biogeobears使用

install.packages("rexpokit")
install.packages("cladoRcpp")
library(devtools)
devtools::install_github(repo="nmatzke/BioGeoBEARS")

library(optimx)
library(GenSA)
library(FD)
library(snow)
library(parallel)

library(rexpokit)
library(cladoRcpp)
library(BioGeoBEARS)

extdata_dir = np(system.file("extdata", package="BioGeoBEARS"))
extdata_dir
list.files(extdata_dir)

#树文件输入，需要带枝长信息
trfn = np(paste(addslash(extdata_dir), "input.tree", sep=""))
moref(trfn)
#绘制树图
pdffn = "tree.pdf"
pdf(file=pdffn, width=9, height=20)
tr = read.tree(trfn)#这一条很重要，后面需要用到tr这个对象
plot(tr)
title("Zingiber phylogeny (2024)")
axisPhylo()
dev.off()
cmdstr = paste0("open ", pdffn)
system(cmdstr)

#输入地理分布信息
geogfn = np(paste(addslash(extdata_dir), "geo.txt", sep=""))
moref(geogfn)

tipranges = getranges_from_LagrangePHYLIP(lgdata_fn=geogfn)#重要
tipranges
max(rowSums(dfnums_to_numeric(tipranges@df)))
max_range_size = 4

numstates_from_numareas(numareas=7, maxareas=4, include_null_range=TRUE)
#>[1] 99
numstates_from_numareas(numareas=9, maxareas=5, include_null_range=FALSE)
#>[1] 381

##1. 运行基础模型DEG

#新建项目
BioGeoBEARS_run_object = define_BioGeoBEARS_run()

#输入树和分布信息
BioGeoBEARS_run_object$trfn = trfn
BioGeoBEARS_run_object$geogfn = geogfn

#设置分布区域数最大值
BioGeoBEARS_run_object$max_range_size = max_range_size
#设置最小枝长长度，小于这个枝长的末端会被认作直接祖先（没有物种形成事件），默认的适用枝长单位为百万年。
BioGeoBEARS_run_object$min_branchlength = 0.000001
BioGeoBEARS_run_object$include_null_range = TRUE
## set to FALSE for e.g. DEC* model, DEC*+J, etc. DEC*是对DEC的一个修正，能更好的推断物种在局部范围内灭绝

#提速、多核处理
BioGeoBEARS_run_object$on_NaN_error = -1e50
BioGeoBEARS_run_object$speedup = TRUE
BioGeoBEARS_run_object$use_optimx = TRUE ##FALSE用optim()；如果输入GenSA，使用Generalized Simulated Annealing，适用于高次元模型（参数多于5），但有时无法优化简单的模型
BioGeoBEARS_run_object$num_cores_to_use = 1 ##多线程运算，需要library(parallel) 和/或 library(snow)，数据量大的话一般改为2就行了。
BioGeoBEARS_run_object$force_sparse = FALSE #是否使用稀疏矩阵的项，稀疏矩阵对小规模数据的提速不明显，而且会使结果不精确

#加载dispersal multiplier matrix等文本到模型对象中，并会检测的一些错误。
BioGeoBEARS_run_object = readfiles_BioGeoBEARS_run(BioGeoBEARS_run_object)

#获取良好的默认状态设置
BioGeoBEARS_run_object$return_condlikes_table = TRUE
BioGeoBEARS_run_object$calc_TTL_loglike_from_condlikes_table = TRUE
BioGeoBEARS_run_object$calc_ancprobs = TRUE

#检查输入
check_BioGeoBEARS_run(BioGeoBEARS_run_object)

#运行并储存结果
resfn = "322_zingiber121"
res = bears_optim_run(BioGeoBEARS_run_object)
save(res, file=resfn)
resDEC = res

#需要重新载入结果时
#load(resfn)
#resDEC = res 


##2. DEC+J
BioGeoBEARS_run_object = define_BioGeoBEARS_run()
BioGeoBEARS_run_object$trfn = trfn
BioGeoBEARS_run_object$geogfn = geogfn
BioGeoBEARS_run_object$max_range_size = max_range_size
BioGeoBEARS_run_object$min_branchlength = 0.000001
BioGeoBEARS_run_object$include_null_range = TRUE

