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app.R
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app.R
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### Layout for app
library(here)
library(shiny)
library(dplyr)
library(DT)
library(plotly)
library(tidyr)
library(pins)
library(lubridate)
library(markdown)
ui <- fluidPage(
tags$head(tags$style(HTML('* {font-family: "Futura PT Medium"};'))),
titlePanel(
# creating NVI logo in the top of the app and the title following it
windowTitle = "Laksefiskdødelighet",
fluidRow(
column(4, shiny::HTML(
'<a href="https://www.vetinst.no/">
<img src="vet-rgb-2.svg", alt="NVI logo" style="width:auto;height:40px;"></a>'
)),
column(
8,
h3("Statistikk over tap og dødelighet av laks og regnbueørret", style = "color:#1b314f; font-style:bold")
))
),
sidebarLayout(
sidebarPanel(
uiOutput("sidebar_content"),
width = 2),
mainPanel(
navbarPage(title = "", id = "navbar",
#### top level tab monthly losses ####
tabPanel(h5("Månedlige tap"),
tabsetPanel(
type = "tabs",
tabPanel(
"Diagram",
br(),
fluidRow(column(
width = 6,
selectInput("select_year", "Velg år:", list("År" = c(
2023, 2022, 2021, 2020, 2019
)))
),
column(
width = 6,
selectInput("select_month", "Velg måned:", list(
"Måned" = c(
"01",
"02",
"03",
"04",
"05",
"06",
"07",
"08",
"09",
"10",
"11",
"12"
)
))
)),
plotlyOutput("plot_losses_monthly"),
hr(),
shiny::includeMarkdown("www/tab1_table_and_plot_footer.md")
),
tabPanel(
"Tabell",
br(),
uiOutput("tab_filter_m1"),
DTOutput("table_losses_month"),
hr(),
shiny::includeMarkdown("www/tab1_table_and_plot_footer.md")
)
)),
#### top level tab monthly mortality ####
tabPanel(h5("Månedlige dødsrater"),
tabsetPanel(
type = "tabs",
tabPanel(
"Diagram",
br(),
fluidRow(column(
width = 6,
selectInput("select_year_mort", "Velg år:", list("År" = c(
2023, 2022, 2021, 2020, 2019
)))
),
column(
width = 6,
selectInput("select_zone", "Velg zone:", list(
"Zone" = c("1 & 2", "3", "4", "5", "6",
"7", "8", "9", "10", "11", "12 & 13")
),
multiple = TRUE)
)),
plotlyOutput("plot_mortality_month"),
hr(),
shiny::includeMarkdown("www/tab2_plot_footer.md")
),
tabPanel(
"Tabell",
br(),
uiOutput("tab_filter_m2"),
DTOutput("table_mortality_month"),
hr(),
shiny::includeMarkdown("www/tab2_table_footer.md")
)
)),
#### top level tab yearly losses ####
tabPanel(h5("Årlige tap"),
tabsetPanel(
type = "tabs",
tabPanel(
"Diagram",
br(),
selectInput("select_year_losses", "Velg år:", list("År" = c(
2023, 2022, 2021, 2020, 2019
))),
plotlyOutput("plot_losses"),
hr(),
shiny::includeMarkdown("www/tab3_table_and_plot_footer.md")
),
tabPanel(
"Tabell",
br(),
uiOutput("tab_filter"),
DTOutput("table_losses"),
hr(),
shiny::includeMarkdown("www/tab3_table_and_plot_footer.md")
)
)),
#### top level tab yearly mortality####
tabPanel(h5("Årlig dødelighet"),
tabsetPanel(
type = "tabs",
tabPanel(
"Diagram",
br(),
plotlyOutput("plot_mortality"),
hr(),
shiny::includeMarkdown("www/tab4_table_and_plot_footer.md")
),
tabPanel(
"Tabell",
br(),
uiOutput("tab_filter_2"),
DTOutput("table_mortality"),
hr(),
shiny::includeMarkdown("www/tab4_table_and_plot_footer.md")
)
)),
#### top level tab cohorts####
tabPanel(
h5("Produksjonssykluser dødelighet"),
tabsetPanel(
type = "tabs",
tabPanel(
"Diagram",
br(),
column(width = 6,
selectInput(
"select_year_coh", "Velg år:",
list("År" = c(2023, 2022, 2021, 2020, 2019))
)),
br(),
br(),
br(),
br(),
plotlyOutput("plot_cohort"),
