R Markdown

library(readr)
production <- read_csv("C:/Users/LCHIPINDU/OneDrive - CIMMYT/CIMMYT/Dr Paswel/Leonard/Production/production.csv")

## 
## -- Column specification --------------------------------------------------------
## cols(
##   region = col_character(),
##   period = col_character(),
##   country = col_character(),
##   production = col_double(),
##   crop = col_character()
## )

View(production)
attach(production)

## The following object is masked _by_ .GlobalEnv:
## 
##     production

library(ggplot2)

## Warning: package 'ggplot2' was built under R version 4.1.3

library(patchwork)

## Warning: package 'patchwork' was built under R version 4.1.1

library(ggsignif)

## Warning: package 'ggsignif' was built under R version 4.1.2

library(ggpubr)
library(agricolae)
library(easynls)
library(MVN)

## Registered S3 method overwritten by 'GGally':
##   method from   
##   +.gg   ggplot2

## sROC 0.1-2 loaded

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

Production

ea<-subset(production, region=="Eastern Africa")

g1<-ggplot(ea, aes(x=period, y=production, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Production (million tonnes)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=7),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  facet_wrap(~crop)+
  ggtitle("Eastern Africa")+
  theme(plot.title = element_text(hjust = 0.5))+ theme(legend.position = "bottom")
g1

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

## Gnuts East Africa
gnuts_ea<-subset(production, region=="Eastern Africa" & crop=="Groundnut")

a1<-ggplot(gnuts_ea, aes(x= period, y=production)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Groundnut production (million tonnes)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =production), color = "black", size = 2.5,vjust=-0.5)+ facet_wrap(~country, ncol=2)+ theme(legend.position = "none") +
  ggtitle("Eastern Africa")+
  theme(plot.title = element_text(hjust = 0.5))

## Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.

## Warning: Please use the `linewidth` argument instead.

a1

 ## Gnuts in East Africa Line Graph
 
########## Maize
 gnuts_ea_1<-subset(production, region=="Eastern Africa" & crop=="Maize")

a2<-ggplot(gnuts_ea_1, aes(x= period, y=production,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Maize production (million tonnes)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =production), color = "black", size = 2.5,vjust=-0.5)+ facet_wrap(~country, ncol=2)+ theme(legend.position = "none") +
  ggtitle("Eastern Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 a2

########## Millet
 gnuts_ea_2<-subset(production, region=="Eastern Africa" & crop=="Millet")

a3<-ggplot(gnuts_ea_2, aes(x= period, y=production,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Millet production (million tonnes)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =production), color = "black", size = 2.5,vjust=-0.5)+ facet_wrap(~country, ncol=2)+ theme(legend.position = "none") +
  ggtitle("Eastern Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 a3

 ########## Sorghum
 gnuts_ea_3<-subset(production, region=="Eastern Africa" & crop=="Sorghum")

a4<-ggplot(gnuts_ea_3, aes(x= period, y=production,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Sorghum production (million tonnes)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =production), color = "black", size = 2.5,vjust=-0.5)+ facet_wrap(~country, ncol=2)+ theme(legend.position = "none") +
  ggtitle("Eastern Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 a4

West Africa

wa<-subset(production, region=="West Africa")

w1<-ggplot(wa, aes(x=period, y=production, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Production (million tonnes)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=7),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  facet_wrap(~crop)+
  ggtitle("West Africa")+
  theme(plot.title = element_text(hjust = 0.5))+ theme(legend.position = "bottom")
w1

wst_1<-subset(production, region=="West Africa" & crop=="Groundnut")

b1<-ggplot(wst_1, aes(x= period, y=production,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Groundnut production (million tonnes)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =production), color = "black", size = 2,vjust=-0.5)+ facet_wrap(~country, ncol=3)+ theme(legend.position = "none") +
  ggtitle("West Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 b1

 ####################### Maize
 wst_2<-subset(production, region=="West Africa" & crop=="Maize")

b2<-ggplot(wst_2, aes(x= period, y=production,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Maize production (million tonnes)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =production), color = "black", size = 2,vjust=-0.5)+ facet_wrap(~country, ncol=3)+ theme(legend.position = "none") +
  ggtitle("West Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 b2

