R/app_ui.R
In mathedjoe/animaltracker: Animal Tracker
Defines functions
app_ui
### UI the Shiny App
#'
#'Defines a user interface for the 'shiny' app
#'
#'
#'@return ui function for use in a 'shiny' app
#'@noRd
#'
app_ui <- function(){
jsCode <- 'shinyjs.removePolygon = function() {
var event = document.createEvent("Event");
event.initEvent("click", true, true);
var trashButton = document.getElementsByClassName("leaflet-draw-edit-remove");
!trashButton[0].dispatchEvent(event);
var clearButton = document.querySelector(\'[title="Clear all layers"]\');
!clearButton.dispatchEvent(event);
}'
navbarPage(theme = shinythemes::shinytheme("yeti"),
header = div(shinyjs::useShinyjs(),
shinyjs::extendShinyjs(text = jsCode, functions = "removePolygon")),
title = "Animal Tracker",
## DATA PANEL
tabPanel("Data",
sidebarLayout(
sidebarPanel(
h4("1. Upload Data"),
helpText("Select a zip folder on your computer containing .csv files. Please upload data from one
area at a time."),
fileInput("zipInput", "Upload zip file", accept=c(".zip")),
textOutput("numUploaded"),
hr(),
h4("2. Select Data"),
reactivePickerOutput("choose_site") %>% shinycssloaders::withSpinner(),
reactivePickerOutput("choose_ani"),
shinyBS::bsCollapse(id = "restrictOptions",
shinyBS::bsCollapsePanel("Restrict Date/Time/Location",
datePickerOutput("choose_dates"),
timeOutput("min_time"),
timeOutput("max_time"),
reactiveRangeOutput("lat_bounds"),
reactiveRangeOutput("long_bounds")
, value = "restrict_options"),
open = "restrict_options"
),
hr(),
h4("3. Data Processing"),
shinyBS::bsCollapse(id = "uploadOptions", open = "General Options",
shinyBS::bsCollapsePanel("General Options",
checkboxInput("filterBox", label = "Filter bad data points", value = TRUE),
checkboxInput("kalman_enable", label = "Cluster data with Kalman filtering", value = FALSE),
checkboxInput("dbscan_enable", label = "Cluster data with DBSCAN filtering", value = FALSE),
checkboxInput("elevBox", label = "Append USGS Elevation data"),
checkboxInput("weatherBox", label = "Append NOAA Hourly Weather data")
)),
shinyBS::bsCollapse(id = "filterOptions",
shinyBS::bsCollapsePanel("Filter Options",
uiOutput("max_rate"),
uiOutput("max_course"),
uiOutput("max_dist"),
uiOutput("max_clean_time")
), open = "Filter Options"),
shinyBS::bsCollapse(id = "kalmanOptions",
shinyBS::bsCollapsePanel("Kalman Configuration Options",
uiOutput("kalman_max_timestep")
), open = "Kalman Configuration Options"),
shinyBS::bsCollapse(id = "dbscanOptions",
shinyBS::bsCollapsePanel("DBSCAN Configuration Options",
uiOutput("knn_eps"),
uiOutput("knn_k"),
uiOutput("interp")
), open = "DBSCAN Configuration Options"),
shinyBS::bsCollapse(id = "elevOptions",
shinyBS::bsCollapsePanel("Elevation Options",
uiOutput("zoom"),
checkboxInput("slopeBox", label = "Include slope", value = TRUE),
checkboxInput("aspectBox", label = "Include aspect", value = TRUE)
), open = "Elevation Options"),
shinyBS::bsCollapse(id = "weatherOptions",
shinyBS::bsCollapsePanel("Weather Options",
reactivePickerOutput("choose_station"),
shinyWidgets::pickerInput("selected_weather",
label = "Select weather variables",
choices = c("wind direction", "wind speed", "ceiling height",
"visibility distance", "temperature", "dewpoint temperature",
"air pressure", "precipitation depth"),
selected = c("wind direction", "wind speed", "temperature",
"dewpoint temperature", "air pressure"),
multiple = TRUE,
options = list(`actions-box` = TRUE)
)), open = "Weather Options"
),
actionButton("processButton", "Process All"),
actionButton("processSelectedButton", "Process Selected"),
hr(),
h4("4. Download Data"),
helpText("Save data to a (potentially large) .csv file."),
# Button
shinyBS::bsCollapse(id = "downloadOptionsPanel",
shinyBS::bsCollapsePanel("Download Options",
radioButtons("downloadOptions", NULL,
c("Processed (unfiltered) data", "Processed (filtered) data", "Currently selected data"),
selected = "Currently selected data"))
),
downloadButton("downloadData", "Download")
),#sidebarPanel
mainPanel(
leafletOutput("mainmap", height = 640) %>% shinycssloaders::withSpinner(),
htmlOutput("mapinfo"),
br(),
br(),
h4("Display Geographic Features"),