BioGeoBEARS_run_object$on_NaN_error = -1e50
BioGeoBEARS_run_object$speedup = TRUE
BioGeoBEARS_run_object$use_optimx = TRUE
BioGeoBEARS_run_object$num_cores_to_use = 1
BioGeoBEARS_run_object$force_sparse = FALSE

BioGeoBEARS_run_object = readfiles_BioGeoBEARS_run(BioGeoBEARS_run_object)
BioGeoBEARS_run_object$return_condlikes_table = TRUE
BioGeoBEARS_run_object$calc_TTL_loglike_from_condlikes_table = TRUE
BioGeoBEARS_run_object$calc_ancprobs = TRUE

#设定DEC+j模型
#从参数嵌套模型中获取ML参数值（需要建立在DEC模型运算的结果之上）
dstart = resDEC$outputs@params_table["d","est"]
estart = resDEC$outputs@params_table["e","est"]
jstart = 0.0001

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","init"] = dstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","est"] = dstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","init"] = estart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","est"] = estart

#加入j作为自由参数
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","type"] = "free"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","init"] = jstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","est"] = jstart

check_BioGeoBEARS_run(BioGeoBEARS_run_object)

resfn = "322_zingiber121_DEG+J"
res = bears_optim_run(BioGeoBEARS_run_object)
save(res, file=resfn)
resDECj = res

#load(resfn)
#resDECj = res

##3. DIVALIKE

BioGeoBEARS_run_object = define_BioGeoBEARS_run()
BioGeoBEARS_run_object$trfn = trfn
BioGeoBEARS_run_object$geogfn = geogfn
BioGeoBEARS_run_object$max_range_size = max_range_size
BioGeoBEARS_run_object$min_branchlength = 0.000001
BioGeoBEARS_run_object$include_null_range = TRUE

BioGeoBEARS_run_object$on_NaN_error = -1e50
BioGeoBEARS_run_object$speedup = TRUE
BioGeoBEARS_run_object$use_optimx = TRUE
BioGeoBEARS_run_object$num_cores_to_use = 1
BioGeoBEARS_run_object$force_sparse = FALSE

BioGeoBEARS_run_object = readfiles_BioGeoBEARS_run(BioGeoBEARS_run_object)
BioGeoBEARS_run_object$return_condlikes_table = TRUE
BioGeoBEARS_run_object$calc_TTL_loglike_from_condlikes_table = TRUE
BioGeoBEARS_run_object$calc_ancprobs = TRUE

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","init"] = 0.0
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","est"] = 0.0

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ysv","type"] = "2-j"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ys","type"] = "ysv*1/2"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["y","type"] = "ysv*1/2"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","type"] = "ysv*1/2"

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01v","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01v","init"] = 0.5
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01v","est"] = 0.5

# BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","type"] = "free"
# BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","init"] = 0.01
# BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","est"] = 0.01

check_BioGeoBEARS_run(BioGeoBEARS_run_object)

resfn = "Zingiber_DIVALIKE"
res = bears_optim_run(BioGeoBEARS_run_object)
save(res, file=resfn)
resDIVALIKE = res

#load(resfn)
#resDIVALIKE = res

##DIVALIKE+J
BioGeoBEARS_run_object = define_BioGeoBEARS_run()
BioGeoBEARS_run_object$trfn = trfn
BioGeoBEARS_run_object$geogfn = geogfn
BioGeoBEARS_run_object$max_range_size = max_range_size
BioGeoBEARS_run_object$min_branchlength = 0.000001
BioGeoBEARS_run_object$include_null_range = TRUE

BioGeoBEARS_run_object$on_NaN_error = -1e50
BioGeoBEARS_run_object$speedup = TRUE
BioGeoBEARS_run_object$use_optimx = TRUE
BioGeoBEARS_run_object$num_cores_to_use = 1
BioGeoBEARS_run_object$force_sparse = FALSE

