## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# # install.packages('ecochange')
# 
# require('ecochange')
# require('viridis')

## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# # The getGADM() function provides the names of administrative units. By default, it shows level 2 administrative units in the country of Colombia but those settings can be changed through the parameters level and country
# getGADM()
# 
# # List the products that can be downloaded with ecochange
# listGP()
# 
# # Download a layer containing water occurrence for the municipality
# # of Chimichagua
# waterocc=getrsp("Chimichagua", lyrs=c("occurrence"))
# 
# # the object is downloaded by default to a temporary folder.
# # Users can define a different path using the argument path()
# waterocc
# 
# # Let's plot the object
# plot(raster(waterocc), axes = T,
#      main = 'Occurrence (Colombia)')

## ----scene, echo=FALSE, fig.cap="", out.width = '100%'------------------------
knitr::include_graphics("images/scene_01.png")

## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# wo=rsp2ebv('Chimichagua', lyrs = c('occurrence'), mc.cores = detectCores())
# plot(wo, main = 'Occurrence (Municipality of Chimichagua)')

## ----ocu_chimi, echo=FALSE, fig.cap="", out.width = '100%'--------------------
knitr::include_graphics("images/scene_02.png")

## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# # check that the projection is different to the file that was originally downloaded
# crs(raster(waterocc[1]))
# crs(wo[[1]])

## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# ebv <- rsp2ebv('Chimichagua', lyrs = c('treecover2000','lossyear'), mc.cores = detectCores())
# plot(ebv, main = 'Forest cover and loss (Chimichagua)')

## ----treeloss_chimi, echo=FALSE, fig.cap="", out.width = '100%'---------------
knitr::include_graphics("images/scene_03.png")

## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# forExt <- echanges(ebv, eco = 'tree', eco_range=c(95,100), echanges = 'loss', change_vals = c(5,10,20), binary_output=TRUE, mc.cores = detectCores())
# plot(forExt, main = 'Changes in forest cover')

## ----ecochanges_echimi, echo=FALSE, fig.cap="", out.width = '100%'------------
knitr::include_graphics("images/scene_04.png")

## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# defExt <- echanges(ebv, eco = 'tree', eco_range=c(95,100), echanges = 'loss', change_vals = c(5,10,20), binary_output=TRUE, mc.cores = detectCores(),
#                    get_unaffected=FALSE)
# plot(defExt, main = 'Changes in forest loss')

## ----unafectedF_chimi, echo=FALSE, fig.cap="", out.width = '100%'-------------
knitr::include_graphics("images/scene_05.png")

## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# defExtTC <- echanges(ebv, eco = 'tree', eco_range=c(95,100), echanges = 'loss', change_vals = c(5,10,20), binary_output=FALSE, mc.cores = detectCores(), get_unaffected=FALSE)
# plot(defExtTC, main = 'Changes in deforested pixels')

## ----tree_unafectedF_chimi, echo=FALSE, fig.cap="", out.width = '100%'--------
knitr::include_graphics("images/scene_06.png")

## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# library(landscapemetrics)
# list_lsm()

## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# forArea=gaugeIndicator(forExt, ncores=6)
# defArea=gaugeIndicator(defExt, ncores=6)
# forArea
# defArea
# plot(forArea, cex = 1.1, xlab = 'Year', ylab = 'Area (ha)', title = "Ecosystem extents", subtitle = 'Forest cover', fill = 'Pixel \nvalue')
# plot(defArea, cex = 1.1, xlab = 'Year', ylab = '', title = '', subtitle = 'Forest loss', fill = '')

## ----area_unafectedF_chimi, echo=FALSE, fig.cap="", out.width = '100%'--------
knitr::include_graphics("images/scene_065.png")

## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# defAreaTC=gaugeIndicator(defExtTC, ncores=6)
# defAreaTC
# plot(defAreaTC, y = viridis(6), cex = 1.1, xlab = 'Year',
#      ylab = 'Area (ha)', title = 'Forest loss',
#      subtitle = 'Tree-canopy cover values', fill = '(%)')

## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# plot(defAreaTC, type = 'b', cex = 1.1, xlab = 'Year',
# ylab = '',title = '', subtitle = 'Tree-canopy cover distributions', fill = 'Year')

## ----box_area_afectedDefF_chimi, echo=FALSE, fig.cap="", out.width = '100%'----
knitr::include_graphics("images/scene_075.png")

## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# chgstats=EBVstats(defExtTC)
# chgstats

## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# # Let's first calculate forest extent by all tree cover classes for 2019
# ech <- echanges(ebv, eco = 'tree', echanges = 'loss',
#                 change_vals = c(0,20), mc.cores = 2)
# plot(ech, main = 'Forest cover')
# 
# si <- sampleIndicator(ech, mc.cores = detectCores())
# si
# plot(si, main = 'Conditional entropy')

## ----sampleInd_chimi, echo=FALSE, fig.cap="", out.width = '100%'--------------
knitr::include_graphics("images/scene_11.png")

## ----include = TRUE, message=F, warning=F, eval=FALSE-------------------------
# citation('ecochange')