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app.R
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app.R
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library(shiny)
library(shinyvalidate)
library(bs4Dash)
library(waiter)
library(leaflet)
library(RColorBrewer)
library(viridisLite)
library(ggplot2)
library(plotly)
library(DT)
library(tidyr)
library(dplyr)
library(stringr)
library(lemon)
library(rmarkdown)
library(knitr)
library(kableExtra)
library(ks)
library(zip)
library(leaflet.providers)
library(sendmailR)
source("www/scripts/calculate_ratios.R")
source("www/scripts/calculate_model_ages.R")
source("www/scripts/geom_kde2d.R")
source("plot_module.R")
source("update.R")
source("www/scripts/hCaptcha_module.R")
credentials <- readRDS("data/credentials.rds")
providers <- readRDS("data/providers.rds")
use_providers(providers)
tmpdir <- tempdir()
options(shiny.maxRequestSize=25*1024^2)
# load datasets
data_complete <- readRDS("data/database_complete.rds")
data_clean <- readRDS("data/database_clean.rds")
commodities <- data_complete %>%
select(`Metals`) %>%
drop_na() %>%
mutate(sep_num = str_count(`Metals`, ";")) %>%
separate(`Metals`, into = paste0("Metal", seq(1:1+max(.$sep_num))), sep = "; ", fill = "right") %>%
pivot_longer(contains("Metal")) %>%
select(value) %>%
drop_na() %>%
distinct() %>%
pull()
minerals <- data_complete %>%
select(`Minerals`) %>%
drop_na() %>%
mutate(sep_num = str_count(`Minerals`, ";")) %>%
separate(`Minerals`, into = paste0("Mineral", seq(1:1+max(.$sep_num))), sep = "; ", fill = "right") %>%
pivot_longer(contains("Mineral")) %>%
select(value) %>%
drop_na() %>%
distinct() %>%
pull()
# UI side -----------------------------------------------------------------
ui <- dashboardPage(
title = "GlobaLID",
fullscreen = TRUE,
dark = TRUE,
scrollToTop = TRUE,
preloader = list(html = spin_1(), color = "#333e48"),
header = dashboardHeader(
title = dashboardBrand(
title = "GlobaLID",
color = "primary",
href = NULL,
image = "logo.svg",
),
status = "white",
border = TRUE,
sidebarIcon = icon("bars"),
controlbarIcon = icon("filter"),
fixed = FALSE,
leftUi = tags$li(class = "dropdown",
tags$head(tags$style(".headerRow{height:40px;}")),
tagList(
fluidRow(
class = "headerRow",
column(
width = 2,
fluidRow(
column(
width = 4,
align = "right",
"Database:"
),
column(
width = 8,
selectizeInput("database", NULL, choices = "Ores & Minerals")
)
)
),
column(
width = 3,
fluidRow(
column(
width = 6,
checkboxInput("data_clean", "Only reliable data", value = TRUE)
),
column(
width = 6,
checkboxInput("location_accuracy", "Only exact locations")
)
)
),
column(
width = 2,
fluidRow(
column(
width = 5,
align = "right",
"Subset by"
),
column(
width = 7,
selectizeInput("group", NULL, choices = c("Country" = "Country",
"Province" = "Political province/region",
"Mining area" = "Mining area",
"Mining site" = "Mining site",
"Tect./geol. super unit" = "Tectonic/geolog. super unit",
"Tect./geol. unit" = "Tectonic/geolog. unit",
"Tect./geol. sub unit" = "Tectonic/geolog. subunit",
"Deposit type" = "Deposit type"),
selected = "Mining area")
)
)
),
column(
width = 2,
checkboxInput("data_unknown", "Exclude 'unknown's", value = FALSE)
),
column(
width = 2,
conditionalPanel(
condition = "input.sidebar == 'graphs'",
tagList(
fluidRow(
column(width = 6,
align = "right",
"Colour palette:"),
column(
width = 6,
selectizeInput("palette", NULL,
choices = list(
"Viridis and similar" = list("viridis", "magma", "inferno", "plasma", "cividis"),
"ColourBrewer: diverging" = list("BrBG", "PiYG", "PRGn", "PuOr", "RdBu", "RdGy", "RdYlBu", "RdYlGn", "Spectral"),
"ColourBrewer: sequential" = list("Blues", "BuGn", "BuPu", "GnBu", "Greens", "Greys", "Oranges", "OrRd", "PuBu", "PuBuGn", "PuRd", "Purples", "RdPu", "Reds", "YlGn", "YlGnBu", "YlOrBr", "YlOrRd"),
"ColourBrewer: qualitative" = list("Accent", "Dark2", "Paired", "Pastel1", "Pastel2", "Set1", "Set2", "Set3")
)
)
)
)
)
)
)
)
)
),
rightUi = NULL
),
sidebar = dashboardSidebar(
skin = "light",
status = "primary",
elevation = 3,
