index.Rmd

---
title: "MBON Pole to Pole Project"
editor_options:
  chunk_output_type: console
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = F, message = F, warning = F, fig.width=9.5, fig.height=12)
```
<br>
<br>
<font size="5">
Welcome! We are developing a Community of Practice across the Americas to assess marine biodiversity and ecosystem change using field and space observations.
<br>
<br>
Learn about ongoing biodiversity monitoring efforts contributing to the network by clicking markers on the map

```{r}
if (!require(librarian)){
  install.packages("librarian")
  library(librarian)
}
shelf(
  glue, here, htmltools, leaflet, markdown, rnaturalearth, sf, tidyverse)

countries <- ne_countries(
  scale = "small", type = "countries", returnclass = "sf",
  continent= c("North America", "South America")) %>%
  mutate(
    mapcolor7 = as.factor(as.character(mapcolor7))) %>% 
  st_set_crs(4326)

sites_csv <- here("data/sites.csv")

sites <- read_csv(sites_csv, col_types=cols()) %>%
  st_as_sf(coords = c("lon", "lat"), crs = 4326)

b <- sf::st_bbox(sites)

pal <- colorFactor("Set2", countries$mapcolor7)
```

```{r}
sites <- read_csv(sites_csv, col_types=cols()) %>%
  st_as_sf(coords = c("lon", "lat"), crs = 4326) %>%
  mutate(
    md = glue("**{name}**<br>Org: {org}<br>Country: {str_to_upper(country)}<br>↪[ Visit](z_{id}.html)"),
    html = map_chr(md, function(x) HTML(markdownToHTML(text=x, fragment.only=T))))
#View(sites)

leaflet(countries) %>%
  addProviderTiles(
    providers$Esri.OceanBasemap,
    options = providerTileOptions(opacity = 0.5)) %>%
  addPolygons(
    stroke = FALSE, smoothFactor = 0.2, fillOpacity = 0.8,
    fillColor = ~pal(mapcolor7),
    label = ~admin) %>%
  addMarkers(
    data = sites,
    popup = ~html, label = ~htmlEscape(name)) %>%
  fitBounds(b[['xmin']], b[['ymin']], b[['xmax']], b[['ymax']])
```

```{r}
# poly_tbl <- c(40014, 40061, 40015, 40016, 40013, 40011, 40003, 21000, 20001)
# 
# for (i in 1:length(poly_tbl))
# {
#   area_code <- poly_tbl[i]
#   
#   ## Total
#   total = occurrence(areaid = area_code, taxonid = c(51, 1806, 882, 3))
#   csv <- here(glue("data/obis/obis_{area_code}.csv"))
#   write.csv(total, file = csv)
# }
```