 #####################
 
 
 
 
####################### Millet
 wst_3<-subset(production, region=="West Africa" & crop=="Millet")

b3<-ggplot(wst_3, aes(x= period, y=production,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Millet production (million tonnes)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =production), color = "black", size = 2,vjust=-0.5)+ facet_wrap(~country, ncol=3)+ theme(legend.position = "none") +
  ggtitle("West Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 b3

 ####################### Sorghum
 wst_4<-subset(production, region=="West Africa" & crop=="Sorghum")

b4<-ggplot(wst_4, aes(x= period, y=production,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Sorghum production (million tonnes)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =production), color = "black", size = 2,vjust=-0.5)+ facet_wrap(~country, ncol=3)+ theme(legend.position = "none") +
  ggtitle("West Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 b4

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

East and West Africa Total Production

ew_1<-subset(production, country== "Total W.A")

z1<-ggplot(ew_1, aes(x= period, y=production,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Total production (million tonnes)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =production), color = "black", size = 2,vjust=-0.5)+ facet_wrap(~crop, ncol=2)+ theme(legend.position = "none") +
  ggtitle("Total Production:West Africa")+
  theme(plot.title = element_text(hjust = 0.5))

z1

######## EA
ew_2<-subset(production, country== ".Total E.A")

z2<-ggplot(ew_2, aes(x= period, y=production,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Total production (million tonnes)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =production), color = "black", size = 2,vjust=-0.5)+ facet_wrap(~crop, ncol=2)+ theme(legend.position = "none") +
  ggtitle("Total Production:Eastern Africa")+
  theme(plot.title = element_text(hjust = 0.5))

z2

Yield

yield <- read_csv("C:/Users/LCHIPINDU/OneDrive - CIMMYT/CIMMYT/Dr Paswel/Leonard/Yield/yield.csv")

## 
## -- Column specification --------------------------------------------------------
## cols(
##   region = col_character(),
##   period = col_character(),
##   country = col_character(),
##   yield = col_double(),
##   crop = col_character()
## )

View(yield)
attach(yield)

## The following object is masked _by_ .GlobalEnv:
## 
##     yield

## The following objects are masked from production:
## 
##     country, crop, period, region

############ East Africa
ea_yld<-subset(yield, region=="Eastern Africa")

y1<-ggplot(ea_yld, aes(x=period, y=yield, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Yield (Mt/Ha)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=7),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  facet_wrap(~crop)+
  ggtitle("Eastern Africa")+
  theme(plot.title = element_text(hjust = 0.5))+ theme(legend.position = "bottom")
y1

################# West Africa
ea_yld_2<-subset(yield, region=="West Africa")

y2<-ggplot(ea_yld_2, aes(x=period, y=yield, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Yield (Mt/Ha)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=7),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  facet_wrap(~crop)+
  ggtitle("West Africa")+
  theme(plot.title = element_text(hjust = 0.5))+ theme(legend.position = "bottom")
y2

####
#da=y1+y2+plot_layout(ncol = 1)
#ggsave("Yield_EA_WA_v1.pdf",da, width = 6, height =6, dpi=700)

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

## Gnuts East Africa
gnts<-subset(yield, region=="Eastern Africa" & crop=="Groundnut")

x1<-ggplot(gnts, aes(x= period, y=yield,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Groundnut Yield (Mt/Ha)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =yield), color = "black", size = 2.5,vjust=-0.5)+ facet_wrap(~country, ncol=3)+ theme(legend.position = "none") +
  ggtitle("Eastern Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 x1

########## Maize
 mz<-subset(yield, region=="Eastern Africa" & crop=="Maize")

x2<-ggplot(mz, aes(x= period, y=yield,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Maize yield (Mt/Ha)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =yield), color = "black", size = 2.5,vjust=-0.5)+ facet_wrap(~country, ncol=3)+ theme(legend.position = "none") +
  ggtitle("Eastern Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 x2

########## Millet
 millet<-subset(yield, region=="Eastern Africa" & crop=="Millet")

x3<-ggplot(millet, aes(x= period, y=yield,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Millet yield (Mt/Ha)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =yield), color = "black", size = 2.5,vjust=-0.5)+ facet_wrap(~country, ncol=3)+ theme(legend.position = "none") +
  ggtitle("Eastern Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 x3

