How to get the info of a (one) LTER Site by knowing the DEIMS.ID
Alessandro Oggioni, Paolo Tagliolato
Source:vignettes/site_information.Rmd
site_information.RmdFor each LTER site the information are provided, by site manager, into DEIMS-SDR registry (see https://deims.org). The LTER site’s information are 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:
siteAffiliations <- ReLTER::get_site_info(
deimsid = 'https://deims.org/f30007c4-8a6e-4f11-ab87-569db54638fe',
category = 'Affiliations'
)
# network(s) where the site is involved in
knitr::kable(
siteAffiliations$affiliation.networks[[1]]$network,
caption = "The list of the network(s) in which the site is listed"
)| name | id |
|---|---|
| ILTER | https://deims.org/networks/ |
| LTER Europe | https://deims.org/networks/ |
| LTER Italia (Italy) | https://deims.org/networks/ |
# project(s) where the site is involved in
knitr::kable(
siteAffiliations$affiliation.projects[[1]],
caption = "The list of the project(s) in which the site is listed"
)| label | uri |
|---|---|
| LIFEPLAN | https://cordis.europa.eu/project/id/856506 |
| NETLAKE Cost Action ES1201 | NA |
| eLTER (H2020) | https://cordis.europa.eu/project/id/654359 |
| eLTER PLUS (H2020) - RA | https://cordis.europa.eu/project/id/871128 |
| eLTER PLUS (H2020) - TA | https://cordis.europa.eu/project/id/871128 |
| eLTER PLUS (H2020) - VA | https://cordis.europa.eu/project/id/871128 |
| eLTER catalogue | NA |
Get boundaries info of the LTER site:
If the aim is to obtain the info about the geographic extent covering the area of all measurements, you can:
siteBoundaries <- ReLTER::get_site_info(
deimsid = "https://deims.org/f30007c4-8a6e-4f11-ab87-569db54638fe",
category = "Boundaries"
)
tmap::tmap_mode("view")## tmap mode set to interactive viewing
tmap::tm_basemap("OpenStreetMap") +
tmap::tm_shape(siteBoundaries) +
tmap::tm_polygons(col = "skyblue", alpha = 0.25, border.col = "blue")Get Contacts info of the LTER site:
If the aim is to obtain the info about the reference to the contact person responsible for the site, the organisation operating the site and its monitoring programme(s), the reference to the organisation or the responsible national authority for funding and strategic decisions about the site or the full name of the person(s) or organisation(s) who created the documentation for the site, you can:
siteContact <- ReLTER::get_site_info(
deimsid = "https://deims.org/f30007c4-8a6e-4f11-ab87-569db54638fe",
category = "Contacts"
)
# site manager(s)
knitr::kable(
siteContact$generalInfo.siteManager[[1]],
caption = "The list of the manager(s) of site"
)| type | name | orcid | |
|---|---|---|---|
| person | Michela Rogora | michela.rogora@irsa.cnr.it | NA |
# operating organisation of site
knitr::kable(
siteContact$generalInfo.operatingOrganisation[[1]],
caption = "The list of the operating organization of the site"
)| type | name | url |
|---|---|---|
| organisation | CNR Water Research Institute | http://www.irsa.cnr.it |
# metadata provider(s) of site
knitr::kable(
siteContact$generalInfo.metadataProvider[[1]],
caption = "The list of the metadata provider(s) of site"
)| type | name | orcid | |
|---|---|---|---|
| person | Alessandro Oggioni | oggioni.a@irea.cnr.it | https://orcid.org/0000-0002-7997-219X |
| person | Cristiana Callieri | c.callieri@ise.cnr.it | NA |
| person | Manuela Coci | m.coci@ise.cnr.it | NA |
| person | Marina Manca | m.manca@ise.cnr.it | NA |
# funding agency(ies) of site
knitr::kable(
siteContact$generalInfo.fundingAgency[[1]],
caption = "The list of the funding agency(ies) of site"
)| type | name | url |
|---|---|---|
| organisation | CIPAIS | http://www.cipais.org/ |
| organisation | CNR Water Research Institute | http://www.irsa.cnr.it |
The same approach could be used for other category information.