fileInput("kmzInput", "Upload kmz file to display fences, etc.", accept=c(".kmz")),
h4("Add Water Sources"),
fileInput("waterInput", "Upload kmz file to compute distance to water", accept=c(".kmz")),
h4("Recent Data"),
reactivePickerOutput("choose_recent"),
textOutput("nrow_recent"),
br(),
tableOutput("head_recent")
) #mainPanel
) #sidebarLayout
), #end data panel
## PLOTS PANEL
tabPanel("Plots",
actionButton("generateGif", "Create movement animation"),
imageOutput("animatedPlot"),
reactivePlotOutput("plot_elevation_line"),
reactivePlotOutput("plot_samplerate_hist"),
reactivePlotOutput("plot_rate_violin"),
reactivePlotOutput("plot_time_heatmap")
),# end plots panel
## ANALYSIS PANEL
tabPanel("Analysis",
sidebarLayout(
sidebarPanel(
h4("Variables"),
staticPickerOutput("choose_cols"),
hr(),
h4("Summary Statistics"),
staticPickerOutput("choose_stats")
),
mainPanel(
h2("Statistical Summary of Selected Data"),
helpText("To change the sample, switch to the Data panel."),
statsLabelOutput("elevation_title"),
statsOutput("elevation"),
statsLabelOutput("speed_title"),
statsOutput("speed"),
statsLabelOutput("timediff_title"),
statsOutput("timediff"),
statsLabelOutput("course_title"),
statsOutput("course"),
statsLabelOutput("coursediff_title"),
statsOutput("coursediff"),
statsLabelOutput("distance_title"),
statsOutput("distance"),
statsLabelOutput("rate_title"),
statsOutput("rate"),
statsLabelOutput("slope_title"),
statsOutput("slope"),
statsLabelOutput("aspect_title"),
statsOutput("aspect")
)
)
),# end analysis panel
## Secondary navigation "More" Panel
navbarMenu("More",
## ABOUT PANEL
tabPanel("About",
p("This app is part of a larger project to integrate GPS tracking data for animals (e.g., cattle) with data management and visualization tools. If you're interesting in joining our efforts, please reach out to one of the collaborators."),
h2("Get the Code"),
p("The code for this Shiny App and related functions is stored on github. "),
a(h4("View Code", class = "btn btn-default action-button" ,
style = "fontweight:600"), target = "_blank",
href = 'https://github.com/mathedjoe/animaltracker'),
h2("Usage"),
p("The following R code will install the package and run this app in your browser. (For more advanced usage, please consult the documentation and codebase, or reach out to the contributors.)"),
code("install.packages('devtools') # (if not already installed)", tags$br(),
"devtools::install_github('mathedjoe/animaltracker') # installs the package", tags$br(),
"library(animaltracker) # loads the package", tags$br(),
"run_shiny_animaltracker() # runs the app"),
h2("Contributors"),
tags$ul(
tags$li("Sergio Arispe (lead researcher), Oregon State University,", a("sergio.arispe@oregonstate.edu", href='mailto:Sergio.Arispe@oregonstate.edu'),
HTML(", "), a("website",href = 'https://extension.oregonstate.edu/people/sergio-arispe', target="_blank" )),
tags$li("Joe Champion (lead developer), Boise State University,", a("joechampion@boisestate.edu", href='mailto:joechampion@boisestate.edu'),
HTML(", "), a("website",href = 'https://math.boisestate.edu/jchampion/', target="_blank" )),
tags$li("Thea Sukianto (student assistant), Boise State University,", a("TheophiliaSukian@u.boisestate.edu", href='mailto:TheophiliaSukian@u.boisestate.edu')),
tags$li("Chithkala Dhulipati (student assistant), Boise State University,", a("chithkaladhulipa@u.boisestate.edu ", href='mailto:chithkaladhulipa@u.boisestate.edu')),
tags$li("Joseph Goodwin (student assistant), Oregon State University,", a("jgoodwin9628@gmail.com", href='mailto:jgoodwin9628@gmail.com')),
tags$li("Sebastian Benjamin (student assistant), Oregon State University,", a("sebastiancbenjamin@gmail.com", href='mailto:sebastiancbenjamin@gmail.com')),
tags$li("Connor Wilson (student assistant), Oregon State University,", a("connor.wilson48@gmail.com", href='mailto:connor.wilson48@gmail.com')),
tags$li("Dylan Mikesell (researcher), Boise State University,", a("dylanmikesell@boisestate.edu", href='mailto:dylanmikesell@boisestate.edu'))
)
))
)
}
mathedjoe/animaltracker documentation built on Aug. 12, 2021, 7:46 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions app_ui