sidebarMenu(
id = "sidebar",
menuItem(
"Map",
tabName = "map",
icon = icon("map-marked-alt")
),
menuItem(
"Explore",
tabName = "graphs",
icon = icon("chart-bar")
),
menuItem(
"Upload data",
tabName = "upload",
icon = icon("upload")
),
menuItem(
"Download",
tabName = "download",
icon = icon("download")
),
menuItem(
"References",
tabName = "references",
icon = icon("book")
),
menuItem(
"Instructions",
tabName = "instructions",
icon = icon("book-open")
),
menuItem(
"Resources",
tabName = "resources",
icon = icon("code")
),
menuItem(
"About",
tabName = "about",
icon = icon("info-circle")
),
menuItem(
"News",
tabName = "news",
icon = icon("newspaper")
),
menuItem(
"Contribute",
tabName = "contribute",
icon = icon("file-upload")
),
menuItem(
"Legal Notice & Privacy",
tabName = "imprint",
icon = icon("balance-scale")
),
menuItem(
"Disclaimer",
tabName = "disclaimer",
icon = icon("exclamation-triangle")
)#,
#menuItem( # activate when bug is solved, update heading of Legal notice item, update imprint.rmd
# "Privacy",
# href = "https://dse.cortina-consult.com/privacy/6140aab59b531",
# newTab = TRUE,
# icon = icon("user-shield")
#)
)
),
controlbar = dashboardControlbar(
skin = "light",
pinned = TRUE,
collapsed = FALSE,
overlay = FALSE,
#width = "25vw",
column(
width = 12,
align = "center",
uiOutput("filter_countryOut"),
uiOutput("filter_provinceOut"),
uiOutput("filter_areaOut"),
uiOutput("filter_siteOut"),
hr(style = "border-top: 1px solid #adb5bd;"),
uiOutput("filter_geolAgeOut"),
uiOutput("filter_mineralOut"),
uiOutput("filter_commodityOut"),
uiOutput("filter_instrumentOut"),
uiOutput("filter_yearOut")
)
),
footer = dashboardFooter(
left = a(
href = "mailto:globalid@bergbaumuseum.de?subject=GlobaLID Web App",
target = "_blank", "Contact the GlobaLID Core team"
),
right = paste("Database status:", format(update_database,"%d %B %Y"))
),
body = dashboardBody(
use_waiter(),
# Matomo script ----
tags$head(tags$script(type = "text/javascript",
"var _paq = window._paq = window._paq || [];",
'/* tracker methods like "setCustomDimension" should be called before "trackPageView" */',
'_paq.push(["setDoNotTrack", true]);
_paq.push(["disableCookies"]);',
"_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {",
'var u="https://stats.thga.de/";',
"_paq.push(['setTrackerUrl', u+'matomo.php']);
_paq.push(['setSiteId', '12']);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.async=true; g.src=u+'matomo.js'; s.parentNode.insertBefore(g,s);
})();"
)),
tags$style(HTML("
.dataTables_wrapper .dataTables_length, .dataTables_wrapper .dataTables_filter, .dataTables_wrapper .dataTables_info, .dataTables_wrapper .dataTables_processing, .dataTables_wrapper .dataTables_paginate, .dataTables_wrapper .dataTables_paginate .paginate_button.current:hover {
color: #6c757d;}
.dataTables_wrapper .dataTables_paginate .paginate_button{
box-sizing:border-box;display:inline-block;min-width:1.5em;padding:0.5em 1em;margin-left:2px;text-align:center;text-decoration:none !important;cursor:pointer;
*cursor:hand;color:#808080 !important;border:1px solid transparent;border-radius:2px}
.dataTables_length select {color: #000000; background-color: #adb5bd}
.dataTables_filter input {color: #000000; background-color: #adb5bd}
thead {color: #6c757d;}
tbody {color: #6c757d;}"
)),
tabItems(
tabItem(
tabName = "map",
fluidRow(
bs4Card(
title = "Plots",
width = 3,
maximizable = TRUE,
selectInput("preview_control", label = NULL, width = "100%",
choices = list("204Pb normalised" = "A", "206Pb normalised" = "B", "Age Model" = "C")),
plotOutput("preview", height = "70vh")
),
bs4Card(
title = "Map",
width = 9,
maximizable = TRUE,
fluidRow(
column(
width = 7,
fluidRow(
column(
width = 3,
align = "right",
"Jump to (lat/lon)"
),
column(
width = 3,
numericInput("jump_lat", label = NULL, value = 51.48867, min = -90, max = 90, step = 0.1)
),
column(
width = 3,
numericInput("jump_lon", label = NULL, value = 7.21685, min = -180, max = 180, step = 0.1)
),
column(
width = 3,
align = "left",
actionButton("jump_button", "Go!")
