_shiny/incidence_difference_calculator_beta/ui.R
In SACEMA/inctools: Incidence Estimation Tools
# Incidence Estimation Tools (Shiny webapps).
# Copyright (C) 2017-2019, Lamin Juwara, individual contributors and
# Stellenbosch University.
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version. This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details. You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
library(shiny)
# Define UI
shinyUI(fluidPage(
# Application title
titlePanel("Incidence Difference Calculator"),
br(),
sidebarLayout(
sidebarPanel(
fluidPage(
wellPanel(
fluidRow(column(9, downloadButton('downloadData', 'Download Results')))
),
# wellPanel(fluidRow(
# column(12,
# radioButtons("case", label = h3("Scenario Type:"),
# c(" Same MDRI, same FRR estimates in the two surveys" = 1,
# " Same MDRI, but different FRR estimates in the two surveys" = 2,
# " Different MDRI and FRR estimates in the two surveys" = 3)),
# selected = 1)
# )),
wellPanel( # fluid page for the assay parameters
fluidPage(
h3("Assay Parameters"),
###
fluidRow(
column(6,
numericInput("MDRI_1",
label = h5("MDRI estimate for survey 1 (days)"),
min = 0,
max = 720,
step = 1,
value = 240),
numericInput("MDRI_2",
label = h5("MDRI estimate for survey 2 (days)"),
min = 0,
max = 720,
step = 1,
value = 240),
numericInput("FRR_1",
label = h5("FRR estimate for survey 1 (%)"),
min = 0,
max = 100,
step = 0.1,
value = 1),
numericInput("FRR_2",
label = h5("FRR estimate for survey 2 (%)"),
min = 0,
max = 100,
step = 0.1,
value = 1),
selectInput("COV_MDRI",
label = h5("Covariance of MDRI values"),
choices = c(0,1),
selected = 0
)
),
column(6,
numericInput("RSE_MDRI_1", label = h5("RSE of MDRI estimate for survey 1 (%)"), value = 5, step = 0.1),
numericInput("RSE_MDRI_2", label = h5("RSE of MDRI estimate for survey 2(%)"), value = 5, step = 0.1),
numericInput("RSE_FRR_1", label = h5("RSE of FRR estimate for survey 1 (%)"), value = 20, step = 0.1),
numericInput("RSE_FRR_2", label = h5("RSE of FRR estimate for survey 2 (%)"), value = 20, step = 0.1),
selectInput("COV_FRR",
label = h5("Covariance of FRR values"),
choices = c(0,1),
selected = 0
)
)
),
fluidRow(column(9,
numericInput("BigT", label = h5("Cut-off BigT T (days)"), value = 730, step = 10)
))
)
),
# wellPanel(
# # fluid page for the assay parameters
# fluidPage(
# h3("Assay Parameters"),
# fluidRow(
# column(6,
# conditionalPanel(
# condition = "input.case != 3",
# numericInput("MDRI",
# label = h5("MDRI estimate (days)"),
# min = 0,
# max = 720,
# step = 1,
# value = 240)
# ),
# conditionalPanel(
# condition = "input.case == 3",
# numericInput("MDRI_1",
# label = h5("MDRI estimate for survey 1 (days)"),
# min = 0,
# max = 720,
# step = 1,
# value = 240)
# ),
# conditionalPanel(
# condition = "input.case == 1",
# numericInput("FRR",
# label = h5("FRR estimate (%)"),
# min = 0,
# max = 100,
# step = 0.1,
# value = 1)
# ),
# conditionalPanel(
# condition = "input.case != 1",
# numericInput("FRR_1",
# label = h5("FRR estimate for survey 1 (%)"),
# min = 0,
# max = 100,
# step = 0.1,
# value = 1)
# )
# ),
# column(6,
# conditionalPanel(
# condition = "input.case != 3",
# numericInput("RSE_MDRI", label = h5("RSE of MDRI estimate (%)"), value = 5, step = 0.1)
# ),
# conditionalPanel(
# condition = "input.case == 3",
# numericInput("RSE_MDRI_1", label = h5("RSE of MDRI estimate for survey 1 (%)"), value = 5, step = 0.1)
# ),
# conditionalPanel(
# condition = "input.case == 1",
# numericInput("RSE_FRR", label = h5("RSE of FRR estimate (%)"), value = 20, step = 0.1)
# ),
# conditionalPanel(
# condition = "input.case != 1",
# numericInput("RSE_FRR_1", label = h5("RSE of FRR estimate for survey 1 (%)"), value = 20, step = 0.1)
# )
# )
# ),
# fluidRow(
# column(6,
# conditionalPanel(
# condition = "input.case == 3",
# numericInput("MDRI_2",
# label = h5("MDRI estimate for survey 2 (days)"),
# min = 0,
# max = 720,
# step = 1,
# value = 240)
# ),
# conditionalPanel(
# condition = "input.case != 1",
# numericInput("FRR_2",
# label = h5("FRR estimate for survey 2 (%)"),
# min = 0,
# max = 100,
# step = 0.1,
# value = 1)
# )
# ),
# column(6,
# conditionalPanel(
# condition = "input.case == 3",
# numericInput("RSE_MDRI_2", label = h5("RSE of MDRI estimate for survey 2(%)"), value = 5, step = 0.1)
# ),
# conditionalPanel(
# condition = "input.case != 1",
# numericInput("RSE_FRR_2", label = h5("RSE of FRR estimate for survey 2 (%)"), value = 20, step = 0.1)
# )
# )
#
# ),
#
# fluidRow(
# column(10,numericInput("BigT", label = h5("Cut-off time T (days)"), value = 730, step = 10)
# )))
# ),
wellPanel(
fluidPage(
h3("Survey Parameters"),
fluidRow(
column(6,
numericInput("PrevH_1", label = h5("Prevalence of HIV infection in survey 1 (%)"), value = 20, step = 0.1, min=0, max = 100),
numericInput("PrevR_1", label = h5("Prevalence of recent infections among positives in survey 1 (%)"), value = 10, step = 0.1, min=0, max = 100)
),
column(6,
numericInput("RSE_PrevH_1", label = h5("RSE of Prevalence HIV infection in survey 1 (%)"), value = 2.8, step = 0.1, min=0, max = 100),
numericInput("RSE_PrevR_1", label = h5("RSE of Prevalence of recent infections among positives 1 (%)"), value = 9.8, step = 0.1, min=0, max = 100))
# )
),
# wellPanel(
fluidRow(
column(6,
numericInput("PrevH_2", label = h5("Prevalence of HIV infection in survey 2 (%)"), value = 21, step = 0.1, min=0, max = 100),
numericInput("PrevR_2", label = h5("Prevalence of recent infections among positives in survey 2 (%)"), value = 13, step = 0.1, min=0, max = 100)
),
column(6,
numericInput("RSE_PrevH_2", label = h5("RSE of Prevalence HIV infection in survey 2 (%)"), value = 3, step = 0.1, min=0, max = 100),
numericInput("RSE_PrevR_2", label = h5("RSE of Prevalence of recent infections among positives 2 (%)"), value = 9.5, step = 0.1, min=0, max = 100))
# )
)
)
)
)
# )
),
mainPanel(
fluidRow(
column(12,
img(src='SACEMA_logo.jpg', align = "right", height = "75px")
#img(src='mcgill.png', align = "right", height = "40px"),
)),
fluidRow(
tabsetPanel(type = "tabs",
tabPanel("Incidence Difference", tableOutput("tab"),
p(""),
p(style = "color:black", strong('Parameter Definitions')),
br(style = "color:grey","compare: surveys compared"),
br(style = "color:grey","Diff: point estimate of the estimated difference (p.a)"),
br(style = "color:grey","CI.Diff.low: lower limit of confidence interval "),
br(style = "color:grey","CI.Diff.up: Upper limit of confidence interval"),
br(style = "color:grey","RSE.Diff: RSE of difference estimate"),
br(style = "color:grey","RSE.Diff.inf.SS: RSE of the difference estimate at the infinite sample size"),
br(style = "color:grey","p.value: P-value for incidence estimate "),
br(style = "color:grey","p.value.inf.SS: P-value at infinite sample size"),
br(),
br()),
tabPanel("User Guide", value='tab3_val', id = 'tab3',
wellPanel(includeHTML("incidence_difference_calculator.html"))
#includeHTML("incidence_difference_calculator.html")
),
tabPanel("About", value='tab4_val', id = 'tab4',
wellPanel( p(""),
p(HTML("calculates the point estimate of incidence difference, the
95% and p-value for incidence difference, from two surveys.")),
p("Contributors:"),
tags$ul(
tags$li("Lamin Juwara"),
tags$li("Eduard Grebe"),
tags$li("Stefano Ongarello"),
tags$li("Cari van Schalkwyk"),
tags$li("Alex Welte")
),
p(em("Built using", a(strong("inctools"), href = "https://cran.r-project.org/web/packages/inctools/index.html", target = "_blank")))
)
)
)
)
)
)
))
SACEMA/inctools documentation built on Dec. 18, 2021, 11:56 a.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.
