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app.R
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### Copyright (C) 2017-2024 Alvaro Santamaria-Gomez, 12 May 2017
###
### This program is free software: you can redistribute it and/or modify
### it under the terms of the GNU General Public License as published by
### the Free Software Foundation, either version 3 of the License, or
### any later version.
###
### This program is distributed in the hope that it will be useful,
### but WITHOUT ANY WARRANTY; without even the implied warranty of
### MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
### GNU General Public License for more details.
###
### You should have received a copy of the GNU General Public License
### along with this program. If not, see <https://www.gnu.org/licenses/>.
# Loading packages ####
suppressPackageStartupMessages(suppressMessages(suppressWarnings({
library(data.table, verbose = F, quietly = T)
library(dlm, verbose = F, quietly = T)
library(fields, verbose = F, quietly = T)
library(lubridate, verbose = F, quietly = T)
library(magrittr, verbose = F, quietly = T)
library(markdown, verbose = F, quietly = T)
library(matrixStats, verbose = F, quietly = T)
library(mnormt, verbose = F, quietly = T)
library(numDeriv, verbose = F, quietly = T)
library(pracma, verbose = F, quietly = T)
library(psych, verbose = F, quietly = T)
library(RColorBrewer, verbose = F, quietly = T)
library(RCurl, verbose = F, quietly = T)
library(XML, verbose = F, quietly = T)
library(jsonlite, verbose = F, quietly = T)
library(shinyBS, verbose = F, quietly = T)
library(shinycssloaders, verbose = F, quietly = T)
library(shinyjs, verbose = F, quietly = T)
library(shinythemes, verbose = F, quietly = T)
library(shiny, verbose = F, quietly = T)
library(spectral, verbose = F, quietly = T)
library(strucchange, verbose = F, quietly = T)
library(tseries, verbose = F, quietly = T)
})))
# Function to check and load packages if installed
check_load <- function(packages) {
for (package in packages) {
if (package %in% rownames(installed.packages())) {
suppressPackageStartupMessages(suppressMessages(suppressWarnings(do.call('library', list(package = package, verbose = F, quietly = T)))))
}
}
}
# Shinyapps & local version
# suppressPackageStartupMessages(suppressMessages(suppressWarnings({
# library(mvcwt, verbose = F, quietly = T)
# library(leaflet, verbose = F, quietly = T)
# library(geojsonio, verbose = F, quietly = T)
# library(Rcpp, verbose = F, quietly = T)
# library(RcppArmadillo, verbose = F, quietly = T)
# library(RcppEigen, verbose = F, quietly = T)
# })))
# GitHub version
optionalPackages <- c(
"mvcwt",
"leaflet",
"geojsonio",
"Rcpp",
"RcppArmadillo",
"RcppEigen"
)
check_load(optionalPackages)
# GUI addons ####
# Help popups (based on https://github.com/daattali/ddpcr/blob/master/inst/shiny/ui/helpers.R)
helpPopup <- function(content, title = NULL, anchor = NULL) {
if (is.null(anchor)) {
a(#href = "#",
class = "popover-link",
`data-toggle` = "popover",
`data-title` = title,
`data-content` = content,
`data-html` = "true",
`data-trigger` = "hover",
`data-placement` = "auto right",
`data-container` = "body",
`data-animation` = "true",
`data-delay` = "show: 100, hide: 500",
icon("circle-question")
)
} else {
a(href = paste0("about.html#",anchor), target = "_blank",
class = "popover-link",
`data-toggle` = "popover",
`data-title` = title,
`data-content` = content,
`data-html` = "true",
`data-trigger` = "hover",
`data-placement` = "auto right",
`data-container` = "body",
`data-animation` = "true",
`data-delay` = "show: 100, hide: 500",
icon("circle-question")
)
}
}
helpPopupHeader <- function(content, title = NULL) {
a(#href = "#",
class = "popover-link",
`data-toggle` = "popover",
`data-title` = title,
`data-content` = content,
`data-html` = "true",
`data-trigger` = "hover",
`data-placement` = "auto right",
`data-container` = "body",
`data-animation` = "true",
`data-delay` = "show: 100, hide: 500",
icon("circle-question", class = "headerIcon")
)
}
# Working spinner (based on https://github.com/daattali/advanced-shiny/blob/master/busy-indicator/helpers.R)
withBusyIndicatorUI <- function(button) {
id <- button[['attribs']][['id']]
div(
shinyjs::useShinyjs(),
singleton(tags$head(
tags$style(withBusyIndicatorCSS)
)),
`data-for-btn` = id,
button,
span(
class = "btn-loading-container",
shinyjs::hidden(
img(src = "ajax-loader-bar.gif", class = "btn-loading-indicator"),
icon("check", class = "btn-done-indicator")
)
),
shinyjs::hidden(
div(class = "btn-err",
div(icon("circle-exclamation"),
tags$b("Error: "),
span(class = "btn-err-msg")
)
)
)
)
}
# CSS class for disabled tabs
withBusyIndicatorCSS <- "
.btn-loading-container {
margin-left: 10px;
font-size: 1.2em;
}
.btn-done-indicator {
color: #61D04F;
}
.btn-err {
margin-top: 10px;
color: #DF536B;
}"
# Mobile detector (from https://g3rv4.com/2017/08/shiny-detect-mobile-browsers)
mobileDetect <- function(inputId, value = 0) {
tagList(
singleton(tags$head(tags$script(src = "mobile.js"))),
tags$input(id = inputId,
class = "mobile-element",
type = "hidden")
)
}
# Disable tab click (based on https://stackoverflow.com/questions/40741691/rshiny-disabling-tabs-adding-text-to-tabs)
css <- '