)
)
)
),
leafletOutput("map_box", height = "70vh")
)
)
),
tabItem(
tabName = "graphs",
plotExploreUI("plot1", "Plot 1", "207Pb/204Pb"),
plotExploreUI("plot2", "Plot 2", "208Pb/204Pb")
),
tabItem(
tabName = "upload",
fluidRow(
bs4Card(
title = "Upload Form",
width = 3,
maximizable = TRUE,
uiOutput("file_upload"),
hr(style = "border-top: 1px solid #adb5bd;"),
h5("Parameters:"),
radioButtons("sep", "Separator",
choices = c(Comma = ",",
Semicolon = ";",
Tab = "\t"),
selected = ","),
radioButtons("dec", "Decimal sign",
choices = c(Point = ".",
Comma = ","),
selected = "."),
radioButtons("quote", "Quote",
choices = c(None = "",
"Double Quote" = '"',
"Single Quote" = "'"),
selected = '"'),
hr(style = "border-top: 1px solid #adb5bd;"),
fluidRow(
column(
width = 6,
actionButton("autopick", "Match database"),
),
column(
width = 6,
actionButton("upload_reset", "Reset"),
align = "right"
)
)
),
tabBox(
id = "upload_check",
width = 9,
side = "left",
maximizable = TRUE,
tabPanel(
title = "Data Viewer",
DT::dataTableOutput("upload_preview")
),
tabPanel(
title = "Instructions",
includeMarkdown("doc/upload.md")
)
)
)
),
tabItem(
tabName = "download",
bs4Card(
title = "Download plots and datasets",
width = 12,
collapsible = FALSE,
fluidRow(
column(
width = 5,
fluidRow(
checkboxInput("download_plot1", "Plot 1")
),
fluidRow(
column(
width = 6,
numericInput("download_plot1_width", "Width", value = 15, min = 0, max = 50)
),
column(
width = 6,
numericInput("download_plot1_height", "Height", value = 10, min = 0, max = 50)
)
)
),
column(
width = 1
),
column(
width = 5,
fluidRow(
checkboxInput("download_plot2", "Plot 2")
),
fluidRow(
column(
width = 6,
numericInput("download_plot2_width", "Width", value = 15, min = 0, max = 50)
),
column(
width = 6,
numericInput("download_plot2_height", "Height", value = 10, min = 0, max = 50)
)
)
)
),
hr(style = "border-top: 1px solid #adb5bd;"),
fluidRow(
column(
width = 5,
fluidRow(
checkboxInput("download_combineh", "Horizontally combined")
),
fluidRow(
column(
width = 6,
numericInput("download_combineh_width", "Width", value = 20, min = 0, max = 50)
),
column(
width = 6,
numericInput("download_combineh_height", "Height", value = 15, min = 0, max = 50)
)
)
),
column(
width = 1
),
column(
width = 5,
fluidRow(
checkboxInput("download_combinev", "Vertically combined")
),
fluidRow(
column(
width = 6,
numericInput("download_combinev_width", "Width", value = 15, min = 0, max = 50)
),
column(
width = 6,
numericInput("download_combinev_height", "Height", value = 20, min = 0, max = 50)
)
)
)
),
"Please make sure that the plots have identical legends: only the legend of plot 1 will be shown.",
hr(style = "border-top: 1px solid #adb5bd;"),
fluidRow(
column(
width = 4,
selectInput("download_unit", "Unit of plot size", choices = c("cm", "mm", "in"))
),
column(
width = 4,
numericInput("download_dpi", "Resolution (dpi)", value = 300, min = 72, max = 4800)
),
column(
width = 4,
selectInput("download_plot_filetype", "File type", choices = c("tiff", "jpg", "png", "pdf", "eps"))
)
),
hr(style = "border-top: 3px solid #adb5bd;"),
fluidRow(
column(
width = 4,
fluidRow(
checkboxInput("download_dataset", "Dataset used in plots")
),
fluidRow(
checkboxInput("download_upload", "Enhanced uploaded data")
)
),
column(
width = 4,
selectInput("download_data_filetype", "File type - data", choices = c("txt - tab sep." = "txt", "csv - comma sep." = "csv1", "csv - semicolon sep." = "csv2"))
),
column(
width = 4,
selectInput("download_references_filetype", "File type - References", choices = c("docx" = "docx", "txt" = "txt"))
)
),
hr(style = "border-top: 3px solid #adb5bd;"),
fluidRow(
column(
width = 10,
tags$b("Caution: ", style = "color: red;"),
"3D scatterplots will result in the download of an empty plot. Use the snapshot tool in the interactive plot instead."
