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app.R
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app.R
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# clear memory to free up space
gc()
library(shiny)
library(shinyWidgets) # for updating buttons
library(shinyjs) # for enabling/disabling download buttons
library(shinybusy) # to show progress when processing a full time series
library(leaflet) # for creating map
library(leafpm) # for drawing/editing polygons on the map (replacing leaflet.extras)
library(fst) # for speedier data file loading
library(minpack.lm) # to use nlsLM for gaussian fit
library(sf) # to make polygons into simple feature collections (sfc)
library(sp) # convert sfc to spatial to use sp::over() to extract pixels in polygons
library(ggplot2) # for the density and time series plots
library(ggpp) # for overlaying tables and text on plots
library(dplyr) # for formatting data tables
library(oceancolouR) # for shifted_gaussian() and pad0()
library(terra) # for making rasters
# other required packages: raster, leafem, quantreg, fs (functions called using :: notation)
source("rateOfChange.R") # rate of change (ROC) function for model fit
source("threshold.R") # threshold function for model fit
source("gaussFit.R") # gaussian function for model fit
source("full_run.R") # contains function to run full time series with current settings
source("functions.R") # extra functions
source("00_input_variables.R") # load pre-defined variables
# deprecated shinyWidgets function
# https://github.com/dreamRs/shinyWidgets/blob/26838f9e9ccdc90a47178b45318d110f5812d6e1/R/setSliderColor.R
setSliderColor <- function(color, sliderId) {
# the css class for ionrangeslider starts from 0
# therefore need to remove 1 from sliderId
sliderId <- sliderId - 1
# create custom css background for each slider selected by the user
sliderCol <- lapply(sliderId, FUN = function(i) {
paste0(
".js-irs-", i, " .irs-single,",
" .js-irs-", i, " .irs-from,",
" .js-irs-", i, " .irs-to,",
" .js-irs-", i, " .irs-bar-edge,",
" .js-irs-", i,
" .irs-bar{ border-color: transparent;background: ", color[i+1],
"; border-top: 1px solid ", color[i+1],
"; border-bottom: 1px solid ", color[i+1],
";}"
)
})
# insert this custom css code in the head of the shiy app
custom_head <- tags$head(tags$style(HTML(as.character(sliderCol))))
return(custom_head)
}
#*******************************************************************************
# UI ####
ui <- fluidPage(
# For hiding download buttons if data hasn't been loaded yet
useShinyjs(),
# styling
tags$head(tags$style(HTML(sidebar_tags_style))),
inlineCSS(list("#applysettings" = "margin-top: -15px")),
tags$style(".shiny-file-input-progress {display: none}
.irs-grid-text {font-size: 14px; color: white; bottom: -10px; top: 12px;}"),
# old polygon removal code
tags$div(remove_custom_poly),
# color and style for sliderInput (note this does not affect sliderTextInput)
chooseSliderSkin("Flat", color="#00cc00"),
# needed for zlim sliderTextInput
setSliderColor("#00cc00", sliderId=1),
titlePanel("Satellite Data Visualization"),
fluidRow(
sidebarPanel(width=3,
#*******************************************************************
# UI MAIN SETTINGS ####
helpText(HTML(bhelp$settings_file), width=widget_width, style=label_text_style_main_options),
br(),
fileInput(inputId="settings_file", label=NULL, multiple=FALSE, accept=".txt", width=widget_width),
actionButton(inputId="applysettings", label="Apply settings", style=button_style),
uiOutput("help_settings_file", width=widget_width, style="white-space: normal;"),
hr(),
helpText(HTML(bhelp$main_settings), width=widget_width, style=label_text_style_main_options),
br(),br(),
helpText("Region", width=widget_width, style=label_text_style_main_options),
selectInput(inputId="region", label=NULL, choices=regions, selected=default_region, width=widget_width),
helpText("Satellite and variable", width=widget_width, style=label_text_style_main_options),
selectInput(inputId="sat_alg", label=NULL, choices=default_sat_algs, selected=default_sat_algs[1], width=widget_width),
helpText(bhelp$concentration_type, width=widget_width, style=paste(label_text_style_main_options, "margin-bottom: 20px;")),
radioButtons(inputId="concentration_type", label=NULL, choices=concentration_types, selected="full", width=widget_width),
conditionalPanel(condition = "input.concentration_type == 'model1'",
radioGroupButtons(inputId = "cell_size_model1", label=NULL,
choices=cell_sizes_model1, selected = "small", width=widget_width)),
conditionalPanel(condition = "input.concentration_type == 'model2'",
radioGroupButtons(inputId = "cell_size_model2", label=NULL,
choices=cell_sizes_model2, selected = "small", width=widget_width)),
br(),
helpText("Year", width=widget_width, style=label_text_style_main_options),
selectInput(inputId = "year", label=NULL, choices=rev(default_years), width=widget_width),
helpText("Data composite length", width=widget_width, style=label_text_style_main_options),
selectInput(inputId = "composite", label=NULL, choices=composites, width=widget_width),
helpText("Log-transform data", width=widget_width, style=label_text_style_main_options),
switchInput(inputId = "log_chla", label=HTML("log<sub>10</sub>"), value=TRUE, onStatus = "success"),
