im", label = withMathJax("$$\\mu_{I_m}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.0500),
sliderInput(inputId = "sc.mu.is", label = withMathJax("$$\\mu_{I_s}$$"),
min = 0.000, max = 1.000, step = 0.0001, value = 0.3000)
)
)
),
## =================== SEIRD_Age ====================== ##
conditionalPanel(condition="input.simulation == 'SEIRDAge_params'",
# input contact matrices
fileInput(inputId = "age.contact.files", label = "Load contact matrices and population (.rda format)",
accept = ".rda", multiple = TRUE, placeholder = "Please select files all at once"),
# select country from the contact matrix info (allow one only)
selectInput(inputId = "age.country", label = "Select country",
choices = NULL, multiple = FALSE),
# transmission params
box(title = "Transmission parameters",
width= "100%", background = "black",
# beta
box(title = withMathJax("$$\\beta$$"),
id = "age.params.beta",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "age.beta", label = withMathJax("$$\\beta$$"),
min = 0.000, max = 1.500, step = 0.0001, value = beta_default)
),
# kappa
box(title = withMathJax("$$\\kappa$$"),
id = "age.params.kappa",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "age.kappa", label = withMathJax("$$\\kappa$$"),
min = 0.000, max = 1.000, step = 0.0001, value = parameters$kappa)
),
# gamma
box(title = withMathJax("$$\\gamma$$"),
id = "age.params.gamma",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "age.gamma", label = withMathJax("$$\\gamma$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$gamma)
),
# mu
box(title = withMathJax("$$\\mu$$"),
id = "age.params.mu",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "age.mu", label = withMathJax("$$\\mu$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$mu)
)
)
),
## ===================== SEIRDV ======================= ##
conditionalPanel(condition="input.simulation == 'SEIRDV_params'",
# transmission params
box(title = "Transmission parameters",
width= "100%", background = "black",
# beta
box(title = withMathJax("$$\\beta$$"),
id = "vac.params.beta",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.beta", label = withMathJax("$$\\beta$$"),
min = 0.0000, max = 1.5000, step = 0.0001, value = beta_default)
),
# kappa
box(title = withMathJax("$$\\kappa$$"),
id = "vac.params.kappa",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.kappa", label = withMathJax("$$\\kappa$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$kappa)
),
# gamma
box(title = withMathJax("$$\\gamma$$"),
id = "vac.params.gamma",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.gamma", label = withMathJax("$$\\gamma$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$gamma)
),
# mu
box(title = withMathJax("$$\\mu$$"),
id = "vac.params.mu",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.mu", label = withMathJax("$$\\mu$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$mu)
),
# nu (vac rate)
box(title = withMathJax("$$\\nu$$"),
id = "vac.params.nu",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.nu", label = withMathJax("$$\\nu$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = 0.4000)
),
# delta (rate of immunity loss)
box(title = withMathJax("$$\\delta_V$$"),
id = "vac.params.delta.v",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.delta.v", label = withMathJax("$$\\delta_V$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = 0.1000)
),
box(title = withMathJax("$$\\delta_R$$"),
id = "vac.params.delta.r",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.delta.r", label = withMathJax("$$\\delta_R$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = 0.0500)
),
box(title = withMathJax("$$\\delta_{VR}$$"),
id = "vac.params.delta.vr",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "vac.delta.vr", label = withMathJax("$$\\delta_{VR}$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = 0.0200)
)
)
),
## =================== SEIRD_RU ===================== ##
conditionalPanel(condition="input.simulation == 'SEIRD_RU_params'",
# input contact matrices
fileInput(inputId = "ru.contact.files", label = "Load contact matrices and demographic data (.rda format)",
accept = ".rda", multiple = TRUE, placeholder = "Please select files all at once"),
# select country from the contact matrix info (allow one only)
selectInput(inputId = "ru.country", label = "Select country",
choices = NULL, multiple = FALSE),
# transmission params
box(title = "Transmission parameters",
width= "100%", background = "black",
# beta
box(title = withMathJax("$$\\beta$$"),