),
column(
width = 2,
downloadButton("download"),
align = "right"
)
)
)
),
tabItem(
tabName = "references",
includeMarkdown("doc/references.md")
),
tabItem(
tabName = "instructions",
includeMarkdown("doc/instructions.md")
),
tabItem(
tabName = "resources",
includeMarkdown("doc/resources.md")
),
tabItem(
tabName = "about",
includeMarkdown("doc/about.md")
),
tabItem(
tabName = "news",
includeMarkdown("doc/news.md")
),
tabItem(
tabName = "imprint",
includeMarkdown("doc/imprint.md")
),
tabItem(
tabName = "disclaimer",
includeMarkdown("doc/disclaimer.md")
),
tabItem(
tabName = "contribute",
fluidRow(
bs4Card(
title = "Data upload",
width = 4,
maximizable = TRUE,
fluidRow(
column(
width = 6,
fileInput("contribute_data", "Data (.csv, .txt)",
accept = c("text/csv", "text/comma-separated-values,text/plain", ".csv", ".txt")
),
radioButtons("contribute_sep", "Separator",
choices = c(Comma = ",",
Semicolon = ";",
Tab = "\t"),
selected = ","),
radioButtons("contribute_dec", "Decimal sign",
choices = c(Point = ".",
Comma = ","),
selected = "."),
radioButtons("contribute_quote", "Quote",
choices = c(None = "",
"Double Quote" = '"',
"Single Quote" = "'"),
selected = '"'
)
),
column(
width = 6,
textInput("contribute_user", "Contributor"),
radioButtons("contribute_type", "Type of Contribution",
choices = c("New data" = "new",
"Update data" = "update"
),
selected = "update"
),
conditionalPanel(condition = "input.contribute_type == 'new'",
tagList(
fileInput("contribute_publication", "Publications (.pdf)",
accept = c("application/pdf", ".pdf")
),
textInput("contribute_doi", "DOI (or 'n/a')"),
textInput("contribute_citation", "Full citation")
)
)
)
),
hr(style = "border-top: 1px solid #adb5bd;"),
textAreaInput("contribute_comments", "Comments to data", rows = 3, placeholder = "Enter short summary of the contribution here")
),
tabBox(
id = "contribute_check",
width = 8,
side = "left",
maximizable = TRUE,
tabPanel(
title = "Instructions",
includeMarkdown("doc/contribute.md")
),
tabPanel(
title = "Data Viewer",
DT::dataTableOutput("contribute_data_preview")
),
tabPanel(
title = "Check & Submit",
h5("I confirm that"),
checkboxGroupInput("contribute_checklist", NULL,
choiceNames = c("The data are correct to the best of my knowledge",
"Submission of the data does not violate any copyright",
"The data were correctly parsed",
"The data are UTF-8 encoded",
"The data are following the notation of GlobaLID",
"The data do not contain malicious code."),
choiceValues = letters[1:6]),
actionButton("contribute_submit", "Submit")
)
)
)
)
)
)
)
# Server side -------------------------------------------------------------
server <- function(input, output, session) {
# Input validation --------------------------------------------------------
iv <- InputValidator$new()
general_iv <- InputValidator$new()
general_iv$add_rule("group", sv_in_set(c("Country", "Political province/region", "Mining area", "Mining site", "Tectonic/geolog. super unit", "Tectonic/geolog. unit", "Tectonic/geolog. subunit", "Deposit type")))
general_iv$add_rule("sidebar", sv_in_set(c("map", "graphs", "upload", "download", "references", "instructions", "resources", "about", "contribute", "imprint")))
database_iv <- InputValidator$new()
database_iv$add_rule("database", ~ if(. != "Ores & Minerals") "Do not hack the app.")
database_iv$add_rule("data_clean", ~ if(!is.logical(.)) "Do not hack the app.")
database_iv$add_rule("location_accuracy", ~ if(!is.logical(.)) "Do not hack the app.")
database_iv$add_rule("data_unknown", ~ if(!is.logical(.)) "Do not hack the app.")