hr(),
shiny::includeMarkdown("www/tab5_plot_footer.md")
),
tabPanel(
"Tabell",
br(),
uiOutput("tab_filter_c"),
DTOutput("table_cohort"),
hr(),
shiny::includeMarkdown("www/tab5_table_footer.md")
)
)
),
#### top level tab calculator####
tabPanel(
h5("Dødelighetskalkulator"),
value = "calc",
verbatimTextOutput("result_text"),
plotOutput("mortality_plot")
),
#### top level tab calculator_2 ####
tabPanel(
h5("Dødelighetskalkulator for utvidet periode"),
value = "calc_cum",
plotOutput("cumulative_risk_plot"),
verbatimTextOutput("result_text_cum")
),
#### top level tab about####
tabPanel(h5("Om statistikken"),
column(width = 9,
shiny::includeMarkdown("www/about.md")))
)
)
)
)
#####
server <- function(input, output) {
#### UI for tab losses monthly ####
observeEvent(input$geo_group, {
if (input$geo_group == "zone") {
output$tab_filter_m1 <-
renderUI(
tagList(
fluidRow(
column(
width = 4,
selectizeInput(
"select_years_table3",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
),
column(
width = 4,
selectizeInput(
"select_month_table3",
"Velg flere måneder:",
c(
"jan",
"feb",
"mar",
"apr",
"mai",
"jun",
"jul",
"aug",
"sep",
"okt",
"nov",
"des"
),
selected = c(
"jan"
),
multiple = T
)
),
column(
width = 4,
selectizeInput(
"select_area3",
"Velg Omrade",
c(1:13),
selected = c(1:13),
multiple = TRUE
)
)
)
)
)
} else if (input$geo_group == "fylke") {
output$tab_filter_m1 <-
renderUI(
tagList(
fluidRow(
column(
width = 4,
selectizeInput(
"select_years_table3",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
),
column(
width = 4,
selectizeInput(
"select_month_table3",
"Velg flere måneder:",
c(
"jan",
"feb",
"mar",
"apr",
"mai",
"jun",
"jul",
"aug",
"sep",
"okt",
"nov",
"des"
),
selected = c(
"jan"
),
multiple = T
)
),
column(
width = 4,
selectizeInput(
"select_area3",
"Velg Omrade",
c("Agder", "Møre og Romsdal",
"Nordland", "Rogaland",
"Troms og Finnmark",
"Trøndelag", "Vestland"),
selected = c("Agder", "Møre og Romsdal",
"Nordland", "Rogaland",
"Troms og Finnmark",
"Trøndelag", "Vestland"),
multiple = TRUE
)
)
)
)
)
} else {
output$tab_filter_m1 <-
renderUI(
tagList(
fluidRow(
column(
width = 6,
selectizeInput(
"select_years_table3",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
),
column(
width = 4,
selectizeInput(
"select_month_table3",
"Velg flere måneder:",
c(
"jan",
"feb",
"mar",
"apr",
"mai",
"jun",
"jul",
"aug",
"sep",
"okt",
"nov",
"des"
),
selected = c(
"jan"
),
multiple = T
)
))))
}
})
#### UI for tab mortality monthly ####
observeEvent(input$geo_group, {
if (input$geo_group == "zone") {
output$tab_filter_m2 <-
renderUI(
tagList(
fluidRow(
column(
width = 4,
selectizeInput(
"select_years_table4",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
),
column(
width = 4,
selectizeInput(
"select_month_table4",
"Velg flere måneder:",
c(
"jan",
"feb",
"mar",
"apr",
"mai",
"jun",
"jul",
"aug",
"sep",
"okt",
"nov",
"des"
),
selected = c(
"jan"
),
multiple = T
)
),
column(
width = 4,
selectizeInput(
"select_area4",
"Velg område",
c("1 & 2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12 & 13"),
selected = c("1 & 2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12 & 13"),
multiple = TRUE
)
)
)
)
)
} else if (input$geo_group == "fylke") {
output$tab_filter_m2 <-
renderUI(
tagList(
fluidRow(
column(
width = 4,
selectizeInput(
"select_years_table4",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
),
column(
width = 4,