siteGeneral <- ReLTER::get_site_info(
deimsid = "https://deims.org/f30007c4-8a6e-4f11-ab87-569db54638fe",
category = "General"
)
siteGeneral## # A tibble: 1 × 21
## title uri geoCo…¹ country geoEl…² geoEl…³ geoEl…⁴ geoEl…⁵ gener…⁶ gener…⁷
## <chr> <chr> <chr> <list> <dbl> <int> <int> <chr> <chr> <chr>
## 1 Lago Ma… http… POINT … <chr> 194. 186 4633 msl "Lake … Operat…
## # … with 11 more variables: generalInfo.status.uri <chr>,
## # generalInfo.yearEstablished <int>, generalInfo.yearClosed <lgl>,
## # generalInfo.hierarchy.parent <list>, generalInfo.hierarchy.children <lgl>,
## # generalInfo.siteName <chr>, generalInfo.shortName <chr>,
## # generalInfo.siteType <chr>, generalInfo.protectionLevel <lgl>,
## # generalInfo.landUse <lgl>, generalInfo.images <list>, and abbreviated
## # variable names ¹geoCoord, ²geoElev.avg, ³geoElev.min, ⁴geoElev.max, …
siteInfrastructure <- ReLTER::get_site_info(
deimsid = "https://deims.org/f30007c4-8a6e-4f11-ab87-569db54638fe",
category = "Infrastructure"
)
siteInfrastructure$generalInfo.collection## [[1]]
## collectionLabel collectionURI
## 1 6 - 10 beds NA
## 2 > 5 places NA
## 3 Boat NA
## 4 Cable based NA
## 5 Central station(s) NA
## 6 Paper NA
## 7 Proprietary file format NA
## 8 Relational database NA
## 9 Sensor Web Enablement (SWE) NA
## 10 Spatial data file (GIS) NA
## 11 Telephone line NA
## 12 XML database NA
siteEnvCharacts <- ReLTER::get_site_info(
deimsid = "https://deims.org/f30007c4-8a6e-4f11-ab87-569db54638fe",
category = "EnvCharacts"
)
siteEnvCharacts## # A tibble: 1 × 26
## title uri geoCo…¹ country geoEl…² geoEl…³ geoEl…⁴ geoEl…⁵ envCh…⁶ envCh…⁷
## <chr> <chr> <chr> <list> <dbl> <int> <int> <chr> <dbl> <lgl>
## 1 Lago Ma… http… POINT … <chr> 194. 186 4633 msl 12.4 NA
## # … with 16 more variables: envCharacteristics.airTemperature.unit <chr>,
## # envCharacteristics.airTemperature.referencePeriod <lgl>,
## # envCharacteristics.precipitation.yearlyAverage <int>,
## # envCharacteristics.precipitation.monthlyAverage <lgl>,
## # envCharacteristics.precipitation.unit <chr>,
## # envCharacteristics.precipitation.referencePeriod <lgl>,
## # envCharacteristics.biogeographicalRegion <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
Get list of parameters or related resources declared to the LTER site:
siteObsProp <- ReLTER::get_site_info(
deimsid = "https://deims.org/f30007c4-8a6e-4f11-ab87-569db54638fe",
category = "observedProperties"
)
# parameter(s) collected in the site
knitr::kable(
siteObsProp$observedProperties[[1]],
caption = "The list of the funding agency(ies) of site"
)
siteRelateRes <- ReLTER::get_site_info(
deimsid = "https://deims.org/f30007c4-8a6e-4f11-ab87-569db54638fe",
category = "RelateRes"
)
# resource(s) related to the site (e.g. datasets, activities)
knitr::kable(
siteRelateRes$relatedResources[[1]],
caption = "The list of the funding agency(ies) of site"
)| relatedResourcesTitle | relatedResourcesChanged | uri |
|---|---|---|
| Biovolume of Phytoplankton in Lake Maggiore site code IT_SI001137_within the period 1981 - 2010 | 2021-08-25 16:38:00 | https://deims.org/dataset/d9e94776-e7a8-11e2-a655-005056ab003f |
| 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 | 2023-01-20 14:38:00 | https://deims.org/dataset/c857c8e2-48aa-4dcd-a7fb-e089bd4c5c4e |
| Water discharge of River Ticino, Lake Maggiore outlet, 1988-2018 | 2023-01-21 07:09:00 | https://deims.org/dataset/fb3a8fec-0c1f-4c3a-81d5-364c7e6078c4 |
| 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.