database_iv$add_rule("filter_country", sv_in_set(unique(data_complete$Country)))
database_iv$add_rule("filter_province", sv_in_set(unique(data_complete$`Political province/region`)))
database_iv$add_rule("filter_area", sv_in_set(unique(data_complete$`Mining area`)))
database_iv$add_rule("filter_site", sv_in_set(unique(data_complete$`Mining site`)))
database_iv$add_rule("filter_geolAge", sv_in_set(unique(data_complete$`Geol. period`)))
database_iv$add_rule("filter_instrument", sv_in_set(unique(data_complete$`Instrument used`)))
database_iv$add_rule("filter_year", sv_integer(allow_multiple = TRUE))
database_iv$add_rule("filter_year", sv_between(min(data_complete$year, na.rm = TRUE), max(data_complete$year, na.rm = TRUE)))
database_iv$add_rule("filter_commodity", sv_in_set(commodities))
database_iv$add_rule("filter_mineral", sv_in_set(minerals))
map_iv <- InputValidator$new()
map_iv$add_rule("preview_control", sv_in_set(LETTERS[1:3]))
map_iv$add_rule("jump_lat", sv_numeric())
map_iv$add_rule("jump_lat", sv_between(-90, 90))
map_iv$add_rule("jump_lon", sv_numeric())
map_iv$add_rule("jump_lon", sv_between(-180, 180))
plot_iv <- InputValidator$new()
plot_iv$add_rule("palette", sv_in_set(c("viridis", "magma", "inferno", "plasma", "cividis", "BrBG", "PiYG", "PRGn", "PuOr", "RdBu", "RdGy", "RdYlBu", "RdYlGn", "Spectral", "Blues", "BuGn", "BuPu", "GnBu", "Greens", "Greys", "Oranges", "OrRd", "PuBu", "PuBuGn", "PuRd", "Purples", "RdPu", "Reds", "YlGn", "YlGnBu", "YlOrBr", "YlOrRd", "Accent", "Dark2", "Paired", "Pastel1", "Pastel2", "Set1", "Set2", "Set3")))
upload_iv <- InputValidator$new()
upload_iv$add_rule("sep", sv_in_set(c(",", ";", "\t")))
upload_iv$add_rule("dec", sv_in_set(c(",", ".")))
upload_iv$add_rule("quote", sv_in_set(c("'", '"', "")))
download_iv <- InputValidator$new()
download_iv$add_rule("download_plot1", ~ if(!is.logical(.)) "Do not hack the app.")
download_iv$add_rule("download_plot1_width", sv_integer())
download_iv$add_rule("download_plot1_width", sv_between(0, 50))
download_iv$add_rule("download_plot1_height", sv_integer())
download_iv$add_rule("download_plot1_height", sv_between(0, 50))
download_iv$add_rule("download_plot2", ~ if(!is.logical(.)) "Do not hack the app.")
download_iv$add_rule("download_plot2_width", sv_integer())
download_iv$add_rule("download_plot2_width", sv_between(0, 50))
download_iv$add_rule("download_plot2_height", sv_integer())
download_iv$add_rule("download_plot2_height", sv_between(0, 50))
download_iv$add_rule("download_combineh", ~ if(!is.logical(.)) "Do not hack the app.")
download_iv$add_rule("download_combineh_width", sv_integer())
download_iv$add_rule("download_combineh_width", sv_between(0, 50))
download_iv$add_rule("download_combineh_height", sv_integer())
download_iv$add_rule("download_combineh_height", sv_between(0, 50))
download_iv$add_rule("download_combinev", ~ if(!is.logical(.)) "Do not hack the app.")
download_iv$add_rule("download_combinev_width", sv_integer())
download_iv$add_rule("download_combinev_width", sv_between(0, 50))
download_iv$add_rule("download_combinev_height", sv_integer())
download_iv$add_rule("download_combinev_height", sv_between(0, 50))
download_iv$add_rule("download_unit", sv_in_set(c("cm", "in", "mm")))
download_iv$add_rule("download_dpi", sv_integer())
download_iv$add_rule("download_dpi", sv_between(72, 4800))
download_iv$add_rule("download_plot_filetype", sv_in_set(c("tiff", "jpg", "png", "pdf", "eps")))
download_iv$add_rule("download_dataset", ~ if(!is.logical(.)) "Do not hack the app.")
download_iv$add_rule("download_upload", ~ if(!is.logical(.)) "Do not hack the app.")
download_iv$add_rule("download_data_filetype", sv_in_set(c("txt", "csv1", "csv2")))
download_iv$add_rule("download_references_filetype", sv_in_set(c("docx", "txt")))
contribute_iv <- InputValidator$new()
contribute_iv$add_rule("contribute_sep", sv_in_set(c(",", ";", "\t")))
contribute_iv$add_rule("contribute_dec", sv_in_set(c(",", ".")))
