Obtaining information about many LTER Sites

Alessandro Oggioni

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

By get_network_* functions:

Five functions were developed to access and download informationof an entire eLTER network.

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 spatial coordinates of the sites belonging to the network selected. A map of the sites can be produced.

library(dplyr)
library(leaflet)
library(ReLTER)

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

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

The list of site for LTER-Italy network

title	changed	uri	coordinates
Acquatina - Italy	2023-10-25T21:48:55+0200	https://deims.org/8e1909ae-afc0-4207-9314-68e234d57405	POINT (18.24 40.44)
Torgnon grassland Tellinod (IT19 Aosta Valley) - Italy	2023-10-27T10:46:01+0200	https://deims.org/a03ef869-aa6f-49cf-8e86-f791ee482ca9	POINT (7.579028 45.84606)
Renon BOL1 - Italy	2023-10-27T10:44:32+0200	https://deims.org/5d32cbf8-ab7c-4acb-b29f-600fec830a1d	POINT (11.4336 46.5868)
Collelongo-Selva Piana ABR1 - Italy	2023-07-24T16:06:23+0200	https://deims.org/9b1d144a-dc37-4b0e-8cda-1dda1d7667da	POINT (13.5881 41.8494)
Colognole TOS1 - Italy	2023-10-26T13:52:46+0200	https://deims.org/fdd9b462-d2a9-441a-80a1-f4e8947f5577	POINT (10.4386 43.5094)
Tarvisio FRI2 - Italy	2023-10-27T10:45:36+0200	https://deims.org/5907d0b6-7b4d-4260-a669-4bc0f61d1696	POINT (13.5933 46.4894)
Val Masino LOM1 - Italy	2023-10-27T10:46:51+0200	https://deims.org/68a5673c-9172-48cc-88e5-b9408b203309	POINT (9.59829 46.24215)
Alimini - Italy	2023-10-26T13:51:11+0200	https://deims.org/765cad42-25da-4893-b4cc-eb1f393b4b47	POINT (18.441 40.202)
Appennino centrale: Gran Sasso d’Italia - Italy	2023-07-24T14:20:51+0200	https://deims.org/c0738b00-854c-418f-8d4f-69b03486e9fd	POINT (13.55498 42.44625)
Appennino centrale: Velino-Duchessa - Italy	2023-07-24T14:20:48+0200	https://deims.org/12c79ecb-7890-4b75-9655-0883dacd8a29	POINT (13.3682 42.15693)

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

## Error in path.expand(path): invalid 'path' argument

Get other information sites in the network:

Four additional functions were implemented to obtain site information in the network. Each function gets 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.

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

# Table of the network's related resources
knitr::kable(
  head(listRelatedResources, 10),
  caption = "The list of sites for LTER-Italy network"
)

The list of sites for LTER-Italy network

relatedResourcesTitle	uri	relatedResourcesChanged
NA	NA	NA
LTER_EU_IT_077 Soil Temperature	https://deims.org/dataset/a84c3800-0384-11e5-870c-005056ab003f	2020-01-07 14:49:00
Deposition of N-NH4 and N-NO3 Renon Bol1 1985-207	https://deims.org/dataset/6499a7cc-df94-45ac-92ed-62f43360411d	2020-02-27 09:38:00
LTER Collelongo-Selva Piana, Italy, Vegetation data 1999-2016	https://deims.org/dataset/28fe3227-fb9f-4e73-9a2a-30c07e90104d	2019-12-20 13:21:00
LTER Collelongo-Selva Piana, Italy, Precipitation and Throughfall data 1998-2017	https://deims.org/dataset/d1497375-56f5-4140-a399-adfb32f925af	2020-09-02 13:43:00
LTER Val Masino, Italy, Vegetation data 1999-2012	https://deims.org/dataset/67727a8a-fe1f-44eb-88b5-bf98bc443104	2019-12-20 13:21:00
LTER Val Masino LOM1, Italy, Precipitation and throughfall data 1997-2015	https://deims.org/dataset/94b8f6fb-2cba-4b45-90e2-afd45b3e655e	2019-12-20 13:21:00
LTER_EU_IT_021: Vegetation monitoring by 10x10 m permanent plots	https://deims.org/dataset/1f49ee00-198f-11e5-a766-005056ab003f	2022-11-19 11:10:00
LTER_EU_IT_025: Vegetation monitoring by 10x10 permanent plots	https://deims.org/dataset/0c540fe8-1984-11e5-a766-005056ab003f	2019-11-29 11:31:00
LTER_EU_IT_025: Soil and air temperature measurement	https://deims.org/dataset/9edc9b28-1984-11e5-a766-005056ab003f	2019-11-29 11:31:00

By get_site_info function:

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

The example below shows how to select, from the list of LTER-Italy sites, only those with a lake environment and map those sites.

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

allSitesBounds <- lapply(sites$uri, function(s) {
  get_site_info(s, category = "Boundaries")
})
allSitesBounds <- do.call(rbind, allSitesBounds) # Creates an `sf` object

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

## Error in path.expand(path): invalid 'path' argument

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

# Using sites from previous example
allSitesContacts <- lapply(sites$uri, function(s) {
  get_site_info(s, category = "Contacts")
})
allSitesContacts <- do.call(rbind, allSitesContacts)

contacts <- tibble::tibble(
  siteName = NA,
  managerName = NA,
  managerEmail = NA,
  managerORCID = NA
)

for (i in seq_along(allSitesContacts)) {
  contacts <- contacts %>% 
    tibble::add_row(
      siteName = allSitesContacts$title[[i]],
      managerName = allSitesContacts$siteManager[[1]]$name,
      managerEmail = allSitesContacts$siteManager[[1]]$email,
      managerORCID = allSitesContacts$siteManager[[1]]$orcid
    )
}
# Contacts table
knitr::kable(
  head(contacts, 10),
  caption = "List of the contacts"
)

List of the contacts

siteName	managerName	managerEmail	managerORCID
NA	NA	NA	NA
Lago Bidighinzu - Italy	NA	NA	NA
Lago Braies - Italy	NA	NA	NA
Lago Cedrino - Italy	NA	NA	NA
Lago Cuga - Italy	NA	NA	NA
Lago di Candia - Italy	NA	NA	NA
Lago di Como - Italy	NA	NA	NA
Lago di Garda - Italy	NA	NA	NA
Lago di Orta - Italy	NA	NA	NA
LTSER Lago di Tovel - Italy	NA	NA	NA