rm(list=ls())
setwd("/Users/beatriceelohorifie/Documents/Module 8")
options(max.print=2000000)

#################################################################
##                    Install R packages                       ##
##                    A smart function                         ##
#################################################################

check.packages <- function(pkg){
  new.pkg <- pkg[!(pkg%in%installed.packages()[,"Package"])]
  if (length(new.pkg))
    install.packages(new.pkg, dependencies = TRUE)
  sapply(pkg, require, character.only = TRUE)
}
packages <- c('DiallelAnalysisR' )
check.packages(packages)

### Diallel analysis from Striga infested field####
Data1 <- read.csv("QG_Mod8_ALA8.1_ds1.csv", header = TRUE)
Data1$Cross1 <- factor(Data1$Cross1)
Data1$Cross2 <- factor(Data1$Cross2)
Data1$Rep    <- factor(Data1$Rep)

str(Data1)
names(Data1)


fm1 <-
  Griffing(
    y      = Pheno
  , Rep    = Rep
  , Cross1 = Cross1
  , Cross2 = Cross2
  , data   = Data1
  , Method = 4
  , Model  = 1
  )

fm1
names(fm1)
fm1$Means
fm1$ANOVA
fm1$Genetic.Components
fm1$Effects
fm1$StdErr

### Diallel analysis from non-striga infested field####
Data2 <- read.csv("QG_Mod8_ALA8.1_ds2.csv", header = TRUE)
Data2$Cross1 <- factor(Data2$Cross1)
Data2$Cross2 <- factor(Data2$Cross2)
Data2$Rep    <- factor(Data2$Rep)

str(Data2)
names(Data2)


fm2 <-
  Griffing(
      y      = Pheno
    , Rep    = Rep
    , Cross1 = Cross1
    , Cross2 = Cross2
    , data   = Data2
    , Method = 4
    , Model  = 1
  )

fm2
names(fm2)
fm2$Means
fm2$ANOVA
fm2$Genetic.Components
fm2$Effects
fm2$StdErr

combinedstr <- read.csv("QG_Mod8_ALA8.1_ds2.csv", header = TRUE)
combinedstr$Cross1 <- factor(combinedstr$Cross1)
combinedstr$Cross2 <- factor(combinedstr$Cross2)
combinedstr$Rep    <- factor(combinedstr$Rep)

str(combinedstr)
names(combinedstr)


fm3 <-
  Griffing(
    y      = Pheno
    , Rep    = Rep
    , Cross1 = Cross1
    , Cross2 = Cross2
    , data   = combinedstr
    , Method = 4
    , Model  = 1
  )

fm3
names(fm3)
fm3$Means
fm3$ANOVA
fm3$Genetic.Components
fm3$Effects
fm3$StdErr