.disabled {
background: default !important;
cursor: not-allowed !important;
pointer-events: none;
color: gray62 !important;
}'
# show & check plotAll popup
showPopup <- "shinyjs.showPopup = function(file) { overview = window.open('' + file + '', 'plotAll', 'popup=yes, width=1000, height=800, menubar=no, resizable=yes, status=no, titlebar=no, toolbar=no'); }"
checkPopup <- "shinyjs.checkPopup = function() { var status = 'FALSE'; if (typeof overview === 'object') { status = !overview.closed; } Shiny.onInputChange('overview', status);}"
# Update file names from URL/remote (based on https://stackoverflow.com/questions/62626901/r-shiny-change-text-fileinput-after-upload)
update_series <- "
Shiny.addCustomMessageHandler('filename', function(txt) {
var target = $('#series').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); "
update_series2 <- "
Shiny.addCustomMessageHandler('filename2', function(txt) {
var target = $('#series2').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); "
update_sitelog <- "
Shiny.addCustomMessageHandler('log', function(txt) {
var target = $('#log').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); "
update_soln <- "
Shiny.addCustomMessageHandler('soln', function(txt) {
var target = $('#soln').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); "
update_custom <- "
Shiny.addCustomMessageHandler('custom', function(txt) {
var target = $('#custom').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); "
update_step <- "
Shiny.addCustomMessageHandler('step', function(txt) {
var target = $('#step').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); "
update_step2 <- "
Shiny.addCustomMessageHandler('step2', function(txt) {
var target = $('#step2').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); "
update_trendRef <- "
Shiny.addCustomMessageHandler('trendRef', function(txt) {
var target = $('#trendRef').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); "
# Hide loading page splash, from https://stackoverflow.com/questions/35599470/shiny-dashboard-display-a-dedicated-loading-page-until-initial-loading-of
load_data <- function(seconds) {
Sys.sleep(seconds)
shinyjs::hide("loading_page")
shinyjs::show("main_content")
}
# Setting the layout of the plots in the visualization panel
tabContents <- function(tabNum) {
if (tabNum == 1) {
tabName <- uiOutput("tabName1")
} else if (tabNum == 2) {
tabName <- uiOutput("tabName2")
} else if (tabNum == 3) {
tabName <- uiOutput("tabName3")
}
tabPanel(div(style = "font-size: 20px;",tabName), value = tabNum,
tags$style(type = "text/css", "
body {padding-top: 60px;}
#side-panel,.navbar-nav {-webkit-user-select: none; -ms-user-select: none; user-select: none;}
.shiny-html-output {-webkit-user-select: text; -ms-user-select: text; user-select: text;}
"),
hidden(div(id = paste0("zoomin",tabNum), style = "margin-bottom: -3em; margin-top: 2em; color: #DF536B; font-weight: bold; margin-right: 30px; font-size: 10px; text-align: right; position: relative; z-index: 1;", "Zoomed in")),
withSpinner(
plotOutput(paste0("plot",tabNum), click = "plot_1click", dblclick = dblclickOpts("plot_2click", delay = 1000), brush = brushOpts(id = "plot_brush", resetOnNew = T, fill = "#DF536B", stroke = "gray62", opacity = '0.5', clip = T)),
type = getOption("spinner.type", default = 1),
color = getOption("spinner.color", default = "#0080ff"),
size = getOption("spinner.size", default = 2),
color.background = getOption("spinner.color.background", default = "#ffffff"),
custom.css = FALSE, proxy.height = if (grepl("height:\\s*\\d", "plot1")) NULL else "400px"
),
conditionalPanel(
condition = "output.run",
withSpinner(
plotOutput(paste0("res",tabNum), click = "plot_1click", dblclick = dblclickOpts("res_2click", delay = 1000), brush = brushOpts(id = "res_brush", resetOnNew = T, fill = "#2297E6", stroke = "gray62", opacity = '0.5', clip = T)),
type = getOption("spinner.type", default = 1),
color = getOption("spinner.color", default = "#0080ff"),
size = getOption("spinner.size", default = 2),
color.background = getOption("spinner.color.background", default = "#ffffff"),
custom.css = FALSE, proxy.height = if (grepl("height:\\s*\\d", "res1")) NULL else "400px"
)
),
conditionalPanel(
condition = "input.filter == true && input.low !== input.high && output.residuals == false && input.series2filter == 1",
withSpinner(
plotOutput(paste0("vondrak",tabNum), click = "plot_1click", dblclick = "res_2click", brush = brushOpts(id = "vondrak_brush", resetOnNew = T, fill = "#2297E6", stroke = "gray62", opacity = '0.5', clip = T)),
type = getOption("spinner.type", default = 1),
color = getOption("spinner.color", default = "#0080ff"),
size = getOption("spinner.size", default = 2),
color.background = getOption("spinner.color.background", default = "#ffffff"),
custom.css = FALSE, proxy.height = if (grepl("height:\\s*\\d", "res1")) NULL else "400px"
)
),
verbatimTextOutput(paste0("plot",tabNum,"_info"), placeholder = F),
conditionalPanel(
condition = "output.rate",
withSpinner(
plotOutput(paste0("rate",tabNum), click = "plot_1click", dblclick = "rate_2click", brush = brushOpts(id = "rate_brush", resetOnNew = T, fill = "#2297E6", stroke = "gray62", opacity = '0.5', clip = T)),
