agridat: Agricultural Datasets

# summerby.multi.uniformity.R

# The Excel workbook tab labeled 20x100 links is for the larger-plot data
# and is not included in agridat

libs(agridat,desplot,dplyr,lattice,readxl,reshape2,rio)

setwd("c:/drop/rpack/agridat/data-raw")

d1 <- read_excel("summerby.multi.uniformity.xlsx","r222", col_names=FALSE)
d2 <- read_excel("summerby.multi.uniformity.xlsx","r223", col_names=FALSE)
d3 <- read_excel("summerby.multi.uniformity.xlsx","r224", col_names=FALSE)
d4 <- read_excel("summerby.multi.uniformity.xlsx","r225", col_names=FALSE)
d5 <- read_excel("summerby.multi.uniformity.xlsx","r226", col_names=FALSE)
d6 <- read_excel("summerby.multi.uniformity.xlsx","r322", col_names=FALSE)
d7 <- read_excel("summerby.multi.uniformity.xlsx","r324", col_names=FALSE)
d8 <- read_excel("summerby.multi.uniformity.xlsx","r323", col_names=FALSE)
d9 <- read_excel("summerby.multi.uniformity.xlsx","r326", col_names=FALSE)
d10 <- read_excel("summerby.multi.uniformity.xlsx","r425", col_names=FALSE)
d11 <- read_excel("summerby.multi.uniformity.xlsx","r424", col_names=FALSE)
d12 <- read_excel("summerby.multi.uniformity.xlsx","r425", col_names=FALSE)
d13 <- read_excel("summerby.multi.uniformity.xlsx","r525", col_names=FALSE)
d14 <- read_excel("summerby.multi.uniformity.xlsx","r524", col_names=FALSE)
d15 <- read_excel("summerby.multi.uniformity.xlsx","r527", col_names=FALSE)
d16 <- read_excel("summerby.multi.uniformity.xlsx","r526", col_names=FALSE)

d1 %<>% as.matrix %>% `colnames<-`(1:ncol(d1)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R2",year=1922,crop="maize")
d2 %<>% as.matrix %>% `colnames<-`(1:ncol(d2)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R2",year=1923,crop="maize")
d3 %<>% as.matrix %>% `colnames<-`(1:ncol(d3)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R2",year=1924,crop="maize")
d4 %<>% as.matrix %>% `colnames<-`(1:ncol(d4)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R2",year=1925,crop="maize")
d5 %<>% as.matrix %>% `colnames<-`(1:ncol(d5)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R2",year=1926,crop="maize")
d6 %<>% as.matrix %>% `colnames<-`(1:ncol(d6)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R3",year=1922,crop="oats")
d7 %<>% as.matrix %>% `colnames<-`(1:ncol(d7)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R3",year=1924,crop="oats")
d8 %<>% as.matrix %>% `colnames<-`(1:ncol(d8)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R3",year=1923,crop="oats")
d9 %<>% as.matrix %>% `colnames<-`(1:ncol(d9)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R3",year=1926,crop="oats")
d10 %<>% as.matrix %>% `colnames<-`(1:ncol(d10)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R4",year=1925,crop="alfalfa")
d11 %<>% as.matrix %>% `colnames<-`(1:ncol(d11)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R4",year=1924,crop="alfalfa")
d12 %<>% as.matrix %>% `colnames<-`(1:ncol(d12)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R4",year=1926,crop="mangels")
d13 %<>% as.matrix %>% `colnames<-`(1:ncol(d13)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R5",year=1925,crop="oats")
d14 %<>% as.matrix %>% `colnames<-`(1:ncol(d14)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R5",year=1924,crop="oats")
d15 %<>% as.matrix %>% `colnames<-`(1:ncol(d15)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R5",year=1927,crop="mangels")
d16 %<>% as.matrix %>% `colnames<-`(1:ncol(d16)) %>% melt %>% rename(col=Var1,row=Var2,yield=value) %>% mutate(range="R5",year=1926,crop="oats")

dat <- dplyr::bind_rows(d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16)
head(dat)

# Adjust row numbers so that they are similar to the layout on p. 8
# and page 13 of Summerby
dat <- mutate(dat,
              row = ifelse(range=="R5", row+18, row),
              row = ifelse(range=="R4", row+12, row),
              row = ifelse(range=="R3", row+6, row) )

# Export

summerby.multi.uniformity <- dat
kw::agex(summerby.multi.uniformity)

## ---------------------------------------------------------------------------

dat <- summerby.multi.uniformity

libs(desplot)
dat <- mutate(dat, env=paste(range, year, crop))
desplot(dat, yield ~ col*row|env, aspect=(5*20)/(35*20))
qqmath( ~ yield|env, data=dat)

# Show all ranges for a single year.
dat %>% filter(year==1924) %>% desplot(yield ~ col*row, aspect=23/35, main="1924")

# Compare the variance for each dataset in Summerby, page 18, column (a)
# with what we calculate.  Very slight differences.
# libs(dplyr)
# dat %>% group_by(range,year) %>% summarize(var=var(yield))
## range  year       var  summerby
##  1 R2     1922  82404      82404
##  2 R2     1923 254780.    254780  
##  3 R2     1924 111978.    111978  
##  4 R2     1925  84515.     84515  
##  5 R2     1926 101008.    100960  
##  6 R3     1922 185031.    185031  
##  7 R3     1923 154777.    154784
##  8 R3     1924 252451.    252451  
##  9 R3     1926 472087.    472088  
## 10 R4     1924     19.3       19.341 
## 11 R4     1925     14.2       14.234 
## 12 R4     1926     14.2       14.236 
## 13 R5     1924 134472.    134472  
## 14 R5     1925 289001.    289026  
## 15 R5     1926 131714.    131714  
## 16 R5     1927      8.62       8.622