selectizeInput(
"select_month_table4",
"Velg flere måneder:",
c(
"jan",
"feb",
"mar",
"apr",
"mai",
"jun",
"jul",
"aug",
"sep",
"okt",
"nov",
"des"
),
selected = c(
"jan"
),
multiple = T
)
),
column(
width = 4,
selectizeInput(
"select_area4",
"Velg Område:",
c("Agder", "Møre og Romsdal",
"Nordland", "Rogaland",
"Troms og Finnmark",
"Trøndelag", "Vestland"),
selected = c("Agder", "Møre og Romsdal",
"Nordland", "Rogaland",
"Troms og Finnmark",
"Trøndelag", "Vestland"),
multiple = TRUE
)
)
)
)
)
} else {
output$tab_filter_m2 <-
renderUI(
tagList(
fluidRow(
column(
width = 6,
selectizeInput(
"select_years_table4",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
),
column(
width = 4,
selectizeInput(
"select_month_table4",
"Velg flere måneder:",
c(
"jan",
"feb",
"mar",
"apr",
"mai",
"jun",
"jul",
"aug",
"sep",
"okt",
"nov",
"des"
),
selected = c(
"jan"
),
multiple = T
)
))))
}
})
#### UI for tab losses yearly ####
observeEvent(input$geo_group, {
if (input$geo_group == "zone") {
output$tab_filter <-
renderUI(
tagList(
fluidRow(
column(
width = 6,
selectizeInput(
"select_years_table1",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
),
column(
width = 6,
selectizeInput(
"select_area1",
"Velg Omrade",
c(1:13),
selected = c(1:13),
multiple = TRUE
)
)
)
)
)
} else if (input$geo_group == "fylke") {
output$tab_filter <-
renderUI(
tagList(
fluidRow(
column(
width = 6,
selectizeInput(
"select_years_table1",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
),
column(
width = 6,
selectizeInput(
"select_area1",
"Velg Omrade",
c("Agder", "Møre og Romsdal",
"Nordland", "Rogaland",
"Troms og Finnmark",
"Trøndelag", "Vestland"),
selected = c("Agder", "Møre og Romsdal",
"Nordland", "Rogaland",
"Troms og Finnmark",
"Trøndelag", "Vestland"),
multiple = TRUE
)
)
)
)
)
} else {
output$tab_filter <-
renderUI(
tagList(
fluidRow(
column(
width = 6,
selectizeInput(
"select_years_table1",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
))))
}
})
#### UI for tab mortality yearly ####
observeEvent(input$geo_group, {
if (input$geo_group == "zone") {
output$tab_filter_2 <-
renderUI(
tagList(
fluidRow(
column(
width = 6,
selectizeInput(
"select_years_table2",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
),
column(
width = 6,
selectizeInput(
"select_area2",
"Velg Omrade",
c(1:13),
selected = c(1:13),
multiple = TRUE
)
)
)
)
)
} else if (input$geo_group == "fylke") {
output$tab_filter_2 <-
renderUI(
tagList(
fluidRow(
column(
width = 6,
selectizeInput(
"select_years_table2",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
),
column(
width = 6,
selectizeInput(
"select_area2",
"Velg Omrade",
c("Agder", "Møre og Romsdal",
"Nordland", "Rogaland",
"Troms og Finnmark",
"Trøndelag", "Vestland"),
selected = c("Agder", "Møre og Romsdal",
"Nordland", "Rogaland",
"Troms og Finnmark",
"Trøndelag", "Vestland"),
multiple = TRUE
)
)
)
)
)
} else {
output$tab_filter_2 <-
renderUI(
tagList(
fluidRow(
column(
width = 6,
selectizeInput(
"select_years_table2",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
))))
}
})
#### UI for tab cohorts ####
observeEvent(input$geo_group, {
if (input$geo_group == "zone") {
output$tab_filter_c <-
renderUI(
tagList(
fluidRow(
column(
width = 6,
selectizeInput(
"select_years_table5",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
),
column(
width = 6,
selectizeInput(
"select_locs",
"Velg Omrade",
c(1:13),
selected = c(1:13),