# this will be enabled if data is available for the combination of variables selected above
disabled(actionButton(inputId = "load", label = "Load data", style=button_style)),
uiOutput("help_load", width=widget_width, style = "white-space: normal;"),
br(),
shinyjs::hidden(div(id="hiddenPanel",
#*******************************************************************
# UI POLYGON ####
actionButton(inputId="polygonButton", label="Polygon",
"data-toggle"='collapse', "data-target"='#polygonDiv', style=button_style),
div(id = 'polygonDiv', class="collapse",
br(),
selectInput(inputId = 'box',
label=HTML("<font style=\"font-size: 14px; color: #555555; font-weight: bold;\">Choose a polygon</font>"),
choices=poly_choices[[default_region]], selected = 'custom', width=widget_width),
conditionalPanel(condition = "input.box =='custom'",
helpText(bhelp$box_custom, width=widget_width, style=help_text_style),
div(style="display: inline-block; vertical-align:top; align:center; width: 58%;",
textInput(inputId = "custom_name", label=NULL, value=NULL)),
div(style="display: inline-block; width: 40%",
actionButton(inputId="applyname", label="Apply", style=button_style)),
helpText(bhelp$box_method, width=widget_width, style=help_text_style),
radioButtons(inputId = "latlon_method", label=NULL,
choices=latlon_methods, selected = "drawPoly", width=widget_width),
conditionalPanel(condition = "input.latlon_method =='drawPoly'",
helpText(bhelp$box_draw, width=widget_width, style=help_text_style)),
conditionalPanel(condition = "input.latlon_method =='typeCoords'",
helpText(HTML(bhelp$box_type), width=widget_width, style=help_text_style)),
conditionalPanel(condition = "input.latlon_method =='loadShapefile'",
helpText(HTML(bhelp$box_shp), width=widget_width, style=help_text_style),
fileInput(inputId = "shapefile", label=NULL,
multiple=TRUE, accept=c('.shp','.dbf','.sbn','.sbx','.shx','.prj', '.qix'), width=widget_width)),
conditionalPanel(condition = "input.latlon_method =='typeCoords'",
helpText(HTML("<font style=\"font-size: 12px; color: #555555; font-weight: bold;\">List of latitudes:</font>"),
width=widget_width, style=paste(help_text_style, "margin-bottom: -2px; margin-top: -5px;")),
textInput(inputId = "manual_lats", label=NULL,
value = "", width=widget_width, placeholder = "42.6, 43, 42, 40.4, 40, 42.6"),
helpText(HTML("<font style=\"font-size: 12px; color: #555555; font-weight: bold;\">List of longitudes:</font>"),
width=widget_width, style=paste(help_text_style, "margin-bottom: -2px; margin-top: -5px;")),
textInput(inputId = "manual_lons", label=NULL,
value = "", width=widget_width, placeholder = "-61, -59, -55, -57, -60.4, -61"),
actionButton(inputId='createTypedPoly', label='Create polygon',width=widget_width)),
uiOutput("shapefile_button", width=widget_width, style = "white-space: normal;"),
uiOutput("help_latlon", width=widget_width, style = "white-space: normal;"),
br()),
br()
), # closes polygon panel
#*******************************************************************
# UI STATISTICS ####
actionButton(inputId="statsButton", label="Statistics",
"data-toggle"='collapse', "data-target"='#statsDiv', style=button_style),
div(id = 'statsDiv', class="collapse",
br(),
helpText(HTML(bhelp$percent), width=widget_width, style=help_text_style),
numericInput(inputId = 'percent', label=NULL, value=10, min=0, max=100, width=widget_width),
helpText(HTML(bhelp$outlier), width=widget_width, style=help_text_style),
selectInput(inputId='outlier', label=NULL, choices=outliers, selected = 'none', width=widget_width),
helpText(HTML(bhelp$dailystat), width=widget_width, style=help_text_style),
selectInput(inputId = 'dailystat', label=NULL, choices=dailystats, selected = 'average', width=widget_width),
helpText(HTML(bhelp$pixrange), width=widget_width, style=help_text_style),
div(style="display: inline-block; vertical-align:top; width: 50px;",
textInput(inputId = "pixrange1", label=NULL, value=NA)),
div(style="display: inline-block; vertical-align:top; width: 10px;",
helpText(HTML(paste0("<font style=\"font-size: 14px; color: #555555;\">–</font>")))),
div(style="display: inline-block; vertical-align:top; width: 50px;",
textInput(inputId = "pixrange2", label=NULL, value=NA)),
div(style="display: inline-block;vertical-align:top; width: 60px;",
actionButton(inputId="applypixrange", label="Apply", style=button_style)),
br(),br()
), # closes stats panel
#*******************************************************************
# UI MODEL FIT ####
actionButton(inputId="bfButton", label="Model fit",
"data-toggle"='collapse', "data-target"='#bfDiv', style=button_style),
div(id = 'bfDiv', class="collapse",
helpText(bhelp$bf_desc, width=widget_width, style="white-space: normal; font-size: 14px; font-weight: bold;"),
br(),
helpText(bhelp$bf, width=widget_width, style=help_text_style),
selectInput(inputId='fitmethod', label=NULL, choices=fitmethods, selected='gauss', width=widget_width),
selectInput(inputId='bloomShape', label=NULL, choices=bloomShapes, selected='symmetric', width=widget_width),
selectInput(inputId='smoothMethod', label=NULL, choices=smoothMethods, selected='nofit', width=widget_width),
conditionalPanel(condition = "input.smoothMethod == 'loess'",
helpText(HTML(bhelp$loessSpan), width=widget_width, style=help_text_style),
numericInput(inputId = 'loessSpan', label=NULL, value=0.3, min=0.04, max=1, step=0.02, width=widget_width)),