BioGeoBEARS_run_object = readfiles_BioGeoBEARS_run(BioGeoBEARS_run_object)
BioGeoBEARS_run_object$return_condlikes_table = TRUE
BioGeoBEARS_run_object$calc_TTL_loglike_from_condlikes_table = TRUE
BioGeoBEARS_run_object$calc_ancprobs = TRUE


dstart = resDIVALIKE$outputs@params_table["d","est"]
estart = resDIVALIKE$outputs@params_table["e","est"]
jstart = 0.0001

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","init"] = dstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","est"] = dstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","init"] = estart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","est"] = estart

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","init"] = 0.0
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","est"] = 0.0

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ysv","type"] = "2-j"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ys","type"] = "ysv*1/2"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["y","type"] = "ysv*1/2"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","type"] = "ysv*1/2"

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01v","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01v","init"] = 0.5
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01v","est"] = 0.5

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","type"] = "free"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","init"] = jstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","est"] = jstart

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","min"] = 0.00001
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","max"] = 1.99999

check_BioGeoBEARS_run(BioGeoBEARS_run_object)

resfn = "Zingiber_DIVALIKE+J"
res = bears_optim_run(BioGeoBEARS_run_object)
save(res, file=resfn)
resDIVALIKEj =res

#load(resfn)
#
## 5. BAYAREALIKE

BioGeoBEARS_run_object = define_BioGeoBEARS_run()
BioGeoBEARS_run_object$trfn = trfn
BioGeoBEARS_run_object$geogfn = geogfn
BioGeoBEARS_run_object$max_range_size = max_range_size
BioGeoBEARS_run_object$min_branchlength = 0.000001
BioGeoBEARS_run_object$include_null_range = TRUE

BioGeoBEARS_run_object$on_NaN_error = -1e50
BioGeoBEARS_run_object$speedup = TRUE
BioGeoBEARS_run_object$use_optimx = TRUE
BioGeoBEARS_run_object$num_cores_to_use = 1
BioGeoBEARS_run_object$force_sparse = FALSE

BioGeoBEARS_run_object = readfiles_BioGeoBEARS_run(BioGeoBEARS_run_object)
BioGeoBEARS_run_object$return_condlikes_table = TRUE
BioGeoBEARS_run_object$calc_TTL_loglike_from_condlikes_table = TRUE
BioGeoBEARS_run_object$calc_ancprobs = TRUE

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","init"] = 0.0
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","est"] = 0.0

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","init"] = 0.0
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","est"] = 0.0

# BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","type"] = "free"
# BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","init"] = 0.01
# BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","est"] = 0.01

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ysv","type"] = "1-j"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ys","type"] = "ysv*1/1"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["y","type"] = "1-j"

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01y","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01y","init"] = 0.9999
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01y","est"] = 0.9999

check_BioGeoBEARS_run(BioGeoBEARS_run_object)

resfn = "Zingiber_BAYAREALIKE"
res = bears_optim_run(BioGeoBEARS_run_object)
save(res, file=resfn)
resBAYAREALIKE = res

#load(resfn)
#resBAYAREALIKE = res

##6. BAYAREALIKE+J
BioGeoBEARS_run_object = define_BioGeoBEARS_run()
BioGeoBEARS_run_object$trfn = trfn
BioGeoBEARS_run_object$geogfn = geogfn
BioGeoBEARS_run_object$max_range_size = max_range_size
BioGeoBEARS_run_object$min_branchlength = 0.000001
BioGeoBEARS_run_object$include_null_range = TRUE

BioGeoBEARS_run_object$on_NaN_error = -1e50
BioGeoBEARS_run_object$speedup = TRUE
BioGeoBEARS_run_object$use_optimx = "GenSA"
BioGeoBEARS_run_object$num_cores_to_use = 1
BioGeoBEARS_run_object$force_sparse = FALSE

BioGeoBEARS_run_object = readfiles_BioGeoBEARS_run(BioGeoBEARS_run_object)
BioGeoBEARS_run_object$return_condlikes_table = TRUE
BioGeoBEARS_run_object$calc_TTL_loglike_from_condlikes_table = TRUE
BioGeoBEARS_run_object$calc_ancprobs = TRUE