 ########## Sorghum
 sorg<-subset(yield, region=="Eastern Africa" & crop=="Sorghum")

x4<-ggplot(sorg, aes(x= period, y=yield,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Sorghum yield (Mt/Ha)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =yield), color = "black", size = 2.5,vjust=-0.5)+ facet_wrap(~country, ncol=3)+ theme(legend.position = "none") +
  ggtitle("Eastern Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 x4

Crop Yield West Africa

## Gnuts west Africa
gnts<-subset(yield, region=="West Africa" & crop=="Groundnut")

x1<-ggplot(gnts, aes(x= period, y=yield,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Groundnut yield (Mt/Ha)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =yield), color = "black", size = 2.5,vjust=-0.5)+ facet_wrap(~country, ncol=2)+ theme(legend.position = "none") +
  ggtitle("West Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 x1

########## Maize
 mz<-subset(yield, region=="West Africa" & crop=="Maize")

x2<-ggplot(mz, aes(x= period, y=yield,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Maize yield (Mt/Ha)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =yield), color = "black", size = 2.5,vjust=-0.5)+ facet_wrap(~country, ncol=2)+ theme(legend.position = "none") +
  ggtitle("West Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 x2

########## Millet
 millet<-subset(yield, region=="West Africa" & crop=="Millet")

x3<-ggplot(millet, aes(x= period, y=yield,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Millet yield (Mt/Ha)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =yield), color = "black", size = 2.5,vjust=-0.5)+ facet_wrap(~country, ncol=2)+ theme(legend.position = "none") +
  ggtitle("West Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 x3

 ########## Sorghum
 sorg<-subset(yield, region=="West Africa" & crop=="Sorghum")

x4<-ggplot(sorg, aes(x= period, y=yield,fill=period)) +
geom_bar(stat="identity", color="black", position=position_dodge(),fill="blue")+
  xlab("")+
  ylab("Sorghum yield (Mt/Ha)")+
  theme_bw()+
  theme(plot.title=element_text(size=8,face="bold"),
        axis.text.x=element_text(angle=45,hjust=1,size=7,color="black"),
        axis.text.y=element_text(size=9,color="black"))+
theme(legend.background = element_rect(fill="white", size=0.5, linetype="solid", 
                                  colour ="black"))+
  geom_text(aes(label =yield), color = "black", size = 2.5,vjust=-0.5)+ facet_wrap(~country, ncol=2)+ theme(legend.position = "none") +
  ggtitle("West Africa")+
  theme(plot.title = element_text(hjust = 0.5))

 x4

burkina <- read_csv("C:/Users/LCHIPINDU/OneDrive - CIMMYT/CIMMYT/Dr Paswel/Leonard/Calorie/burkina.csv")

## 
## -- Column specification --------------------------------------------------------
## cols(
##   region = col_character(),
##   period = col_character(),
##   crop = col_character(),
##   calorie = col_double()
## )

View(burkina)
attach(burkina)

## The following objects are masked from yield:
## 
##     crop, period, region

## The following objects are masked from production:
## 
##     crop, period, region

cols <- c("black", "#E69F00", "#56B4E9", "#009E73", "#00AFBB", "#0072B2", "#D55E00", "#800020","green")

Burkina Faso Calorie Consumption

p1 <- ggplot(data = burkina, aes(x = period, y = calorie)) +
  geom_col(aes(fill = crop), width = 0.5)+
  theme_bw()+
  theme(axis.text.x = element_text(face="bold", color="black", 
                           size=8))+
  theme(axis.text.y = element_text(face="bold", color="black", 
                           size=8))+

  ylab("Calorie Consumption (Kg/Capita/Yr)")+
  xlab("")+
scale_fill_manual(values = c("black", "#E69F00", "#56B4E9", "#009E73", "#00AFBB", "#0072B2", "#D55E00", "#800020","green"))+
  theme(legend.position="bottom",legend.justification="left")+coord_flip()+
  ggtitle("Burkina Faso")+
  theme(plot.title = element_text(hjust = 0.5))
 
p1

#+ scale_fill_discrete(breaks=c(“Yams”, “Sorghum and products”, “Rice (milled equivalent)”, “Potatoes”, “Millet and products”, “Maize and products”, “Cassava”,“Bananas”,“Plantains”))

