Making three plots, one for each cultivar

Create three separate data sets; one for each cultivar

> fungicide.tidy.TwentyOneThirtySevenWheat <- fungicide.tidy[which(fungicide.tidy$Cultivar == "TwentyOneThirtySevenWheat" ), ]
> fungicide.tidy.CutterWheat <- fungicide.tidy[which(fungicide.tidy$Cultivar == "CutterWheat"), ]
> fungicide.tidy.JaggerWheat <- fungicide.tidy[which(fungicide.tidy$Cultivar == "JaggerWheat"), ]

Create a vector for the dates

> jdate <- fungicide.tidy.TwentyOneThirtySevenWheat[which(fungicide.tidy.TwentyOneThirtySevenWheat$Experiment == "fungicide"), "Julian.Date"]

Create vectors for each treatement and cultvar

> TwentyOneThirtySevenWheat.fungicide <- fungicide.tidy.TwentyOneThirtySevenWheat[which(fungicide.tidy.TwentyOneThirtySevenWheat$Experiment == "fungicide"), "Severity"]
> TwentyOneThirtySevenWheat.control <- fungicide.tidy.TwentyOneThirtySevenWheat[which(fungicide.tidy.TwentyOneThirtySevenWheat$Experiment == "control"), "Severity"]
> CutterWheat.fungicide <- fungicide.tidy.CutterWheat[which(fungicide.tidy.CutterWheat$Experiment == "fungicide"), "Severity"]
> CutterWheat.control <- fungicide.tidy.CutterWheat[which(fungicide.tidy.CutterWheat$Experiment == "control"), "Severity"]
> JaggerWheat.fungicide <- fungicide.tidy.JaggerWheat[which(fungicide.tidy.JaggerWheat$Experiment == "fungicide"), "Severity"]
> JaggerWheat.control <- fungicide.tidy.JaggerWheat[which(fungicide.tidy.JaggerWheat$Experiment == "control"), "Severity"]
> 
> par(mfrow = c(3, 1),
+     mar = c(2, 2, 2, 2),
+     lab = c(5, 5, 7))
> 
> plot(
+   TwentyOneThirtySevenWheat.fungicide ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "TwentyOneThirtySevenWheat",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "purple",
+   pch = 25,
+   ylim = c(0, 50)
+ )
> 
> points(
+   TwentyOneThirtySevenWheat.control ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "Control",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "red",
+   pch = 24,
+   ylim = c(0, 50)
+ )
> legend(
+   "topleft",
+   col = c("purple", "red"),
+   pch = c(25, 24),
+   legend = c("Fungicide", "Control")
+ )
> 
> 
> plot(
+   CutterWheat.fungicide ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "CutterWheat",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "purple",
+   pch = 25,
+   ylim = c(0, 50)
+ )
> points(
+   CutterWheat.control ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "Control",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "red",
+   pch = 24,
+   ylim = c(0, 50)
+ )
> legend(
+   "topleft",
+   col = c("purple", "red"),
+   pch = c(25, 24),
+   legend = c("Fungicide", "Control")
+ )
> 
> 
> 
> plot(
+   JaggerWheat.fungicide ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "JaggerWheat",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "purple",
+   pch = 25,
+   ylim = c(0, 50)
+ )
> points(
+   JaggerWheat.control ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "Control",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "red",
+   pch = 24,
+   ylim = c(0, 50)
+ )
> legend(
+   "topleft",
+   col = c("purple", "red"),
+   pch = c(25, 24),
+   legend = c("Fungicide", "Control")
+ )

Change the symbols so that they are “histogram-like”

> par(mfrow = c(3, 1),
+     mar = c(2, 2, 2, 2),
+     lab = c(5, 5, 7))
> 
> 
> plot(
+   TwentyOneThirtySevenWheat.fungicide ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "TwentyOneThirtySevenWheat",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "purple",
+   pch = 25,
+   ylim = c(0, 50),
+   type = "h"
+ )
> lines(
+   TwentyOneThirtySevenWheat.control ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "Control",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "red",
+   pch = 24,
+   ylim = c(0, 50),
+   type = "h"
+ )
> legend(
+   "topleft",
+   col = c("purple", "red"),
+   pch = c(25, 24),
+   legend = c("Fungicide", "Control")
+ )
> 
> 
> plot(
+   CutterWheat.fungicide ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "CutterWheat",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "purple",
+   pch = 25,
+   ylim = c(0, 50),
+   type = "h"
+ )
> lines(
+   CutterWheat.control ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "Control",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "red",
+   pch = 24,
+   ylim = c(0, 50),
+   type = "h"
+ )
> legend(
+   "topleft",
+   col = c("purple", "red"),
+   pch = c(25, 24),
+   legend = c("Fungicide", "Control")
+ )
> 
> 
> 
> plot(
+   JaggerWheat.fungicide ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "JaggerWheat",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "purple",
+   pch = 25,
+   ylim = c(0, 50),
+   type = "h"
+ )
> lines(
+   JaggerWheat.control ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "Control",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "red",
+   pch = 24,
+   ylim = c(0, 50),
+   type = "h"
+ )
> legend(
+   "topleft",
+   col = c("purple", "red"),
+   pch = c(25, 24),
+   legend = c("Fungicide", "Control")
+ )

