--- title: "Obtaining information about many LTER Sites" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Obtaining information about many LTER Sites} %\VignetteEngine{knitr::knitr} %\usepackage[UTF-8]{inputenc} author: "Alessandro Oggioni" --- Taking into account the guide on ["How to obtain site info?"](./site_information.html), here are two examples on how to aggregate information of many eLTER sites. ## By get_network_* functions: {#firstExample} 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 ), the [`get_network_sites`](https://docs.ropensci.org/ReLTER/reference/get_network_sites.html) 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. ```r 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" ) ``` Table: 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) | ```r 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`](https://docs.ropensci.org/ReLTER/reference/get_network_envcharacts.html) * Observed properties by [`get_network_observedProperties`](https://docs.ropensci.org/ReLTER/reference/get_network_observedProperties.html) * Related resources by [`get_network_related_resources`](https://docs.ropensci.org/ReLTER/reference/get_network_related_resources.html) 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. ```r 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" ) ``` Table: 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](#firstExample)), or by using any DEIMS ID list, through the [`get_site_info`](https://docs.ropensci.org/ReLTER/reference/get_site_info.html) function (already described [here](./site_information.html)). The example below shows how to select, from the list of LTER-Italy sites, only those with a lake environment and map those sites. ```r sites <- as_tibble(listItaSites) %>% filter(grepl("Lago", title)) %>% filter(!row_number() %in% c(1, 21, 22)) allSitesBounds <- lapply(sites$uri, function(s) { get_site_info(s, category = "Boundaries") }) allSitesBounds <- do.call(rbind, allSitesBounds) # Creates an `sf` object # Map leaflet(data = allSitesBounds) %>% addPolygons() %>% addProviderTiles(provider = "CartoDB.PositronNoLabels", group = "Basemap", layerId = 123) %>% addTiles( "http://{s}.basemaps.cartocdn.com/light_only_labels/{z}/{x}/{y}.png") ``` ``` ## Error in path.expand(path): invalid 'path' argument ``` Using the same LTER-Italy sites list, the next example provide a contact list of all lake site managers. ```r # Using sites from previous example allSitesContacts <- lapply(sites$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" ) ``` Table: 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 |