type = getOption("spinner.type", default = 1),
color = getOption("spinner.color", default = "#0080ff"),
size = getOption("spinner.size", default = 2),
color.background = getOption("spinner.color.background", default = "#ffffff"),
custom.css = FALSE, proxy.height = if (grepl("height:\\s*\\d", "res1")) NULL else "400px"
)
),
conditionalPanel(
condition = "input.filter == true && input.low !== input.high && output.residuals == true && input.series2filter == 2",
withSpinner(
plotOutput(paste0("Vondrak",tabNum), click = "plot_1click", dblclick = "res_2click", brush = brushOpts(id = "vondrak_brush", resetOnNew = T, fill = "#2297E6", stroke = "gray62", opacity = '0.5', clip = T)),
type = getOption("spinner.type", default = 1),
color = getOption("spinner.color", default = "#0080ff"),
size = getOption("spinner.size", default = 2),
color.background = getOption("spinner.color.background", default = "#ffffff"),
custom.css = FALSE, proxy.height = if (grepl("height:\\s*\\d", "res1")) NULL else "400px"
)
),
conditionalPanel(
condition = "input.waveform == true && input.waveformPeriod.length > 0",
withSpinner(
plotOutput(paste0("waveform",tabNum), click = "plot_1click", dblclick = "waveform_2click", brush = brushOpts(id = "waveform_brush", resetOnNew = T, fill = "#2297E6", stroke = "gray62", opacity = '0.5', clip = T)),
type = getOption("spinner.type", default = 1),
color = getOption("spinner.color", default = "#0080ff"),
size = getOption("spinner.size", default = 2),
color.background = getOption("spinner.color.background", default = "#ffffff"),
custom.css = FALSE, proxy.height = if (grepl("height:\\s*\\d", "res1")) NULL else "400px"
)
),
conditionalPanel(
condition = "input.printLog == true",
verbatimTextOutput(paste0("changes_ant",tabNum), placeholder = F),
verbatimTextOutput(paste0("changes_rec",tabNum), placeholder = F)
),
conditionalPanel(
condition = "input.printSinfo == true",
verbatimTextOutput(paste0("changes_ant",tabNum,"s"), placeholder = F),
verbatimTextOutput(paste0("changes_rec",tabNum,"s"), placeholder = F)
),
conditionalPanel(
condition = "input.printSoln == true",
verbatimTextOutput(paste0("changes_ant",tabNum,"so"), placeholder = F),
verbatimTextOutput(paste0("changes_rec",tabNum,"so"), placeholder = F)
),
conditionalPanel(
condition = "input.printCustom == true",
verbatimTextOutput(paste0("changes_ant",tabNum,"c"), placeholder = F)
),
conditionalPanel(
condition = "input.model.length > 0 || input.midas == true || input.entropy == true || input.optionSecondary == 1",
verbatimTextOutput(paste0("summary",tabNum), placeholder = F)
),
conditionalPanel(
condition = "input.histogram == true && input.histogramType > 0",
plotOutput(paste0("hist",tabNum)),
verbatimTextOutput(paste0("stats",tabNum))
),
conditionalPanel(
condition = "input.midas == true",
plotOutput(paste0("midas_hist",tabNum))
),
div(id = paste0("lomb",tabNum), style = "margin-top: 1em",
conditionalPanel(
condition = "input.spectrumOriginal == true || input.spectrumModel == true || input.spectrumResiduals == true || input.spectrumFilter == true || input.spectrumFilterRes == true",
withSpinner(
plotOutput(paste0("res",tabNum,"_espectral"), click = "lomb_1click", dblclick = dblclickOpts("lomb_2click", delay = 1000), brush = brushOpts(id = "lomb_brush", resetOnNew = T, fill = "#2297E6", stroke = "gray62", opacity = '0.5', clip = T, delay = 600)),
type = getOption("spinner.type", default = 1),
color = getOption("spinner.color", default = "#0080ff"),
size = getOption("spinner.size", default = 2),
color.background = getOption("spinner.color.background", default = "#ffffff"),
custom.css = FALSE, proxy.height = if (grepl("height:\\s*\\d", "res1")) NULL else "400px"
),
downloadLink(paste0("downloadSpectrum",tabNum), div(id = paste0("downloadlink",tabNum), style = "margin-top:0em; margin-bottom:2em; font-size: 10px; text-align: right;","Get periodogram data")),
verbatimTextOutput(paste0("lomb",tabNum,"_info"), placeholder = F)
)
),
div(id = paste0("wl",tabNum),
conditionalPanel(
condition = "input.wavelet == true && input.waveletType.length > 0",
withSpinner(
plotOutput(paste0("wavelet",tabNum), click = "wavelet_1click"),
type = getOption("spinner.type", default = 1),
color = getOption("spinner.color", default = "#0080ff"),
size = getOption("spinner.size", default = 2),
color.background = getOption("spinner.color.background", default = "#ffffff"),
custom.css = FALSE, proxy.height = if (grepl("height:\\s*\\d", "res1")) NULL else "400px"
),
verbatimTextOutput(paste0("wavelet",tabNum,"_info"), placeholder = F)
)
)
)
}
# Setting the layout of the model and the residual series for all the components simultaneously
tab3Contents <- function(series) {
if (series == "3D") {
tabNum <- 4
tabName <- uiOutput("tabName4")
} else if (series == "residuals") {
tabNum <- 5
tabName <- uiOutput("tabName5")
}
tabPanel(div(style = "font-size: 20px;",tabName), value = tabNum,
tags$style(type = "text/css", "
body {padding-top: 60px;}
#side-panel,.navbar-nav {-webkit-user-select: none; -ms-user-select: none; user-select: none;}
