---
title: "Obtain information about one LTER Site using the DEIMS ID"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Obtain information about one LTER Site using the DEIMS ID}
  %\VignetteEngine{knitr::knitr}
  %\usepackage[UTF-8]{inputenc}
  bibliography: ./references/occurrences_into_site_refs.bib
author: "Alessandro Oggioni, Paolo Tagliolato"
---

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`](https://docs.ropensci.org/ReLTER/reference/get_site_info.html) 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: 


```r
# 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

```r
# 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: 


```r
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: 


```r
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

```r
# 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

```r
# 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

```r
# 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.


```r
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>, …
```

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

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

```
## NULL
```

```r
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

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


```r
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)"
)
```



Table: 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 |

```r
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"
)
```



Table: 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](./sites_information.html).