使用沃尔丹开发的ENMtools进行空间分析

## 利用enmtools构建数据分析：
setwd("E:/")
## 以西藏沙棘为例：
library(ENMTools)
library(raster)
env <- raster::getData('worldclim', var='bio', res=10)
env <- crop(env, extent(-10, 17, 39, 48))
plot(env[[1]])
# 1000m =1km=30s =0.5min = 1/120度；

monticola.path <- paste(system.file(package="ENMTools"), "/monticola.csv", sep='')
monticola <- enmtools.species(species.name = "monticola", 
                              presence.points = read.csv(monticola.path))
monticola$range <- background.raster.buffer(monticola$presence.points, 50000, mask = env)
monticola$background.points <- background.points.buffer(points = monticola$presence.points,
                                                        radius = 20000, n = 1000, mask = env[[1]])


monticola.glm <- enmtools.glm(species = monticola, env = env, f = pres ~ bio1 + bio12 + bio7, test.prop = 0.2)
data(iberolacerta.clade)
data(euro.worldclim)
monticola <- iberolacerta.clade$species$monticola

plot(monticola)


library(rgbif)
library(ape)

tree.path <- paste(system.file(package="ENMTools"), "/StarBEAST_MCC.species.txt", sep='')

hisp.anoles <- read.nexus(file = tree.path)

keepers <- c("brevirostris", "marron", "caudalis", "websteri", "distichus")

hisp.anoles <- drop.tip(phy = hisp.anoles, tip = hisp.anoles$tip.label[!hisp.anoles$tip.label %in% keepers])
plot(hisp.anoles)

hisp.anoles$tip.label

install.packages("ggtree")
library(ggtree)
file <- system.file("extdata/BEAST", "beast_mcc.tree", package="ggtree")
beast <- read.beast(file)
beast

get.fields(beast)
ggtree(beast, ndigits = 2, branch.length = 'none') + geom_text(aes(x = branch, label = length_0.95_HPD), vjust = -.5, color = 'firebrick')

######### 导入的数据通过 fortify函数能够转换为 data.frame
beast_data <- fortify(beast)
head(beast_data)


################ PAML
brstfile <- system.file("extdata/PAML_Baseml", "rst", package="ggtree")
brst <- read.paml_rst(brstfile)
brst

p <- ggtree(brst) +
  geom_text(aes(x = branch, label = marginal_AA_subs), vjust=-.5, color='steelblue') +
  theme_tree2()
print(p)

##
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("ggtree")

library(ggtree)
set.seed(2017-02-16)
tree <- rtree(50)



library(rgbif)
library(ape)

tree.path <- paste(system.file(package="ENMTools"), "/StarBEAST_MCC.species.txt", sep='')

hisp.anoles <- read.nexus(file = tree.path)

keepers <- c("brevirostris", "marron", "caudalis", "websteri", "distichus")

hisp.anoles <- drop.tip(phy = hisp.anoles, tip = hisp.anoles$tip.label[!hisp.anoles$tip.label %in% keepers])
plot(hisp.anoles)

hisp.anoles$edge
hisp.anoles$edge.length