.shiny-html-output {-webkit-user-select: text; -ms-user-select: text; user-select: text;}
"),
hidden(div(id = paste0("zoomin",tabNum), style = "margin-bottom: -3em; margin-top: 2em; color: #DF536B; font-weight: bold; margin-right: 30px; font-size: 10px; text-align: right; position: relative; z-index: 1;", "Zoomed in")),
div(style = "margin: 2em 0em -4em 4em; font-weight: bold; font-size: 14px; text-align: left; position: relative; z-index: 1;", uiOutput(paste0("component",tabNum,"1"))),
withSpinner(
plotOutput(paste0("plot",tabNum,1), click = paste0("plot",tabNum,"1_1click"), dblclick = dblclickOpts(paste0("plot",tabNum,"1_2click"), delay = 1000), brush = brushOpts(id = paste0("plot",tabNum,"1_brush"), resetOnNew = T, fill = "#DF536B", stroke = "gray62", opacity = '0.5', clip = T)),
type = getOption("spinner.type", default = 1),
color = getOption("spinner.color", default = "#0080ff"),
size = getOption("spinner.size", default = 2),
color.background = getOption("spinner.color.background", default = "#ffffff"),
custom.css = FALSE, proxy.height = if (grepl("height:\\s*\\d", "plot1")) NULL else "400px"
),
div(style = "margin-top: 1.5em;",
div(style = "margin: 0em 0em -4em 4em; font-weight: bold; font-size: 14px; text-align: left; position: relative; z-index: 1;", uiOutput(paste0("component",tabNum,"2"))),
withSpinner(
plotOutput(paste0("plot",tabNum,2), click = paste0("plot",tabNum,"2_1click"), dblclick = dblclickOpts(paste0("plot",tabNum,"2_2click"), delay = 1000), brush = brushOpts(id = paste0("plot",tabNum,"2_brush"), resetOnNew = T, fill = "#DF536B", stroke = "gray62", opacity = '0.5', clip = T)),
type = getOption("spinner.type", default = 1),
color = getOption("spinner.color", default = "#0080ff"),
size = getOption("spinner.size", default = 2),
color.background = getOption("spinner.color.background", default = "#ffffff"),
custom.css = FALSE, proxy.height = if (grepl("height:\\s*\\d", "plot1")) NULL else "400px"
)
),
div(style = "margin-top: 1.5em;",
div(style = "margin: 0em 0em -4em 4em; font-weight: bold; font-size: 14px; text-align: left; position: relative; z-index: 1;", uiOutput(paste0("component",tabNum,"3"))),
withSpinner(
plotOutput(paste0("plot",tabNum,3), click = paste0("plot",tabNum,"3_1click"), dblclick = dblclickOpts(paste0("plot",tabNum,"3_2click"), delay = 1000), brush = brushOpts(id = paste0("plot",tabNum,"3_brush"), resetOnNew = T, fill = "#DF536B", stroke = "gray62", opacity = '0.5', clip = T)),
type = getOption("spinner.type", default = 1),
color = getOption("spinner.color", default = "#0080ff"),
size = getOption("spinner.size", default = 2),
color.background = getOption("spinner.color.background", default = "#ffffff"),
custom.css = FALSE, proxy.height = if (grepl("height:\\s*\\d", "plot1")) NULL else "400px"
)
),
verbatimTextOutput(paste0("plot",tabNum,"_info"), placeholder = F)
)
}
# Source C++ functions on a Windows machine
if (all(c("Rcpp", "RcppArmadillo", "RcppEigen") %in% .packages()) && Sys.info()[['sysname']] == "Windows") {
cat(file = stderr(), "Compiling C++ functions for Windows\n")
sourceCpp('functions.cpp', verbose = F)
}
# Shiny/R general options ####
options(shiny.fullstacktrace = T, shiny.maxRequestSize = 60*1024^2, width = 280, max.print = 50)
options(shiny.trace = F)
devmode(F)
options(shiny.autoreload = T, shiny.autoreload.pattern = "app.R")
options(scipen = 4)
Sys.setlocale('LC_ALL','C')
options(shiny.reactlog = F)
# version ####
version <- "SARI enero 2025"
# UI ####
ui <- fluidPage(theme = shinytheme("spacelab"),
mobileDetect('isMobile'),
useShinyjs(),
extendShinyjs(text = showPopup, functions = c("showPopup")),
extendShinyjs(text = checkPopup, functions = c("checkPopup")),
div( style = "text-align: center; display: flex; flex-direction: column; justify-content: space-between; margin: auto",
id = "loading_page",
h1(style = "text-align: center; color: #333333; font-weight: bold", "SARI session established."),
h1(style = "text-align: center; color: #333333; font-weight: bold", "Loading user interface ..."),
div( style = "margin: 0 auto",
img(src = "SARI_logo_animated.gif", width = "80%")
)
),
# tracker analytics
# tags$head(includeScript("matomo.js")),
# bugfix for unsolicited scrolling to top of page when clicking on a fileInput button
# from https://github.com/rstudio/shiny/issues/3327
tags$script(
HTML(
'setTimeout(() => $(".shiny-bound-input[type=\'file\']").css("all","unset").css("display", "none"), 750);'
)
),
# Getting the input elements that are solicited during execution
tags$script(
"$(document).on('shiny:inputchanged', function(event) {
if (event.name !== 'changed') {
Shiny.setInputValue('changed', event.name);
}
});"
),
# HTTP meta and style header tags
tags$style(css),
tags$head(
tags$script(src = "ddpcr.js"),
tags$head(tags$link(rel = "shortcut icon", href = "favicon.png")),
tags$meta(name = "application-name", content = "SARI"),
tags$meta(name = "description", content = "Interactive & online GNSS position time series analysis tool"),
tags$meta(name = "keywords", content = "SARI,sari,GNSS,gnss,GPS,gps,time,series,analysis"),
tags$meta(name = "author", content = "Alvaro Santamaria-Gomez"),
tags$meta(name = "viewport", content = "width=device-width, initial-scale=1.0"),