# Incidence Estimation Tools (Shiny webapps).
# Copyright (C) 2017-2019, Lamin Juwara, individual contributors and
# Stellenbosch University.
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version. This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details. You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
library(shiny)
# Define UI
shinyUI(fluidPage(
# Application title
titlePanel("Incidence Difference Calculator"),
br(),
sidebarLayout(
sidebarPanel(
fluidPage(
wellPanel(
fluidRow(column(9, downloadButton('downloadData', 'Download Results')))
),
# wellPanel(fluidRow(
# column(12,
# radioButtons("case", label = h3("Scenario Type:"),
# c(" Same MDRI, same FRR estimates in the two surveys" = 1,
# " Same MDRI, but different FRR estimates in the two surveys" = 2,
# " Different MDRI and FRR estimates in the two surveys" = 3)),
# selected = 1)
# )),
wellPanel( # fluid page for the assay parameters
fluidPage(
h3("Assay Parameters"),
###
fluidRow(
column(6,
numericInput("MDRI_1",
label = h5("MDRI estimate for survey 1 (days)"),
min = 0,
max = 720,
step = 1,
value = 240),
numericInput("MDRI_2",
label = h5("MDRI estimate for survey 2 (days)"),
min = 0,
max = 720,
step = 1,
value = 240),
numericInput("FRR_1",
label = h5("FRR estimate for survey 1 (%)"),
min = 0,
max = 100,
step = 0.1,
value = 1),
numericInput("FRR_2",
label = h5("FRR estimate for survey 2 (%)"),
min = 0,
max = 100,
step = 0.1,
value = 1),
selectInput("COV_MDRI",
label = h5("Covariance of MDRI values"),
choices = c(0,1),
selected = 0
)
),
column(6,
numericInput("RSE_MDRI_1", label = h5("RSE of MDRI estimate for survey 1 (%)"), value = 5, step = 0.1),
numericInput("RSE_MDRI_2", label = h5("RSE of MDRI estimate for survey 2(%)"), value = 5, step = 0.1),
numericInput("RSE_FRR_1", label = h5("RSE of FRR estimate for survey 1 (%)"), value = 20, step = 0.1),
numericInput("RSE_FRR_2", label = h5("RSE of FRR estimate for survey 2 (%)"), value = 20, step = 0.1),
selectInput("COV_FRR",
label = h5("Covariance of FRR values"),
choices = c(0,1),
selected = 0
)
)
),
fluidRow(column(9,
numericInput("BigT", label = h5("Cut-off BigT T (days)"), value = 730, step = 10)
))
)
),
# wellPanel(
# # fluid page for the assay parameters
# fluidPage(
# h3("Assay Parameters"),
# fluidRow(
# column(6,
# conditionalPanel(
# condition = "input.case != 3",
# numericInput("MDRI",
# label = h5("MDRI estimate (days)"),
# min = 0,
# max = 720,
# step = 1,
# value = 240)
# ),
# conditionalPanel(
# condition = "input.case == 3",
# numericInput("MDRI_1",
# label = h5("MDRI estimate for survey 1 (days)"),
# min = 0,
# max = 720,
# step = 1,
# value = 240)
# ),
# conditionalPanel(
# condition = "input.case == 1",
# numericInput("FRR",
# label = h5("FRR estimate (%)"),
# min = 0,
# max = 100,
# step = 0.1,
# value = 1)
# ),
# conditionalPanel(
# condition = "input.case != 1",
# numericInput("FRR_1",
# label = h5("FRR estimate for survey 1 (%)"),
# min = 0,
# max = 100,
# step = 0.1,
# value = 1)
# )
# ),
# column(6,
# conditionalPanel(
# condition = "input.case != 3",
# numericInput("RSE_MDRI", label = h5("RSE of MDRI estimate (%)"), value = 5, step = 0.1)
# ),
# conditionalPanel(
# condition = "input.case == 3",
# numericInput("RSE_MDRI_1", label = h5("RSE of MDRI estimate for survey 1 (%)"), value = 5, step = 0.1)
# ),
# conditionalPanel(
# condition = "input.case == 1",
# numericInput("RSE_FRR", label = h5("RSE of FRR estimate (%)"), value = 20, step = 0.1)
# ),
# conditionalPanel(
# condition = "input.case != 1",
# numericInput("RSE_FRR_1", label = h5("RSE of FRR estimate for survey 1 (%)"), value = 20, step = 0.1)
# )
# )
# ),
# fluidRow(
# column(6,
# conditionalPanel(
# condition = "input.case == 3",
# numericInput("MDRI_2",
# label = h5("MDRI estimate