Demo2_ReLTER_intro.Rmd

---
title: "Introducing `ReLTER`"
author: "Alessandro Oggioni, Micha Silver, Paulo Tagliolato"
date: "3/01/2023"
output:
  ioslides_presentation:
    smaller: true
    logo: figures/eLTER_logo.png
    css: styles.css
---

```{r relter-setup, include=FALSE, purl=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE)
```

## What is ReLTER

#### As a reminder
  
  - Clone the github repository: https://github.com/micha-silver/ReLTER_demo
  - Review the first video: https://youtu.be/Y037HJH34g4
  - Install `ReLTER` from github:
    
```{r relter-loading, message=FALSE, warning=FALSE}
if (!require("ReLTER", quietly = TRUE))
  remotes::install_github("ropensci/ReLTER")
# Convenient way to load list of additional packages
pkg_list <- c("sf", "terra", "ReLTER", "tmap")
lapply(pkg_list,require, character.only = TRUE)
tmap_options(check.and.fix = TRUE)
tmap_mode("view")
```

----

#### Package Maintainer

```{r relter-maintainer}
library(ReLTER)
maintainer("ReLTER")
```

#### How to cite

```{r relter-citation}
citation("ReLTER")
```

----

#### Package functions

```{r relter-functions}
head(ls("package:ReLTER"), 30)
```

----

#### Categories of functions

  - site specific functions
  - network functions
  - metadata functions
  - taxonomy functions

#### Access to external data

  - Species occurrence
  - Species taxonomy
  - European spatial data
  - MODIS products

----

#### Key functions:
  - `get_ilter_generalinfo()`
  - `get_site_info()`
  - `get_network_sites()`
  - `get_site_speciesOccurrences()`
  - `get_site_ODS()`
  - `get_site_MODIS()`
  

## Examples

Search for DEIMS ID for a particular site. The function `get_ilter_generalinfo` allows to search by country name and site name. Then `get_site_info()` obtains various metadata about a chosen site.

#### For the first example, the **Doñana LTSER Platform** in Spain

```{r relter-donana}
donana = get_ilter_generalinfo(country_name = "Spain",
                              site_name = "Doñana")
(donana_id = donana$uri)
```

----

Plot a basic map of that site. We use the `tmap` package for viewing maps.

```{r relter-plot-donana}
donana_polygon <- get_site_info(donana_id, category = "Boundaries")
tm_basemap("OpenStreetMap.Mapnik") + 
  tm_shape(donana_polygon) +
  tm_fill(col = "blue", alpha = 0.3)
```

---- 

Get species occurrence data for Doñana using the `get_site_speciesOccurrences()` function. This function downloads data from one of the global biodiversity information sites.

In this case, GBIF: https://www.gbif.org/

```{r relter-species-donana}
species_occur <-  get_site_speciesOccurrences(donana_id,
                                              list_DS = "gbif", limit=12)
colnames(species_occur$gbif)
```

----

Display some variables from GBIF

```{r relter-species-variables}
dplyr::select(species_occur$gbif, name, eventDate)
```

----

#### Next example: Metadata from **Loch Kinord** in Scotland.

Note that partial matching is supported by `get_ilter_generalinfo()`. i.e. "United K"

```{r relter-kinord-info}
loch_kinord <- get_ilter_generalinfo(country_name = "United K",
                              site_name = "Loch Kinord")
(loch_kinord_id = loch_kinord$uri)
loch_kinord_details <- get_site_info(loch_kinord_id,
                                 c("Contacts", "EnvCharacts", "Parameters"))

print(paste("Site manager:",
            loch_kinord_details$generalInfo.siteManager[[1]]['name'],
            loch_kinord_details$generalInfo.siteManager[[1]]['email']))
```

----

Environment Characteristics

```{r relter-kinord-envcharacteristics}
print(paste("Annual average air temperature:",
            loch_kinord_details$envCharacteristics.airTemperature.yearlyAverage))
print(paste("Annual precipitation:",
            loch_kinord_details$envCharacteristics.precipitation.yearlyAverage))
```

----

Biome, vegetation

```{r relter-kinord-geobonbiome}
print(paste("GeoBonBiome: ",
            loch_kinord_details$envCharacteristics.geoBonBiome))

loch_kinord_vegetation <- loch_kinord_details$envCharacteristics.vegetation
cat("Vegetation: \n", stringr::str_wrap(loch_kinord_vegetation, 70))
```

----

#### Next example: Query the **LTER network in Slovakia**


```{r elter-slovakia, message=FALSE, warning=FALSE}
lter_slovakia_id = "https://deims.org/networks/3d6a8d72-9f86-4082-ad56-a361b4cdc8a0"
lter_slovakia_sites <- get_network_sites(lter_slovakia_id)
lter_slovakia_sites$title
```

----

#### Show map of sites in the network

```{r relter-slovakia-map, message=FALSE, warning=FALSE}
lter_slovakia <- produce_network_points_map(lter_slovakia_id, "SVK")
svk <- readRDS("gadm36_SVK_0_sp.rds")  # downloaded by produce_network_points_map()
tm_basemap("OpenStreetMap.Mapnik") + 
  lter_slovakia + 
  tm_shape(svk) +   tm_borders(col = "blue", lwd = 1) + 
  tm_scale_bar(position = c("right", "bottom"))
```