library(readr)
combined <- read_csv("combined.csv")
## Parsed with column specification:
## cols(
##   management = col_character(),
##   class = col_character(),
##   rank = col_double(),
##   rep = col_double(),
##   blk = col_double(),
##   plot = col_double(),
##   entry = col_double(),
##   pedigree = col_character(),
##   year = col_double(),
##   gyd = col_double(),
##   ad = col_double(),
##   asi = col_double(),
##   ph = col_double(),
##   eh = col_double(),
##   epp = col_double(),
##   np = col_double(),
##   sen1 = col_double(),
##   sen2 = col_double()
## )
View(combined)
attach(combined)
names(combined)
##  [1] "management" "class"      "rank"       "rep"        "blk"       
##  [6] "plot"       "entry"      "pedigree"   "year"       "gyd"       
## [11] "ad"         "asi"        "ph"         "eh"         "epp"       
## [16] "np"         "sen1"       "sen2"
management=as.factor(management)
class=as.factor(class)
rank=as.factor(rank)
pedigree=as.factor(pedigree)
rep=as.factor(rep)
blk=as.factor(blk)
year=as.factor(year)
library(lme4)
## Loading required package: Matrix
library(lmerTest)
## 
## Attaching package: 'lmerTest'
## The following object is masked from 'package:lme4':
## 
##     lmer
## The following object is masked from 'package:stats':
## 
##     step
library(ggplot2)
library(psych)
## 
## Attaching package: 'psych'
## The following objects are masked from 'package:ggplot2':
## 
##     %+%, alpha
library(agricolae)
require(MASS)
## Loading required package: MASS
library(Hmisc)
## Loading required package: lattice
## Loading required package: survival
## Loading required package: Formula
## 
## Attaching package: 'Hmisc'
## The following object is masked from 'package:psych':
## 
##     describe
## The following objects are masked from 'package:base':
## 
##     format.pval, units
library(lubridate) # for working with dates
## 
## Attaching package: 'lubridate'
## The following object is masked from 'package:base':
## 
##     date
library(scales)   # to access breaks/formatting functions
## 
## Attaching package: 'scales'
## The following objects are masked from 'package:psych':
## 
##     alpha, rescale
## The following object is masked from 'package:readr':
## 
##     col_factor
library(gridExtra) # for arranging plots
library(ggthemes)

Graphical presentation

theme_set(theme_gray(base_size =12))
ggplot(combined, aes(x = management, y =gyd, colour = class)) + 
    geom_boxplot(size=1.2,varwidth = TRUE) + 
    geom_point(data = combined, aes(y = mean(gyd))) +
    geom_line(data = combined, aes(y =mean(gyd), group = class))+ylab("Maize Grain yield [t/ha]") + 
  xlab("Management")+theme(legend.position = c(0.2, 0.85))

#############################################################

theme_set(theme_gray(base_size =12))
m <- ggplot(data=combined,aes(x=management, y=gyd, colour = class))
m + geom_violin(size=1.1,shape=8)+ geom_boxplot(width=.3, outlier.size=0)+ylab("Maize Grain yield [kg/ha]") + xlab("Management")+theme(legend.position = c(0.2, 0.85))
## Warning: Ignoring unknown parameters: shape

#######AD
theme_set(theme_gray(base_size =12))
ggplot(combined, aes(x = management, y =ad, colour = class)) + 
    geom_boxplot(size=1.0,varwidth = TRUE) + 
    geom_point(data = combined, aes(y = mean(gyd))) +
    geom_line(data = combined, aes(y =mean(gyd), group = class))+ylab("AD") + 
  xlab("Management")

########ASI
theme_set(theme_gray(base_size =12))
ggplot(combined, aes(x = management, y =asi, colour = class)) + 
    geom_boxplot(size=1.2,varwidth = TRUE) + 
    geom_point(data = combined, aes(y = mean(gyd))) +
    geom_line(data = combined, aes(y =mean(gyd), group = class))+ylab("ASI") + 
  xlab("Management")

#########PH
theme_set(theme_gray(base_size =12))
ggplot(combined, aes(x = management, y =ph, colour = class)) + 
    geom_boxplot(size=1.2,varwidth = TRUE) + 
    geom_point(data = combined, aes(y = mean(gyd))) +
    geom_line(data = combined, aes(y =mean(gyd), group = class))+ylab("PH") + xlab("Management")

##################EH
theme_set(theme_gray(base_size =12))
ggplot(combined, aes(x = management, y =eh, colour = class)) + 
    geom_boxplot(size=1.2,varwidth = TRUE) + 
    geom_point(data = combined, aes(y = mean(gyd))) +
    geom_line(data = combined, aes(y =mean(gyd), group = class))+ylab("EH") + xlab("Management")

