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Obtain list of contacts from several DEIMS ID's (in csv file)

Alessandro Oggioni, Paolo Tagliolato

Source: vignettes/multi_sites_contacts.Rmd
multi_sites_contacts.Rmd

Starting from the DEIMS-SDR “Advanced Search - Sites” interface, users can download a csv file of the sites. Some filters can be used for selecting sites based on countries, projects, Biome, etc. The list of selected sites can be downloaded in csv format.

This vignette begins with such a csv file, and shows how to:

  1. Obtain contacts details, and spatial info for all sites (limited to 7 sites)
  2. Display in a table
  3. Prepare of map of those sites

List of the contacts 

library(ReLTER)
library(dplyr)
library(sf)
library(leaflet)
site_results <- read.csv("./data/site_contacts_data.csv", sep = ";") %>%
  as_tibble() %>% 
  mutate(url = paste0("https://deims.org/", DEIMS.ID)) %>%
  top_n(10) %>%
  unique()

# contacts <- site_results$url %>%
#   purrr::map_dfr(.f = function(x) {
#     x %>% ReLTER::get_site_info(category = "Contacts") %>%
#       dplyr::select(title, uri, siteManager, geoCoord) %>%
#       tidyr::unnest()
#   }) %>%
#   dplyr::mutate(
#     site = paste0("[", title, "](", uri, ")"),
#     contact = paste0("[", name, "](mailto:", email, ")")
#   ) %>%
#   unique()
#})

contacts <- lapply(site_results$url, function(u) {
  contact_info <- ReLTER::get_site_info(u, c("Contacts", "Boundary"))
  sm <- as.data.frame(contact_info$siteManager)
  cntt <- data.frame(site = paste0("[", contact_info$title, "](", contact_info$uri, ")"),
                  contact = paste0("[", sm$name, "](mailto:", sm$email, ")"),
                  geoCoord = contact_info$geoCoord)
  return(cntt)
  })
contacts <- do.call(rbind, contacts)

# Contacts table
knitr::kable(contacts[, c("site", "contact")],
  #(contacts %>% dplyr::select(site, contact)),
  caption = "List of the contacts",
  booktabs = TRUE, longtable = TRUE
)
List of the contacts
site contact
Beatenberg - Switzerland
Colognole TOS1 - Italy
Jussy - Switzerland
Krkonose/Karkonosze - Czechia
Krofdorf - Germany
Oulanka Research Station (Oulanka LTER) - Finland
Salmopol - Poland

Map of the sites 

site_results_geo <- st_as_sf(
      contacts,
      wkt = "geoCoord"
    )

listItaSitesMap <- leaflet(site_results_geo) %>%
  addTiles() %>%
  addCircleMarkers(
    data = site_results_geo,
    radius = 3,
    weight = 2,
    opacity = 0.5,
    fill = TRUE,
    fillOpacity = 0.2,
    popup = paste0(
      '<b>eLTER site: </b><br><a href="',
      site_results_geo$uri, '">', site_results_geo$title, '</a><br>',
      '<b>Contact:</b> <br><a href="mailto:', site_results_geo$email, '">',
      site_results_geo$name, '</a>'
    )
  )
listItaSitesMap
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