examples/vt_anlaysis_test.R

In austinjcase/BreedR: An R package for managing a breeding program

# laoding the raw files
library(devtools)
library(roxygen2)
library(BreedR)
library(plyr)

#####
exp_odb<-read.csv("/Volumes/CFANS/AGRO/Oat_Lab/Oat_Database/ODB/expt_26apr18.csv", head=T,stringsAsFactors = F) # experiemntial description file
fld_odb<-read.csv("/Volumes/CFANS/AGRO/Oat_Lab/Oat_Database/ODB/field_2may18.csv", head=T, stringsAsFactors = F) # field phnoetype  file
qual_odb<-read.csv("/Volumes/CFANS/AGRO/Oat_Lab/Oat_Database/ODB/post_harvest_27apr18.csv", head=T, stringsAsFactors = F) # quality phnoetype  file
#####


?vt_analysis()
head(fld_odb)
head(exp_odb)
# running the function

#with the cut offs
test_out<-vt_analysis(exp_data = exp_odb, fld_data = fld_odb, qual_data = qual_odb,
            trial_type = "vt", 
            yr1 = 2017, yr2 = 2016, yr3 = 2015,
            trait_sel = "yield",
            exclude = c("vt_2017_stp", "vt_2016_stp", "vt_2017_kim", "vt_2015_was" ,"vt_2017_roc" ),
            expt_obj = "agro", cut_offs = c(50, 300))


head(test_out)



test_out<-vt_analysis(exp_data = exp_odb, fld_data = fld_odb, qual_data = qual_odb,
                      trial_type = "vt", 
                      yr1 = 2017, yr2 = NULL, yr3 = NULL,
                      trait_sel = "yield",
                      exclude = c("vt_2017_stp", "vt_2016_stp", "vt_2017_kim", "vt_2015_was" ,"vt_2017_roc" ),
                      expt_obj = "agro", cut_offs = c(50, 300))


test_out<-vt_analysis(exp_data = exp_odb, fld_data = fld_odb, qual_data = qual_odb,
                      trial_type = "umopn", 
                      yr1 = 2016, yr2 = NULL, yr3 = NULL,
                      trait_sel = "yield",
                      expt_obj = "agro")

rm(test_out)

#without cut offs
test_out<-vt_analysis(exp_data = exp_odb, fld_data = fld_odb, qual_data = qual_odb,
                        trial_type = "vt", yr1 = 2017, yr2 = 2016, yr3 = 2015,
                        trait_sel = "yield",
                        exclude = c("vt_2017_stp", "vt_2016_stp", "vt_2017_kim", "vt_2015_was" ,"vt_2017_roc" ),
                        expt_obj = "agro", cut_offs = NULL)


rm(test_out)

#test weight
test_out<-vt_analysis(exp_data = exp_odb, fld_data = fld_odb, qual_data = qual_odb,
                      trial_type = "vt", yr1 = 2017, yr2 = 2016, yr3 = 2015,
                      trait_sel = "test_weight",
                      exclude = c("vt_2017_stp", "vt_2016_stp", "vt_2017_kim", "vt_2015_was" ,"vt_2017_roc" ),
                      expt_obj = "agro", cut_offs = NULL)
rm(test_out)


# just one year
test_out<-vt_analysis(exp_data = exp_odb, fld_data = fld_odb, qual_data = qual_odb,
                      trial_type = "vt", yr1 = 2017,
                      trait_sel = "yield",
                      expt_obj = "agro", cut_offs = c(50, 300))
rm(test_out)

# just two years
test_out<-vt_analysis(exp_data = exp_odb, fld_data = fld_odb, qual_data = qual_odb,
                      trial_type = "vt", yr1 = 2017, yr2=2016,
                      trait_sel = "yield",
                      expt_obj = "agro", cut_offs = c(50, 300))
rm(test_out)