### UI the Shiny App
#'
#'Defines a user interface for the 'shiny' app
#'
#'
#'@return ui function for use in a 'shiny' app
#'@noRd
#'
app_ui <- function(){
jsCode <- 'shinyjs.removePolygon = function() {
var event = document.createEvent("Event");
event.initEvent("click", true, true);
var trashButton = document.getElementsByClassName("leaflet-draw-edit-remove");
!trashButton[0].dispatchEvent(event);
var clearButton = document.querySelector(\'[title="Clear all layers"]\');
!clearButton.dispatchEvent(event);
}'
navbarPage(theme = shinythemes::shinytheme("yeti"),
header = div(shinyjs::useShinyjs(),
shinyjs::extendShinyjs(text = jsCode, functions = "removePolygon")),
title = "Animal Tracker",
## DATA PANEL
tabPanel("Data",
sidebarLayout(
sidebarPanel(
h4("1. Upload Data"),
helpText("Select a zip folder on your computer containing .csv files. Please upload data from one
area at a time."),
fileInput("zipInput", "Upload zip file", accept=c(".zip")),
textOutput("numUploaded"),
hr(),
h4("2. Select Data"),
reactivePickerOutput("choose_site") %>% shinycssloaders::withSpinner(),
reactivePickerOutput("choose_ani"),
shinyBS::bsCollapse(id = "restrictOptions",
shinyBS::bsCollapsePanel("Restrict Date/Time/Location",
datePickerOutput("choose_dates"),
timeOutput("min_time"),
timeOutput("max_time"),
reactiveRangeOutput("lat_bounds"),
reactiveRangeOutput("long_bounds")
, value = "restrict_options"),
open = "restrict_options"
),
hr(),
h4("3. Data Processing"),
shinyBS::bsCollapse(id = "uploadOptions", open = "General Options",
shinyBS::bsCollapsePanel("General Options",
checkboxInput("filterBox", label = "Filter bad data points", value = TRUE),
checkboxInput("kalman_enable", label = "Cluster data with Kalman filtering", value = FALSE),
checkboxInput("dbscan_enable", label = "Cluster data with DBSCAN filtering", value = FALSE),
checkboxInput("elevBox", label = "Append USGS Elevation data"),
checkboxInput("weatherBox", label = "Append NOAA Hourly Weather data")
)),
shinyBS::bsCollapse(id = "filterOptions",
shinyBS::bsCollapsePanel("Filter Options",
uiOutput("max_rate"),
uiOutput("max_course"),
uiOutput("max_dist"),
uiOutput("max_clean_time")
), open = "Filter Options"),
shinyBS::bsCollapse(id = "kalmanOptions",
shinyBS::bsCollapsePanel("Kalman Configuration Options",
uiOutput("kalman_max_timestep")
), open = "Kalman Configuration Options"),
shinyBS::bsCollapse(id = "dbscanOptions",
shinyBS::bsCollapsePanel("DBSCAN Configuration Options",
uiOutput("knn_eps"),
uiOutput("knn_k"),
uiOutput("interp")
), open = "DBSCAN Configuration Options"),
shinyBS::bsCollapse(id = "elevOptions",
shinyBS::bsCollapsePanel("Elevation Options",
uiOutput("zoom"),
checkboxInput("slopeBox", label = "Include slope", value = TRUE),
checkboxInput("aspectBox", label = "Include aspect", value = TRUE)
), open = "Elevation Options"),
shinyBS::bsCollapse(id = "weatherOptions",
shinyBS::bsCollapsePanel("Weather Options",
reactivePickerOutput("choose_station"),
shinyWidgets::pickerInput("selected_weather",
label = "Select weather variables",
choices = c("wind direction", "wind speed", "ceiling height",
"visibility distance", "temperature", "dewpoint temperature",
"air pressure", "precipitation depth"),
selected = c("wind direction", "wind speed", "temperature",
"dewpoint temperature", "air pressure"),
multiple = TRUE,
options = list(`actions-box` = TRUE)
)), open = "Weather Options"
),
actionButton("processButton", "Process All"),
actionButton("processSelectedButton", "Process Selected"),
hr(),
h4("4. Download Data"),
helpText("Save data to a (potentially large) .csv file."),
# Button
shinyBS::bsCollapse(id = "downloadOptionsPanel",
shinyBS::bsCollapsePanel("Download Options",
radioButtons("downloadOptions", NULL,
c("Processed (unfiltered) data", "Processed (filtered) data", "Currently selected data"),
selected = "Currently selected data"))
),
downloadButton("downloadData", "Download")
),#sidebarPanel
mainPanel(
leafletOutput("mainmap", height = 640) %>% shinycssloaders::withSpinner(),
htmlOutput("mapinfo"),
br(),
br(),
h4("Display Geographic Features"),
fileInput("kmzInput", "Upload kmz file to display fences, etc.", accept=c(".kmz")),