contribute_iv$add_rule("contribute_quote", sv_in_set(c("'", '"', "")))
contribute_iv$add_rule("contribute_user", sv_regex("<|>", "Must not contain < or >.", invert = TRUE))
contribute_iv$add_rule("contribute_type", sv_in_set(c("new", "update")))
contribute_iv$add_rule("contribute_doi", sv_regex("<|>", "Must not contain < or >.", invert = TRUE))
contribute_iv$add_rule("contribute_citation", sv_regex("<|>", "Must not contain < or >.", invert = TRUE))
contribute_iv$add_rule("contribute_comments", sv_regex("<|>", "Must not contain < or >.", invert = TRUE))
contribute_iv$add_rule("contribute_checklist", sv_in_set(letters[1:6]))
iv$add_validator(database_iv)
iv$add_validator(general_iv)
iv$add_validator(map_iv)
iv$add_validator(plot_iv)
iv$add_validator(upload_iv)
iv$add_validator(download_iv)
iv$add_validator(contribute_iv)
iv$enable()
# Modal popup on start ----------------------------------------------------
showModal(
modalDialog(
title = "Welcome to GlobaLID!",
h6("Welcome to the prototype of the GlobaLID web application."),
div("We are currently developing the full version of GlobaLID. Visit ",
a(href = "https://archmetaldbm.github.io/Globalid/", target="_blank", "our webpage"),
"to learn more about GlobaLID and the current state of the work."),
div("In the meanwhile, we appreciate if you send us any feedback or suggestions you might have",
a(href = "mailto:globalid@bergbaumuseum.de?subject=Feedback to GlobaLID Web App", "by mail"),
"."),
div(tags$b("Thank you!")),
footer = modalButton("Close"),
easyClose = TRUE,
fade = FALSE
)
)
# Status handler ----------------------------------------------------------
status <- reactiveValues(reset = TRUE)
observeEvent(input$upload_reset, {
status$reset <- TRUE
autopick_data <- NULL
filter$country <- NULL
filter$province <- NULL
filter$area <- NULL
})
observeEvent(input$upload_file, {
status$reset <- FALSE
})
# Databases: Reference data ----------------------------------------------
# The input variable "database" is saved and allocated to choose from different datasets, must be validated if it becomes active
database <- reactive({
req(database_iv$is_valid(), general_iv$is_valid())
if (input$data_clean) {data <- data_clean} else {data <- data_complete}
data <- data %>%
filter(if(!is.null(input$filter_country)) Country %in% input$filter_country else TRUE) %>%
filter({
if (!is.null(input$filter_province) | !is.null(input$filter_area)) {
(if(!is.null(input$filter_province)) `Political province/region` %in% input$filter_province else `Political province/region` == TRUE) |
(if(!is.null(input$filter_area)) `Mining area` %in% input$filter_area else `Mining area` == TRUE)
} else {
TRUE
}
}) %>%
filter(if(!is.null(input$filter_site)) `Mining site` %in% input$filter_site else TRUE) %>%
filter(if(!is.null(input$filter_commodity)) str_detect(`Metals`, str_c(input$filter_commodity, collapse = "|")) else TRUE) %>%
filter(if(!is.null(input$filter_mineral)) str_detect(`Minerals`, str_c(input$filter_mineral, collapse = "|")) else TRUE) %>%
filter(if(!is.null(input$filter_geolAge)) `Geol. period` %in% input$filter_geolAge else TRUE) %>%
filter(if(!is.null(input$filter_instrument)) `Instrument used` %in% input$filter_instrument else TRUE) %>%
filter(if(!is.null(input$filter_year)) between(year, input$filter_year[1], input$filter_year[2]) else TRUE) %>%
filter(if(all(!is.null(input$data_unknown), input$data_unknown)) !.data[[input$group]] == "unknown" else TRUE) %>%
filter(if(all(!is.null(input$location_accuracy), input$location_accuracy)) {str_detect(`Location precision`, "exact|Exact")} else TRUE)
if (dim(data)[1] == 0) {data <- NULL}
data
})
# Databases: user data --------------------------------------------------
custom_data <- reactive({
req(upload_iv$is_valid())
if (!status$reset) {
validate(need(tools::file_ext(input$upload_file$datapath) %in% c("csv", "txt"), "Please upload a csv or txt file."))
tryCatch(
upload_data <- read.delim(
input$upload_file$datapath,
header = TRUE,
sep = input$sep,
quote = input$quote,
dec = input$dec
),
error = function(e) "A problem occurred while parsing your file. Please chose the appropriate parameters for reading your data."
