bdc: Bavarian Data Cube

## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE, eval=F,
  results="asis", echo=F, warning=F, message=F, comment = NA,
  fig.width=10, fig.height=8, fig.path="../figures/"
)

## ----load_pkgs----------------------------------------------------------------
#  library(tidyverse)
#  library(lubridate)
#  library(ggspatial)
#  library(ggsci)
#  library(ggthemes)
#  library(patchwork)
#  library(zoo)
#  
#  # Define standard colour scheme
#  bluewhitered <- colorRampPalette(c("#009392","#39b185","#9ccb86","#e9e29c","#eeb479","#e88471","#cf597e"))(255)

## -----------------------------------------------------------------------------
#  # Load shapefile of Bavaria
#  data("bavaria", package="bdc")

## ---- fig.width=10, fig.height=5----------------------------------------------
#  data("amphibians_bav", package="bdc")
#  data("bird_bav", package="bdc")
#  data("gard_reptiles_bav", package="bdc")
#  data("mammals_bav", package="bdc")
#  data("odonata_bav", package="bdc")
#  data("reptiles_bav", package="bdc")
#  
#  data("tk25_grid", package="bdc")
#  tk25_grid <- tk25_grid %>% raster::rasterFromXYZ()
#  raster::projection(tk25_grid) <- sp::CRS("+init=epsg:31468")
#  tk25_grid <- raster::projectRaster(tk25_grid, crs=sp::CRS("+init=epsg:4326"))
#  
#  #nrow(amphibians_bav); sum(amphibians_bav$presence)
#  
#  amphi <- raster::rasterize(amphibians_bav, tk25_grid) %>% raster::mask(tk25_grid) %>%
#    raster::rasterToPoints() %>% data.frame()
#  bird <- raster::rasterize(bird_bav, tk25_grid) %>% raster::mask(tk25_grid) %>%
#    raster::rasterToPoints() %>% data.frame()
#  mam <- raster::rasterize(mammals_bav, tk25_grid) %>% raster::mask(tk25_grid) %>%
#    raster::rasterToPoints() %>% data.frame()
#  odo <- raster::rasterize(odonata_bav, tk25_grid) %>% raster::mask(tk25_grid) %>%
#    raster::rasterToPoints() %>% data.frame()
#  rep <- raster::rasterize(reptiles_bav, tk25_grid) %>% raster::mask(tk25_grid) %>%
#    raster::rasterToPoints() %>% data.frame()
#  gard_rep <- raster::rasterize(gard_reptiles_bav, tk25_grid) %>% raster::mask(tk25_grid) %>%
#    raster::rasterToPoints() %>% data.frame()
#  
#  #colnames(bird)
#  
#  # Plot species richness of individual taxa
#  p1 <- amphi %>% ggplot() + geom_tile(aes(x=x,y=y,fill=layer)) +
#    scale_fill_gradientn(name="Amphibian SR", colours=bluewhitered) +
#    geom_sf(data=bavaria, fill=NA) + coord_sf() + labs(x="", y="")
#  p2 <- bird %>% ggplot() + geom_tile(aes(x=x,y=y,fill=layer)) +
#    scale_fill_gradientn(name="Bird SR", colours=bluewhitered) +
#    geom_sf(data=bavaria, fill=NA) + coord_sf() + labs(x="", y="")
#  p3 <- mam %>% ggplot() + geom_tile(aes(x=x,y=y,fill=layer)) +
#    scale_fill_gradientn(name="Mammal SR", colours=bluewhitered) +
#    geom_sf(data=bavaria, fill=NA) + coord_sf() + labs(x="", y="")
#  p4 <- odo %>% ggplot() + geom_tile(aes(x=x,y=y,fill=layer)) +
#    scale_fill_gradientn(name="Odonata SR", colours=bluewhitered) +
#    geom_sf(data=bavaria, fill=NA) + coord_sf() + labs(x="", y="")
#  p5 <- rep %>% ggplot() + geom_tile(aes(x=x,y=y,fill=layer)) +
#    scale_fill_gradientn(name="Reptile SR", colours=bluewhitered) +
#    geom_sf(data=bavaria, fill=NA) + coord_sf() + labs(x="", y="")
#  
#  p1 + p2 + p3 + p4 + p5
#  rm(list=ls()); invisible(gc())