In oggioniale/ReLTER: An Interface for the eLTER Community

Taking into account the guide on "How to obtain site info?", here is offered two examples on how to aggregate information of many eLTER sites.

By get_network_* functions: {#firstExample}

Through the 5 functions developed for get network information, access and download of some information of an entire eLTER network can be made.

Get general information of the network's sites:

Knowing the network elTER id (DEIMS ID of the Network, e.g. LTER-Italy https://deims.org/network/7fef6b73-e5cb-4cd2-b438-ed32eb1504b3), the get_network_sites can download general info, such as name, DEIMS.iD and coordinates of the sites belonging to the network selected. A map of the sites can be returned.

library(dplyr)

listItaSites <- ReLTER::get_network_sites(
 networkDEIMSID =
   "https://deims.org/network/7fef6b73-e5cb-4cd2-b438-ed32eb1504b3"
) %>%
  dplyr::filter(!grepl('^IT', title))

knitr::kable(
  listItaSites[1:10, ],
  caption = "The list of site for LTER-Italy network"
)

listItaSitesMap <- leaflet::leaflet(listItaSites) %>%
  leaflet::addProviderTiles(provider = "CartoDB.PositronNoLabels",
                            group = "Basemap",
                            layerId = 123) %>%
  leaflet::addTiles("http://{s}.basemaps.cartocdn.com/light_only_labels/{z}/{x}/{y}.png") %>%
  leaflet::addCircleMarkers(
    data = listItaSites,
    radius = 3,
    weight = 2,
    opacity = 0.5,
    fill = TRUE,
    fillOpacity = 0.2
  )
listItaSitesMap

Get other information of the network's sites:

Another 4 functions are been implemented to obtain network's sites information. Each functions get specific information:

Environmental characteristics by get_network_envcharacts
Observed properties by get_network_observedProperties
Related resources by get_network_related_resources

The following example perform the request to get all related resources (e.g. activities, datasets, etc.) of the network. The output is a table containing the title, id and time stamp of the last changes of the related resources shared by the network's sites.

listRelatedResources <- ReLTER::get_network_related_resources(
  networkDEIMSID = "https://deims.org/network/7fef6b73-e5cb-4cd2-b438-ed32eb1504b3"
)

# Table of the network's related resources
knitr::kable(
  listRelatedResources,
  caption = "The list of site for LTER-Italy network"
)

By get_site_info function:

Starting by the list of the LTER-Italy network's sites (see first example above), or by using any DEIMS ID list, through the get_site_info function (already described here).

In the example below is proposed the selection, from the list of LTER-Italy sites, only the lakes environments and the map of these sites is made.

library(dplyr)
sites <- as_tibble(
  listItaSites
) %>%
  filter(grepl("Lago", title)) %>%
  filter(!row_number() %in% c(1, 21, 22))

allSiteBound <- lapply(
    as.list(
      sites$uri
    ),
    ReLTER::get_site_info,
    category = "Boundaries"
  )

# Map
sites_map <- leaflet::leaflet(allSiteBound) %>%
  leaflet::addProviderTiles(provider = "CartoDB.PositronNoLabels",
                            group = "Basemap",
                            layerId = 123) %>%
  leaflet::addTiles("http://{s}.basemaps.cartocdn.com/light_only_labels/{z}/{x}/{y}.png")

groups <- length(allSiteBound)

for (i in 1:groups) {
  site_polygon <- allSiteBound[[i]]
  sites_map <- sites_map %>%
    leaflet::addPolygons(
      data = site_polygon,
      popup = ~ title,
      group = i
    )
}
sites_map

Using the same LTER-Italy sites list, the next example provide a contact list of all lake site managers.

library(dplyr)
sites <- as_tibble(
  listItaSites
) %>%
  filter(grepl("Lago", title)) %>%
  filter(!row_number() %in% c(1, 21, 22))

allSiteContact <- lapply(
    as.list(
      sites$uri
    ),
    ReLTER::get_site_info,
    category = "Contacts"
  )
contacts <- tibble::tibble(
  siteName = NA,
  managerName = NA,
  managerEmail = NA,
  managerORCID = NA
)
for (i in seq_len(length(allSiteContact))) {
  contacts <- contacts %>% 
    tibble::add_row(
      siteName = allSiteContact[[i]]$title,
      managerName = allSiteContact[[i]]$generalInfo.siteManager[[1]]$name,
      managerEmail = allSiteContact[[i]]$generalInfo.siteManager[[1]]$email,
      managerORCID = allSiteContact[[i]]$generalInfo.siteManager[[1]]$orcid
    )
}
# Contacts table
knitr::kable(
  contacts,
  caption = "List of the contacts"
)