helpText(bhelp$fit_days, width=widget_width, style=help_text_style),
sliderInput(inputId='t_range', min=1, max=365, value=c(31,274), ticks=FALSE,
label=HTML("<font style=\"font-size: 14px; color: #555555; font-weight: bold;\">t<sub>range</sub></font>")),
sliderInput(inputId='tm_limits', min=1, max=365, value=c(91,181), ticks=FALSE,
label=HTML("<font style=\"font-size: 14px; color: #555555; font-weight: bold;\">t<sub>max</sub></font>")),
sliderInput(inputId='ti_limits', min=1, max=365, value=c(60,151), ticks=FALSE,
label=HTML("<font style=\"font-size: 14px; color: #555555; font-weight: bold;\">t<sub>start</sub></font>")),
conditionalPanel(condition = "input.fitmethod == 'gauss'",
helpText(HTML(bhelp$fit_tstart_method), width=widget_width, style=help_text_style),
radioButtons(inputId = "ti_threshold_type", label=NULL, choices=ti_threshold_types, selected = "percent_thresh", width=widget_width),
conditionalPanel(condition = "input.ti_threshold_type == 'percent_thresh'",
helpText(HTML(bhelp$fit_ti_threshold_percent), width=widget_width, style=help_text_style),
numericInputIcon(inputId="ti_threshold_percent", label=NULL, value=20, min=0.01, max=90, step=5, icon=list(NULL,icon("percent")), width="75%")),
conditionalPanel(condition = "input.ti_threshold_type == 'constant_thresh'",
helpText(HTML(bhelp$fit_ti_threshold_constant), width=widget_width, style=help_text_style),
numericInput(inputId="ti_threshold_constant", label=NULL, value=0.1, min=0.01, max=5, step=0.05, width="75%")),
helpText(HTML(bhelp$fit_tmax), width=widget_width, style=help_text_style),
switchInput(inputId='tm', label=HTML('t<sub>max</sub>'), value=FALSE, onStatus="success"),
helpText(HTML(bhelp$fit_beta), width=widget_width, style=help_text_style),
switchInput(inputId='beta', label='\u03B2t', value=FALSE, onStatus="success"),
helpText(bhelp$fit_weights, width=widget_width, style=help_text_style),
switchInput(inputId='use_weights', label='weights', value=FALSE, onStatus="success"),
helpText(HTML(bhelp$fit_bkrnd), width=widget_width, style=help_text_style),
checkboxInput(inputId="rm_bkrnd", label="Remove background", value=TRUE, width=widget_width),
helpText(HTML(bhelp$fit_flags), width=widget_width, style=help_text_style),
actionButton(inputId="flagdescriptions", label="Flag descriptions", style=button_style),
br(),br(),
helpText(HTML(bhelp$fit_flag1), width=widget_width, style=help_text_style),
div(style="display: inline-block; vertical-align:top; width: 50px; margin-top: -10px;",
textInput(inputId="flag1_lim1", label=NULL, value=0.75)),
div(style="display: inline-block; vertical-align:top; width: 10px; margin-top: -10px;",
helpText(HTML(paste0("<font style=\"font-size: 14px; color: #555555;\">–</font>")))),
div(style="display: inline-block; vertical-align:top; width: 50px; margin-top: -10px;",
textInput(inputId="flag1_lim2", label=NULL, value=1.25)),
div(style="display: inline-block;vertical-align:top; width: 60px; margin-top: -10px;",
actionButton(inputId="apply_flag1_lim", label="Apply", style=button_style)),
helpText(HTML(bhelp$fit_flag2), width=widget_width,style=help_text_style),
div(style="display: inline-block; vertical-align:top; width: 50px; margin-top: -10px;",
textInput(inputId="flag2_lim1", label=NULL, value=0.85)),
div(style="display: inline-block; vertical-align:top; width: 10px; margin-top: -10px;",
helpText(HTML(paste0("<font style=\"font-size: 14px; color: #555555;\">–</font>")))),
div(style="display: inline-block; vertical-align:top; width: 50px; margin-top: -10px;",
textInput(inputId="flag2_lim2", label=NULL, value=1.15)),
div(style="display: inline-block;vertical-align:top; width: 60px; margin-top: -10px;",
actionButton(inputId="apply_flag2_lim", label="Apply", style=button_style))),
conditionalPanel(condition = "input.fitmethod == 'thresh'",
helpText(HTML(bhelp$fit_threshcoef), width=widget_width, style=help_text_style),
numericInput(inputId='threshcoef', label=NULL, value=1.05, min=1.00, width=widget_width),
helpText(HTML(bhelp$fit_threshcoefnote), width=widget_width, style=help_text_style)),
), # closes model fit panel
br(),br(),hr(),
#*******************************************************************
# UI SAVE OPTIONS ####
helpText(HTML(bhelp$fullrun1), width=widget_width, style=help_text_style),
checkboxInput(inputId = "fullrunoutput_png", value=TRUE, width=widget_width,
label=HTML("<font style=\"white-space: normal; font-size: 10px;\">time series plots (.png),</font>")),
div(style="margin-top: -15px; line-height: 90%;",
checkboxInput(inputId = "fullrunoutput_statcsv", value=TRUE, width=widget_width,
label=HTML("<font style=\"white-space: normal; font-size: 10px;\">tables of statistics (.csv),</font>"))),
div(style="margin-top: -15px; line-height: 90%;",
disabled(checkboxInput(
inputId = "fullrunoutput_paramcsv", value=TRUE, width=widget_width,
label=HTML("<font style=\"white-space: normal; font-size: 10px;\">a single .csv file containing the fitted parameters for all selected years and polygons, and</font>")))),
div(style="margin-top: -15px; line-height: 90%;",
disabled(checkboxInput(
inputId = "fullrunoutput_settingcsv", value=TRUE, width=widget_width,
label=HTML("<font style=\"white-space: normal; font-size: 10px;\">a .csv file containing the settings used for the time series, for reference.</font>")))),
helpText(HTML(bhelp$fullrun2), width=widget_width, style=help_text_style),
