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library(MMGS)
?MMGS
?LbyE_calculate
library(MMGS)
devtools::use_vignette("MMGS-tutorial")
?use_vignette
usethis::use_vignette("MMGS-tutorial")
library(rhub)
install.packages("rhub")
library("rhub")
?rhub
rhub::check_for_cran("MMGS")
getwd()
rhub::check_for_cran("E:/10.devR/MMGS")
getwd()
devtools::check_win_devel("E:/10.devR/MMGS")
?MMPrdM
library(MMGS)
?MMPrdM
library(MMGS)
?MMPrdM
Regression %>% left_join(MSE)
library(MMGS)
data(trait)
data(geno)
data(env_info)
data("PTT_PTR")
env_trait<-env_trait_calculate(data=trait,trait="FTgdd",env="env_code")
LbyE<-LbyE_calculate(data=trait,trait="FTgdd",env="env_code",line="line_code")
LbyE_corrplot(LbyE=LbyE)
etl<-LbyE_Reshape(data=env_trait,env="env_code",LbyE=LbyE)
etl_plotter(data=etl,trait=env_trait)
Regression<-Reg(LbyE = LbyE, env_trait = env_trait)
Reg_plotter(Reg = Regression)
result<-line_trait_mean(data=trait,trait="FTgdd",mean=env_trait,LbyE=LbyE,row=2)
MSE<-result[[1]]
ltm<-result[[2]]
mse_plotter(MSE)
Regression %>% left_join(MSE)
Regression dplyr::%>% left_join(MSE)
library(dpolyr)
library(dplyr)
Regression dplyr::%>% left_join(MSE)
Regression %>% left_join(MSE)
head(Regression %>% left_join(MSE))
Mean_trait_plot(Regression,MSE)
pop_cor<-Exhaustive_search(data=env_trait, env_paras=PTT_PTR, searching_daps=122,
p=1, dap_x=122,dap_y=122,LOO=0,Paras=Paras)
Paras <- colnames(PTT_PTR)[-c(1:4)]
pop_cor<-Exhaustive_search(data=env_trait, env_paras=PTT_PTR, searching_daps=122,
p=1, dap_x=122,dap_y=122,LOO=0,Paras=Paras)
#全局变量.data
#Exhaustive_plotter(Correlation=pop_cor,dap_x=122, dap_y=122,p=1,Paras=Paras)
envMeanPara<-envMeanPara(data=env_trait, env_paras=PTT_PTR, maxR_dap1=18,
maxR_dap2=43, Paras=Paras)
#全局变量.data
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
Paras <- colnames(PTT_PTR)[-c(1:4)]
pop_cor<-Exhaustive_search(data=env_trait, env_paras=PTT_PTR, searching_daps=122,
p=1, dap_x=122,dap_y=122,LOO=0,Paras=Paras)
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
warnings()
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
dplyr::pull(envMeanPara, `1`)
dplyr::pull(envMeanPara, 5)
dplyr::pull(envMeanPara, 6)
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
dplyr::pull(envMeanPara, 6)
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
source("E:/10.devR/MMGS/R/08.Cross_vadiation.R")
out<-MMGP(pheno=pheno, geno=geno,
env=env_info,para=envMeanPara,
Para_Name=Para[1], depend="PEI",
SVM_cost=100,gamma=10,
model="RR",reshuffle=1,methods="RM.G")
out<-MMGP(pheno=LbyE, geno=geno,
env=env_info,para=envMeanPara,
Para_Name=Para[1], depend="PEI",
SVM_cost=100,gamma=10,
model="RR",reshuffle=1,methods="RM.G")
Para<-gsub(".*_","", colnames(pop_cor)[cols[1]])
cols<-which(abs(pop_cor[, -c(1:4)]) == max(abs(pop_cor[, -c(1:4)])), arr.ind = TRUE)[1,2]+4
Para<-gsub(".*_","", colnames(pop_cor)[cols[1]])
out<-MMGP(pheno=LbyE, geno=geno,
env=env_info,para=envMeanPara,
Para_Name=Para[1], depend="PEI",
SVM_cost=100,gamma=10,
model="RR",reshuffle=1,methods="RM.G")
source("E:/10.devR/MMGS/R/08.Cross_vadiation.R")
out[[2]]
out[[3]]
source("E:/10.devR/MMGS/R/08.Cross_vadiation.R")
MMGP(pheno=LbyE, geno=geno,
env=env_info,para=envMeanPara,
Para_Name=Para[1], depend="PEI",
SVM_cost=100,gamma=10,
model="rrBLUP",reshuffle=1,methods="RM.G")
source("E:/10.devR/MMGS/R/08.Cross_vadiation.R")
MMGP(pheno=LbyE, geno=geno,
env=env_info,para=envMeanPara,
Para_Name=Para[1], depend="PEI",
SVM_cost=100,gamma=10,
model="rrBLUP",reshuffle=1,methods="RM.G")
source("E:/10.devR/MMGS/R/08.Cross_vadiation.R")
MMGP(pheno=LbyE, geno=geno,
env=env_info,para=envMeanPara,
Para_Name=Para[1], depend="PEI",
SVM_cost=100,gamma=10,
model="rrBLUP",reshuffle=1,methods="RM.G")
source("E:/10.devR/MMGS/R/08.Cross_vadiation.R")
MMGP(pheno=LbyE, geno=geno,