)
validate(need(ncol(upload_data) >= 2, "A problem occurred while parsing your file. Please chose the appropriate parameters for reading your data."))
colnames(upload_data) <- stringr::str_to_lower(colnames(upload_data))
colnames(upload_data) <- stringr::str_replace_all(colnames(upload_data), pattern = ".*6.*4.*", "206Pb/204Pb")
colnames(upload_data) <- stringr::str_replace_all(colnames(upload_data), pattern = ".*7.*4.*", "207Pb/204Pb")
colnames(upload_data) <- stringr::str_replace_all(colnames(upload_data), pattern = ".*8.*4.*", "208Pb/204Pb")
colnames(upload_data) <- stringr::str_replace_all(colnames(upload_data), pattern = ".*4.*6.*", "204Pb/206Pb")
colnames(upload_data) <- stringr::str_replace_all(colnames(upload_data), pattern = ".*7.*6.*", "207Pb/206Pb")
colnames(upload_data) <- stringr::str_replace_all(colnames(upload_data), pattern = ".*8.*6.*", "208Pb/206Pb")
colnames(upload_data) <- stringr::str_replace_all(colnames(upload_data), pattern = ".*6.*7.*", "206Pb/207Pb")
colnames(upload_data) <- stringr::str_replace_all(colnames(upload_data), pattern = ".*8.*7.*", "208Pb/207Pb")
colnames(upload_data) <- stringr::str_replace_all(colnames(upload_data), pattern = ".*lat.*", "latitude")
colnames(upload_data) <- stringr::str_replace_all(colnames(upload_data), pattern = ".*l.*ng.*", "longitude")
colnames(upload_data) <- stringr::str_replace_all(colnames(upload_data), pattern = ".*ample.*", "sample")
colnames(upload_data) <- stringr::str_replace_all(colnames(upload_data), pattern = ".*gr.*", "group")
if ("sample" %in% names(upload_data)) {upload_data$sample <- as.character(upload_data$sample)}
if ("group" %in% names(upload_data)) {upload_data$group <- as.character(upload_data$group)}
validate(need(length(setdiff(names(upload_data), c("206Pb/204Pb", "207Pb/204Pb", "208Pb/204Pb", "204Pb/206Pb", "207Pb/206Pb", "208Pb/206Pb", "206Pb/207Pb", "208Pb/207Pb", "latitude", "longitude", "sample", "group"))) == 0, "One or more columns in your data set are not supported by GlobaLID. For a list of supported columns, see chapter 'Upload and display of your data' in the instructions."))
if ("206Pb/204Pb" %in% names(upload_data)) {validate(need(is.numeric(upload_data$`206Pb/204Pb`), "Columns for isotope ratios must contain only numeric values."))}
if ("207Pb/204Pb" %in% names(upload_data)) {validate(need(is.numeric(upload_data$`207Pb/204Pb`), "Columns for isotope ratios must contain only numeric values."))}
if ("208Pb/204Pb" %in% names(upload_data)) {validate(need(is.numeric(upload_data$`208Pb/204Pb`), "Columns for isotope ratios must contain only numeric values."))}
if ("204Pb/206Pb" %in% names(upload_data)) {validate(need(is.numeric(upload_data$`204Pb/206Pb`), "Columns for isotope ratios must contain only numeric values."))}
if ("207Pb/206Pb" %in% names(upload_data)) {validate(need(is.numeric(upload_data$`207Pb/206Pb`), "Columns for isotope ratios must contain only numeric values."))}
if ("208Pb/206Pb" %in% names(upload_data)) {validate(need(is.numeric(upload_data$`208Pb/206Pb`), "Columns for isotope ratios must contain only numeric values."))}
if ("206Pb/207Pb" %in% names(upload_data)) {validate(need(is.numeric(upload_data$`206Pb/207Pb`), "Columns for isotope ratios must contain only numeric values."))}
if ("208Pb/207Pb" %in% names(upload_data)) {validate(need(is.numeric(upload_data$`208Pb/207Pb`), "Columns for isotope ratios must contain only numeric values."))}
if ("latitude" %in% names(upload_data)) {
validate(need(is.numeric(upload_data$latitude), "Columns for coordinates must contain only numeric values."))
validate(need({min(upload_data$latitude, na.rm = TRUE) >= -90 & max(upload_data$latitude, na.rm = TRUE) <= 90}, "One or more of the latitude coordinates is out of bounds."))
validate(need("longitude" %in% names(upload_data), "Please provide also the coordinates for the longitude or no coordinates at all."))
}
if ("longitude" %in% names(upload_data)) {
validate(need(is.numeric(upload_data$longitude), "Columns for coordinates must contain only numeric values."))
validate(need({min(upload_data$longitude, na.rm = TRUE) >= -180 & max(upload_data$longitude, na.rm = TRUE) <= 180}, "One or more of the longitude coordinates is out of bounds."))
validate(need("latitude" %in% names(upload_data), "Please provide also the coordinates for the latitude or no coordinates at all."))