sliderInput(inputId="fullrunyears", label=NULL, min=min(default_years), max=max(default_years), value=range(default_years), ticks=FALSE, step=1, sep = ""),
pickerInput(inputId="fullrunboxes", label="Select your polygons", choices=multipoly_choices[[default_region]], selected="custom",
options=list(`actions-box`=TRUE,size=10,`selected-text-format`="count > 3"), multiple=TRUE, width=widget_width),
br(),
actionButton(inputId = "fullrun_process", label = "Run time series", style=button_style),
uiOutput("fullrun_fname", width=widget_width, style = "white-space: normal;"),
disabled(downloadButton(outputId = "fullrun_download", label = "Download results (.zip)", style=button_style)),
br(),br(),
disabled(downloadButton(outputId = "savesettings", label = "Save settings (.txt)", style=button_style))
)) # close side panel that's hidden when data hasn't been loaded yet
),
#***********************************************************************
# UI DISPLAY ####
mainPanel(width=9,
div(style="margin-bottom: -30px; margin-left: 4px; margin-right: 7px;",
plotOutput(outputId='datebar',height="40px",width='100%')),
sliderInput(inputId="yearday_slide", label=NULL, min=1, max=365, value=1,
animate=animationOptions(interval=4000), ticks=TRUE, width='100%'),
leafletOutput(outputId='fullmap', height='700px'),
div(style="display: inline-block; vertical-align:top; width: 74%; margin-top: 5px;",
sliderTextInput(inputId="zlim", label=NULL, choices=default_colscale, selected=default_zlim, grid=TRUE, width="100%")),
div(style="display: inline-block; vertical-align:top; width: 25%; margin-top: 5px;",
actionButton(inputId="applyzlim", label="Apply color scale", style=button_style)),
br(),
htmlOutput(outputId="poly_title"),
br(),
div(style="display: inline-block; vertical-align:top; width: 82%; margin-top: 5px;",
plotOutput(outputId='chla_hist',height='360px')),
div(style="display: inline-block; vertical-align:top; width: 17%; margin-top: 27px;",
tableOutput(outputId="chla_hist_df")),
disabled(downloadButton(outputId="savedensplot",label="Download density plot (.png)",style=button_style)),
br(),br(),
div(style="display: inline-block; vertical-align:top; width: 82%; margin-top: 5px;",
plotOutput(outputId='bloomfit',height='440px',click='bloomfit_click')),
div(style="display: inline-block; vertical-align:top; width: 17%; margin-top: 27px; font-size:80%;",
tableOutput(outputId="bloomfit_df")),
disabled(downloadButton(outputId="savebloomfit",label="Download time series plot (.png)",style=button_style)),
disabled(downloadButton(outputId="saveannualstats",label="Download time series table of statistics (.csv)",style=button_style)),
disabled(downloadButton(outputId="savebloomparams",label="Download fit parameters (.csv)",style=button_style)),
br(),br()
)
) # closes fluidRow
)
#*******************************************************************************
server <- function(input, output, session) {
# 2023-05-01 When I close the app, sometimes R stops responding. Can't find any issues with the code that could be causing it, and it appears totally random - often it does, sometimes it doesn't. This line is required to make sure the app stops and doesn't crash R on the way out.
# https://community.rstudio.com/t/r-crashes-when-closing-shiny-app-window-instead-of-clicking-red-stop-button-in-rstudio/131951/2
session$onSessionEnded(function() stopApp())
# Create a list of reactive values to collect widget input after running checks on it.
state <- reactiveValues()
# initialize some defaults so the code doesn't break
state$data_loaded <- FALSE
state$region <- default_region
state$predefined_polys <- predefined_polys[[default_region]]
state$sat_alg <- default_sat_algs[1]
state$variable <- default_variable
state$cell_model_option <- default_variable$cell_model_option
state$concentration_type <- "full"
state$cell_size_model1 <- state$cell_size_model2 <- "small"
state$year <- as.numeric(format(Sys.Date(),"%Y"))
state$composite <- 1
state$log_chla <- TRUE
state$doy_vec <- 1:365
state$sschla <- matrix(nrow=1,ncol=365)
state$colscale <- default_colscale
state$zlim <- ifelse(rep(default_variable$log,2),log10(default_variable$zlim),default_variable$zlim)
state$flag1_lim1 <- 0.75
state$flag1_lim2 <- 1.25
state$flag2_lim1 <- 0.85
state$flag2_lim2 <- 1.15
state$pixrange1 <- -Inf
state$pixrange2 <- Inf
state$latlon_method <- "drawPoly"
state$draw_toolbar <- TRUE
state$latlon_invalid <- state$latlon_toolarge <- FALSE
state$newpoly <- state$editedpoly <- NULL
state$ti_threshold <- state$tt_threshold <- 0.2
state$fullrun_fname <- NULL
state$box <- state$fullrunboxes <- "custom"
state$custom_name <- ""
state$help_load_txt <- state$help_latlon_txt <- state$help_settings_file_txt <- ""
state$secondary_settings <- NULL
state$draw_programmatically <- state$applyname_programmatically <- FALSE
# These are used to check which specific inputs have been updated in the code block
# below that hides the left panel if any of the main inputs have changed.
state$current_sat_algs <- default_sat_algs
state$current_years <- default_years
# Used for deleting typed or shapefile polygons
state$typed_polys_deleted <- 0
state$shapefile_polys_deleted <- 0
state$shapefile <- NULL
# START SCREEN POPUP
observe({
showModal(modalDialog(
title = "Satellite Data Visualization",
HTML(startup_popup), easyClose=TRUE, footer=modalButton("OK")
))
})