Tanzania Calorie Consumption

tanzania <- read_csv("C:/Users/LCHIPINDU/OneDrive - CIMMYT/CIMMYT/Dr Paswel/Leonard/Calorie/tanzania.csv")

## 
## -- Column specification --------------------------------------------------------
## cols(
##   region = col_character(),
##   period = col_character(),
##   crop = col_character(),
##   calorie = col_double()
## )

View(tanzania)
attach(tanzania)

## The following objects are masked from burkina:
## 
##     calorie, crop, period, region

## The following objects are masked from yield:
## 
##     crop, period, region

## The following objects are masked from production:
## 
##     crop, period, region

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

p2 <- ggplot(data = tanzania, aes(x = period, y = calorie)) +
  geom_col(aes(fill = crop), width = 0.5)+
  theme_bw()+
  theme(axis.text.x = element_text(face="bold", color="black", 
                           size=8))+
  theme(axis.text.y = element_text(face="bold", color="black", 
                           size=8))+

  ylab("Calorie Consumption (Kg/Capita/Yr)")+
  xlab("")+
scale_fill_manual(values = c("black", "#E69F00", "#56B4E9", "#009E73", "#00AFBB", "#0072B2", "#D55E00", "#800020","green"))+
  theme(legend.position="bottom",legend.justification="left")+coord_flip()+
  ggtitle("Tanzania")+
  theme(plot.title = element_text(hjust = 0.5))
 
p2

Ethiopia Calorie Consumption

ethiopia <- read_csv("C:/Users/LCHIPINDU/OneDrive - CIMMYT/CIMMYT/Dr Paswel/Leonard/Calorie/ethiopia.csv")

## 
## -- Column specification --------------------------------------------------------
## cols(
##   region = col_character(),
##   period = col_character(),
##   crop = col_character(),
##   calorie = col_double()
## )

View(ethiopia)
attach(ethiopia)

## The following objects are masked from tanzania:
## 
##     calorie, crop, period, region

## The following objects are masked from burkina:
## 
##     calorie, crop, period, region

## The following objects are masked from yield:
## 
##     crop, period, region

## The following objects are masked from production:
## 
##     crop, period, region

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

p4 <- ggplot(data = ethiopia, aes(x = period, y = calorie)) +
  geom_col(aes(fill = crop), width = 0.5)+
  theme_bw()+
  theme(axis.text.x = element_text(face="bold", color="black", 
                           size=8))+
  theme(axis.text.y = element_text(face="bold", color="black", 
                           size=8))+

  ylab("Calorie Consumption (Kg/Capita/Yr)")+
  xlab("")+
scale_fill_manual(values = c("black", "#E69F00", "#56B4E9", "#009E73", "#00AFBB", "#0072B2", "#D55E00", "#800020","green"))+
  theme(legend.position="bottom",legend.justification="left")+coord_flip()+
  ggtitle("Ethiopia")+
  theme(plot.title = element_text(hjust = 0.5))
 
p4

Ghana Calorie Consumption

ghana <- read_csv("C:/Users/LCHIPINDU/OneDrive - CIMMYT/CIMMYT/Dr Paswel/Leonard/Calorie/ghana.csv")

## 
## -- Column specification --------------------------------------------------------
## cols(
##   region = col_character(),
##   period = col_character(),
##   crop = col_character(),
##   calorie = col_double()
## )

View(ghana)
attach(ghana)

