Obtain information about one LTER Site using the DEIMS ID

For each LTER site the information is provided by the site manager in the DEIMS-SDR registry (see https://deims.org). The LTER site information is grouped into main sections, the most important ones are:

Affiliations,
Boundaries,
Contacts,
Environmental characteristics,
General,
Infrastructure,
Parameters,
Relate resources.

For more details about the site data model please visit https://deims.org/models/?id=site.

The get_site_info function of {ReLTER} allows to download details about a specific site, through the DEIMS-SDR sites API and the DEIMS.ID (https://deims.org/docs/deimsid.html).

Get affiliation info of the LTER site:

If the aim is to obtain the info about in which networks/RIs the site is listed, you can:

# For this example, the Lago Maggiore in Italy
deimsid <- 'https://deims.org/f30007c4-8a6e-4f11-ab87-569db54638fe'
siteAffiliations <- ReLTER::get_site_info(deimsid = deimsid,
  category = 'Affiliations'
)
# network(s) where the site is involved in
knitr::kable(
  siteAffiliations$networks[[1]],
  caption = "The list of the network(s) in which the site is listed"
)

Table: The list of the network(s) in which the site is listed

# project(s) where the site is involved in
knitr::kable(
  siteAffiliations$projects[[1]],
  caption = "The list of the project(s) in which the site is listed"
)

Table: The list of the project(s) in which the site is listed

Get boundaries info of the LTER site:

Get information about the geographic extent of the site:

library(leaflet)
siteBoundaries <- ReLTER::get_site_info(deimsid = deimsid,
  category = "Boundaries"
)

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

## Error in structure(list(options = options), leafletData = data): object 'sitesBoundaries' not found

Get Contacts info of the LTER site:

Get information about the contact person responsible for the site, the organisation operating the site and its monitoring programs, the reference to the organisation or the responsible national authority for funding and strategic decisions about the site , full name of the person(s) or organisation(s) who created the documentation for the site:

siteContact <- ReLTER::get_site_info(deimsid = deimsid,
  category = "Contacts"
)
# site manager(s)
knitr::kable(
  siteContact$siteManager[[1]],
  caption = "The list of the manager(s) of site"
)

Table: The list of the manager(s) of site

# operating organisation of site
knitr::kable(
  siteContact$operatingOrganisation[[1]],
  caption = "The list of the operating organization of the site"
)

Table: The list of the operating organization of the site

# metadata provider(s) of site
knitr::kable(
  siteContact$metadataProvider[[1]],
  caption = "The list of the metadata provider(s) of site"
)

Table: The list of the metadata provider(s) of site

# funding agency(ies) of site
knitr::kable(
  siteContact$fundingAgency[[1]],
  caption = "The list of the funding agency(ies) of site"
)

Table: The list of the funding agency(ies) of site

The same approach could be used for other category information.

siteGeneral <- ReLTER::get_site_info(deimsid = deimsid,
  category = "General"
)
siteGeneral

## # A tibble: 1 × 24
##   title            uri   geoCoord country geoElev.avg geoElev.min geoElev.max geoElev.unit
##   <chr>            <chr> <chr>    <list>        <dbl>       <int>       <int> <chr>       
## 1 Lago Maggiore -… http… POINT (… <chr>          194.         186        4633 msl         
## # ℹ 16 more variables: generalInfo.abstract <chr>, generalInfo.citation <lgl>,
## #   generalInfo.relatedIdentifiers <lgl>, generalInfo.status.label <chr>,
## #   generalInfo.status.uri <chr>, generalInfo.yearEstablished <int>,
## #   generalInfo.yearClosed <lgl>, generalInfo.hierarchy.parent <list>,
## #   generalInfo.hierarchy.children <lgl>, generalInfo.relatedSites <list>,
## #   generalInfo.siteName <chr>, generalInfo.shortName <chr>, generalInfo.siteType <chr>,
## #   generalInfo.protectionLevel <lgl>, generalInfo.landUse <lgl>, …

siteInfrastructure <- ReLTER::get_site_info(deimsid = deimsid, 
  category = "Infrastructure"
)
siteInfrastructure$collection[[1]]

## Warning: Unknown or uninitialised column: `collection`.

## NULL

siteEnvCharacts <- ReLTER::get_site_info(deimsid = deimsid, 
  category = "EnvCharacts"
)
siteEnvCharacts