######################EPP

theme_set(theme_gray(base_size =12))
ggplot(combined, aes(x = management, y =epp, colour = class)) + 
    geom_boxplot(size=1.2,varwidth = TRUE) + 
    geom_point(data = combined, aes(y = mean(gyd))) +
    geom_line(data = combined, aes(y =mean(gyd), group = class))+ylab("EPP") + xlab("Management")

####################np

theme_set(theme_gray(base_size =12))
ggplot(combined, aes(x = management, y =np, colour = class)) + 
    geom_boxplot(size=1.2,varwidth = TRUE) + 
    geom_point(data = combined, aes(y = mean(gyd))) +
    geom_line(data = combined, aes(y =mean(gyd), group = class))+ylab("NP") + xlab("Management")

###################sen1
theme_set(theme_gray(base_size =12))
ggplot(combined, aes(x = management, y =sen1, colour = class)) + 
    geom_boxplot(size=1.2,varwidth = TRUE) + 
    geom_point(data = combined, aes(y = mean(gyd))) +
    geom_line(data = combined, aes(y =mean(gyd), group = class))+ylab("SEN_1") + xlab("Management")
## Warning: Removed 60 rows containing non-finite values (stat_boxplot).

##########################SEN2

theme_set(theme_gray(base_size =12))
ggplot(combined, aes(x = management, y =sen2, colour = class)) + 
    geom_boxplot(size=1.2,varwidth = TRUE) + 
    geom_point(data = combined, aes(y = mean(gyd))) +
    geom_line(data = combined, aes(y =mean(gyd), group = class))+ylab("SEN_2") + xlab("Management")
## Warning: Removed 60 rows containing non-finite values (stat_boxplot).

theme_set(theme_gray(base_size =12))
ggplot(combined, aes(x = year, y =gyd, colour = class)) + 
    geom_boxplot(size=1.2,varwidth = TRUE) + 
    geom_point(data = combined, aes(y = mean(gyd))) +
    geom_line(data = combined, aes(y =mean(gyd), group = class))+ylab("Maize Grain yield [t/ha]") + 
  xlab("year")+theme(legend.position = c(0.2, 0.85))+facet_wrap(.~management)

ggplot(combined, aes(x = year , y = gyd, color = class)) +  
  geom_point(size=3,  aes(shape=class)) + 
  geom_smooth(method=lm, position = "jitter", aes(fill=class), level = 0.95)+ylab("Maize grain yield [t/ha]") + 
  xlab("Year")+geom_abline(xintercept = 0, linetype=2, color = "red", size=1)+theme(legend.position = c(0.85, 0.85))
## Warning: Ignoring unknown parameters: xintercept

###########################ad

ggplot(combined, aes(x = year , y = ad, color = class)) +  
  geom_point(size=3,  aes(shape=class)) + 
  geom_smooth(method=lm, position = "jitter", aes(fill=class), level = 0.95)+ylab("ad") + xlab("Year")+geom_abline(xintercept = 0, linetype=2, color = "red", size=1)
## Warning: Ignoring unknown parameters: xintercept

#######################asi
ggplot(combined, aes(x = year , y = asi, color = class)) +  
  geom_point(size=3,  aes(shape=class)) + 
  geom_smooth(method=lm, position = "jitter", aes(fill=class), level = 0.95)+ylab("ASI") + xlab("Year")+geom_abline(xintercept = 0, linetype=2, color = "red", size=1)
## Warning: Ignoring unknown parameters: xintercept

######################ph
ggplot(combined, aes(x = year , y = ph, color = class)) +  
  geom_point(size=3,  aes(shape=class)) + 
  geom_smooth(method=lm, position = "jitter", aes(fill=class), level = 0.95)+ylab("PH") + xlab("Year")+geom_abline(xintercept = 0, linetype=2, color = "red", size=1)
## Warning: Ignoring unknown parameters: xintercept

##################### EH
ggplot(combined, aes(x = year , y = eh, color = class)) +  
  geom_point(size=3,  aes(shape=class)) + 
  geom_smooth(method=lm, position = "jitter", aes(fill=class), level = 0.95)+ylab("EH") + xlab("Year")+geom_abline(xintercept = 0, linetype=2, color = "red", size=1)
## Warning: Ignoring unknown parameters: xintercept

#####################EPP
ggplot(combined, aes(x = year , y = epp, color = class)) +  
  geom_point(size=3,  aes(shape=class)) + 
  geom_smooth(method=lm, position = "jitter", aes(fill=class), level = 0.95)+ylab("EPP") + xlab("Year")+geom_abline(xintercept = 0, linetype=2, color = "red", size=1)
## Warning: Ignoring unknown parameters: xintercept

#########################np

ggplot(combined, aes(x = year , y =np, color = class)) +  
  geom_point(size=3,  aes(shape=class)) + 
  geom_smooth(method=lm, position = "jitter", aes(fill=class), level = 0.95)+ylab("NP") + xlab("Year")+geom_abline(xintercept = 0, linetype=2, color = "red", size=1)
## Warning: Ignoring unknown parameters: xintercept

###############################