tags$html(lang = "en"),
tags$style(HTML("
.help {color: #2297E6; font-weight: bold;}
.UIoption {color: #F5C710; font-weight: bold;}
.warning {color: #DF536B; font-weight: bold;}
.popover {min-width: 21%; color: #ffffff; background-color: #474949; font-size: medium; position: absolute; z-index: 9999;}
.arrow { border-left-color: #8447cf; }
.navbar-nav { width: 98%;}
.navbar-nav li:nth-child(9) { float: right }
.navbar-nav li:nth-child(8) { float: right }
.navbar-nav li:nth-child(2) { width: 17%; }
.navbar-nav li:nth-child(1) { width: 17%; }
.tabbable > .nav > li[class=active] > a { background-color: #333333; color:white; }
.shiny-notification { word-break: break-word; color: #ffffff; background-color: #446e9b; font-size: large; font-weight: bold; border: 3px solid #333333; padding: 10px 8px 10px 10px; margin: 2px; }
.shiny-notification-warning { color: #ffffff; }
.shiny-notification-error { color: #F5C710; }
.shiny-notification-message { color: #ffffff; background-color: #446e9b; font-size: large; font-weight: bold; border: 3px solid #333333; padding: 10px 8px 10px 10px; margin: 2px; position:fixed; top: 0; left: calc(28%); width: 71%}
.shiny-notification-close:hover { color: #ffffff; }
.fa-caret-down { float: right; }
.headerIcon { color: #ffffff;}
/*.shiny-text-output { text-wrap-mode: wrap;}*/
")
),
tags$style(type = "text/css", "#inline label{ display: table-cell; text-align: left; vertical-align: middle; padding: 0px 20px;} #inline .form-group { display: table-row; padding: 0px 20px;}"),
tags$style(type = 'text/css', 'form.well { height: 96vh; overflow-y: auto; width: 100%}'),
tags$style(".modal-body {padding: 10px}
.modal-content {-webkit-border-radius: 6px !important;-moz-border-radius: 6px !important;border-radius: 6px !important;}
.modal-dialog { width: 90%; max-width: 600px; vertical-align: center;}
.modal { color: #333333; font-weight: bold; text-align: center; padding-right:10px; padding-top: 24px;}"),
# Getting user screen size (from https://stackoverflow.com/questions/36995142/get-the-size-of-the-window-in-shiny)
# tags$script('
# var size = [0, 0];
# var tactile = 9;
# $(document).on("shiny:connected", function(e) {
# size[0] = window.outerWidth;
# size[1] = window.outerHeight;
# tactile = navigator.maxTouchPoints;
# Shiny.onInputChange("tactile", tactile);
# Shiny.onInputChange("size", size);
# });
# $(window).resize(function(e) {
# size[0] = window.outerWidth;
# size[1] = window.outerHeight;
# Shiny.onInputChange("size", size);
# });
# '),
# scrolling a block of the left panel to the center of the screen when it is open
tags$script('
document.addEventListener("click", function(event) {
if (event.target.parentElement) {
if (event.target.parentElement.getAttribute("data-toggle") === "collapse") {
const id = event.target.parentElement.href.split("#")[1];
const target = document.getElementById(id);
setTimeout(function() {
target.scrollIntoView({ behavior: "smooth", block: "center" });
}, 300);
}
}
});
'),
# closing the overview window if left open on exit
tags$script('
window.onbeforeunload = closingCode;
function closingCode(){
if (typeof overview === "object") {
if (!overview.closed) {
overview.close();
}
}
return null;
}
'),
# update fileInput file names from URL
tags$script(HTML(update_series)),
tags$script(HTML(update_series2)),
tags$script(HTML(update_sitelog)),
tags$script(HTML(update_soln)),
tags$script(HTML(update_custom)),
tags$script(HTML(update_step)),
tags$script(HTML(update_step2)),
tags$script(HTML(update_trendRef)),
# confirm click on refresh button
# uiOutput("refresh")
),
hidden(
div(id = "main_content",
sidebarLayout(position = "left", fluid = T,
div( id = "menu_all",
# Sidebar menu ####
sidebarPanel(
width = 4,
style = "position:fixed;width:inherit;",
id = "side-panel",
bsCollapse(id = "menu", open = c(1), multiple = T,
# Expandable/collapsible blocks
# * Input data and format ####
bsCollapsePanel(value = 1,
tags$h4(style = "color:white;", icon("database", class = "headerIcon", lib = "font-awesome"), div(style = "color: white; display: inline; text-decoration-line: inherit;", "Input data and format"),
div(style = "float: right; margin-right: 10px;",
helpPopupHeader("This block allows uploading and setting the series format, if necessary, before plotting.<br><br>
Load a series from a local file using the <span class='UIoption'>browse file</span> button or from a remote file using the <span class='UIoption'>server</span>, <span class='UIoption'>product</span>, and <span class='UIoption'>station</span> options.<br><br>
When loading a local file, ensure that the <span class='UIoption'>series format</span>, <span class='UIoption'>time units</span>, and <span class='UIoption'>series units</span> are correct before plotting.<br><br>
Check the series format before plotting with the <span class='UIoption'>show series header</span> option.<br><br>
Activate or deactivate the series error bars with the <span class='UIoption'>use error bars</span> option.<br><br>
Reduce the sampling of the series with the <span class='UIoption'>reduce sampling</span> option.<br><br>
See more details in the </i><span class='help'>help</span> tab."))