#***************************************************************************
# APPLY SETTINGS FILE ####
# If user uploads an existing settings file, read the settings and apply them. Either:
# 1. All the main settings are the same but some secondary settings (i.e. in the hidden panel)
# might be changed, in which case you just need to change those settings, or
# 2. Some main settings are different - update them and programmatically click the "load"
# button, then apply the secondary settings.
# If a valid custom polygon is present in the settings file, extract the coordinates and apply them
# to the typeCoords option, programmatically clicking the "Create polygon" button.
# Afterwards, reset state$secondary_settings to NULL, and "programmatic" button clicking
# variables to FALSE.
observeEvent(input$applysettings, {
help_settings_file_txt <- ""
file <- input$settings_file
ext <- tools::file_ext(file$datapath)
# check the extension
if (ext == "txt") {
# try to load the file
file_contents <- try(read.table(file$datapath, header = TRUE, sep="\\"), silent=TRUE)
if (class(file_contents)!="try-error") {
# check the file contents
if (all(colnames(file_contents)==c("setting_id","value","setting_description","value_description", "variable_type"))) {
# get updated values of main input buttons
main_ids <- c("region","sat_alg","concentration_type","cell_size_model1","cell_size_model2","year","composite","log_chla")
main_inds <- file_contents$setting_id %in% main_ids
primary_settings <- file_contents[main_inds,]
new_inputs <- format_settings_to_load(primary_settings)
# check if data actually exists for this combo
if (dexist(new_inputs$region,new_inputs$sat_alg,new_inputs$year)) {
state$secondary_settings <- file_contents[!main_inds,]
current_inputs <- reactiveValuesToList(input)
current_inputs <- current_inputs[match(names(new_inputs),names(current_inputs))]
ci <- as.character(unname(unlist(current_inputs)))
ni <- as.character(unname(unlist(new_inputs)))
if (identical(ci,ni)) { # main settings haven't changed, just check secondary settings
update_secondary_settings()
if (!state$data_loaded) {
state$help_load_txt <- ""
enable("load")
shinyjs::click("load")
}
} else { # main settings have changed, update them and then update secondary settings after data loads
nir <- new_inputs$region
nisa <- new_inputs$sat_alg
updateSelectInput(session, inputId="region", selected=nir)
updateSelectInput(session, inputId="sat_alg", selected=nisa, choices=sat_algs[[nir]])
updateRadioButtons(session, inputId="concentration_type", selected=new_inputs$concentration_type)
updateRadioGroupButtons(session, inputId="cell_size_model1", selected=new_inputs$cell_size_model1)
updateRadioGroupButtons(session, inputId="cell_size_model2", selected=new_inputs$cell_size_model2)
updateSelectInput(session, inputId="year", selected=new_inputs$year, choices=rev(years[[nir]][[nisa]]))
updateSelectInput(session, inputId="composite", selected=new_inputs$composite)
updateSwitchInput(session, inputId="log_chla", value=new_inputs$log_chla)
}
} else {
help_settings_file_txt <- "No data available for the region/satellite/algorithm/year in the settings file."
}
} else {
help_settings_file_txt <- "Invalid file contents."
}
} else {
help_settings_file_txt <- "Invalid input file."
}
} else {
help_settings_file_txt <- "Please select a PhytoFit settings file with extension .txt."
}
state$help_settings_file_txt <- help_settings_file_txt
})
output$help_settings_file <- renderPrint({
helpText(state$help_settings_file_txt, width=widget_width, style=error_text_style)
})
# function to apply secondary settings, either by themselves (if main settings haven't changed), or after main settings have been updated and data reloaded
update_secondary_settings <- eventReactive(state$secondary_settings, {
ssdf <- state$secondary_settings
if (!is.null(ssdf)) {
# update polygon input
predefined_polygon <- ssdf$value[ssdf$setting_id=="box"]
custom_polygon <- ssdf$value[ssdf$setting_id=="polystr"]
updateSelectInput(session, inputId="box", choices=poly_choices[[state$region]], selected=predefined_polygon)
# if it's a custom box, update lat/lon input and add it to the map and stats using the "typeCoords" method
if (predefined_polygon=="custom" & !is.na(custom_polygon)) {
custom_polygon_name <- trimws(ssdf$value[ssdf$setting_id=="custom_name"])
spdf_name <- ifelse(nchar(custom_polygon_name) > 0,custom_polygon_name,"custom")
updateRadioButtons(session, inputId="latlon_method", selected="typeCoords")
spdf <- st_sf(tibble(poly_id="custom",group=NA,name=spdf_name,label=spdf_name,geometry=st_as_sfc(custom_polygon)))
st_crs(spdf) <- "EPSG:4326"
pcp_coords <- st_coordinates(spdf)
updateTextInput(session, inputId="manual_lats", value=pcp_coords[,2])
updateTextInput(session, inputId="manual_lons", value=pcp_coords[,1])
# set a variable to automatically click "createTypedPoly" after the lats/lons are updated
state$draw_programmatically <- TRUE
# if the custom polygon has a name, apply it
if (nchar(custom_polygon_name) > 0) {
updateTextInput(session, inputId="custom_name", value=custom_polygon_name)
state$applyname_programmatically <- TRUE
}
}
# update the box state variable as well
# this is needed because the input choices/widget will be updated during this round of reactive updates,
# then the stats will be calculated, but the actual box state won't be updated until next round, so it
# won't be calculating the right stats (if you change region, this will make it crash)
state$box <- predefined_polygon
# format remaining secondary settings for updating
ssdf <- ssdf[!(ssdf$setting_id %in% c("box","custom_name","polystr")),]
ssdf <- format_settings_to_load(ssdf)
vals <- ssdf$values
ids <- ssdf$ids
# YEARDAY_SLIDER
updateSliderInput(session, inputId = "yearday_slide", value = ssdf$yearday_slide, step = state$composite)
# FULL_RUN
updateCheckboxInput(session, inputId="fullrunoutput_png", value=ssdf$fullrunoutput_png)
updateCheckboxInput(session, inputId="fullrunoutput_statcsv", value=ssdf$fullrunoutput_statcsv)