#从参数嵌套模型中获取ML参数值
dstart = resBAYAREALIKE$outputs@params_table["d","est"]
estart = resBAYAREALIKE$outputs@params_table["e","est"]
jstart = 0.0001

#输入d，e参数起始值
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","init"] = dstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","est"] = dstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","init"] = estart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","est"] = estart

#无子集共域
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","init"] = 0.0
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["s","est"] = 0.0

#无隔离成种
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","init"] = 0.0
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["v","est"] = 0.0

#允许创始事件
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","type"] = "free"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","init"] = jstart
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","est"] = jstart

#BAYAREALIKE+J模型下，j的上限为1
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","max"] = 0.99999
#调整参数关联性
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ysv","type"] = "1-j"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["ys","type"] = "ysv*1/1"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["y","type"] = "1-j"

#允许广域的同域物种形成，范围成种。子代范围总与祖先一致。
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01y","type"] = "fixed"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01y","init"] = 0.9999
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["mx01y","est"] = 0.9999

#微调参数上下界，防止崩溃
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","min"] = 0.0000001
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["d","max"] = 4.9999999

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","min"] = 0.0000001
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["e","max"] = 4.9999999

BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","min"] = 0.00001
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","max"] = 0.99999

check_BioGeoBEARS_run(BioGeoBEARS_run_object)

resfn = "Zingiber_BAYAREALIKE+J"
res = bears_optim_run(BioGeoBEARS_run_object)
save(res, file=resfn)
resBAYAREALIKEj =res

#load(resfn)
#resBAYAREALIKEj = res



##绘图
pdffn = "321_zingiber.pdf"
pdf(pdffn, width=10, height=16)

analysis_titletxt ="BioGeoBEARS DEC on 321_zingiber"
results_object = resDEC
scriptdir = np(system.file("extdata/a_scripts", package="BioGeoBEARS")) #根据树调整边幅

res2 = plot_BioGeoBEARS_results(results_object, analysis_titletxt, addl_params=list("j"), plotwhat="text", label.offset=0.45, tipcex=0.7, statecex=0.7, splitcex=0.6, titlecex=0.8, plotsplits=TRUE, cornercoords_loc=scriptdir, include_null_range=TRUE, tr=tr, tipranges=tipranges)
plot_BioGeoBEARS_results(results_object, analysis_titletxt, addl_params=list("j"), plotwhat="pie", label.offset=0.45, tipcex=0.7, statecex=0.7, splitcex=0.6, titlecex=0.8, plotsplits=TRUE, cornercoords_loc=scriptdir, include_null_range=TRUE, tr=tr, tipranges=tipranges)

dev.off()
cmdstr = paste("open ", pdffn, sep="")
system(cmdstr)


pdffn = "321_zingiber_DEC+G.pdf"
pdf(pdffn, width=30, height=30)
analysis_titletxt ="BioGeoBEARS DEC+J on 321_zingiber"
results_object = resDECj
scriptdir = np(system.file("extdata/a_scripts", package="BioGeoBEARS"))
res1 = plot_BioGeoBEARS_results(results_object, analysis_titletxt, addl_params=list("j"), plotwhat="text", label.offset=0.45, tipcex=0.7, statecex=0.7, splitcex=0.6, titlecex=0.8, plotsplits=TRUE, cornercoords_loc=scriptdir, include_null_range=TRUE, tr=tr, tipranges=tipranges)
plot_BioGeoBEARS_results(results_object, analysis_titletxt, addl_params=list("j"), plotwhat="pie", label.offset=0.45, tipcex=0.7, statecex=0.7, splitcex=0.6, titlecex=0.8, plotsplits=TRUE, cornercoords_loc=scriptdir, include_null_range=TRUE, tr=tr, tipranges=tipranges)


dev.off()
cmdstr = paste("open ", pdffn, sep="")
system(cmdstr)