),
div(style = "padding: 0px 0px; margin-top:-2em",
fluidRow(
column(4,
br(),
div(style = "font-weight: bold", "Input series file"),
div(style = "margin-right: -1em", uiOutput("fileSeries1"))
),
column(8,
fileInput(inputId = "series", label = "", multiple = F, buttonLabel = "Browse file ...", placeholder = "Empty")
)
)
),
fluidRow(
column(4,
selectInput(inputId = "server1", label = "Input series server", choices = list("", "RENAG", "FORMATER", "SONEL", "IGS", "EUREF", "EPOS", "NGL", "JPL", "EARTHSCOPE", "SIRGAS", "EOSTLS", "PSMSL"), selected = "", multiple = F, selectize = T)
),
column(4,
selectizeInput(inputId = "product1", label = "Product", choices = list(""), selected = "", multiple = F, options = list(maxItems = 1))
),
column(4,
withBusyIndicatorUI(
uiOutput("showStation1")
)
)
),
conditionalPanel(
condition = "output.series1",
div(style = "padding: 0px 0px",
fluidRow(
column(3,
div(style = "font-weight: bold", "Series ID",
helpPopup("This text field shows the GNSS station ID(s) extracted from the file name(s) of the primary and secondary series.<br>
The GNSS station ID(s) are used for extracting the corresponding metadata.<br>
Edit the station ID(s) if necessary.", anchor = "series-id"))
),
column(6,
textInput(inputId = "ids", label = NULL, value = "")
)
)
),
div(style = "padding: 0px 0px; margin-top: 1em",
fluidRow(
column(4,
div(style = "font-weight: bold", "Series format",
helpPopup("This option sets the series file format. Select 1D if the other file formats are unknown.", anchor = "format"))
),
column(8,
radioButtons(inputId = "format", label = NULL, choices = list("NEU/ENU" = 1, "PBO" = 2, "NGL" = 3, "1D" = 4), selected = 1, inline = T, width = "auto"),
)
)
),
conditionalPanel(
condition = "input.format == 4",
fluidRow(
column(6,
selectInput(inputId = "separator", label = "Column separation", choices = list("Blank/Tab" = 1, "Comma" = 2, "Semi-colon" = 3), selected = 1, multiple = F, selectize = T)
),
column(6,
div(style = "font-weight: bold", "Column selection",
helpPopup("Enter the column number for the epochs, data and error bars in the series file.", anchor = "format")
),
div(style = "margin-top:-1em",
fluidRow(
column(4,
textInput(inputId = "epoch", label = "", value = "1")
),
column(4, offset = -2,
textInput(inputId = "variable", label = "", value = "2")
),
column(4, offset = -2,
textInput(inputId = "errorBar", label = "", value = "3")
)
)
)
)
)
),
div(style = "padding: 0px 0px; margin-top:-0em",
fluidRow(
column(5,
div(style = "margin-top:1em",
radioButtons(inputId = "tunits",
div("Time units",
helpPopup("This option sets the units of the time axis.<br>These units define the periods of time in several options.", anchor = "tunits")),
choices = list("Days" = 1, "Weeks" = 2, "Years" = 3), selected = "", inline = F)
),
div(
radioButtons(inputId = "sunits",
div("Series units",
helpPopup("This option sets the units of the variable in the time series.<br>They are used to define the units of the estimated parameters.", anchor = "tunits")),
choices = list("?" = 0, "m" = 1, "mm" = 2), selected = 0, inline = T)
)
),
column(6, offset = 1,
checkboxInput(inputId = "sigmas", label = "Use error bars", value = T),
checkboxInput(inputId = "header",
div("Show series header",
helpPopup("Before plotting the series, this option shows the first lines of the series file.<br>After plotting the series, this option shows the first lines of the series data in the plot.", anchor = "header")),
value = F),
conditionalPanel(
condition = "input.header == true",
sliderInput(inputId = "lines", label = "Number of lines", min = 1, max = 50, value = 10))
)
)
),
fluidRow(
column(6,
checkboxInput(inputId = "average",
div("Reduce sampling",
helpPopup("This option computes the moving average of the series for a given non-overlapping time pediod.<br>
The new sampling period must have a value between the time series sampling and half the time series length.<br>
The new sampling period must be given in the same units as the time axis of the series.<br>
Expressions are allowed starting by <span class='UIoption'>=</span>,<br>
as in <span class='UIoption'>=7/365.25</span>, for a week period in units of years.", anchor = "average")),
value = F)
),
column(6,
div(style = "padding: 0px 0px; margin-top:1em",
conditionalPanel(
condition = "input.average == true",
textInput(inputId = "step", label = "Averaging time period", value = "")
)
)
)
),
conditionalPanel(
condition = "output.data",
div(style = "padding: 0px 0px; margin-top: -1em",
tags$hr(style = "border-color: #333333; border-top: 1px solid #333333;")
),
checkboxInput(inputId = "showmap",
div("Show location map",
helpPopup("If the series header contains the station coordinates, or they are included in a public database, or they are provided by the user in the 'Plate motion model' option, this option will show a map with the station's location together with the tectonic plate boundaries.", anchor = "map")),
value = F),
conditionalPanel(
condition = "input.showmap == false",
