BreedStats: Genetic values and predictions for breeding

In jbkey730/BreedStats: Genetic values and predictions for breeding

Genetic values and predictions for breeding

Description

A group of functions for breeding statistics. It uses ASReml algorithms for spatial adjustments and breeding value types of analysis. Simulated (simulate=T) data is avaiable to utilize the functions.

Usage

 BV(fdp,wdp, ws, doHybridID, doPedigreeChange, InventoryPedigree, doReduceNonCodes, doField, doLmer, ytData, doGCABV, year, A, B, C, Prop, Choice, D, R, X, E, Q, V, doDNN, GEM, date, s0, s1, s2, s3, s4, s5, seas0, seas1, seas2, seas3, seas4, seas5, doYear, folder, simulate)

 inbredChar(dpf, gdp, hdp, year, l_year, h_year, doAdjInbredData, simulate, prepImages)

 sim_yielddata(BV.MC.Entry,seed)

 oneRepIBDSpatial(numOfReps = rep, numOfEntry = plot, ebn = EBN, numOfChecks=Checks)

 spaEBN(year="21",fdp="R:/Breeding/MT_TP/Models/AL_Adjustments/",spaDF=load_Data(x,simulate),namesSeq)

 xgblinearBV(hdp, fdp, s0, s1, s2, s3, s4, s5, seas0, seas1, seas2, seas3, seas4, seas5, inbred,
 rounds, eta, lambda, alpha, male )

Arguments

doLmer	uses lme4 to run breeding values analysis (0.9999 r2 to ASReml)
doField	Switches from year to field effect
doHybridID	Runs BV analysis with LINE as random
doGCABV	Runs BV analysis with MALE and FEMALE as random
x	date in "11_8_2021" format, export out of prism must be used with a spatial analysis design setup from function oneRepIBDSpatial()
simulate	T or F, when T sample data will be used
fdp	final data path of output file
wdp	working data path for breeding value pedigrees
ws	working sheet for yield trial master catalog output from PRISM
dpf	path file for inbred data_ (5 output files)
gdp	goss's dath path for inbred data exported from PRISM yield trial master catalog
hdp	inbred data path for inbred data exported from PRISM nursery master catalog
folder	year or folder to put files into fdp
numOfReps	list of numbers of reps for entry list book
numOfEntry	list of number of entries per entry list book
ebn	list of names for entry books
numOfChecks	list of checks per entry list book
inbred	list of male inbreds to filter with
male	list of male inbreds to include with predicitons file

Author(s)

Jacob Lamkey

References

https://www.github.com/jbkey730/BreedStats

Examples

#########################
#SIMULATED DATA DEMO
#########################
######################################################################################################
######Rscript for Alpha Lattice Designs
######################################################################################################
invisible(gc(reset=T)) #cleans memory "garbage collector"
memory.limit(size=16071)
######################################################################################################
######The following packages need to be loaded
######Load packages:  #
library(BreedStats)
library(tidyverse)
library(data.table)
library(asreml)

cl=parallel::detectCores()
cl <- makePSOCKcluster(cl)
registerDoParallel(cl)

#dimField = 48*50 #2400 plots
#num of plots in Entry List
fdp = "C:/Users/jake.lamkey/Documents/"

plotListOneRep = c(36,36,36,48, 48,36,36,36)
RepListOneRep = c(8,6,4,9, 10,8,10,4)
ebn = c("TP21B681","TP21B682","TP21B683","TP21B721", "TP21B722","TP21B723","TP21B725","TP21B727")
numOfChecks = c(4,4,4,4, 4,4,5,4)

length(plotListOneRep)
length(RepListOneRep)
length(ebn)
length(numOfChecks)

data.files=as.factor(ebn)

bind.linked.male.peds=foreach(i=(1:length(plotListOneRep)),
                              .packages=c("dplyr","DiGGer","stats"),
                              .export=c("mutate","filter","setNames","group_by","summarise",
                                        "ibDiGGer","getDesign","corDiGGer","desPlot")
) 

#for(i in 1:length(plotListOneRep)){

  EBN = ebn[[i]]

  pdf(file = paste0(fdp,"B_YTDesign_",i ,EBN,"OneReplicated.pdf"), paper="special", width = 8.5,
                          height = 11, family="Times", pointsize=11, bg="white", fg="black")

  plot = plotListOneRep[[i]]
  rep = RepListOneRep[[i]]
  Checks = numOfChecks[[i]]
  oneRepIBDSpatial(numOfReps = rep, numOfEntry = plot, ebn = EBN, numOfChecks=Checks)

  dev.off()