## 7.AICc test model
restable = NULL
teststable = NULL
#建空表储存比较结果

LnL_2 = get_LnL_from_BioGeoBEARS_results_object(resDEC)
LnL_1 = get_LnL_from_BioGeoBEARS_results_object(resDECj)
numparams1 = 3
numparams2 = 2
stats = AICstats_2models(LnL_1, LnL_2, numparams1, numparams2)
stats
res2 = extract_params_from_BioGeoBEARS_results_object(results_object=resDEC, returnwhat="table", addl_params=c("j"), paramsstr_digits=4)
res1 = extract_params_from_BioGeoBEARS_results_object(results_object=resDECj, returnwhat="table", addl_params=c("j"), paramsstr_digits=4)
rbind(res2, res1)
tmp_tests = conditional_format_table(stats)
restable = rbind(restable, res2, res1)
teststable = rbind(teststable, tmp_tests)

LnL_2 = get_LnL_from_BioGeoBEARS_results_object(resDIVALIKE)
LnL_1 = get_LnL_from_BioGeoBEARS_results_object(resDIVALIKEj)
numparams1 = 3
numparams2 = 2
stats = AICstats_2models(LnL_1, LnL_2, numparams1, numparams2)
stats
res2 = extract_params_from_BioGeoBEARS_results_object(results_object=resDIVALIKE, returnwhat="table", addl_params=c("j"), paramsstr_digits=4)
res1 = extract_params_from_BioGeoBEARS_results_object(results_object=resDIVALIKEj, returnwhat="table", addl_params=c("j"), paramsstr_digits=4)
rbind(res2, res1)
conditional_format_table(stats)
tmp_tests = conditional_format_table(stats)
restable = rbind(restable, res2, res1)
teststable = rbind(teststable, tmp_tests)

LnL_2 = get_LnL_from_BioGeoBEARS_results_object(resBAYAREALIKE)
LnL_1 = get_LnL_from_BioGeoBEARS_results_object(resBAYAREALIKEj)
numparams1 = 3
numparams2 = 2
stats = AICstats_2models(LnL_1, LnL_2, numparams1, numparams2)
stats
res2 = extract_params_from_BioGeoBEARS_results_object(results_object=resBAYAREALIKE, returnwhat="table", addl_params=c("j"), paramsstr_digits=4)
res1 = extract_params_from_BioGeoBEARS_results_object(results_object=resBAYAREALIKEj, returnwhat="table", addl_params=c("j"), paramsstr_digits=4)
rbind(res2, res1)
conditional_format_table(stats)
tmp_tests = conditional_format_table(stats)
restable = rbind(restable, res2, res1)
teststable = rbind(teststable, tmp_tests)

#合并表格
teststable$alt = c("DEC+J", "DIVALIKE+J", "BAYAREALIKE+J")
teststable$null = c("DEC", "DIVALIKE", "BAYAREALIKE")
row.names(restable) = c("DEC", "DEC+J", "DIVALIKE", "DIVALIKE+J", "BAYAREALIKE", "BAYAREALIKE+J")
restable = put_jcol_after_ecol(restable)
restable
teststable

#储存
save(restable, file="restable_v1.Rdata")
load(file="restable_v1.Rdata")

save(teststable, file="teststable_v1.Rdata")
load(file="teststable_v1.Rdata")

#write.table(restable, file="restable.txt", quote=FALSE, sep="\t")
#write.table(unlist_df(teststable), file="teststable.txt", quote=FALSE, sep="\t")


restable2 = restable

AICtable = calc_AIC_column(LnL_vals=restable$LnL, nparam_vals=restable$numparams)
restable = cbind(restable, AICtable)
restable_AIC_rellike = AkaikeWeights_on_summary_table(restable=restable, colname_to_use="AIC")
restable_AIC_rellike = put_jcol_after_ecol(restable_AIC_rellike)
restable_AIC_rellike

samplesize = length(tr$tip.label)
AICtable = calc_AICc_column(LnL_vals=restable$LnL, nparam_vals=restable$numparams, samplesize=samplesize)
restable2 = cbind(restable2, AICtable)
restable_AICc_rellike = AkaikeWeights_on_summary_table(restable=restable2, colname_to_use="AICc")
restable_AICc_rellike = put_jcol_after_ecol(restable_AICc_rellike)
restable_AICc_rellike

image.png

最后编辑于：2024.03.23 04:53:25

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