add 2021 IDN fish data and include year selector

Rare-Technology · Nov 4, 2021 · d812799 · d812799
1 parent fb6539e
commit d812799
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Showing 15 changed files with 176 additions and 49 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -22,6 +22,7 @@ importFrom(shiny,tagList)
 importFrom(shinyWidgets,dropdown)
 importFrom(shinyWidgets,multiInput)
 importFrom(shinyWidgets,pickerInput)
+importFrom(shinyWidgets,radioGroupButtons)
 importFrom(shinyWidgets,switchInput)
 importFrom(shinyWidgets,updatePickerInput)
 importFrom(shinyjs,extendShinyjs)

diff --git a/R/mod_main.R b/R/mod_main.R
@@ -36,7 +36,7 @@ mainUI <- function(id){
     tabsetPanel(
       id = ns('tabs'),
       tabPanel("Start", startUI("startUI")),
-      tabPanel('Coral Reefs', plotUI('plotUI')),
+      tabPanel('Fish', plotUI('plotUI')),
       tabPanel('Mangrove Forests', mangroveUI('mangroveUI')),
       tabPanel('Map', mapUI('mapUI'))
       # tabPanel('Report', reportUI('reportUI'))

diff --git a/R/mod_plot.R b/R/mod_plot.R
@@ -29,16 +29,16 @@ plotServer <- function(id, rv){
       sel_maa <- rv$sel_maa
       y_scale <- rv$sel_yscale
       sel_geom <- rv$sel_geom
-      sel_dates <- rv$sel_dates
+      sel_year <- rv$sel_year
 
       if (is.null(sel_maa)) {
         div(class="warning_message", "No managed access area selected.")
       } else {
         p <- switch(rv$sel_metric,
-              "Fish Biomass" = plot_biomass(data_filtered, sel_family, sel_geom),
-              "Fish Density" = plot_density(data_filtered, sel_family, sel_geom),
-              "Fish Diversity" = plot_diversity(data_filtered, sel_family, sel_geom),
-              "Fish Size" = plot_size(data_filtered, sel_family, sel_geom)
+              "Fish Biomass" = plot_biomass(data_filtered, sel_year, sel_family, sel_geom),
+              "Fish Density" = plot_density(data_filtered, sel_year, sel_family, sel_geom),
+              "Fish Diversity" = plot_diversity(data_filtered, sel_year, sel_family, sel_geom),
+              "Fish Size" = plot_size(data_filtered, sel_year, sel_family, sel_geom)
         )
         p$facet$params$free$y <- y_scale
         rv$current_plot <- p

diff --git a/R/mod_plot_utils_fish_biomass.R b/R/mod_plot_utils_fish_biomass.R
@@ -1,7 +1,8 @@
-plot_biomass <- function(data_filtered, sel_family, sel_geom) {
+plot_biomass <- function(data_filtered, sel_year, sel_family, sel_geom) {
   data_aggreg <- data_filtered %>% 
-                  dplyr::filter(family %in% sel_family) %>% 
-                  aggregate_data(., 'biomass_kg_ha')
+    dplyr::filter(family %in% sel_family) %>% 
+    dplyr::filter(year == sel_year) %>% 
+    aggregate_data(., 'biomass_kg_ha')
 
   if (sel_geom == 'Bar plots') {
     data_summary <- summarySE(data_aggreg, 'biomass_kg_ha')

diff --git a/R/mod_plot_utils_fish_density.R b/R/mod_plot_utils_fish_density.R
@@ -1,7 +1,8 @@
-plot_density <- function(data_filtered, sel_family, sel_geom) {
+plot_density <- function(data_filtered, sel_year, sel_family, sel_geom) {
   data_aggreg <- data_filtered %>% 
-                  dplyr::filter(family %in% sel_family) %>% 
-                  aggregate_data(., 'density_ind_ha')
+    dplyr::filter(family %in% sel_family) %>% 
+    dplyr::filter(year == sel_year) %>% 
+    aggregate_data(., 'density_ind_ha')
   if (sel_geom == 'Bar plots') {
     data_summary <- summarySE(data_aggreg, 'density_ind_ha')
 

