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  #                                                            #
  # A Script for the Analysis of:                              #
  # Echinacea pallida and Echinacea angustifolia               #
  # reciprical crosses performed during the summer of 2011     #
  #                                                            #
  # Second Version                                             #
  #                                                            #
  ##############################################################
  #                                                            #
  # @Author: Nicholas Goldsmith                                #
  # @Professor: Stuart Wagenius                                #
  # @Collaborators:                                            #
  # @Date 2 August 2011                                        #
  #                                                            #
  ##############################################################
  #                                                            #
  # Table of Contents:                                         #
  # 1) Importing the Data                                      #
  # 2) The Data                                                #
  # 3) Questions for the Data                                  #
  # . Examining these questions, A through E                   #
  #                                                            #
  ##############################################################
  
  # 1) Importing the Data
  crossData <- read.csv("http://blog.lib.umn.edu/wage0005/echinacea/CSV_recip_Crosses.csv")
  
  # 2) The Data
  #crossData$Pallida = E. pallida ID (Ex. PAL1001)
  #crossData$Angustifolia = E. angustifolia ID (Ex. 18_967)
  #crossData$PalColor = color the bracts on E. pallida was painted (Ex. AQA)
  #crossData$PalColorDate = Date the E. pallida bracts were painted
  #crossData$PalNumBract = Number of E. pallida bracts painted
  #crossData$PalDateCross = Date the E. pallida was pollinated
  #crossData$PalnumCross = Number of styles pollinated
  #crossData$PalNumShrivel = Number of E. pallida styles that shriveled
  #crossData$PalPercentShrivel = Percentage of E. pallida styles that shriveled
  #crossData$PalComp = Compatability of the cross with E. pallida as the maternal plant with: 0 = incompatible, 1 = compatible, 99 = unsure
  #crossData$AngColor = color the bracts on E. angustifolia was painted (Ex. AQA)
  #crossData$AngColorDate = Date the E. angustifolia bracts were painted
  #crossData$AngNumBract = Number of E. angustifolia bracts painted
  #crossData$AngDateCross = Date the E. angustifolia was pollinated
  #crossData$AngnumCross = Number of styles pollinated
  #crossData$AngNumShrivel = Number of E. angustifolia styles that shriveled
  #crossData$AngPercentShrivel = Percentage of E. angustifolia styles that shriveled
  #crossData$AngComp = Compatability of the cross with E. angustifolia as the maternal plant with: 0 = incompatible, 1 = compatible, 99 = unsure
  
  # 3) Questions for the data
  # a. Does E. pallida cause shriveling in E. angustifolia?
  # a.a ) Does E. angustifolia cause shriveling in E. pallida?
  # b. Is there evidence of S alleles in common between the two species?
  # c. Is there are difference in compatability between the two species depending on which one is maternal/paternal?
  # d. Are certain E. pallida plants more likely to be compatible maternal plants than others?
  # e. Are certain E. pallida plants more likely to be compatible paternal plants than others?
  
  # A) Does E. pallida cause shriveling in E. angustifolia?
  windows() #Makes a window for the historgram
  hist(crossData$AngPercentShrivel, breaks=seq(0,100,by=((100)*(1/3))), xlab="Percent styles shriveling", main="Style shriveling in Echinacea angustifolia") #Histogram when E. angustolia is the maternal plant
  
  # A.a) Does E. angustifolia cause shriveling in E. pallida?
  windows() #Makes a window for the histogram
  hist(crossData$PalPercentShrivel, breaks=seq(0,100,by=((100)*(1/3))), xlab="Percent styles shriveling", main="Style shriveling in Echinacea pallida") #Histogram when E. pallida is the maternal plant
  
  # B) Is there evidence of S alleles in common between the two species?
  # The histograms showing the shriveling occurs also appears to show this, right?
  
  # C) Is there are difference in compatability between the two species depending on which one is maternal/paternal?
  crossPalSubset <- subset(crossData, PalComp != 99)
  crossAngSubset <- subset(crossData, AngComp != 99)
  #table(crossPalSubset$PalComp,crossAngSubset$AngComp)
  #chisq.test(table(crossPalSubset$PalComp,crossAngSubset$AngComp))
  #In the following series of steps I will get the number of compatible and incompatible crosses for each species
  numPalComp <- subset (crossData, PalComp == 1)
  palAndComp = length(numPalComp$PalComp)
  numAngComp <- subset(crossData, AngComp == 1)
  angAndComp = length(numAngComp$AngComp)
  numPalIncomp <- subset (crossData, PalComp == 0)
  palAndIncomp = length(numPalIncomp$PalComp)
  numAngIncomp <- subset (crossData, AngComp == 0)
  angAndIncomp = length(numAngIncomp$AngComp)
  #constructing a matrix with this information
  compTable <- matrix (c(palAndComp, angAndComp, palAndIncomp, angAndIncomp), ncol=2, byrow=TRUE)
  rownames(compTable)<-c("Compatible", "Incompatible")
  colnames(compTable)<-c("E. pallida", "E. angustifolia")
  compTable
  #Performing the Chi Squared
  chisq.test(compTable)
  
  # D) Are certain E. pallida plants more likely to be compatible maternal plants than others?
  table(crossPalSubset$Pallida,crossPalSubset$PalComp)
  fisher.test(table(crossPalSubset$Pallida,crossPalSubset$PalComp))
  
  # E) Are certain E. pallida plants more likely to be compatible paternal plants than others?
  table(crossAngSubset$Pallida,crossAngSubset$AngComp)
  fisher.test(table(crossAngSubset$Pallida,crossAngSubset$AngComp))