}

stopCluster(cl)



###############################Examine Data##################################

spaDF = load_Data(x = "11_8_2021",simulate=T ) #merge incomplete block analysis from onerepIBDspatial with data

AL.traits = spaEBN(year = "21",
                   fdp = "C:/Users/jake.lamkey/Documents/",#"R:/Breeding/MT_TP/Models/AL_Adjustments/",
                   spaDF = spaDF,
                   namesSeq =   c(3:5) #ear, plt, tw, ym, yield####not included yet gs, moist, rl
                  )


######################################################################################################
######Inbred Characterization Analysis
######################################################################################################
 var4=2021
 var2 = 2017
 var3=2021

suppressWarnings(suppressMessages(
inbredChar(
          dpf = "C:/Users/jake.lamkey/Documents/Inbred Data_", #"R:/Breeding/MT_TP/Models/shed_silk/Inbred Data_",
          gdp = gdp,
          hdp = hdp,
          year= var4,
          l_year = var2,
          h_year = var3,
          doAdjInbredData = T,
          simulate=T
)))

fdp = paste0("C:/Users/jake.lamkey/Documents")
year= "Simulate"
if(!dir.exists(paste0(fdp,"/",year))){
  dir.create(paste0(fdp,"/",year))
}
######################################################################################################
######diallel breeding value analysis
######################################################################################################

x="11_8_2021"
ws = paste0('R:/Breeding/MT_TP/Models/Data/Department Data/YT_BV Yield Trial Master Catalog ',x, ".csv")
wdp = paste0("C:/Users/jake.lamkey/Documents")
varA ="True"
varB ="False"
varC ="False"
varProp ="True"
varChoice ="False"
varD ="False"
varR ="False"
varX ="False"
varE ="False"
varQ ="False"
varV ="False"
varGEM ="False"
s0=T
s1 =T
s2 =T
s3 =F
s4 =F
s5 =F

seas0 = 21
seas1 = 20
seas2 = 19
seas3 = ""
seas4 = ""
seas5 = ""

doYear="True"
folder=year

#vdp = 'R:/Breeding/MT_TP/Models/Data/Department Data/Variety.male.female.xlsx'
#folder= "21S"
A = if(varA== "True"){varA=T}else(varA=F)#varA,
B = if(varB== "True"){varB=T}else(varB=F)#varB,
C = if(varC==T){varC=T}else(varC=F)#varC,
Prop =if(varProp== "True"){varProp=T}else(varProp=F)# varProp,
Choice =if(varChoice== "True"){varChoice=T}else(varChoice=F)# varChoice,
D=if(varD== "True"){varD=T}else(varD=F)#varD,
R=if(varR== "True"){varR=T}else(varR=F)#varR,
X=if(varX== "True"){varX=T}else(varX=F)#varX,
E=if(varE== "True"){varE=T}else(varE=F)#varE,
Q=if(varQ== "True"){varQ=T}else(varQ=F)#varQ,
V=if(varV== "True"){varV=T}else(varV=F)#varV,
GEM=if(varGEM=="True"){varGEM=T}else(varGEM=F)#VarGEM,

cat("var1=",var1,"varA=",varA,"varB=",varB,"varC=",varC,"varProp=",varProp,"varChoice=",varChoice,"varFolder=",varFolder,
    "seas1=",seas1,"seas2=",seas2,"seas3=",seas3,"seas4=",seas4,"seas5=",seas5,"seas0=",seas0,"s0=",s0,"s1=",s1,"s2=",s2,"s3=",
    s3,"s4=",s4,"s5=",s5,"\n")

cat(A, B, C, Prop, Choice, D, R, X, E, Q, V, GEM,"\n")
sink()