diff --git a/R/mod_plot_utils_fish_diversity.R b/R/mod_plot_utils_fish_diversity.R
@@ -1,6 +1,7 @@
-plot_diversity <- function(data_filtered, sel_family, sel_geom) {
+plot_diversity <- function(data_filtered, sel_year, sel_family, sel_geom) {
   data_aggreg <- data_filtered %>% 
     dplyr::filter(family %in% sel_family) %>% 
+    dplyr::filter(year == sel_year) %>% 
     aggregate_data(., 'species')
   if (sel_geom == 'Bar plots') {
     data_summary <- summarySE(data_aggreg, 'species')

diff --git a/R/mod_plot_utils_fish_size.R b/R/mod_plot_utils_fish_size.R
@@ -1,13 +1,14 @@
-plot_size <- function(data_filtered, sel_family, sel_geom) {
+plot_size <- function(data_filtered, sel_year, sel_family, sel_geom) {
 
   data_aggreg <- data_filtered %>% 
     dplyr::filter(family %in% sel_family) %>% 
-    aggregate_data(., 'sizeclass')
+    dplyr::filter(year == sel_year) %>% 
+    aggregate_data(., 'size_class')
 
   if (sel_geom == "Bar plots") {
     data_summary <- summarySE(data_aggreg, 'density_ind_ha', for.size=TRUE)
     ggplot2::ggplot(data=data_summary,
-                    aes(sizeclass, density_ind_ha),
+                    aes(size_class, density_ind_ha),
                     na.rm = TRUE) +
       facet_wrap('ma_name') +
       geom_bar(aes(fill = location_status), position=position_dodge(),
@@ -16,7 +17,7 @@ plot_size <- function(data_filtered, sel_family, sel_geom) {
   } else {
     data_local <- get_local_data(data_aggreg, 'density_ind_ha', for.size=TRUE)
     ggplot2::ggplot(data=data_local,
-                    aes(sizeclass, group=location_status),
+                    aes(size_class, group=location_status),
                     na.rm = TRUE) +
       facet_wrap('ma_name') +
       geom_density(aes(fill=location_status), size=0.3, alpha=0.5) +

diff --git a/R/mod_plot_utils_selection.R b/R/mod_plot_utils_selection.R
@@ -51,11 +51,11 @@ aggregate_data <- function(data_filtered, metric) {
                 data = .,
                 FUN = mean)
 
-  } else if (metric == 'sizeclass') {
+  } else if (metric == 'size_class') {
     # idea: for each size class, you can expect to see `density_ind_ha` many 
     # fish per hectare.
     aggregate(density_ind_ha ~ country + ma_name + location_status + location_name + 
-                transect_no + sizeclass, data=data_filtered, FUN=sum)
+                transect_no + size_class, data=data_filtered, FUN=sum)
   }
 }
 
@@ -66,27 +66,27 @@ get_local_data <- function(data_aggreg, metric, for.size=FALSE) {
   if (metric %in% c("biomass_kg_ha", "density_ind_ha", "dbh_cm", "sapling_tree_density_ind_m2")) {
     groupvars <- c('country', 'ma_name', 'location_status', 'location_name')
     if (for.size) {
-      groupvars <- append(groupvars, 'sizeclass')
+      groupvars <- append(groupvars, 'size_class')
     }
     formula <- paste(metric, paste(groupvars, collapse=" + "), sep=" ~ ") %>% 
       as.formula()
     aggregate(formula, data=data_aggreg, FUN=mean)
-  } else { # sizeclass
+  } else { # size_class
     aggregate(density_ind_ha ~ country + ma_name + location_status +
-                location_name + sizeclass, data=data_aggreg, FUN=mean)
+                location_name + size_class, data=data_aggreg, FUN=mean)
   }
 }
 summarySE <- function(data_aggreg, metric, for.size=FALSE, for.tree=FALSE) {
 