id = "ru.params.beta",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "ru.beta", label = withMathJax("$$\\beta$$"),
min = 0.0000, max = 1.5000, step = 0.0001, value = beta_default)
),
# kappa
box(title = withMathJax("$$\\kappa$$"),
id = "ru.params.kappa",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "ru.kappa", label = withMathJax("$$\\kappa$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$kappa)
),
# gamma
box(title = withMathJax("$$\\gamma$$"),
id = "ru.params.gamma",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "ru.gamma", label = withMathJax("$$\\gamma$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$gamma)
),
# mu
box(title = withMathJax("$$\\mu$$"),
id = "ru.params.mu",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "ru.mu", label = withMathJax("$$\\mu$$"),
min = 0.0000, max = 1.0000, step = 0.0001, value = parameters$mu)
),
# C (connectedness)
box(title = withMathJax("Connectedness"),
id = "ru.params.c",
width = "100%", background = "black",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = TRUE,
sliderInput(inputId = "ru.c", label = withMathJax("Connectedness"),
min = 0.0000, max = 1.0000, step = 0.0001, value = 0.1000)
)
)
)
)
body = dashboardBody(
shinyjs::useShinyjs(),
# extendShinyjs(text = jscode, functions = c("winprint")),
tabsetPanel(
id = "simulation",
## ==================== SEIRD ======================== ##
tabPanel(title="SEIRD", value='SEIRD_params',
div(class = "col-sm-12 col-md-12 col-lg-10",
fluidRow(
box(width = 6,
title="Model",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
# actionButton(inputId = "control.params.beta", label = withMathJax("$\\beta$")),
box(width = "100%",
title = "Diagram",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
h5("Please click on the transmission parameters you want to modify on the diagram below:"),
grVizOutput(outputId = "model_flowchart"),
verbatimTextOutput(outputId = "SEIRD.param.desc")
),
box(width = "100%",
title = "SEIRD ODE system",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
fluidPage(
uiOutput(outputId = 'dS'),
uiOutput(outputId = 'dE'),
uiOutput(outputId = 'dI'),
uiOutput(outputId = 'dR'),
uiOutput(outputId = 'dD')
)
),
box(width = "100%",
title = "Basic Reproduction Number",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
verbatimTextOutput(outputId = "R0")
)
),
# actionButton("slider.hide.beta", "hide beta"),
box(width = 6,
title="Simulation",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "Download simulation results",
collapsible = FALSE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
downloadButton("download.SEIRD", "Download"),
#downloadButton("download.SEIRD.changes", "Changes")
),
box(width = "100%",
title = "States",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRD.states")
),
box(width = "100%",
title = "Daily Incidence and Deaths",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRD.changes")
)
)
)
)
),
## ====================== SEIaImIsRD ============================== ##
tabPanel(title="SEIaImIsRD", value='SEIaImIsRD_params',
div(class = "col-sm-12 col-md-12 col-lg-10",
fluidRow(
box(width = 6,
title="Model",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "Diagram",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
h5("Please click on the transmission parameters you want to modify on the diagram below:"),
grVizOutput(outputId = "sc_model_flowchart"),
verbatimTextOutput(outputId = "SEIaImIsRD.param.desc")
),
box(width = "100%",
title = "SEIaImIsRD ODE system",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
fluidPage(uiOutput(outputId = 'sc.dS'),
uiOutput(outputId = 'sc.dE'),
uiOutput(outputId = 'sc.dI'),
uiOutput(outputId = 'sc.dR'),
uiOutput(outputId = 'sc.dD')
)
),
box(width = "100%",
title = "Basic Reproduction Number",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
verbatimTextOutput(outputId = "sc.R0")
)
),
box(width = 6,
title="Simulation",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "States",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIaImIsRD.states")
),
box(width = "100%",
title = "Daily Incidence and Deaths",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIaImIsRD.changes")
)
)
)
)
),
## ====================== SEIRDAge ============================ ##
tabPanel(title="SEIRDAge", value='SEIRDAge_params',
div(class = "col-sm-12 col-md-12 col-lg-10", # row-sm-12 row-md-6 row-lg-auo",
fluidRow(
box(width = 6,
title="Model",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "Diagram",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