## The following objects are masked from ethiopia:
## 
##     calorie, crop, period, region

## The following objects are masked from tanzania:
## 
##     calorie, crop, period, region

## The following objects are masked from burkina:
## 
##     calorie, crop, period, region

## The following objects are masked from yield:
## 
##     crop, period, region

## The following objects are masked from production:
## 
##     crop, period, region

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

p5 <- ggplot(data = ghana, aes(x = period, y = calorie)) +
  geom_col(aes(fill = crop), width = 0.5)+
  theme_bw()+
  theme(axis.text.x = element_text(face="bold", color="black", 
                           size=8))+
  theme(axis.text.y = element_text(face="bold", color="black", 
                           size=8))+

  ylab("Calorie Consumption (Kg/Capita/Yr)")+
  xlab("")+
scale_fill_manual(values = c("black", "#E69F00", "#56B4E9", "#009E73", "#00AFBB", "#0072B2", "#D55E00", "#800020","green"))+
  theme(legend.position="bottom",legend.justification="left")+coord_flip()+
  ggtitle("Ghana")+
  theme(plot.title = element_text(hjust = 0.5))
 
p5

Mali Calorie Consumption

mali <- read_csv("C:/Users/LCHIPINDU/OneDrive - CIMMYT/CIMMYT/Dr Paswel/Leonard/Calorie/mali.csv")

## 
## -- Column specification --------------------------------------------------------
## cols(
##   region = col_character(),
##   period = col_character(),
##   crop = col_character(),
##   calorie = col_double()
## )

View(mali)
attach(mali)

## The following objects are masked from ghana:
## 
##     calorie, crop, period, region

## The following objects are masked from ethiopia:
## 
##     calorie, crop, period, region

## The following objects are masked from tanzania:
## 
##     calorie, crop, period, region

## The following objects are masked from burkina:
## 
##     calorie, crop, period, region

## The following objects are masked from yield:
## 
##     crop, period, region

## The following objects are masked from production:
## 
##     crop, period, region

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

p6 <- ggplot(data = mali, aes(x = period, y = calorie)) +
  geom_col(aes(fill = crop), width = 0.5)+
  theme_bw()+
  theme(axis.text.x = element_text(face="bold", color="black", 
                           size=8))+
  theme(axis.text.y = element_text(face="bold", color="black", 
                           size=8))+

  ylab("Calorie Consumption (Kg/Capita/Yr)")+
  xlab("")+
scale_fill_manual(values = c("black", "#E69F00", "#56B4E9", "#009E73", "#00AFBB", "#0072B2", "#D55E00", "#800020","green"))+
  theme(legend.position="bottom",legend.justification="left")+coord_flip()+
  ggtitle("Mali")+
  theme(plot.title = element_text(hjust = 0.5))
 
p6

Nigeria Calorie Consumption

nigeria <- read_csv("C:/Users/LCHIPINDU/OneDrive - CIMMYT/CIMMYT/Dr Paswel/Leonard/Calorie/nigeria.csv")

## 
## -- Column specification --------------------------------------------------------
## cols(
##   region = col_character(),
##   period = col_character(),
##   crop = col_character(),
##   calorie = col_double()
## )

View(nigeria)
attach(nigeria)

## The following objects are masked from mali:
## 
##     calorie, crop, period, region

## The following objects are masked from ghana:
## 
##     calorie, crop, period, region

## The following objects are masked from ethiopia:
## 
##     calorie, crop, period, region

## The following objects are masked from tanzania:
## 
##     calorie, crop, period, region

## The following objects are masked from burkina:
## 
##     calorie, crop, period, region

## The following objects are masked from yield:
## 
##     crop, period, region

## The following objects are masked from production:
## 
##     crop, period, region

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

p7 <- ggplot(data = nigeria, aes(x = period, y = calorie)) +
  geom_col(aes(fill = crop), width = 0.5)+
  theme_bw()+
  theme(axis.text.x = element_text(face="bold", color="black", 
                           size=8))+
  theme(axis.text.y = element_text(face="bold", color="black", 
                           size=8))+

  ylab("Calorie Consumption (Kg/Capita/Yr)")+
  xlab("")+
scale_fill_manual(values = c("black", "#E69F00", "#56B4E9", "#009E73", "#00AFBB", "#0072B2", "#D55E00", "#800020","green"))+
  theme(legend.position="bottom",legend.justification="left")+coord_flip()+
  ggtitle("Nigeria")+
  theme(plot.title = element_text(hjust = 0.5))
 
p7

Uganda Calorie Consumption

uganda <- read_csv("C:/Users/LCHIPINDU/OneDrive - CIMMYT/CIMMYT/Dr Paswel/Leonard/Calorie/uganda.csv")

