-
Notifications
You must be signed in to change notification settings - Fork 1
/
app.R
144 lines (110 loc) · 4.67 KB
/
app.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
library(tidyverse)
library(shiny)
library(shinythemes)
library(leaflet)
library(mapview)
# render mapview doesn't work; this function works
myRenderMapview <- function(expr, env = parent.frame(), quoted = FALSE){
if (!quoted)
expr = substitute(mapview:::mapview2leaflet(expr))
htmlwidgets::shinyRenderWidget(expr, leafletOutput, env,
quoted = TRUE)
}
# read layer
aus_SA2 <- sf::read_sf("shiny-resources/aus_SA2.gpkg") %>%
dplyr::select(SA2_CODE21, SA2_NAME21, Region, State, `Incursion risk`, `Climatic suitability`, `Establishment likelihood`, `Tourist pathway`, `Returning resident pathway`, `Visiting friends & family pathway`, `Sea cargo pathway`, `Natural dispersal pathway`, `Budwood pathway`)
roads <- sf::read_sf("shiny-resources/roads.gpkg")
# layers
all_layers <- c("Incursion risk", "Climatic suitability", "Establishment likelihood", "Tourist pathway", "Returning resident pathway", "Visiting friends & family pathway", "Sea cargo pathway", "Natural dispersal pathway", "Budwood pathway")
data <-
aus_SA2 %>%
tibble::as_tibble() %>%
dplyr::select(-geom)
org_counts <-
data %>%
dplyr::count(State) %>%
dplyr::pull(n)
names(org_counts) <- sort(unique(data$State))
ui <- shinyUI(
navbarPage("Citrus Biosecurity",
selected = "Risk maps",
theme = shinytheme("flatly"),
# Panel 1 -----------------------------------------------------------------
tabPanel(
"Risk maps",
splitLayout(
selectizeInput(inputId = "select_map",
label = "Select layer",
options = list(dropdownParent = 'body',
create = 0),
choices = all_layers),
sliderInput(inputId = "select_quant_map",
label = "Select cutoff (quantile)",
min = 0,
max = 1,
value = 0,
round = -2)
),
# map prediction maps
uiOutput("maps")
),
# Panel 2 -----------------------------------------------------------------
tabPanel(
"Top risk",
splitLayout(
selectizeInput(inputId = "select_filt",
label = "Select filter",
options = list(dropdownParent = 'body',
create = 0),
choices = all_layers),
sliderInput(inputId = "select_quant_dt",
label = "Select cutoff (quantile)",
min = 0,
max = 1,
value = 0.9,
round = -2)
),
# filtered table
tableOutput("table_ui")
)
)
)
server <- function(input, output, session){
map <- reactive({
mapview(map.types = "Esri.WorldStreetMap", roads, layer.name = "Roads", legend = FALSE, label = roads$name, hide = TRUE) +
aus_SA2 %>%
dplyr::filter(.data[[input$select_map]] >= quantile(.data[[input$select_map]], .env$input$select_quant_map)) %>%
mapview(layer.name = input$select_map,
zcol = input$select_map,
label = aus_SA2$SA2_NAME21,
col.regions = viridis::inferno(n = 100))
})
# the maps
output$maps <- renderUI({
myRenderMapview(map())
})
tab <- reactive({
data <- data %>%
dplyr::group_by(State) %>%
dplyr::filter(.data[[input$select_filt]] >= quantile(.data[[input$select_filt]], .env$input$select_quant_dt)) %>%
dplyr::arrange(State, dplyr::desc(.data[[input$select_filt]]))
counts <- data %>%
dplyr::count(State) %>%
dplyr::pull(n)
names(counts) <- sort(unique(data$State))
filt_states <- names(which(!(org_counts - counts == 0)))
data <- data %>%
filter(State %in% filt_states)
})
output$table_ui <- renderUI({
if(nrow(tab()) == 0)
return("All SA2 above cutoff - select different value")
DT::DTOutput("table")
})
output$table <- DT::renderDT({tab()},
filter = "top",
options = list(
pageLength = 20
))
}
shinyApp(ui, server)