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multivariate_analysis.R
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multivariate_analysis.R
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# Load required library
library(dplyr)
library(tidyr)
library(tidyverse)
library(gridExtra)
library(ggplot2)
########### DATE SET #########
NO3 <-read.csv('TOGUCHI_NO3.csv', header = T, check.names = T)
ECS <-read.csv('TOGUCHI_EC.csv', header = T, check.names = T)
head(NO3,2)
head(ECS,2)
##################################################################################
# Example of Blocks schedule of crop growth
## BLOCK vid PLANT START HARVEST START END HARVEST ##
## C v1 2017-07-18 2017-09-18 ?2017-11-27 (until) ##
## D v1 2017-05-26 2017-07-25 2017-10-16 ##
## F v1 2017-08-16 2017-10-23 ?2017-11-27 ##
## F v2 2017-08-16 ? ##
################################################################################
## START AND END DATES of 'start of Plant' to 'Start of harvesting'
End_C_After <- as.Date("2017-11-27")
start_C_After <- as.Date("2017-09-18")
End_D_After <- as.Date("2017-10-10")
start_D_After <- as.Date("2017-07-25")
End_F_After <- as.Date("2017-11-27")
start_F_After <- as.Date("2017-10-23")
##### Function to Filter Date ###############
filterDate <- function(df,x,y){
df$Date <- as.Date.factor(df$Date, format = "%Y-%m-%d")
df[df$Date >= x & df$Date <= y,]
}
## C Block V1 Variety ####
C_EC_DF_After <- filterDate(subset(ECS, Block == 'C'),start_C_After,End_C_After)
C_NO3_DF_After <- filterDate(subset(NO3, Block == 'C'),start_C_After,End_C_After)
##### D Block V1 Variety #####
D_EC_DF_After <- filterDate(subset(ECS, Block == 'D'),start_D_After,End_D_After)
D_NO3_DF_After <- filterDate(subset(NO3, Block == 'D'),start_D_After,End_D_After)
##### F Block V1 variety ######
F_EC_DF_After <- filterDate(subset(ECS, Block == 'F'),start_F_After,End_F_After)
F_NO3_DF_After <- filterDate(subset(NO3, Block == 'F'),start_F_After,End_F_After)
# Bind the three Blocks C,D,F
EC_CDF_After <-dplyr::bind_rows(C_EC_DF_After,D_EC_DF_After,F_EC_DF_After)
NO3_CDF_After <-dplyr::bind_rows(C_NO3_DF_After,D_NO3_DF_After,F_NO3_DF_After)
head(NO3_CDF_After,2)
## PLOT 1 ##
p1_After <- ggplot(aes(y=EC, x=Date),data = EC_CDF_After) +
geom_line(aes(color=Block)) + labs(x=NULL, y='EC') +
theme(legend.position="none",
panel.grid.minor.x = element_blank()) +
theme_bw()
p1_After
ggsave(filename = "toguchi_p1_After.JPEG",p1_After)
## PLOT 2 ##
p4_After <- ggplot(aes(y=Measure, x=Date),data = NO3_CDF_After) +
geom_line(aes(color=Block))+ labs(x='Date', y='NO3') +
theme(legend.position="none",
panel.grid.minor.x = element_blank()) +
theme_bw()
p4_After
ggsave(filename = "toguchi_p4_After.JPEG",p4_After)
## PLOT 3 Combined ##
g_After <- grid.arrange(p1_After,p4_After, ncol= 1)
ggsave(filename = "toguchi_EC_NO3.JPEG",g_After)