## 
## -- Column specification --------------------------------------------------------
## cols(
##   region = col_character(),
##   period = col_character(),
##   crop = col_character(),
##   calorie = col_double()
## )

View(uganda)
attach(uganda)

## The following objects are masked from nigeria:
## 
##     calorie, crop, period, region

## The following objects are masked from mali:
## 
##     calorie, crop, period, region

## The following objects are masked from ghana:
## 
##     calorie, crop, period, region

## The following objects are masked from ethiopia:
## 
##     calorie, crop, period, region

## The following objects are masked from tanzania:
## 
##     calorie, crop, period, region

## The following objects are masked from burkina:
## 
##     calorie, crop, period, region

## The following objects are masked from yield:
## 
##     crop, period, region

## The following objects are masked from production:
## 
##     crop, period, region

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

p8 <- ggplot(data = uganda, aes(x = period, y = calorie)) +
  geom_col(aes(fill = crop), width = 0.5)+
  theme_bw()+
  theme(axis.text.x = element_text(face="bold", color="black", 
                           size=8))+
  theme(axis.text.y = element_text(face="bold", color="black", 
                           size=8))+

  ylab("Calorie Consumption (Kg/Capita/Yr)")+
  xlab("")+
scale_fill_manual(values = c("black", "#E69F00", "#56B4E9", "#009E73", "#00AFBB", "#0072B2", "#D55E00", "#800020","green"))+
  theme(legend.position="bottom",legend.justification="left")+coord_flip()+
  ggtitle("Uganda")+
  theme(plot.title = element_text(hjust = 0.5))
 
p8

Imports and Exports Plots

Imports

import_export <- read_csv("C:/Users/LCHIPINDU/OneDrive - CIMMYT/CIMMYT/Dr Paswel/Leonard/Exports and Imports/import_export.csv")

## 
## -- Column specification --------------------------------------------------------
## cols(
##   region = col_character(),
##   period = col_character(),
##   country = col_character(),
##   export = col_double(),
##   import = col_double(),
##   crop = col_character(),
##   units = col_character()
## )

View(import_export)
attach(import_export)

## The following objects are masked from uganda:
## 
##     crop, period, region

## The following objects are masked from nigeria:
## 
##     crop, period, region

## The following objects are masked from mali:
## 
##     crop, period, region

## The following objects are masked from ghana:
## 
##     crop, period, region

## The following objects are masked from ethiopia:
## 
##     crop, period, region

## The following objects are masked from tanzania:
## 
##     crop, period, region

## The following objects are masked from burkina:
## 
##     crop, period, region

## The following objects are masked from yield:
## 
##     country, crop, period, region

## The following objects are masked from production:
## 
##     country, crop, period, region

east<-subset(import_export, region=="Eastern Africa")
#####################

################# Eastern  Africa

ea1<-ggplot(east, aes(x=period, y=export, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Export (000 tonnes)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=7),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  facet_wrap(~crop)+
  ggtitle("Eastern Africa")+
  theme(plot.title = element_text(hjust = 0.5))
ea1

## Warning: Removed 12 rows containing missing values (`geom_line()`).

## Warning: Removed 25 rows containing missing values (`geom_point()`).

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

west_1<-subset(import_export, region=="West Africa")
#####################
################# West Africa

wt_1<-ggplot(west_1, aes(x=period, y=export, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Export (000 tonnes)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=7),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  facet_wrap(~crop)+
  ggtitle("West Africa")+
  theme(plot.title = element_text(hjust = 0.5))
wt_1

## Warning: Removed 7 rows containing missing values (`geom_line()`).

## Warning: Removed 27 rows containing missing values (`geom_point()`).

Imports

east_imp<-subset(import_export, region=="Eastern Africa")
#####################

################# Eastern  Africa

m1<-ggplot(east_imp, aes(x=period, y=import, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Import (000 tonnes)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=7),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  facet_wrap(~crop)+
  ggtitle("Eastern Africa")+
  theme(plot.title = element_text(hjust = 0.5))
m1