}
upload_data <- LI_ratios_all(upload_data)
upload_data <- cbind(upload_data, LI_model_age(upload_data$`206Pb/204Pb`, upload_data$`207Pb/204Pb`, upload_data$`208Pb/204Pb`, model = "all"))
if ("group" %in% colnames(upload_data)) {
upload_data$tooltip <- upload_data$group
} else {upload_data$group <- "This study"}
if ("sample" %in% colnames(upload_data)) {
upload_data$tooltip <- paste(upload_data$group, upload_data$sample, sep = "<br>")
} else {
upload_data$tooltip <- upload_data$group
}
upload_data
} else {
NULL
}
})
# Auto-Pick data based on upload ------------------------------------------
filter <- reactiveValues(
country = NULL,
province = NULL,
area = NULL
)
observeEvent(input$autopick, {
autopick_data <- reactive({
req(custom_data())
if (input$data_clean) {data <- data_clean} else {data <- data_complete}
suppressWarnings(
filter(data, between(`206Pb/204Pb`, min(custom_data()$`206Pb/204Pb`), max(custom_data()$`206Pb/204Pb`))) %>%
union(filter(data, between(`207Pb/204Pb`, min(custom_data()$`207Pb/204Pb`), max(custom_data()$`207Pb/204Pb`)))) %>%
union(filter(data, between(`208Pb/204Pb`, min(custom_data()$`208Pb/204Pb`), max(custom_data()$`208Pb/204Pb`)))) %>%
union(filter(data, between(`206Pb/207Pb`, min(custom_data()$`206Pb/207Pb`), max(custom_data()$`206Pb/207Pb`)))) %>%
union(filter(data, between(`208Pb/207Pb`, min(custom_data()$`208Pb/207Pb`), max(custom_data()$`208Pb/207Pb`)))) %>%
union(filter(data, between(`204Pb/206Pb`, min(custom_data()$`204Pb/206Pb`), max(custom_data()$`204Pb/206Pb`)))) %>%
union(filter(data, between(`207Pb/206Pb`, min(custom_data()$`207Pb/206Pb`), max(custom_data()$`207Pb/206Pb`)))) %>%
union(filter(data, between(`208Pb/206Pb`, min(custom_data()$`208Pb/206Pb`), max(custom_data()$`208Pb/206Pb`))))
)
})
filter$country <- unique(autopick_data()$Country)
filter$province <- unique(autopick_data()$`Political province/region`)
filter$area <- unique(autopick_data()$`Mining area`)
})
# Data filter: Control Panel Output ---------------------------------------
output$filter_countryOut <- renderUI({
if (input$data_clean) {data <- data_clean} else {data <- data_complete}
selectizeInput("filter_country", "Countries",
choices = sort(unique(data$Country)),
selected = filter$country, multiple = TRUE)
})
output$filter_provinceOut <- renderUI({
if (input$data_clean) {data <- data_clean} else {data <- data_complete}
selectizeInput("filter_province", "Modern provinces (of selected countries)",
choices = unique(data$`Political province/region`[data$Country %in% input$filter_country]),
selected = filter$province, multiple = TRUE)
})
output$filter_areaOut <- renderUI({
if (input$data_clean) {data <- data_clean} else {data <- data_complete}
selectizeInput("filter_area", "Mining Area (of selected countries)",
choices = unique(data$`Mining area`[data$Country %in% input$filter_country]),
selected = filter$area, multiple = TRUE)
})
output$filter_siteOut <- renderUI({
if (input$data_clean) {data <- data_clean} else {data <- data_complete}
selectizeInput("filter_site", "Sites (of selected mining areas and provinces)",
choices = unique(data$`Mining site`[data$`Political province/region` %in% input$filter_province | data$`Mining area` %in% input$filter_area]),
selected = NULL, multiple = TRUE)
})
output$filter_geolAgeOut <- renderUI({
if (input$data_clean) {data <- data_clean} else {data <- data_complete}
selectizeInput("filter_geolAge", "Geological Age",
choices = unique(data %>% filter(if(!is.null(input$filter_country)) Country %in% input$filter_country else TRUE) %>%
filter({
if (!is.null(input$filter_province) | !is.null(input$filter_area)) {
(if(!is.null(input$filter_province)) `Political province/region` %in% input$filter_province else `Political province/region` == TRUE) |
(if(!is.null(input$filter_area)) `Mining area` %in% input$filter_area else `Mining area` == TRUE)
} else {
TRUE
}
}) %>%
filter(if(!is.null(input$filter_site)) `Mining site` %in% input$filter_site else TRUE) %>%
pull(`Geol. period`)),
selected = NULL, multiple = TRUE)
})
output$filter_commodityOut <- renderUI({
if (input$data_clean) {data <- data_clean} else {data <- data_complete}