   groupvars1 <- c('country', 'ma_name', 'location_status', 'location_name')
   groupvars2 <- groupvars1[-length(groupvars1)]
   if (for.size) {
-    groupvars1 <- append(groupvars1, 'sizeclass')
-    groupvars2 <- append(groupvars2, 'sizeclass')
+    groupvars1 <- append(groupvars1, 'size_class')
+    groupvars2 <- append(groupvars2, 'size_class')
     # changing metric to 'count' to use in the following aggregates w/o changing
     # the code much. maybe clunky to do so and it may be better to just set metric
     # to 'count' from the beginning, but from a readability/comprehension standpoint,
-    # I think it makes sense to keep metric as 'sizeclass' in the beginning,
+    # I think it makes sense to keep metric as 'size_class' in the beginning,
     # as it makes it very clear that the surrounding code is in regard to fish size
   }
 
@@ -108,7 +108,7 @@ summarySE <- function(data_aggreg, metric, for.size=FALSE, for.tree=FALSE) {
   # take mean across locations
   data_summary <- aggregate(formula2, data=data_loc, FUN=mean)
 
-  if (!for.size) { # ie not sizeclass
+  if (!for.size) { # ie not size_class
     data_summary$N <- aggregate(formula2, data=data_loc, FUN=length) %>% 
       dplyr::pull(metric)
     data_summary$SD <- aggregate(formula2, data=data_loc, FUN=sd) %>% 

diff --git a/R/mod_side_display.R b/R/mod_side_display.R
@@ -7,7 +7,7 @@
 #' @noRd 
 #'
 #' @importFrom shiny NS tagList
-#' @importFrom shinyWidgets pickerInput multiInput switchInput
+#' @importFrom shinyWidgets pickerInput multiInput switchInput radioGroupButtons
 #' @importFrom leaflet providers
 sidebarDisplayUI <- function(id){
   ns <- NS(id)
@@ -24,7 +24,7 @@ sidebarDisplayServer <- function(id, rv){
       ui <- NULL #list()
       current_tab <- rv$current_tab
 
-      if (current_tab == 'Coral Reefs') {
+      if (current_tab == 'Fish') {
         ui <- tagList(
           div(class="sidetitle", "Plotting"),
           selectInput(ns('sel_metric'),
@@ -54,20 +54,8 @@ sidebarDisplayServer <- function(id, rv){
                         `selected-text-format` = "count > 3"
                       ),
                       multiple = TRUE
-          ),
-          # switchInput(ns("sel_date"),
-          #             "Plot dates")
-          # don't need this right now
-          # pickerInput(ns('sel_species'),
-          #             'Fish species',
-          #             choices = LETTERS,
-          #             options = list(
-          #               `actions-box` = TRUE,
-          #               `selected-text-format` = "count > 2"
-          #             ),
-          #             multiple = TRUE
-          # )
-        ) # tagList
+          )
+        )
       } else if(current_tab == "Mangrove Forests") {
         ui <- tagList(
           div(class = "sidetitle", "Plotting"),
@@ -87,6 +75,14 @@ sidebarDisplayServer <- function(id, rv){
           )
         )
       }
+      ui <- tagList(ui,
+        radioGroupButtons(
+          ns("sel_year"),
+          "Year",
+          choices = get_year_choices(rv$sel_country, rv$data_full$fish),
+          selected = max(get_year_choices(rv$sel_country, rv$data_full$fish))
+        )
+      )
 
       if (current_tab == 'Map') {
 
@@ -148,6 +144,11 @@ sidebarDisplayServer <- function(id, rv){
       # rv$data_map <- get_biomass_loc(rv$data_aggreg)
     }, ignoreInit = TRUE
     )
+
+    observeEvent(input$sel_year, {
+      rv$sel_year <- input$sel_year
+    }, ignoreInit = TRUE
+    )
   })
 }
 

diff --git a/R/mod_side_display_utils_selection.R b/R/mod_side_display_utils_selection.R
@@ -5,4 +5,12 @@ get_display_choices <- function(sel_maa, data_full) {
     unique() %>% 
     as.vector() %>% 
     sort()
+}
+
+get_year_choices <- function(sel_country, data_full) {
+  data_full %>% 
+    dplyr::filter(country == sel_country) %>% 
+    dplyr::pull(year) %>% 
+    unique() %>% 
+    sort()
 }
diff --git a/R/mod_side_geography.R b/R/mod_side_geography.R
@@ -22,7 +22,7 @@ sidebarGeoServer <- function(id, rv){
     output$geo <- renderUI({
       current_tab <- rv$current_tab
 