div(style = "padding: 0px 0px; margin-top: -1em", htmlOutput("information2"))
),
conditionalPanel(
condition = "input.showmap == true",
fluidRow(
column(6,
div(style = "padding: 0px 0px; margin-top: -1em", htmlOutput("information1"))
),
column(6,
div(style = "margin-top: -3em;",
withSpinner(
uiOutput("map"),
type = getOption("spinner.type", default = 1),
color = getOption("spinner.color", default = "#0080ff"),
size = getOption("spinner.size", default = 2),
color.background = getOption("spinner.color.background", default = "#ffffff"),
custom.css = FALSE, proxy.height = if (grepl("height:\\s*\\d", "plot1")) NULL else "175px"
)
)
)
)
)
)
),
style = "primary"),
# * Plot controls ####
bsCollapsePanel(value = 2,
tags$h4(style = "color:white;", icon("gamepad", class = "headerIcon", lib = "font-awesome"), div(style = "color: white; display: inline; text-decoration-line: inherit;", "Plot controls"),
div(style = "float: right; margin-right: 10px;",
helpPopupHeader("This block allows plotting/resetting the time series with the <span class='UIoption'>plot</span> and <span class='UIoption'>reset</span> buttons.<br><br>
The <span class='UIoption'>overview</span> button opens a new browser window containing a plot of the three coordinate components, if available.<br><br>
Outliers can be excluded manually or automatically with the <span class='UIoption'>toggle</span> and <span class='UIoption'>auto toggle</span> buttons.<br><br>
Removed outliers can be restored with the <span class='UIoption'>reset toggle</span> button.<br><br>
The <span class='UIoption'>truncate</span> option removes the beginning and/or end of the series.<br><br>
The <span class='UIoption'>all components</span> option allows removing the outliers from all the components (if more than one) simultaneously or for each component individually.<br><br>
The <span class='UIoption'>permanent</span> option allows deleting permanently (i.e., not possible to be restored) the next outliers flagged to be toggled or truncated.<br><br>
The <span class='UIoption'>include in file</span> option keeps the excluded outliers in the downloaded results file as commented lines.<br><br>
The <span class='UIoption'>scrolling</span> option enables/disables the vertical scrolling of the left panel.<br><br>
See more details in the <span class='help'>help</span> tab."))
),
fluidRow(
column(2, style = 'padding:0px 1px 0px 10px;', align = "left",
actionButton(inputId = "plot", label = "Plot", icon = icon("eye", class = NULL, lib = "font-awesome"), style = "font-size: small")
),
column(3, style = 'padding:0px 1px 0px 1px;', align = "left",
actionButton(inputId = "plotAll", label = "Overview", icon = icon("bars", class = NULL, lib = "font-awesome"), style = "font-size: small")
),
column(2, style = 'padding:0px 1px 0px 1px;', align = "right",
actionButton(inputId = "reset", label = "Reset", icon = icon("trash", class = NULL, lib = "font-awesome"), style = "font-size: small; color: #F5C710; font-weight: bold")
),
column(2, style = 'padding:0px 1px 0px 1px;', align = "right",
actionButton(inputId = "remove", label = "Toggle", icon = icon("ban", class = NULL, lib = "font-awesome"), style = "font-size: small")
),
column(3, style = 'padding:0px 10px 0px 0px;', align = "right",
actionButton(inputId = "delete_excluded", label = "Reset toggle", icon = icon("backward", class = NULL, lib = "font-awesome"), style = "font-size: small")
)
),
div(style = "padding: 0px 0px; margin-top:1em",
fluidRow(
column(4,
checkboxInput(inputId = "cut",
div("Truncate", style = "font-weight: bold",
helpPopup("This option reduces the time axis of the series by removing all points before and/or after the provided epochs.", anchor = "cut")),
value = F)
),
conditionalPanel(
condition = "input.cut == true",
column(4,
textInput(inputId = "cutStart", label = "Before", value = "")
),
column(4,
textInput(inputId = "cutEnd", label = "After", value = "")
)
)
)
),
div(style = "padding: 0px 0px; margin-top:1em",
fluidRow(
column(4,
textInput(inputId = "thresholdRes",
div("Residual",
helpPopup("Enter the threshold to delete all the points with larger absolute residual.", anchor = "threshold")),
value = NULL)
),
column(4, style = "padding:0px 10px 0px 0px;", align = "left",
textInput(inputId = "thresholdResN",
div("Norm. residual",
helpPopup("Enter the threshold to delete all the points with larger normalized absolute residual.<br>
The residuals values are normalized by their error bars.", anchor = "threshold")),
value = NULL)
),
column(4, style = "padding:0px 10px 0px 0px; margin-top:1.75em", align = "right",
actionButton(inputId = "removeAuto", label = "Auto toggle", icon = icon("car", class = NULL, lib = "font-awesome"), style = "font-size: small")
)
)
),
fluidRow(
column(3,
div(style = "font-weight: bold", "Plot type")
),
column(8,
radioButtons(inputId = "symbol", label = NULL, choices = list("Points" = 0, "Lines" = 1, "Points & Lines" = 2), selected = 0, inline = T)
)
),
div(style = "font-weight: bold", "Plot options"),
fluidRow(
column(4,