## Warning: Removed 12 rows containing missing values (`geom_line()`).

## Warning: Removed 18 rows containing missing values (`geom_point()`).

west_imp<-subset(import_export, region=="West Africa")
#####################

################# Eastern  Africa

m2<-ggplot(west_imp, aes(x=period, y=import, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Import (000 tonnes)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=7),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  facet_wrap(~crop)+
  ggtitle("West Africa")+
  theme(plot.title = element_text(hjust = 0.5))
m2

## Warning: Removed 7 rows containing missing values (`geom_point()`).

Additional Species

## mean function
wtp_mean<-function(production,upper_limit=max(
  production)*1.5){
  return(
    data.frame(
      y=4,
      label=paste(
        'Mean=',round(mean(production),0),'\n',
        'Median=',round(median(production),0),'\n',
        'n=',length(production),'\n')
      )
    )
}


# Density plots with semi-transparent fill
zbx<-ggplot(ea, aes(x=log(production), fill=crop)) + geom_density(alpha=.5)+
  facet_wrap(~country,ncol=4)+
    geom_vline(data=ea, aes(xintercept=mean(log(production)),  colour=crop),
               linetype="dashed", size=0.5)+
  
  theme(axis.text.x = element_text(face="bold", color="black", 
                           size=9),
          axis.text.y = element_text(face="bold", color="black", 
                           size=9))+
  theme_bw()+
  xlab("Log (Production(Million tonnes))")+
  ylab("Density")+
       theme(legend.position = c(.9, .8))

## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.

## Warning: Please use `linewidth` instead.

zbx

### Boxplot

ggplot(ea, aes(x = crop, y = log(production))) + 
  geom_boxplot(data=ea, aes(color=crop, fill=crop), outlier.colour="black", outlier.shape=16, outlier.size=2, color="black")+
  facet_wrap(~country, ncol=4)+
  theme_bw()+
  xlab("")+
  stat_summary(fun.y=mean,geom="point",shape=9,size=2,color="blue")+
  ylab("Log (Production(Million tonnes))")+
  theme(legend.position="")+
  
  theme(axis.text.x = element_text(angle=45,hjust=1, face="bold", color="black", 
                           size=8),
          axis.text.y = element_text(face="bold", color="black", 
                           size=9))+
  stat_summary(
    fun.data=wtp_mean,
    geom="text",
    hjust=0.5,
    vjust=0.9,
    size=1.5,
    color="black")

## Warning: The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.

## Warning: Please use the `fun` argument instead.

https://onezero.blog/combining-multiple-ggplot2-plots-for-scientific-publications/

Put the plot on the the area by row and column position.

Intergrating the plots , other option instead on patchwork package.

print(plot1, vp = viewport(layout.pos.row = 1, layout.pos.col = 1)) print(plot2, vp = viewport(layout.pos.row = 1, layout.pos.col = 2)) print(plot3, vp = viewport(layout.pos.row = 2, layout.pos.col = 1)) print(plot4, vp = viewport(layout.pos.row = 2, layout.pos.col = 2))

Consumption Trends

calo <- read_csv("C:/Users/LCHIPINDU/OneDrive - CIMMYT/CIMMYT/Dr Paswel/Leonard/Calorie/calorie_consumption_data.csv")

## 
## -- Column specification --------------------------------------------------------
## cols(
##   country = col_character(),
##   region = col_character(),
##   period = col_character(),
##   crop = col_character(),
##   calorie = col_double()
## )

View(calo)
attach(calo)

## The following objects are masked from import_export:
## 
##     country, crop, period, region

## The following objects are masked from uganda:
## 
##     calorie, crop, period, region

## The following objects are masked from nigeria:
## 
##     calorie, crop, period, region

## The following objects are masked from mali:
## 
##     calorie, crop, period, region

## The following objects are masked from ghana:
## 
##     calorie, crop, period, region

## The following objects are masked from ethiopia:
## 
##     calorie, crop, period, region

## The following objects are masked from tanzania:
## 
##     calorie, crop, period, region

## The following objects are masked from burkina:
## 
##     calorie, crop, period, region

## The following objects are masked from yield:
## 
##     country, crop, period, region

## The following objects are masked from production:
## 
##     country, crop, period, region

Gnuts Trends

## Gnuts East Africa
gnts_cw<-subset(calo, region=="Eastern Africa" & crop=="Sorghum")

 s1<-ggplot(gnts_cw, aes(x=period, y=calorie, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Consumption (kg/capita/yr)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=8),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  ggtitle("Eastern Africa: Sorghum")+
  theme(plot.title = element_text(hjust = 0.5))+
       theme(legend.position = c(.8, .5))
 s1

