## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, eval = FALSE, fig.align="center")

## ----eval=TRUE----------------------------------------------------------------
# install.packages('disdat')
# devtools::install_github('rspatial/disdat')
library(disdat)


## ----eval=TRUE, paged.print=TRUE----------------------------------------------
awt <- disBg("AWT")
head(awt)

## -----------------------------------------------------------------------------
# library(GGally)
# 
# ggcorr(awt[, 7:ncol(awt)],
#        method = c("pairwise", "spearman"),
#        label = TRUE,
#        label_size = 3,
#        label_color = "white",
#        digits = 2) +
#   theme(legend.justification = c(1, 0),
#         legend.position = c(0.5, 0.7),
#         legend.direction = "horizontal") +
#   guides(fill = guide_colorbar(barwidth = 9,
#                                barheight = 1,
#                                title.position = "top",
#                                title.hjust = 0.5,
#                                title = "Spearman correlation"))

## ----eval=TRUE, out.width = 600, echo=F, fig.align="center"-------------------
knitr::include_graphics("../man/figures/corr_plot.png")

## -----------------------------------------------------------------------------
# library(ggplot2)
# 

## ----eval=TRUE----------------------------------------------------------------
# create density plot for species presence-only vs background data
# first prepare the species records in the right format for the tidyverse package:
po <- disPo("AWT") # presence-only data
bg <- disBg("AWT") # background data
spdata <- rbind(po, bg)
spdata$occ <- as.factor(spdata$occ)
levels(spdata$occ) <- c("Landscape", "Species")
levels(spdata$occ)


## -----------------------------------------------------------------------------
# # now plot the data - specify the variable by its column name, as seen below in "aes(x = bc01,.....)"
# ggplot(data = spdata, aes(x = bc01, fill = occ)) +
#   geom_density(alpha = 0.4) +
#   xlab("Annual mean temperature") +
#   scale_fill_brewer(palette = "Dark2") +
#   guides(fill = guide_legend(title = "")) +
#   theme_bw()
# 

## ----eval=TRUE, out.width = 600, echo=F, fig.align="center"-------------------
knitr::include_graphics("../man/figures/density_plot.png")

## -----------------------------------------------------------------------------
# library(sf)
# library(tidyverse)
# 
# # presence-only data
# awt_sf <- st_as_sf(disPo("AWT"), coords = c("x", "y"), crs = 28355)
# 
# # a function to calculate the min distance (excluding self-distance)
# mindist <- function(x) {
#   mindis <- vector(mode = "numeric", length = nrow(x))
#   for(i in 1:nrow(x)){
#     mindis[i] <- min(x[i, -i])
#   }
#   return(mindis)
# }
# 
# awt_min_dist <- awt_sf %>%
#   group_by(spid) %>%
#   nest() %>%
#   mutate(distM = map(data, ~st_distance(x = .)),
#          minDist = map(distM, ~mindist(x = .)),
#          meanDist = map_dbl(minDist, ~mean(x = .)))
# 

## ----eval=TRUE, out.width = 400, echo=FALSE-----------------------------------
knitr::include_graphics("../man/figures/boxplot.jpeg")

## -----------------------------------------------------------------------------
# library(disdat)
# library(sf)
# library(tmap)
# library(grid)
# 
# # loading the data
# r <- disBorder("NSW") # a polygon file showing border of the region
# podata <- disPo("NSW") # presence-only data
# padata <- disPa("NSW", "db") # presence-absence of group db for species 'nsw14'
# 
# # select the species to plot
# species <- "nsw14"
# # convert the data.frame to sf objects for plotting
# po <- st_as_sf(podata[podata$spid == species, ], coords = c("x", "y"), crs = 4326) # subset the species
# pa <- st_as_sf(padata, coords = c("x", "y"), crs = 4326)
# 
# # create map showing training data
# train_sample <- tm_shape(r) + # create tmap object
#   tm_polygons() + # add the border
#   tm_shape(po) + # create tmap object for the points to overlay
#   tm_dots(size = 0.2, col = "blue", alpha = 0.6, legend.show = FALSE) + # add the points
#   tm_compass(type = "8star", position = c("left", "top")) + # add north arrow
#   tm_layout(main.title = "Training data", main.title.position = "center") + # manage the layout
#   tm_grid(lwd = 0.2, labels.inside.frame = FALSE, alpha = 0.4, projection = 4326, # add the grid
#           labels.format = list(big.mark = ",", fun = function(x){paste0(x, "º")})) # add degree symbol
# 
# # create map showing testing data
# pa[,species] <- as.factor(padata[,species])
# test_sample <- tm_shape(r) +
#   tm_polygons() +
#   tm_shape(pa) +
#   tm_dots(species, size = 0.2, palette = c("red", "blue"), title = "Occurrence", alpha = 0.6) +
#   tm_layout(main.title = "Testing data", main.title.position = "center") +
#   tm_grid(lwd = 0.2, labels.inside.frame = FALSE, alpha = 0.4, projection = 4326,
#           labels.format = list(big.mark = ",", fun = function(x){paste0(x, "º")}))
# 
# # create a layout for putting the maps side-by-side
# grid.newpage()
# pushViewport(viewport(layout=grid.layout(1,2)))
# print(train_sample, vp=viewport(layout.pos.col = 1))
# print(test_sample, vp=viewport(layout.pos.col = 2))
# 

## ----eval=TRUE, echo=FALSE----------------------------------------------------
knitr::include_graphics("../man/figures/tmap.png")

## ----eval=TRUE, fig.height=5, fig.width=6, message=FALSE, warning=FALSE-------
library(mapview)
library(sf)

# get presence-absence data
padata <- disPa(region = "NSW", group = "db") 
# use disCRS for each region for its crs code (EPSG)
disCRS("NSW", format = "EPSG")
# convert the data.frame to sf objects for plotting
pa <- st_as_sf(padata, coords = c("x", "y"), crs = 4326)
# select a species to plot
species <- "nsw14"

# plot presence-absence data
# you can add: map.types = "Esri.WorldImagery"
mapview(pa, zcol = species)