env=env_info,para=envMeanPara,
Para_Name=Para[1], depend="PEI",
SVM_cost=100,gamma=10,
model="rrBLUP",reshuffle=1,methods="RM.G")
source("E:/10.devR/MMGS/R/08.Cross_vadiation.R")
(pheno=LbyE, geno=geno,
MMGP(pheno=LbyE, geno=geno,
env=env_info,para=envMeanPara,
Para_Name=Para[1], depend="PEI",
SVM_cost=100,gamma=10,
model="rrBLUP",reshuffle=1,methods="RM.G")
source("E:/10.devR/MMGS/R/09.Predict_Envs.R")
source("E:/10.devR/MMGS/R/08.Cross_vadiation.R")
source("E:/10.devR/MMGS/R/09.Predict_Envs.R")
out<-MMGP(pheno=LbyE, geno=geno,
env=env_info,para=envMeanPara,
Para_Name=Para[1], depend="PEI",
SVM_cost=100,gamma=10,
model="GBLUP",reshuffle=1,methods="RM.G")
out[[3]]
out[[2]]
out[[1]]
source("E:/10.devR/MMGS/R/09.Predict_Envs.R")
source("E:/10.devR/MMGS/R/08.Cross_vadiation.R")
out<-MMGP(pheno=LbyE, geno=geno,
env=env_info,para=envMeanPara,
Para_Name=Para[1], depend="PEI",
SVM_cost=100,gamma=10,
model="GBLUP",reshuffle=1,methods="RM.G")
source("E:/10.devR/MMGS/R/08.Cross_vadiation.R")
source("E:/10.devR/MMGS/R/09.Predict_Envs.R")
source("E:/10.devR/MMGS/R/08.Cross_vadiation.R")
out<-MMGP(pheno=LbyE, geno=geno,
env=env_info,para=envMeanPara,
Para_Name=Para[1], depend="PEI",
SVM_cost=100,gamma=10,
model="GBLUP",reshuffle=1,methods="RM.G")
source("E:/10.devR/MMGS/R/06.Exhaustive_searfch_plotter.R")
out[[3]]
out[[2]]
source("E:/10.devR/MMGS/R/06.Exhaustive_searfch_plotter.R")
Exhaustive_plotter(Correlation=pop_cor,dap_x=122, dap_y=122,p=1,Paras=Paras)
source("E:/10.devR/MMGS/R/06.Exhaustive_searfch_plotter.R")
Exhaustive_plotter(Correlation=pop_cor,dap_x=122, dap_y=122,p=1,Paras=Paras)
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
source("E:/10.devR/MMGS/R/06.Exhaustive_searfch_plotter.R")
Exhaustive_plotter(Correlation=pop_cor,dap_x=122, dap_y=122,p=1,Paras=Paras)
source("E:/10.devR/MMGS/R/06.Exhaustive_searfch_plotter.R")
Exhaustive_plotter(Correlation=pop_cor,dap_x=122, dap_y=122,p=1,Paras=Paras)
colnames(pop_cors[,6])
source("E:/10.devR/MMGS/R/06.Exhaustive_searfch_plotter.R")
Exhaustive_plotter(Correlation=pop_cor,dap_x=122, dap_y=122,p=1,Paras=Paras)
source("E:/10.devR/MMGS/R/06.Exhaustive_searfch_plotter.R")
Exhaustive_plotter(Correlation=pop_cor,dap_x=122, dap_y=122,p=1,Paras=Paras)
source("E:/10.devR/MMGS/R/06.Exhaustive_searfch_plotter.R")
Exhaustive_plotter(Correlation=pop_cor,dap_x=122, dap_y=122,p=1,Paras=Paras)
source("E:/10.devR/MMGS/R/06.Exhaustive_searfch_plotter.R")
Exhaustive_plotter(Correlation=pop_cor,dap_x=122, dap_y=122,p=1,Paras=Paras)
source("E:/10.devR/MMGS/R/06.Exhaustive_searfch_plotter.R")
Exhaustive_plotter(Correlation=pop_cor,dap_x=122, dap_y=122,p=1,Paras=Paras)
source("E:/10.devR/MMGS/R/06.Exhaustive_searfch_plotter.R")
Exhaustive_plotter(Correlation=pop_cor,dap_x=122, dap_y=122,p=1,Paras=Paras)
source("E:/10.devR/MMGS/R/06.Exhaustive_searfch_plotter.R")
Exhaustive_plotter(Correlation=pop_cor,dap_x=122, dap_y=122,p=1,Paras=Paras)
source("E:/10.devR/MMGS/R/06.Exhaustive_searfch_plotter.R")
source("E:/10.devR/MMGS/R/09.Predict_Envs.R")
source("E:/10.devR/MMGS/R/08.Cross_vadiation.R")
MMGP(pheno=LbyE, geno=geno,
env=env_info,para=envMeanPara,
Para_Name=Para[1], depend="PEI",
SVM_cost=100,gamma=10,
model="GBLUP",reshuffle=1,methods="RM.G")
source("E:/10.devR/MMGS/R/08.Cross_vadiation.R")
out<-MMGP(pheno=LbyE, geno=geno,
env=env_info,para=envMeanPara,
Para_Name=Para[1], depend="PEI",
SVM_cost=100,gamma=10,
model="BA",reshuffle=1,methods="RM.G")
out[[3]]
out[[2]]
source("E:/10.devR/MMGS/R/09.Predict_Envs.R")
source("E:/10.devR/MMGS/R/08.Cross_vadiation.R")
source("E:/10.devR/MMGS/R/09.Predict_Envs.R")
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
envMeanPara_plotter(data=envMeanPara,Paras=Paras)
source("E:/10.devR/MMGS/R/07.envMeanPara_plotter.R")
library(MMGS)
library(help = "MMGS")