tmp_years <- as.numeric(years[[state$region]][[state$sat_alg]])
updateSliderInput(session, inputId="fullrunyears", min=min(tmp_years), max=max(tmp_years), value=ssdf$fullrunyears)
updatePickerInput(session, inputId="fullrunboxes", selected=ssdf$fullrunboxes)
# STATS SETTINGS: percent, outlier, dailystat, pixrange1, pixrange2
updateNumericInput(session, inputId="percent", value=ssdf$percent)
updateSelectInput(session, inputId="outlier", selected=ssdf$outlier)
updateSelectInput(session, inputId="dailystat", selected=ssdf$dailystat)
updateTextInput(session, inputId="pixrange1", value=ssdf$pixrange1)
updateTextInput(session, inputId="pixrange2", value=ssdf$pixrange2)
# MODEL FIT SETTINGS: fitmethod, bloomShape, smoothMethod, loessSpan, t_range, ti_limits, tm_limits, ti_threshold_type,
# ti_threshold_constant, tm, beta, use_weights, rm_bkrnd, flag1_lim1, flag1_lim2, flag2_lim1, flag2_lim2, threshcoef
updateSelectInput(session, inputId="fitmethod", selected=ssdf$fitmethod)
updateSelectInput(session, inputId="bloomShape", selected=ssdf$bloomShape)
updateSelectInput(session, inputId="smoothMethod", selected=ssdf$smoothMethod)
updateNumericInput(session, inputId="loessSpan", value=ssdf$loessSpan)
updateSliderInput(session, inputId="t_range", value=ssdf$t_range)
updateSliderInput(session, inputId="ti_limits", value=ssdf$ti_limits)
updateSliderInput(session, inputId="tm_limits", value=ssdf$tm_limits)
updateRadioButtons(session, inputId="ti_threshold_type", selected=ssdf$ti_threshold_type)
updateNumericInput(session, inputId="ti_threshold_percent", value=ssdf$ti_threshold_percent)
updateNumericInput(session, inputId="ti_threshold_constant", value=ssdf$ti_threshold_constant)
updateSwitchInput(session, inputId="tm", value=ssdf$tm)
updateSwitchInput(session, inputId="beta", value=ssdf$beta)
updateSwitchInput(session, inputId="use_weights", value=ssdf$use_weights)
updateCheckboxInput(session, inputId="rm_bkrnd", value=ssdf$rm_bkrnd)
updateTextInput(session, inputId="flag1_lim1", value=ssdf$flag1_lim1)
updateTextInput(session, inputId="flag1_lim2", value=ssdf$flag1_lim2)
updateTextInput(session, inputId="flag2_lim1", value=ssdf$flag2_lim1)
updateTextInput(session, inputId="flag2_lim2", value=ssdf$flag2_lim2)
updateNumericInput(session, inputId="threscoef", value=ssdf$threshcoef)
# now reset secondary_settings
state$secondary_settings <- NULL
}
})
#***************************************************************************
# HIDE/DISABLE/TOGGLE BUTTONS AND PANELS ####
# if "tm" is on (i.e. day of max. concentration is a parameter in the model fit),
# then the start of the model can't be restricted, so turn off that slider button
observe({
toggleState("ti_limits", condition = !input$tm | input$ti_threshold_type=="constant_thresh")
})
# enable/disable "Run time series" button depending on which boxes are selected and if there are custom coordinates
observe({
frb <- state$fullrunboxes
if (length(frb)==0) {
disable("fullrun_process")
} else if (length(frb)==1) {
if (frb[1] == "custom" & is.null(get_polygon())) {
disable("fullrun_process")
} else {
enable("fullrun_process")
}
} else {
enable("fullrun_process")
}
})
# if a file with predefined settings has not been loaded, disable the "apply settings" button
observe({
if (is.null(input$settings_file)) {
disable("applysettings")
} else {
enable("applysettings")
}
})
# set some options based on user-selected variable
observeEvent(input$sat_alg, {
if (input$sat_alg=="empty_sat_alg") {
updateSwitchInput(session, inputId="log_chla", value=state$log_chla, disabled=FALSE)
state$concentration_type <- "full"
state$cell_model_option <- FALSE
} else {
v <- variables[[strsplit(input$sat_alg,split="_")[[1]][2]]]
if (v$log) {
updateSwitchInput(session, inputId="log_chla", value=state$log_chla, disabled=FALSE)
} else {
updateSwitchInput(session, inputId="log_chla", value=FALSE, disabled=TRUE)
}
state$cell_model_option <- v$cell_model_option
if (state$cell_model_option) {
enable("concentration_type")
enable("cell_size_model1")
enable("cell_size_model2")
} else {
disable("concentration_type")
disable("cell_size_model1")
disable("cell_size_model2")
state$concentration_type <- "full"
}
}
})
# Hide the settings panel if main options have changed but "load" has not been clicked yet.
observeEvent({
input$region
input$sat_alg
input$concentration_type
input$cell_size_model1
input$cell_size_model2
input$year
input$composite
input$log_chla
}, {
hideElement(id = "hiddenPanel", anim = FALSE)
disable("savedensplot")
disable("savebloomfit")
disable("savebloomparams")
disable("saveannualstats")
state$data_loaded <- FALSE
# FOR APPLYING INDIVIDUAL SETTINGS MANUALLY
if (is.null(state$secondary_settings)) {
# if the region has changed, check if you need to update the sat_alg dropdown
new_sat_algs <- sat_algs[[input$region]]
if (!identical(new_sat_algs, state$current_sat_algs)) {
if (state$sat_alg %in% new_sat_algs) {
selected_sat_alg <- state$sat_alg
} else {
selected_sat_alg <- new_sat_algs[1]
}
updateSelectInput(session, inputId = "sat_alg", choices = new_sat_algs, selected = selected_sat_alg)
} else {
selected_sat_alg <- input$sat_alg
}
state$current_sat_algs <- new_sat_algs
# if the region or sat_alg have changed, check if you need to update the year dropdown
new_years <- years[[input$region]][[selected_sat_alg]]
if (!identical(new_years, state$current_years)) {
if (state$year %in% new_years) {
selected_year <- state$year
} else {
selected_year <- max(new_years)
}
updateSelectInput(session, inputId = "year", choices = rev(new_years), selected = selected_year)
} else {
selected_year <- input$year
}
state$current_years <- new_years
# enable/disable load button depending on whether or not data exists for these settings
data_exists <- dexist(input$region, selected_sat_alg, selected_year)
if (data_exists) {
enable("load")
state$help_load_txt <- ""
} else {
disable("load")
state$help_load_txt <- "No data available for the selected options."