## # A tibble: 1 × 26
##   title            uri   geoCoord country geoElev.avg geoElev.min geoElev.max geoElev.unit
##   <chr>            <chr> <chr>    <list>        <dbl>       <int>       <int> <chr>       
## 1 Lago Maggiore -… http… POINT (… <chr>          194.         186        4633 msl         
## # ℹ 18 more variables: envCharacteristics.airTemperature.yearlyAverage <dbl>,
## #   envCharacteristics.airTemperature.monthlyAverage <lgl>,
## #   envCharacteristics.airTemperature.unit <chr>,
## #   envCharacteristics.airTemperature.referencePeriod <lgl>,
## #   envCharacteristics.precipitation.yearlyAverage <int>,
## #   envCharacteristics.precipitation.monthlyAverage <lgl>,
## #   envCharacteristics.precipitation.unit <chr>, …

By selecting the category Infrastructure you can obtain info as:

access type
data policy

By selecting the category Infrastructure you can obtain info as:

air temperature (min, max and average)
precipitation (min, max and average)
biogeographical region
biome
ecosystem type
eunis habitat
geoBon biome
geology
hydrology
soil
vegetation

siteObsProp <- ReLTER::get_site_info(deimsid = deimsid,
  category = "observedProperties"
)
# parameter(s) collected in the site
knitr::kable(
  head(siteObsProp$observedProperties[[1]], 10),
  caption = "List of Observed Properties of site (partial)"
)

List of Observed Properties of site (partial)
observedPropertiesLabel	observedPropertiesUri
DNA sequence	http://vocabs.lter-europe.net/EnvThes/21400
acid neutralising capacity	http://vocabs.lter-europe.net/EnvThes/10310
acid neutralizing capacity of water	http://vocabs.lter-europe.net/EnvThes/22029
air temperature	http://vocabs.lter-europe.net/EnvThes/22035
algae species abundance	http://vocabs.lter-europe.net/EnvThes/10338
ammonium content	http://vocabs.lter-europe.net/EnvThes/10071
atmospheric parameter	http://vocabs.lter-europe.net/EnvThes/20937
available phosphorus	http://vocabs.lter-europe.net/EnvThes/22061
bacillariophyceae abundance	http://vocabs.lter-europe.net/EnvThes/10083
bacillariophyceae biomass	http://vocabs.lter-europe.net/EnvThes/10120

siteRelateRes <- ReLTER::get_site_info(deimsid = deimsid,
  category = "RelateRes"
)
# resource(s) related to the site (e.g. datasets, activities)
knitr::kable(
  siteRelateRes$relatedResources[[1]],
  caption = "List of funding agencies of site"
)

List of funding agencies of site
relatedResourcesTitle	relatedResourcesChanged	uri
Atmospheric deposition in Pallanza, Lake Maggiore watershed, 1980-2018	2023-01-20 14:58:00	https://deims.org/dataset/0ce46362-0aab-482a-b1f0-a444a5dada39
Phytoplankton_Biomass_Lake Maggiore_Ghiffa_station-1984-2018	2020-12-16 10:46:00	https://deims.org/dataset/0ab8425a-d574-4575-8ba9-5275c607b0c5
Water chemistry of Lake Maggiore, Ghiffa station, 1988-2018	2021-11-03 06:10:00	https://deims.org/dataset/69564188-89de-4879-ad88-4aa97c1d005d
Transparency (Secchi depth) of Lake Maggiore, Ghiffa station, 1988-2018	2022-02-16 11:36:00	https://deims.org/dataset/e538c743-2149-49e3-9025-14a04ea7c90d
Chlorophyll a_Lake_Maggiore_Ghiffa_Station-1984-2018	2023-03-03 11:17:00	https://deims.org/dataset/c857c8e2-48aa-4dcd-a7fb-e089bd4c5c4e
Moldaenke FluoroProbe sensor	2022-05-19 21:02:00	https://deims.org/sensors/NA

Finally if you want get info from multiple site, please visit this page.

Alessandro Oggioni, Paolo Tagliolato

Get affiliation info of the LTER site:

Get boundaries info of the LTER site:

Get Contacts info of the LTER site:

About

Community

Resources

Obtain information about one LTER Site using the DEIMS ID

Alessandro Oggioni, Paolo Tagliolato

Get affiliation info of the LTER site:

Get boundaries info of the LTER site:

Get Contacts info of the LTER site:

Get list of parameters or related resources declared to the LTER site: