ecoregion_background_sampler.Rmd

---
title: "Background Points"
author: "Fiona Spooner"
date: "30/10/2019"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(warning = FALSE, message = FALSE)
```

```{r}
library(dplyr)
library(ggplot2)
library(here)
library(lwgeom)
library(readr)
library(sf)
```


```{r}
ecoreg <-
  st_read(here::here("WWF_Ecoregions/official/wwf_terr_ecos.shp"))

ecoreg <- ecoreg %>%
  select(OBJECTID, ECO_NAME)   ##just selecting out the columns we're interested in

occ_files <-
  list.files(
    here::here("GBIF/Occurences/Network_Groups/"),
    pattern = "*.csv",
    full.names = TRUE,
    recursive = TRUE
  )

head(read.csv(occ_files[1]))

```


The function is in two stages, the first stage pulls out the unique longitude and latitude species occurrence points and identifies which ecoregions they are in.

The second stage creates a set number (no_pnts) of random points in these ecoregions which can be used as background points. 

```{r}

background_sampler <- function(occ_file, no_pnts) {
  sf_int <- read_csv(occ_file) %>%
    dplyr::select("decimalLongitude", "decimalLatitude") %>%
    distinct() %>%
    st_as_sf(.,
             coords = c("decimalLongitude", "decimalLatitude"),
             crs = 4326) %>%
    st_intersection(., ecoreg)
  
  bkg_ecoreg <- ecoreg %>%
    filter(ECO_NAME %in% sf_int$ECO_NAME) %>%
    st_sample(., size = no_pnts, type = "random")
  
  print(basename(occ_file))
  return(bkg_ecoreg)
}

```


Checking the background points are where you expect for a random species
```{r}
rsp <- sample(1:length(occ_files),1)

check <- background_sampler(occ_files[rsp], 10000)
pnt_buff <- 0.15

xy <- read_csv(occ_files[rsp]) %>%
  dplyr::select("decimalLongitude", "decimalLatitude") %>%
  distinct() %>%
  st_as_sf(.,
           coords = c("decimalLongitude", "decimalLatitude"),
           crs = 4326) %>%
  st_intersection(., ecoreg)

ggplot(data = ecoreg) +
  geom_sf(aes(fill = ECO_NAME, alpha = 0.6)) +
  geom_sf(data = check, alpha = 0.1) +
  geom_sf(data = xy,
          colour = "red",
          size = 2) +
  coord_sf(
    xlim = c(st_bbox(check)[1] - pnt_buff, st_bbox(check)[3] + pnt_buff),
    ylim = c(st_bbox(check)[2] - pnt_buff, st_bbox(check)[4] + pnt_buff)
  ) +
  theme_bw() +
  theme(legend.position = "none") +
  ggtitle(gsub(".csv", "", paste0(basename(occ_files[rsp]))))

```