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

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('plantbreeding' )
check.packages(packages)

################################################################################
#####install.packages("plantbreeding", repos="http://R-Forge.R-project.org")####
##########library(plantbreeding)  ###############
################################################################################

ds <-read.csv("QG_Mod8_ALA8.2_ds.csv",header=TRUE)
summary(ds)

ds$loc<-factor(ds$loc)
ds$set<-factor(ds$set)
ds$rep<-factor(ds$rep)
ds$female<-factor(ds$female)
ds$male<-factor(ds$male)
summary(ds)

###Dataset for North Carolina Design 2)
ds <- carolina2(dataframe = ds,  set = "set", male = "male", female = "female", 
                 replication = "rep", yvar = "yield")
#########anova(ds$model) # anova 
ds$var.m
ds$var.f
ds$var.mf
ds$var.Af
ds$var.D

###Dataset for North Carolina Design 2)
ds <-read.csv("QG_Mod8_ALA8.3_ds.csv",header=TRUE)
summary(ds)

ds$loc<-factor(ds$loc)
ds$set<-factor(ds$set)
ds$rep<-factor(ds$rep)
ds$female<-factor(ds$female)
ds$male<-factor(ds$male)
summary(ds)

ds <- carolina2(dataframe = ds,  set = "set", male = "male", female = "female", 
                replication = "rep", yvar = "yield")

########anova(ds$model) # anova 

ds$var.m
ds$var.f
ds$var.mf
ds$var.Af
ds$var.D