checkboxInput(inputId = "remove3D",
div("All components", align = "right",
helpPopup("This option allows toggling or deleting the points from all the coordinate components at the same time or separately.", anchor = "3d")),
value = T)
),
column(4,
checkboxInput(inputId = "permanent",
div("Permanent", align = "right",
helpPopup("This option deletes the points from the series permanently.<br>
Deleted points cannot be restored, unless the series are reset and reloaded.", anchor = "permanent")),
value = F)
),
column(4,
checkboxInput(inputId = "add_excluded",
div("Include in file", align = "right",
helpPopup("This option includes the removed points in the downloaded file as commented lines.", anchor = "excluded")),
value = F)
)
),
fluidRow(
column(4,
checkboxInput(inputId = "overflow",
div("Scrolling",
helpPopup("This options enables or disables the vertical scrolling of the left panel.<br>
When the scrolling is disabled, the user can take a screenshot of the full web page.", anchor = "scrolling")),
value = T)
)
),
style = "primary"),
# * Ancillary information ####
bsCollapsePanel(value = 3,
tags$h4(style = "color:white;", icon("upload", class = "headerIcon", lib = "font-awesome"), div(style = "color: white; display: inline; text-decoration-line: inherit;", "Ancillary information"),
div(style = "float: right; margin-right: 10px;",
helpPopupHeader("This block allows for the uploading of files containing complementary information or metadata related to the analysis of the series.<br><br>
The user can upload any of the following possibilities:<br>
a <span class='UIoption'>SARI</span> file,<br>
a GNSS <span class='UIoption'>sitelog</span>,<br>
a GAMIT-like <span class='UIoption'>station.info</span> file,<br>
an IGS-like <span class='UIoption'>soln</span> file,<br>
a <span class='UIoption'>custom</span> offset file,<br>
a <span class='UIoption'>secondary</span> series.<br>
The secondary series can be <span class='UIoption'>shown</span> next to the primary series or used to either <span class='UIoption'>correct</span> the primary series or to <span class='UIoption'>average</span> both the primary and secondary series.<br><br>
Two model predictions can also be plotted or used to correct the primary series: a <span class='UIoption'>plate motion</span> model and a <span class='UIoption'>GIA</span> model.<br><br>
See more details in the <span class='help'>help</span> tab."))
),
## % SARI model ####
conditionalPanel(
condition = "output.tab3D == true",
div(style = "padding: 0px 0px; margin-top:0em",
fluidRow(
column(6,
div(style = "font-weight: bold", "Load SARI model",
helpPopup("This option allows loading a file with the model fitted in a previous analysis with SARI.", anchor = "ancillary-information")
)
)
)
),
br(),
div(style = "text-align: center;", "Select the tab of a coordinate component to enable this option."),
br()
),
conditionalPanel(
condition = "output.tab3D == false",
div(style = "padding: 0px 0px; margin-top:0em",
fluidRow(
column(6,
div(style = "font-weight: bold", "Load SARI model",
helpPopup("This option allows loading a file with the model fitted in a previous analysis with SARI.", anchor = "ancillary-information")
)
)
),
fluidRow(
column(8,
fileInput(inputId = "loadSARI", label = NULL, multiple = F, buttonLabel = "Browse file ...", placeholder = "Empty")
)
)
)
),
## % sitelog ####
div(style = "padding: 0px 0px; margin-top:0em",
fluidRow(
column(6,
div(style = "font-weight: bold", "Input log file",
helpPopup("This option allows loading an IGS-like sitelog file.", anchor = "notes-on-the-equipment-change-logs")
)
),
column(6, align = "right",
uiOutput("sitelog")
)
),
fluidRow(
column(8,
fileInput(inputId = "log", label = NULL, multiple = F, buttonLabel = "Browse file ...", placeholder = "Empty")
),
column(4,
div(style = "padding: 0px 0px; margin-top:0em",
conditionalPanel(
condition = "output.log",
checkboxInput(inputId = "traceLog", label = "Plot changes", value = F),
checkboxInput(inputId = "printLog", label = "List changes", value = F)
)
)
)
)
),
## % station.info ####
div(style = "padding: 0px 0px; margin-top:-1em",
fluidRow(
column(6,
div(style = "font-weight: bold", "Input station.info file",
helpPopup("This option allows loading a GAMIT/GLOBK station.info file.", anchor = "notes-on-the-equipment-change-logs")
)
),
column(6, align = "right",
uiOutput("station.info")
)
),
fluidRow(
column(8,
fileInput(inputId = "sinfo", label = NULL, multiple = F, buttonLabel = "Browse file ...", placeholder = "Empty")
),
column(4,
div(style = "padding: 0px 0px; margin-top:0em",
conditionalPanel(
condition = "output.sinfo",
checkboxInput(inputId = "traceSinfo", label = "Plot changes", value = F),
checkboxInput(inputId = "printSinfo", label = "List changes", value = F)
)
)
)
)
),
## % soln ####
div(style = "padding: 0px 0px; margin-top:-1em",
fluidRow(
column(6,
div(style = "font-weight: bold", "Input soln file",
helpPopup("This option allows loading an IGS-like soln file.", anchor = "notes-on-the-equipment-change-logs")
)
),