-      if (current_tab %in% c("Start", "Coral Reefs", "Map")) {
+      if (current_tab %in% c("Start", "Fish", "Map")) {
         init_country_choices <- INIT$COUNTRY_CHOICES$FISH
         init_subnational_choices <- INIT$SUBNATIONAL_CHOICES$FISH
         init_local_choices <- INIT$LOCAL_CHOICES$FISH
@@ -65,7 +65,7 @@ sidebarGeoServer <- function(id, rv){
         ),
         pickerInput(
           ns('sel_maa'),
-          'Managed access area',
+          'Community',
           choices = init_maa_choices,
           selected = NULL,
           multiple = TRUE,
@@ -96,7 +96,7 @@ sidebarGeoServer <- function(id, rv){
 
     observeEvent(input$sel_country, {
       rv$sel_country <- input$sel_country
-      if (rv$current_tab %in% c("Start", "Coral Reefs", "Map")) {
+      if (rv$current_tab %in% c("Start", "Fish", "Map")) {
         data_country <- rv$data_full$fish %>%
           dplyr::filter(country == input$sel_country)
       } else if (rv$current_tab == "Mangrove Forests") {
@@ -115,7 +115,7 @@ sidebarGeoServer <- function(id, rv){
 
     observeEvent(input$sel_subnational, {
       rv$sel_subnational <- input$sel_subnational
-      if (rv$current_tab %in% c("Start", "Coral Reefs", "Map")) {
+      if (rv$current_tab %in% c("Start", "Fish", "Map")) {
         data_subnational <- rv$data_full$fish %>%
           dplyr::filter(level1_name %in% input$sel_subnational)
       } else if (rv$current_tab == "Mangrove Forests") {
@@ -134,7 +134,7 @@ sidebarGeoServer <- function(id, rv){
 
     observeEvent(input$sel_local, {
       rv$sel_local <- input$sel_local
-      if (rv$current_tab %in% c("Start", "Coral Reefs", "Map")) {
+      if (rv$current_tab %in% c("Start", "Fish", "Map")) {
         data_local <- rv$data_full$fish %>%
           dplyr::filter(level2_name %in% input$sel_local)
       } else if (rv$current_tab == "Mangrove Forests") {
@@ -155,7 +155,7 @@ sidebarGeoServer <- function(id, rv){
 
     observeEvent(input$sel_maa, {
       rv$sel_maa <- input$sel_maa
-      if (rv$current_tab %in% c("Start", "Coral Reefs", "Map")) {
+      if (rv$current_tab %in% c("Start", "Fish", "Map")) {
         rv$data_filtered$fish <- rv$data_full$fish %>%
           dplyr::filter(ma_name %in% input$sel_maa)
       } else if (rv$current_tab == "Mangrove Forests") {

diff --git a/R/utils_init.R b/R/utils_init.R
@@ -6,7 +6,7 @@
 #'
 #' @noRd
 # INIT <-  list()
-# INIT$CURRENT_TAB <- 'Coral Reefs'
+# INIT$CURRENT_TAB <- 'Start'
 # INIT$SEL_METRIC <- 'Fish Biomass'
 # INIT$SEL_GEOM <- "Bar plots"
 # INIT$SEL_YSCALE <- TRUE
@@ -21,6 +21,10 @@
 #   FISH = "HND",
 #   MANGROVES = "Mozambique"
 # )
+# INIT$SEL_YEAR <- fish.surveys %>%
+#   filter(country == INIT$SEL_COUNTRY$FISH) %>%
+#   pull(year) %>%
+#   max()
 # INIT$DATA_FULL <- list(
 #   FISH = fish.surveys %>% dplyr::filter(family != ""),
 #   MANGROVES = mangroves