}
# FOR APPLYING A SETTINGS FILE
# necessary update() functions have already been called in the applysettings code chunk,
# so you don't need to do that here - you can just double-check that data is available
} else {
# reset "current" variables so it knows to change if you manually select
# a region with different sat_algs or years
new_sat_algs <- sat_algs[[input$region]]
if (!identical(new_sat_algs, state$current_sat_algs)) {
if (state$sat_alg %in% new_sat_algs) {
selected_sat_alg <- state$sat_alg
} else {
selected_sat_alg <- new_sat_algs[1]
}
state$current_sat_algs <- new_sat_algs
} else {
selected_sat_alg <- state$sat_alg
}
new_years <- years[[input$region]][[selected_sat_alg]]
if (!identical(new_years, state$current_years)) {state$current_years <- new_years}
enable("load")
state$help_load_txt <- ""
shinyjs::click("load")
}
})
output$help_load <- renderPrint({
helpText(state$help_load_txt, width=widget_width, style=help_text_style)
})
#***************************************************************************
# GET REGION ####
# If region has changed, update predefined polygon choices and state variables
observeEvent(input$region, {
state$region <- input$region
updateSelectInput(session, inputId = "box", choices = poly_choices[[state$region]], selected = "custom")
updatePickerInput(session, inputId = "fullrunboxes", choices = multipoly_choices[[state$region]], selected = "custom")
state$predefined_polys <- predefined_polys[[state$region]]
})
# GET POLYGON ####
observeEvent(input$box,{
if (state$latlon_method == "drawPoly") {
# If switching from predefined to custom polygon, add the draw toolbar to the map.
# If switching from custom to predefined polygon, remove the draw toolbar from the map.
if (state$box != "custom" & input$box == "custom") {
state$draw_toolbar <- TRUE
} else if (state$box == "custom" & input$box != "custom") {
state$draw_toolbar <- FALSE
}
}
state$box <- input$box
})
observeEvent(input$latlon_method, {
state$latlon_method <- input$latlon_method
state$help_latlon_txt <- ""
if (state$latlon_method == "drawPoly") {
state$draw_toolbar <- TRUE
} else {
state$draw_toolbar <- FALSE
}
})
observeEvent({
input$manual_lats
input$manual_lons
}, {
if (state$latlon_method == "typeCoords" & state$draw_programmatically) {
shinyjs::click("createTypedPoly")
state$draw_programmatically <- FALSE
}
})
observeEvent(input$custom_name, {
if (state$applyname_programmatically) {
shinyjs::click("applyname")
state$applyname_programmatically <- FALSE
}
})
observeEvent(input$applyname, {
state$custom_name <- gsub("[^[:alnum:]_.]", "", input$custom_name)
})
# GET MAP COLOUR SCALE ####
observeEvent(input$applyzlim, {
zlim <- input$zlim
if (state$log_chla) {zlim <- log10(zlim)}
state$zlim <- zlim
})
# GET YEAR DAY ####
output$datebar <- renderPlot(pmonth) # date bar at top
observeEvent(input$yearday_slide, {
state$yearday <- input$yearday_slide
# Get some time variables now that yearday is updated
time_variables <- get_time_vars(composite=state$composite, year=state$year,
yearday=state$yearday, dvecs=dvecs)
state$day_label <- time_variables$day_label
state$time_ind <- time_variables$time_ind
})
# GET STATISTICS ####
observeEvent(input$outlier, {
state$outlier <- input$outlier
})
observeEvent(input$dailystat,{
state$dailystat <- input$dailystat
})
observeEvent(input$percent, {
state$percent <- input$percent
})
observeEvent(input$applypixrange, {
state$pixrange1 <- as.numeric(input$pixrange1)
state$pixrange2 <- as.numeric(input$pixrange2)
})