Change the symbols to lines

> par(mfrow = c(3, 1),
+     mar = c(2, 2, 2, 2),
+     lab = c(5, 5, 7))
> 
> plot(
+   TwentyOneThirtySevenWheat.fungicide ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "TwentyOneThirtySevenWheat",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "purple",
+   pch = 25,
+   ylim = c(0, 50),
+   type = "l"
+ )
> lines(
+   TwentyOneThirtySevenWheat.control ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "Control",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "red",
+   pch = 24,
+   ylim = c(0, 50),
+   type = "l"
+ )
> legend(
+   "topleft",
+   col = c("purple", "red"),
+   pch = c(25, 24),
+   legend = c("Fungicide", "Control")
+ )
> 
> 
> plot(
+   CutterWheat.fungicide ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "CutterWheat",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "purple",
+   pch = 25,
+   ylim = c(0, 50),
+   type = "l"
+ )
> lines(
+   CutterWheat.control ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "Control",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "red",
+   pch = 24,
+   ylim = c(0, 50),
+   type = "l"
+ )
> legend(
+   "topleft",
+   col = c("purple", "red"),
+   pch = c(25, 24),
+   legend = c("Fungicide", "Control")
+ )
> 
> 
> 
> plot(
+   JaggerWheat.fungicide ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "JaggerWheat",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "purple",
+   pch = 25,
+   ylim = c(0, 50),
+   type = "l"
+ )
> lines(
+   JaggerWheat.control ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "Control",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "red",
+   pch = 24,
+   ylim = c(0, 50),
+   type = "l"
+ )
> legend(
+   "topleft",
+   col = c("purple", "red"),
+   pch = c(25, 24),
+   legend = c("Fungicide", "Control")
+ )

Change the symbols to points and lines

> pdf("results/Disease.Severity.Fungicide.vs.Control.pdf", width = 8)
> par(mfrow = c(3, 1),
+     mar = c(5, 5, 5, 5),
+     lab = c(5, 5, 7))
> 
> plot(
+   TwentyOneThirtySevenWheat.fungicide ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "TwentyOneThirtySevenWheat",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "purple",
+   pch = 25,
+   ylim = c(0, 50),
+   type = "b"
+ )
> lines(
+   TwentyOneThirtySevenWheat.control ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "Control",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "red",
+   pch = 24,
+   ylim = c(0, 50),
+   type = "b"
+ )
> legend(
+   "topleft",
+   col = c("purple", "red"),
+   pch = c(25, 24),
+   legend = c("Fungicide", "Control")
+ )
> 
> 
> plot(
+   CutterWheat.fungicide ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "CutterWheat",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "purple",
+   pch = 25,
+   ylim = c(0, 50),
+   type = "b"
+ )
> lines(
+   CutterWheat.control ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "Control",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "red",
+   pch = 24,
+   ylim = c(0, 50),
+   type = "b"
+ )
> legend(
+   "topleft",
+   col = c("purple", "red"),
+   pch = c(25, 24),
+   legend = c("Fungicide", "Control")
+ )
> 
> 
> 
> plot(
+   JaggerWheat.fungicide ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "JaggerWheat",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "purple",
+   pch = 25,
+   ylim = c(0, 50),
+   type = "b"
+ )
> lines(
+   JaggerWheat.control ~ jdate,
+   xlab = "Julian Date",
+   ylab = "Disease Severity",
+   main = "Control",
+   cex.lab = 1.5,
+   cex.main = 2,
+   col = "red",
+   pch = 24,
+   ylim = c(0, 50),
+   type = "b"
+ )
> legend(
+   "topleft",
+   col = c("purple", "red"),
+   pch = c(25, 24),
+   legend = c("Fungicide", "Control")
+ )
> 
> dev.off()

quartz_off_screen 
                2 

Reset par at the end so that none of the bells and whistles specified in previous graphs are carried foward to the next graph

> par()

$xlog
[1] FALSE

$ylog
[1] FALSE

$adj
[1] 0.5

$ann
[1] TRUE

$ask
[1] FALSE

$bg
[1] "white"

$bty
[1] "o"

$cex
[1] 1

$cex.axis
[1] 1

$cex.lab
[1] 1

$cex.main
[1] 1.2

$cex.sub
[1] 1

$cin
[1] 0.15 0.20

$col
[1] "black"

$col.axis
[1] "black"

$col.lab
[1] "black"

$col.main
[1] "black"

$col.sub
[1] "black"

$cra
[1] 10.8 14.4

$crt
[1] 0

$csi
[1] 0.2

$cxy
[1] 0.01932990 0.03875969

$din
[1] 9 7

$err
[1] 0

$family
[1] ""

$fg
[1] "black"

$fig
[1] 0 1 0 1

$fin
[1] 9 7

$font
[1] 1

$font.axis
[1] 1

$font.lab
[1] 1

$font.main
[1] 2

$font.sub
[1] 1

$lab
[1] 5 5 7

$las
[1] 0

$lend
[1] "round"

$lheight
[1] 1

$ljoin
[1] "round"

$lmitre
[1] 10

$lty
[1] "solid"

$lwd
[1] 1

$mai
[1] 1.02 0.82 0.82 0.42

$mar
[1] 5.1 4.1 4.1 2.1

$mex
[1] 1

$mfcol
[1] 1 1

$mfg
[1] 1 1 1 1

$mfrow
[1] 1 1

$mgp
[1] 3 1 0

$mkh
[1] 0.001

$new
[1] FALSE

$oma
[1] 0 0 0 0

$omd
[1] 0 1 0 1

$omi
[1] 0 0 0 0

$page
[1] TRUE

$pch
[1] 1

$pin
[1] 7.76 5.16

$plt
[1] 0.09111111 0.95333333 0.14571429 0.88285714

$ps
[1] 12

$pty
[1] "m"

$smo
[1] 1

$srt
[1] 0

$tck
[1] NA

$tcl
[1] -0.5

$usr
[1] 0 1 0 1

$xaxp
[1] 0 1 5

$xaxs
[1] "r"

$xaxt
[1] "s"

$xpd
[1] FALSE

$yaxp
[1] 0 1 5

$yaxs
[1] "r"

$yaxt
[1] "s"

$ylbias
[1] 0.2