add adjustments. Still not figures

R/app_ui.R

@@ -26,46 +26,47 @@ app_ui <- function(request) {
                            # select species of interest
                            selectInput(inputId = "select_spp",
                                        label = "Select species",
-                                       choices = c("Chinook (CH)", "Steelhead (STL)"),
-                                       selected = NULL,
+                                       choices =  data$species,#c("Chinook (CH)", "Steelhead (STL)"),
+                                       selected = NULL,#"Chinook (CH)",
                                        width = "200px",
                                        multiple = T),
                            #select rear type
                            selectInput(inputId = "select_rear",
                                        label = "Select rearing type",
-                                       choices = c("Wild (W)", "Hatchery (H)"),
-                                       selected = NULL,
-                                       width = "200px",
-                                       multiple = T),
-                           # select response metric
-                           selectInput(inputId = "select_metric",
-                                       label = "Select response metric",
-                                       choices = c("Smolt-to-adult return ratio (SAR) ", " Transport to bypass ratio (T:B)"),
-                                       selected = NULL,
+                                       choices = data$rear_type, #c("Wild (W)", "Hatchery (H)"),
+                                       selected =  NULL, #"Wild (W)",
                                        width = "200px",
                                        multiple = T),
+                           # # select response metric
+                           # selectInput(inputId = "select_metric",
+                           #             label = "Select response metric",
+                           #             choices = c("Smolt-to-adult return ratio (SAR) ", " Transport to bypass ratio (T:B)"),
+                           #             selected = "Smolt-to-adult return ratio (SAR) ",
+                           #             width = "200px",
+                           #             multiple = T),
                            # select covariate of interest
                            selectInput(inputId = "select_cov",
                                        label = "Select covariate",
-                                       choices = c("Day of Year (DOY)", "Temperature"),
-                                       selected = NULL,
+                                       choices = data$covariate, #c("Day of Year (DOY)", "Temperature"),
+                                       selected = NULL, #"Day of Year (DOY)",
                                        width = "200px",
                                        multiple = T),
-                           # select years of interest
+                           # select years of interest--currently able to select one year based on function writtten-UPDATE
                            shinyWidgets::pickerInput(inputId = "select_year",
                                        label = "Select years",
-                                       choices = 1993:2018,
+                                       choices = unique(data$year),#1993:2018,
+                                       selected = NULL, #1993:2018,
                                        options = list(`actions-box` = TRUE),
                                        width = "200px",
-                                       multiple = T), #windowPadding = 1 doesn't work
-                           # add button to run after options are selected
-                           actionButton(inputId = 'btn_run_selected',
-                                        label = paste0('Run'),
-                                        icon = icon("wrench")),
-                           ## reset side bar selectoin
-                           actionButton(inputId = 'btn_reset_selected',
-                                        label = 'Reset',
-                                        icon = icon('refresh') )
+                                       multiple = T) #windowPadding = 1 doesn't work
+                           # # add button to run after options are selected
+                           # actionButton(inputId = 'btn_run_selected',
+                           #              label = paste0('Run'),
+                           #              icon = icon("wrench")),
+                           # ## reset side bar selectoin
+                           # actionButton(inputId = 'btn_reset_selected',
+                           #              label = 'Reset',
+                           #              icon = icon('refresh') )
 
                            ),
 

R/fct_get_pred_data.R

@@ -0,0 +1,8 @@
+#' get_pred_data
+#'
+#' @description A fct function
+#'
+#' @return The return value, if any, from executing the function.
+#'
+#' @noRd
+

R/fct_make_plots.R

@@ -0,0 +1,36 @@
+#' make_plots
+#'
+#' @description A fct function
+#'
+#' @return The return value, if any, from executing the function.
+#'
+#' @noRd
+
+
+plot_fx<- function(spp, rtype, cov, SAR_year){
+    data %>%
+    filter(year == SAR_year,
+           species == spp,
+           rear_type == rtype,
+           covariate == cov) %>%
+    ggplot(aes( x= date, color = as.factor(transport), group = year)) +
+    geom_point(aes(y =SAR, fill = as.factor(transport)))+
+    geom_jitter(aes(y =sar.pit, shape = as.factor(transport)), alpha = .7)+
+    geom_lineribbon( aes(y = SAR, ymin =SAR.lo, ymax = SAR.hi, fill = as.factor(transport)), alpha = .25) +
+    labs( x = "Date", y = "SAR", color = NULL,
+          fill = NULL, shape = NULL,
+          title = "Predicted SAR versus observed SAR from PIT tag recoveries",
+          subtitle = paste("Year:",SAR_year)) +
+    scale_color_manual(breaks = c(0, 1),
+                       values = c("steelblue4", "#b47747"),
+                       labels = c("In-river, \npredicted with 95% CI", "Transported, \npredicted with 95% CI"))+
+    scale_fill_manual(breaks = c(0, 1),
+                      values = c("steelblue4", "#b47747"),
+                      labels = c("In-river, \npredicted with 95% CI", "Transported, \npredicted with 95% CI"))+
+    scale_shape_manual(values = c(21,21),
+                       breaks = c(0,1),
+                       labels = c("In-river, observed", "Transported, observed")) +
+    guides(shape = "legend") +
+    theme_minimal()
+
+}

R/mod_Figures.R

@@ -1,4 +1,4 @@
-#' Home UI Function
+#' Figures UI Function
 #'
 #' @description A shiny Module.
 #'
@@ -11,17 +11,65 @@ mod_Figures_ui <- function(id){
   ns <- NS(id)
   tagList(
 
+    fluidPage(
 
+      fluidRow(
+        h2("Header"),
+        shinydashboard::box(
+          title = "X",
+          width = 6,
+          plotOutput(outputId = ns("plot1"))),
+
+        shinydashboard::box(
+          title = "X2",
+          width = 6,
+          plotOutput(outputId = ns("plot2"))
+        )
+      ),
+
+      fluidRow(
+        shinydashboard::box(
+          title = "X",
+          width = 6,
+          plotOutput(outputId = ns("plot3"))),
+
+        shinydashboard::box(
+          title = "X2",
+          width = 6,
+          plotOutput(outputId = ns("plot4"))
+        )
+      )
+    )
   )
 }
 
-#' Home Server Functions
+#' Figures Server Functions
 #'
 #' @noRd
 mod_Figures_server <- function(id){
   moduleServer( id, function(input, output, session){
     ns <- session$ns
 
+     plot1 <- reactive({plot_fx(spp = input$select_spp,
+                     rtype = input$select_rear,
+                     cov = input$select_cov,
+                     SAR_year = input$select_year)})
+     output$plot1 <- renderPlot({
+       plot1()
+    })
+
+    output$plot2 <- renderPlot({
+      shinipsum::random_ggplot(type = "line")
+    })
+
+    output$plot3 <- renderPlot({
+      shinipsum::random_ggplot(type = "line")
+    })
+
+    output$plot4 <- renderPlot({
+      shinipsum::random_ggplot(type = "line")
+    })
+
   })
 }