Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library(graph4lg)
library(igraph)
library(ggplot2)
## ---- eval = FALSE------------------------------------------------------------
# get_graphab()
## ---- echo = FALSE, eval = TRUE-----------------------------------------------
load(file = paste0(system.file('extdata', package = 'graph4lg'),
"/", "res_g.RDa"))
## -----------------------------------------------------------------------------
load(file = paste0(system.file('extdata', package = 'graph4lg'),
"/", "rast_simul50.RDa"))
r.spdf <- as(rast, "SpatialPixelsDataFrame")
r.df <- as.data.frame(r.spdf)
r.df$layer <- as.factor(r.df$rast_simul50)
g <- ggplot(r.df, aes(x=x, y=y)) + geom_tile(aes(fill = layer)) + coord_equal()+
theme_bw()+
#scale_fill_brewer(palette="Dark2")+
scale_fill_manual(values = c("#396D35", "#FB9013", "#EDC951", "#80C342", "black", "#396D35"),
labels = c("0 - Forest", "1 - Shrublands", "2 - Crops",
"3 - Grasslands","4 - Artificial areas", "5 - Forest"),
name = "Land use type")+
labs(x="Longitude",y="Latitude")
g
## ---- eval = FALSE------------------------------------------------------------
# proj_name <- "graphab_example"
#
# graphab_project(proj_name = proj_name,
# raster = "rast_simul50.tif",
# habitat = c(0, 5),
# minarea = 200)
## -----------------------------------------------------------------------------
cost <- data.frame(code = 0:5,
cost = c(1, 5, 60, 40, 1000, 1))
cost
## ---- eval=FALSE--------------------------------------------------------------
#
# graphab_link(proj_name = proj_name,
# distance = "cost",
# cost = cost,
# name = "lkst1",
# topo = "planar")
## ---- eval=FALSE--------------------------------------------------------------
# graphab_graph(proj_name = proj_name,
# linkset = "lkst1",
# name = "graph")
## ---- eval=FALSE--------------------------------------------------------------
# # Global metric: PC
# graphab_metric(proj_name = proj_name,
# graph = "graph",
# metric = "PC",
# dist = 10000,
# prob = 0.05,
# beta = 1,
# cost_conv = TRUE)
## ---- echo = FALSE------------------------------------------------------------
res_g[["PC"]]
## ---- eval=FALSE--------------------------------------------------------------
# f <- graphab_metric(proj_name = proj_name,
# graph = "graph",
# metric = "F",
# dist = 10000,
# prob = 0.05,
# beta = 1,
# cost_conv = FALSE)
## ---- echo = FALSE------------------------------------------------------------
res_g[["F"]][1]
head(res_g[["F"]][[2]])
## ---- eval=FALSE--------------------------------------------------------------
# graphab_modul(proj_name = proj_name,
# graph = "graph",
# dist = 10000,
# prob = 0.05,
# beta = 1)
## -----------------------------------------------------------------------------
# Point data frame
head(pts_pop_simul)
## ---- eval=FALSE--------------------------------------------------------------
# graphab_pointset(proj_name = proj_name,
# linkset = "lkst1",
# pointset = pts_pop_simul)
## ---- echo = FALSE------------------------------------------------------------
head(res_g[["PTSG"]])
## ---- eval=FALSE--------------------------------------------------------------
# get_graphab_linkset(proj_name = proj_name,
# linkset = "lkst1")
## ---- echo = FALSE------------------------------------------------------------
head(res_g[["LK"]])
## ---- eval=FALSE--------------------------------------------------------------
# get_graphab_metric(proj_name = proj_name)
## ---- echo = FALSE------------------------------------------------------------
head(res_g[["MET"]])
## ---- eval=FALSE--------------------------------------------------------------
# land_graph <- graphab_to_igraph(proj_name = proj_name,
# linkset = "lkst1",
# nodes = "patches",
# weight = "cost",
# fig = TRUE,
# crds = TRUE)
#
# crds_patches <- land_graph[[2]]
# land_graph <- land_graph[[1]]
## ---- echo = FALSE------------------------------------------------------------
crds_patches <- res_g[["CRDS"]]
land_graph <- res_g[["LGRAPH"]]
## -----------------------------------------------------------------------------
plot_graph_lg(land_graph,
crds = crds_patches,
mode = "spatial",
node_size = "Area")
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