# GET MODEL FIT VARIABLES ####
observeEvent(input$fitmethod, {
state$fitmethod <- input$fitmethod
# Make sure tmax option starts out as "off" when fit method is changed.
# Needs to be "off" for non-gauss methods so that ti_limits can be adjusted,
# and need to reset it for gauss method anyway, otherwise the whole switch
# disappears when you switch from another method to gauss method.
updateSwitchInput(session, "tm", value = FALSE)
})
observeEvent(input$bloomShape, {
state$bloomShape <- input$bloomShape
})
observeEvent(input$smoothMethod,{
state$smoothMethod <- input$smoothMethod
})
observeEvent(input$loessSpan,{
state$loessSpan <- input$loessSpan
})
# THRESHOLD METHOD SPECIFICALLY
observeEvent(input$threshcoef, {
state$threshcoef <- input$threshcoef
})
observeEvent(input$ti_threshold_type,{
state$ti_threshold_type <- input$ti_threshold_type
})
observeEvent(input$ti_threshold_percent,{
ittt <- input$ti_threshold_percent
if (is.finite(ittt)) {
if (ittt < 0.01) {
ittt <- 0.01
updateNumericInput(session, inputId = "ti_threshold_percent", value = 0.01)
} else if (ittt > 90) {
ittt <- 90
updateNumericInput(session, inputId = "ti_threshold_percent", value = 90)
} else {
state$ti_threshold <- state$tt_threshold <- ittt/100
}
}
})
observeEvent(input$ti_threshold_constant,{
ittt <- input$ti_threshold_constant
if (is.finite(ittt)) {
if (ittt < 0.01) {
ittt <- 0.01
updateNumericInput(session, inputId = "ti_threshold_constant", value = 0.01)
} else if (ittt > 5) {
ittt <- 5
updateNumericInput(session, inputId = "ti_threshold_constant", value = 5)
} else {
state$ti_threshold_constant <- ittt
}
}
})
observeEvent(input$tm,{
state$tm <- input$tm
})
observeEvent(input$beta,{
state$beta <- input$beta
})
observeEvent(input$use_weights,{
state$use_weights <- input$use_weights
})
observeEvent(input$rm_bkrnd,{
state$rm_bkrnd <- input$rm_bkrnd
})
# popup explaining gaussian fit flags
observeEvent(input$flagdescriptions, {
showModal(modalDialog(title="Gaussian fit flag descriptions",HTML(gauss_flag_popup),easyClose=TRUE,footer=modalButton("Close")))
})
observeEvent(input$apply_flag1_lim, {
flag1_lim1 <- as.numeric(input$flag1_lim1)
flag1_lim2 <- as.numeric(input$flag1_lim2)
# Check if values are valid (not NA, NaN, Inf, -Inf, or lim1 > lim2),
# and if so, apply them to the reactive state variables
if (is.finite(flag1_lim1) & is.finite(flag1_lim2) & flag1_lim2 >= flag1_lim1) {
state$flag1_lim1 <- flag1_lim1
state$flag1_lim2 <- flag1_lim2
} else {
# if values are invalid, reset them to the previous values
updateTextInput(session, inputId = "flag1_lim1", value = state$flag1_lim1)
updateTextInput(session, inputId = "flag1_lim2", value = state$flag1_lim2)
}
})
observeEvent(input$apply_flag2_lim, {
flag2_lim1 <- as.numeric(input$flag2_lim1)
flag2_lim2 <- as.numeric(input$flag2_lim2)
# Check if values are valid (not NA, NaN, Inf, -Inf, or flaglim1 > flaglim2),
# and if so, apply them to the reactive state variables
if (is.finite(flag2_lim1) & is.finite(flag2_lim2) & flag2_lim2 >= flag2_lim1) {
state$flag2_lim1 <- flag2_lim1
state$flag2_lim2 <- flag2_lim2
} else {
# if values are invalid, reset them to the previous values
updateTextInput(session, inputId = "flag2_lim1", value = state$flag2_lim1)
updateTextInput(session, inputId = "flag2_lim2", value = state$flag2_lim2)
}
})
# get ranges of days used for fitting and certain parameters
# the t_sliders are dependent on each other, so you might have to update them
# to reflect this - only update their state$ variables once they're all valid
observeEvent({
input$t_range
input$tm_limits
input$ti_limits
}, {
tr1 <- input$t_range[1]
tr2 <- input$t_range[2]
tm1 <- input$tm_limits[1]
tm2 <- input$tm_limits[2]
ti1 <- input$ti_limits[1]
ti2 <- input$ti_limits[2]
update_t_range <- update_tm_limits <- update_ti_limits <- FALSE
# make sure the range of days used in the fit is > the theoretical minimum
# range for a curve (3 days - start, maximum, end)
if (tr1 > 363) {
tr1 <- 363
tr2 <- 365
update_t_range <- TRUE
}
if (abs(tr1 - tr2) < 2) {
tr2 <- tr1 + 2
update_t_range <- TRUE
}
# check for errors in tm_limits - must be within trange
if (tm2 >= tr2) {
tm2 <- tr2 - 1
tm1 <- min(tm1, tm2)
update_tm_limits <- TRUE
}
if (tm1 <= tr1) {
tm1 <- tr1 + 1
tm2 <- max(tm1, tm2)
update_tm_limits <- TRUE
}
# check for errors in ti_limits - must be within trange, and ti and tm limits depend on each other
if (ti1 >= tm1) {
ti1 <- tm1 - 1
update_ti_limits <- TRUE
}
if (ti1 < tr1) {
ti1 <- tr1
ti2 <- max(ti1, ti2)
update_ti_limits <- TRUE
}
if (ti2 >= tm2) {
ti2 <- tm2 - 1
update_ti_limits <- TRUE
}
# if anything needs to be reset, do that here - otherwise, assign them to their state$ variables
if (update_t_range) {
updateSliderInput(session, inputId = 't_range', value = c(tr1, tr2))
} else if (update_tm_limits) {
updateSliderInput(session, inputId = 'tm_limits', value = c(tm1, tm2))
} else if (update_ti_limits) {
updateSliderInput(session, inputId = 'ti_limits', value = c(ti1, ti2))
} else {
state$t_range <- c(tr1, tr2)
state$tm_limits <- c(tm1, tm2)
state$ti_limits <- c(ti1, ti2)
}
})
# Get list of column names for model fit parameters/metrics
get_pnames <- reactive({
pnames <- pnlist[[state$fitmethod]]
if (state$fitmethod=="gauss") {
pnames <- pnames[[state$bloomShape]]
if (!state$beta) {pnames <- pnames[!grepl("beta", pnames)]}
}
return(pnames)
})
# GET "FULL RUN" CHECKBOXES ####
# ignoreNULL is necessary to for cases where all boxes are deselected and fullrunboxes
# is therefore set to NULL - this forces it to trigger anyway so that the "run time series"
# button can be greyed out in this case
observeEvent(input$fullrunboxes, {
state$fullrunboxes <- input$fullrunboxes
}, ignoreNULL = FALSE)
#***************************************************************************
# LOAD DATASET ####
full_data <- eventReactive(input$load, {
show_modal_spinner(spin="atom", color="#112446", text=paste0("Loading data for ",input$year,"..."))
showElement(id = "hiddenPanel", anim = FALSE)