h5("Please click on the transmission parameters you want to modify on the diagram below:"),
grVizOutput(outputId = "age_model_flowchart"),
verbatimTextOutput(outputId = "SEIRDAge.param.desc")
),
box(width = "100%",
title = "SEIRDAge ODE system",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
fluidPage(uiOutput(outputId = 'age.dS'),
uiOutput(outputId = 'age.dE'),
uiOutput(outputId = 'age.dI'),
uiOutput(outputId = 'age.dR'),
uiOutput(outputId = 'age.dD')
)
),
box(width = "100%",
title="Files loaded ",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
verbatimTextOutput(outputId = "age.contact.names")
)
),
box(width = 6,
title="Simulation",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title="Result by compartment groups",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "States",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRDAge.states.by.compartment")
),
box(width = "100%",
title = "Daily Incidence and Deaths",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRDAge.changes.by.compartment")
)
),
box(width = "100%",
title="Result by age groups",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
selectInput(inputId = "age_range.select", label = "Selected age range",
choices = NULL),
box(width = "100%",
title = "States",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRDAge.states.by.age")
),
box(width = "100%",
title = "Daily Incidence and Deaths",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRDAge.changes.by.age")
)
)
)
)
)
),
## ====================== SEIRDV ============================ ##
tabPanel(title="SEIRDV", value='SEIRDV_params',
div(class = "col-sm-12 col-md-12 col-lg-10",
fluidRow(
box(width = 6,
title="Model",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "Diagram",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
h5("Please click on the transmission parameters you want to modify on the diagram below:"),
grVizOutput(outputId = "vac_model_flowchart"),
verbatimTextOutput(outputId = "SEIRDV.param.desc")
),
box(width = "100%",
title = "SEIRDV ODE system",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
fluidPage(uiOutput(outputId = 'vac.dS'),
uiOutput(outputId = 'vac.dE'),
uiOutput(outputId = 'vac.dI'),
uiOutput(outputId = 'vac.dR'),
uiOutput(outputId = 'vac.dV'),
uiOutput(outputId = 'vac.dVR'),
uiOutput(outputId = 'vac.dD')
)
)
),
box(width = 6,
title="Simulation",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "States",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRDV.states")
),
box(width = "100%",
title = "Daily Incidence and Deaths",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRDV.changes")
)
)
)
)
),
## ====================== SEIRD_RU =========================== ##
tabPanel(title="SEIRD_RU", value='SEIRD_RU_params',
div(class = "col-sm-12 col-md-12 col-lg-10",
fluidRow(
box(width = 6,
title="Model",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "Diagram",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
h5("Please click on the transmission parameters you want to modify on the diagram below:"),
grVizOutput(outputId = "ru_model_flowchart"),
verbatimTextOutput(outputId = "SEIRD_RU.param.desc")
),
box(width = "100%",
title = "SEIRD_RU ODE system",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
fluidPage(uiOutput(outputId = 'ru.dS'),
#uiOutput(outputId = 'ru.dS_Y'),
uiOutput(outputId = 'ru.dE'),
#uiOutput(outputId = 'ru.dE_Y'),
uiOutput(outputId = 'ru.dI'),
#uiOutput(outputId = 'ru.dI_Y'),
uiOutput(outputId = 'ru.dR'),
#uiOutput(outputId = 'ru.dR_Y'),
#uiOutput(outputId = 'ru.dC_U'),
#uiOutput(outputId = 'ru.dC_Y'),
uiOutput(outputId = 'ru.dD'),
#uiOutput(outputId = 'ru.dD_Y')
)
),
box(width = "100%",
title = "Basic Reproduction Number",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
verbatimTextOutput(outputId = "ru.R0")
),
box(width = "100%",
title="Files loaded ",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
verbatimTextOutput(outputId = "ru.contact.names")
)
),
box(width = 6,
title="Simulation",
collapsible = TRUE, status = "primary", solidHeader = TRUE, collapsed = FALSE,
box(width = "100%",
title = "States",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRD_RU.states")
),
box(width = "100%",
title = "Daily Incidence and Deaths",
collapsible = TRUE, status = "primary", solidHeader = FALSE, collapsed = FALSE,
plotlyOutput(outputId = "SEIRD_RU.changes")
)
)
)
)
)
)
)
# create ui
ui <- dashboardPage(
title = "CoMo Models",
header = dashboardHeader(title = "CoMo Models"),
sidebar = sidebar,
body = body
)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.