for survey 2 (days)"),
# min = 0,
# max = 720,
# step = 1,
# value = 240)
# ),
# conditionalPanel(
# condition = "input.case != 1",
# numericInput("FRR_2",
# label = h5("FRR estimate for survey 2 (%)"),
# min = 0,
# max = 100,
# step = 0.1,
# value = 1)
# )
# ),
# column(6,
# conditionalPanel(
# condition = "input.case == 3",
# numericInput("RSE_MDRI_2", label = h5("RSE of MDRI estimate for survey 2(%)"), value = 5, step = 0.1)
# ),
# conditionalPanel(
# condition = "input.case != 1",
# numericInput("RSE_FRR_2", label = h5("RSE of FRR estimate for survey 2 (%)"), value = 20, step = 0.1)
# )
# )
#
# ),
#
# fluidRow(
# column(10,numericInput("BigT", label = h5("Cut-off time T (days)"), value = 730, step = 10)
# )))
# ),
wellPanel(
fluidPage(
h3("Survey Parameters"),
fluidRow(
column(6,
numericInput("PrevH_1", label = h5("Prevalence of HIV infection in survey 1 (%)"), value = 20, step = 0.1, min=0, max = 100),
numericInput("PrevR_1", label = h5("Prevalence of recent infections among positives in survey 1 (%)"), value = 10, step = 0.1, min=0, max = 100)
),
column(6,
numericInput("RSE_PrevH_1", label = h5("RSE of Prevalence HIV infection in survey 1 (%)"), value = 2.8, step = 0.1, min=0, max = 100),
numericInput("RSE_PrevR_1", label = h5("RSE of Prevalence of recent infections among positives 1 (%)"), value = 9.8, step = 0.1, min=0, max = 100))
# )
),
# wellPanel(
fluidRow(
column(6,
numericInput("PrevH_2", label = h5("Prevalence of HIV infection in survey 2 (%)"), value = 21, step = 0.1, min=0, max = 100),
numericInput("PrevR_2", label = h5("Prevalence of recent infections among positives in survey 2 (%)"), value = 13, step = 0.1, min=0, max = 100)
),
column(6,
numericInput("RSE_PrevH_2", label = h5("RSE of Prevalence HIV infection in survey 2 (%)"), value = 3, step = 0.1, min=0, max = 100),
numericInput("RSE_PrevR_2", label = h5("RSE of Prevalence of recent infections among positives 2 (%)"), value = 9.5, step = 0.1, min=0, max = 100))
# )
)
)
)
)
# )
),
mainPanel(
fluidRow(
column(12,
img(src='SACEMA_logo.jpg', align = "right", height = "75px")
#img(src='mcgill.png', align = "right", height = "40px"),
)),
fluidRow(
tabsetPanel(type = "tabs",
tabPanel("Incidence Difference", tableOutput("tab"),
p(""),
p(style = "color:black", strong('Parameter Definitions')),
br(style = "color:grey","compare: surveys compared"),
br(style = "color:grey","Diff: point estimate of the estimated difference (p.a)"),
br(style = "color:grey","CI.Diff.low: lower limit of confidence interval "),
br(style = "color:grey","CI.Diff.up: Upper limit of confidence interval"),
br(style = "color:grey","RSE.Diff: RSE of difference estimate"),
br(style = "color:grey","RSE.Diff.inf.SS: RSE of the difference estimate at the infinite sample size"),
br(style = "color:grey","p.value: P-value for incidence estimate "),
br(style = "color:grey","p.value.inf.SS: P-value at infinite sample size"),
br(),
br()),
tabPanel("User Guide", value='tab3_val', id = 'tab3',
wellPanel(includeHTML("incidence_difference_calculator.html"))
#includeHTML("incidence_difference_calculator.html")
),
tabPanel("About", value='tab4_val', id = 'tab4',
wellPanel( p(""),
p(HTML("calculates the point estimate of incidence difference, the
95% and p-value for incidence difference, from two surveys.")),
p("Contributors:"),
tags$ul(
tags$li("Lamin Juwara"),
tags$li("Eduard Grebe"),
tags$li("Stefano Ongarello"),
tags$li("Cari van Schalkwyk"),
tags$li("Alex Welte")
),
p(em("Built using", a(strong("inctools"), href = "https://cran.r-project.org/web/packages/inctools/index.html", target = "_blank")))
)
)
)
)
)
)
))
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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.
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