h4("Add Water Sources"),
fileInput("waterInput", "Upload kmz file to compute distance to water", accept=c(".kmz")),
h4("Recent Data"),
reactivePickerOutput("choose_recent"),
textOutput("nrow_recent"),
br(),
tableOutput("head_recent")
) #mainPanel
) #sidebarLayout
), #end data panel
## PLOTS PANEL
tabPanel("Plots",
actionButton("generateGif", "Create movement animation"),
imageOutput("animatedPlot"),
reactivePlotOutput("plot_elevation_line"),
reactivePlotOutput("plot_samplerate_hist"),
reactivePlotOutput("plot_rate_violin"),
reactivePlotOutput("plot_time_heatmap")
),# end plots panel
## ANALYSIS PANEL
tabPanel("Analysis",
sidebarLayout(
sidebarPanel(
h4("Variables"),
staticPickerOutput("choose_cols"),
hr(),
h4("Summary Statistics"),
staticPickerOutput("choose_stats")
),
mainPanel(
h2("Statistical Summary of Selected Data"),
helpText("To change the sample, switch to the Data panel."),
statsLabelOutput("elevation_title"),
statsOutput("elevation"),
statsLabelOutput("speed_title"),
statsOutput("speed"),
statsLabelOutput("timediff_title"),
statsOutput("timediff"),
statsLabelOutput("course_title"),
statsOutput("course"),
statsLabelOutput("coursediff_title"),
statsOutput("coursediff"),
statsLabelOutput("distance_title"),
statsOutput("distance"),
statsLabelOutput("rate_title"),
statsOutput("rate"),
statsLabelOutput("slope_title"),
statsOutput("slope"),
statsLabelOutput("aspect_title"),
statsOutput("aspect")
)
)
),# end analysis panel
## Secondary navigation "More" Panel
navbarMenu("More",
## ABOUT PANEL
tabPanel("About",
p("This app is part of a larger project to integrate GPS tracking data for animals (e.g., cattle) with data management and visualization tools. If you're interesting in joining our efforts, please reach out to one of the collaborators."),
h2("Get the Code"),
p("The code for this Shiny App and related functions is stored on github. "),
a(h4("View Code", class = "btn btn-default action-button" ,
style = "fontweight:600"), target = "_blank",
href = 'https://github.com/mathedjoe/animaltracker'),
h2("Usage"),
p("The following R code will install the package and run this app in your browser. (For more advanced usage, please consult the documentation and codebase, or reach out to the contributors.)"),
code("install.packages('devtools') # (if not already installed)", tags$br(),
"devtools::install_github('mathedjoe/animaltracker') # installs the package", tags$br(),
"library(animaltracker) # loads the package", tags$br(),
"run_shiny_animaltracker() # runs the app"),
h2("Contributors"),
tags$ul(
tags$li("Sergio Arispe (lead researcher), Oregon State University,", a("sergio.arispe@oregonstate.edu", href='mailto:Sergio.Arispe@oregonstate.edu'),
HTML(", "), a("website",href = 'https://extension.oregonstate.edu/people/sergio-arispe', target="_blank" )),
tags$li("Joe Champion (lead developer), Boise State University,", a("joechampion@boisestate.edu", href='mailto:joechampion@boisestate.edu'),
HTML(", "), a("website",href = 'https://math.boisestate.edu/jchampion/', target="_blank" )),
tags$li("Thea Sukianto (student assistant), Boise State University,", a("TheophiliaSukian@u.boisestate.edu", href='mailto:TheophiliaSukian@u.boisestate.edu')),
tags$li("Chithkala Dhulipati (student assistant), Boise State University,", a("chithkaladhulipa@u.boisestate.edu ", href='mailto:chithkaladhulipa@u.boisestate.edu')),
tags$li("Joseph Goodwin (student assistant), Oregon State University,", a("jgoodwin9628@gmail.com", href='mailto:jgoodwin9628@gmail.com')),
tags$li("Sebastian Benjamin (student assistant), Oregon State University,", a("sebastiancbenjamin@gmail.com", href='mailto:sebastiancbenjamin@gmail.com')),
tags$li("Connor Wilson (student assistant), Oregon State University,", a("connor.wilson48@gmail.com", href='mailto:connor.wilson48@gmail.com')),
tags$li("Dylan Mikesell (researcher), Boise State University,", a("dylanmikesell@boisestate.edu", href='mailto:dylanmikesell@boisestate.edu'))
)
))
)
}
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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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