multiple = TRUE
)
)
)
)
)
} else if (input$geo_group == "fylke") {
output$tab_filter_c <-
renderUI(
tagList(
fluidRow(
column(
width = 6,
selectizeInput(
"select_years_table5",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
),
column(
width = 6,
selectizeInput(
"select_locs",
"Velg Omrade",
c("Agder", "Møre og Romsdal",
"Nordland", "Rogaland",
"Troms og Finnmark",
"Trøndelag", "Vestland"),
selected = c("Agder", "Møre og Romsdal",
"Nordland", "Rogaland",
"Troms og Finnmark",
"Trøndelag", "Vestland"),
multiple = TRUE
)
)
)
)
)
} else {
output$tab_filter_c <-
renderUI(
tagList(
fluidRow(
column(
width = 6,
selectizeInput(
"select_years_table5",
"Velg flere år:",
c(
"2023" = 2023,
"2022" = 2022,
"2021" = 2021,
"2020" = 2020,
"2019" = 2019
),
selected = c(2023),
multiple = T
)
))))
}
})
observeEvent(input$navbar, {
if (input$navbar == "calc") {
output$sidebar_content <-
renderUI(
tagList(
numericInput("beginning_count",
"Antall fisk ved periodens start (f.eks. dag, uke, måned)",
value = 100),
numericInput("end_count", "Antall fisk ved periodens slutt", value = 90),
numericInput("dead_count", "Antall døde fisk i løpet av perioden", value = 5),
actionButton("calculate_button", "Kalkuler")
)
)
} else if (input$navbar == "calc_cum") {
output$sidebar_content <-
renderUI(
tagList(
selectInput(
"period_type",
"Velg periode:",
choices = c(
"Dag" = "day",
"Uke" = "week",
"Måned" = "month"
),
selected = "month"
),
textInput("mortality_input_cum",
"Fyll inn dødsrate for flere perioder (separer perioder ved å bruke komma, og bruk et punktum i stedet for et komma for desimaltall, f.eks. 0.5, 1, 1.5, 2):",
""),
actionButton("calculate_button_cum", "Kalkuler")
)
)
} else {
output$sidebar_content <- renderUI(
tagList(
selectInput("species", "Velg art:",
c("Laks" = "salmon", #should match what is in the data set to use as a selection (for example, "salmon" matches salmon in losses)
"Regnbueørret" = "rainbowtrout"),
selected = c("salmon")),
selectInput("geo_group", "Velg geografisk område:",
c("Fylke" = "fylke",
"Produksjonssone" = "zone",
"Norge" = "all"),
selected = c("zone")),
hr(),
shiny::includeMarkdown("www/sidebar_text.md"))
)
}
})
#### colors ####
myPallete <- c('#cd692c', '#98a762','#dac266','#886b9a')
#### data ####
laksetap_board <- board_connect()
# this is the dataset used for the existing app.
losses <- pin_read(laksetap_board, "vi2451/losses_and_mortality_yearly_data")
# new datasets
losses_monthly_data <- pin_read(laksetap_board, "vi2451/losses_monthly_data")
mortality_rates_monthly_data <- pin_read(laksetap_board, "vi2451/mortality_rates_monthly_data")
mortality_cohorts_data <- pin_read(laksetap_board, "vi2451/mortality_cohorts_data")
#### LOSSES yearly ####
df_losses <-
eventReactive(c(input$species, input$geo_group), {
losses %>%
dplyr::filter(species == input$species &
viz == input$geo_group)
})
# any changes you make to df_losses will affect both the table and the plot,
# if you want to use df_losses write df_losses()
##### Yearly tables need to observe for Norge #####
observeEvent(input$geo_group, {
if (input$geo_group == "all") {
output$table_losses <- DT::renderDT(
datatable(
df_losses() %>%
dplyr::select(
"year",
"area",
"losses",
"doed",
"p.doed",
"ut",
"p.ut",
"romt",
"p.romt",
"ufor",
"p.ufor"
) %>%
dplyr::filter(
year %in% input$select_years_table1
),
#filter = "top",
rownames = F,
colnames = c(
"År",
"Område",
"Total",
"Døde",
"Døde%",