 ##### West Africa: Sorghum
 
 gnts_wa<-subset(calo, region=="West Africa" & crop=="Sorghum")

 s2<-ggplot(gnts_wa, aes(x=period, y=calorie, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Consumption (kg/capita/yr)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=8),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  ggtitle("West Africa: Sorghum")+
  theme(plot.title = element_text(hjust = 0.5))+
       theme(legend.position = c(.3, .4))
 s2

 gfg_comb_1 <- s1+s2
gfg_comb_1

## Maize East Africa
gnts_emz<-subset(calo, region=="Eastern Africa" & crop=="Maize")

 s3<-ggplot(gnts_emz, aes(x=period, y=calorie, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Consumption (kg/capita/yr)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=8),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  ggtitle("Eastern Africa: Maize")+
  theme(plot.title = element_text(hjust = 0.5))+
       theme(legend.position = c(.4, .5))
 s3

 ##### West Africa: Maize
 
 gnts_wmz<-subset(calo, region=="West Africa" & crop=="Maize")

 s4<-ggplot(gnts_wmz, aes(x=period, y=calorie, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Consumption (kg/capita/yr)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=8),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  ggtitle("West Africa: Maize")+
  theme(plot.title = element_text(hjust = 0.5))+
       theme(legend.position = c(.4, .7))
 s4

 gfg_comb <- s3+s4
gfg_comb

 ################### West Africa Sorghum Production line graph
  eg2<-ggplot(wst_4, aes(x=period, y=production, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Production (million tonnes)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=8),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  ggtitle("West Africa: Sorghum")+
  theme(plot.title = element_text(hjust = 0.5))+ theme(legend.position = "bottom")+
       theme(legend.position = c(.2, .7))
eg2

##################### Maize line graphs 
 
  mz1<-ggplot(gnuts_ea_1, aes(x=period, y=production, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Production (million tonnes)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=8),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  ggtitle("Eastern Africa: Maize")+
  theme(plot.title = element_text(hjust = 0.5))+
       theme(legend.position = c(.2, .7))
mz1

 ################### Sorghum Line graph
  eg1<-ggplot(gnuts_ea_3, aes(x=period, y=production, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Production (million tonnes)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=8),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  ggtitle("Eastern Africa: Sorghum")+
  theme(plot.title = element_text(hjust = 0.5))+ theme(legend.position = "bottom")+
       theme(legend.position = c(.2, .7))
eg1

#West Africa Maize line
mz2<-ggplot(wst_2, aes(x=period, y=production, group=country,shape=country)) +
  geom_line(aes(color=country))+
  geom_point(aes(color=country))+
  ylab("Production (million tonnes)")+
  xlab("")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,hjust=1,face="bold",color="black",size=8),
          axis.text.y=element_text(face="bold",color="black",size=8)) +
  ggtitle("West Africa: Maize")+
  theme(plot.title = element_text(hjust = 0.5))+
       theme(legend.position = c(.3, .7))
mz2

 gfg_comb_2 <- eg1+eg2
gfg_comb_2

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

 gfg_comb_3 <- mz1+mz2
gfg_comb_3

AVISA Production and Yield data Time Series

CHIPINDU, Lovemore (CIMMYT-Zimbabwe)

2022-11-22

R Markdown

Production

West Africa

East and West Africa Total Production

Yield

Crop Yield West Africa

Burkina Faso Calorie Consumption

Tanzania Calorie Consumption

Ethiopia Calorie Consumption

Ghana Calorie Consumption

Mali Calorie Consumption

Nigeria Calorie Consumption

Uganda Calorie Consumption

Imports and Exports Plots

Imports

Imports

Additional Species

Put the plot on the the area by row and column position.

Intergrating the plots , other option instead on patchwork package.

Consumption Trends

Gnuts Trends