suppressWarnings(suppressMessages(BV(fdp = fdp, #paste0("R:/Breeding/MT_TP/Models/Breeding Values/",folder),
                                     #fdph = fdph,#paste0("R:/Breeding/MT_TP/Models/Breeding Values/",folder,"/Hybrid"),
                                     wdp = wdp,#paste0("R:/Breeding/MT_TP/Models/Data/Department Data/",folder,"/"),
                                     ws = ws,
                                     #vdp = vdp,
                                     doHybridID=T,
                                     doPedigreeChange =T,
                                     doPedigreeToBecksChange=F,
                                     doGCABV = T,
                                     doWriteFinalPedigrees =F,
                                     year= folder,
                                     folder=folder,
                                     A = A,
                                     B = B,
                                     C = C,
                                     Prop = Prop,
                                     Choice = Choice,
                                     D=D,
                                     R=R,
                                     X=X,
                                     E=E,
                                     Q=Q,
                                     V=V,
                                     GEM=GEM,
                                     doDNN = F,
                                     s0=s0,
                                     s1=s1,
                                     s2=s2,
                                     s3=s3,
                                     s4=s4,
                                     s5=s5,
                                     seas0=seas0,
                                     seas1=seas1,
                                     seas2=seas2,
                                     seas3=seas3,
                                     seas4=seas4,
                                     seas5=seas5,
                                     doYear=if(doYear == "True"){doYear=T}else(doYear=F), #doYear,
                                     simulate=T

)))

######################################################################################################
######Pedigree Adjustments from Inventory
######################################################################################################

fdp = paste0("C:/Users/jake.lamkey/Documents") #FINAL DATA PATH TO WRITE PEDIGREES
wdp = paste0("C:/Users/jake.lamkey/Documents") #WORKING DATA PATH TO CHANGE PEDIGREES

#x="11_8_2021"
#ws = paste0('R:/Breeding/MT_TP/Models/Data/Department Data/YT_BV Yield Trial Master Catalog ',x, ".csv")
date="12_22_2021"
ws = paste0("P:/Temp/PedAdjust ",date,".csv")

#YEARS IN INVENTORY CATALOG
seas0 = 21
seas1 = ""
seas2 = ""
seas3 = ""
seas4 = ""
seas5 = ""


suppressWarnings(suppressMessages(BV(fdp = fdp, #paste0("R:/Breeding/MT_TP/Models/Breeding Values/",folder),
                                     wdp = wdp,#paste0("R:/Breeding/MT_TP/Models/Data/Department Data/",folder,"/"),
                                     ws = ws, date=date,  #LOAD DATA

                                     doPedigreeChange =T, doReduceNonCodes=F, #PEDIGREE SETTINGS
                                     InventoryPedigree = T, ytData=F, simulate=F, #TYPE OF DATA LOADING
                                     doHybridID=F, doGCABV = F,doYear=T, #TYPE OF ANALYSIS
                                     doPedigreeToBecksChange=F,doWriteFinalPedigrees =F,
                                     year= "21S", folder="21S",
                                     A = T,B = F,C = F,Prop = F,Choice = F,D=F,R=F,X=F,E=F,Q=F,V=F,GEM=F, #TESTING LEVEL
                                     doDNN = F,
                                     s0=if(seas0 == ""){s0=F}else(s0=T),
                                     s1=if(seas1 == ""){s1=F}else(s1=T),
                                     s2=if(seas2 == ""){s2=F}else(s2=T),
                                     s3=if(seas3 == ""){s3=F}else(s3=T),
                                     s4=if(seas4 == ""){s4=F}else(s4=T),
                                     s5=if(seas5 == ""){s5=F}else(s5=T),
                                     seas0=seas0,seas1=seas1, seas2=seas2, seas3=seas3,  seas4=seas4, seas5=seas5
                                     #if(doYear == "True"){doYear=T}else(doYear=F) #doYear,
)))

########################################################################################################
######Predictions with xgblinear for a expand.grid type of dataframe including male, female, year, field
########################################################################################################
xgblinearBV(
  hdp = "C:/Users/jake.lamkey/Documents/",
  fdp= "C:/Users/jake.lamkey/Documents/",
  s0=T,
  s1 =T,
  s2 =F,
  s3 =F,
  s4 =F,
  s5 =F,
  seas0 = 21,
  seas1 = 20,
  seas2 = "",
  seas3 = "",
  seas4 = "",
  seas5 = "",

  inbred = "BRS312",
  rounds = 3000,
  eta = 1,
  lambda = 0.0003,
  alpha = 0.0003,
  male =   data.frame(male=c('BSQ033',	'BEX905',
                    'BRQ529',	'BSR095',	'BRU059',
                    'BRQ291',	'BRP251',"BRS312"

  ))

)

jbkey730/BreedStats documentation built on Aug. 28, 2022, 8:22 a.m.