library(ggplot2)
#ggplot2 makes the distribution curve graphs
library(car)
#not sure what car does but I think it works with lattices
library(splitstackshape)
#splitstackshape is an easy package that can help you split columns that have delimiters,
#Original CSV file column labelled "Tray" had entries that needed to be split
picsize5=read.csv('ImageJsize4.csv')
#creates dataframe and reads in the CSV file for sizes
picsize6<-concat.split.multiple(picsize5, "Tray", " ")
#splits the Tray column into Tray_1 with Site Number and Tray_2 with Tray number
foys<-subset(picsize6, Date=="2/26/2014"& Site=="Oyster Bay")
#creates a subset data frame for just the size data from February 26th at Oyster Bay
ggplot(foys, aes(x=Length.mm))+geom_density(aes(group=Tray_1, colour=Tray_1, fill=Tray_1),alpha=0.3)
#creates distribution graph overlays for all populations in Feb at Oyster Bay. Looks cool.
fman<-subset(picsize6, Date=="2/26/2014"& Site=="Manchester")
ggplot(fman, aes(x=Length.mm))+geom_density(aes(group=Tray_1, colour=Tray_1, fill=Tray_1),alpha=0.3)
ffid<-subset(picsize6, Date=="2/28/2014"&Site=="Fidalgo")
ggplot(ffid, aes(x=Length.mm))+geom_density(aes(group=Tray_1, colour=Tray_1, fill=Tray_1),alpha=0.3)
#ffid and fman are just repeating the same subset dataframe command
#and then creating distribution overlay graphs for each site
picsize7=read.csv('imagejsizefixed1.csv')
picsize8<-concat.split.multiple(picsize7, "Tray", " ")
endoys<-subset(picsize8, Date %in% c("7/24/2014", "7/31/2014","8/7/2014","8/14/2014"))
ggplot(endoys, aes(x=Length.mm))+geom_density(aes(group=Tray_1, colour=Tray_1, fill=Tray_1),alpha=0.3)
endfid<-subset(picsize8, Date %in% c("7/25/2014","8/1/2014","8/8/2014","8/15/2014"))
ggplot(endfid, aes(x=Length.mm))+geom_density(aes(group=Tray_1, colour=Tray_1, fill=Tray_1),alpha=0.3)+scale_colour_manual(values=c("#3366CC","#CC66CC","#FF9900"))+scale_colour_fill(values=c("#3366CC","#CC66CC","#FF9900"))
fidn<-subset(picsize8, Site %in% c("Fidalgo","fidalgo")& Tray_1=="2N")
ggplot(fidn, aes(x=Length.mm))+geom_density(aes(group=Date, colour=Date),alpha=0.3)
fidsize<-subset(picsize8, Site %in% c("Fidalgo","fidalgo"))
ggplot(fidsize, aes(x=Length.mm))+geom_density(aes(group=Date, colour=Date),alpha=0.3)+facet_wrap(~Tray_1, ncol=1)
ggplot(mansize, aes(x=Length.mm))+geom_density(aes(group=Tray_1, colour=Tray_1),alpha=0.3)+facet_wrap(~Date, ncol=3)+scale_colour_manual(values=c("#3366CC","#CC66CC","#FF9900"))+scale_fill_manual(values=c("#3366CC","#CC66CC","#FF9900"))
endman<-subset(picsize6, Date == "7/23/2014"| Date == "7/30/2014"| Date=="8/6/2014"|Date=="8/13/2014")
ggplot(endman, aes(x=Length.mm))+geom_density(aes(group=Tray_1, colour=Tray_1, fill=Tray_1),alpha=0.3)+scale_colour_manual(values=c("#3366CC","#CC66CC","#FF9900"))+scale_fill_manual(values=c("#3366CC","#CC66CC","#FF9900"))+ggtitle('End of Summer\nManchester Size Distribution')
endoys<-subset(picsize6, Date %in% c("7/24/2014", "7/31/2014","8/7/2014","8/14/2014"))
ggplot(endoys, aes(x=Length.mm))+geom_density(aes(group=Tray_1, colour=Tray_1, fill=Tray_1),alpha=0.3)+scale_colour_manual(values=c("#3366CC","#CC66CC","#FF9900"))+scale_fill_manual(values=c("#3366CC","#CC66CC","#FF9900"))+ggtitle('End of Summer\nOyster Bay Size Distribution')
endfid<-subset(picsize6, Date %in% c("7/25/2014","8/1/2014","8/8/2014","8/15/2014"))
ggplot(endfid, aes(x=Length.mm))+geom_density(aes(group=Tray_1, colour=Tray_1, fill=Tray_1),alpha=0.3)+scale_colour_manual(values=cou)+scale_fill_manual(values=c("#3366CC","#CC66CC","#FF9900"))+ggtitle('End of Summer\nFidalgo Size Distribution')
ggplot(fidsize, aes(x=Length.mm))+geom_density(aes(group=Date, colour=Date),alpha=0.3)+facet_wrap(~Tray_1, ncol=1)
ggplot(fidsize, aes(x=Length.mm))+geom_density(aes(group=Date, colour=Date, fill=Tray_1),alpha=0.3)+facet_wrap(~Tray_1, ncol=1)
ggplot(fidsize, aes(x=Length.mm))+geom_density(aes(group=Date, colour=Date),alpha=0.3)+facet_wrap(~Tray_1, ncol=1)
mansize<-subset(picsize8, Site %in% c("Manchester","manchester"))
ggplot(mansize, aes(x=Length.mm))+geom_density(aes(group=Date, colour=Date),alpha=0.3)+facet_wrap(~Tray_1, ncol=1)
oyssize<-subset(picsize8, Site %in% c("Oyster Bay","oyster bay"))
ggplot(oyssize, aes(x=Length.mm))+geom_density(aes(group=Date, colour=Date),alpha=0.3)+facet_wrap(~Tray_1, ncol=1)
ggplot(mansize, aes(x=Length.mm))+geom_density(aes(group=Tray_1, colour=Tray_1),alpha=0.3)+facet_wrap(~Date, ncol=3)+scale_colour_manual(values=c("#3366CC","#CC66CC","#FF9900"))+scale_fill_manual(values=c("#3366CC","#CC66CC","#FF9900"))
ggplot(oyssize, aes(x=Length.mm))+geom_density(aes(group=Tray_1, colour=Tray_1),alpha=0.3)+facet_wrap(~Date, ncol=3)+scale_colour_manual(values=c("#3366CC","#CC66CC","#FF9900"))+scale_fill_manual(values=c("#3366CC","#CC66CC","#FF9900"))
oyssize<-subset(picsize8, Site %in% c("Oyster Bay","oyster bay", "Oyster bay"))
ggplot(oyssize, aes(x=Length.mm))+geom_density(aes(group=Tray_1, colour=Tray_1),alpha=0.3)+facet_wrap(~Date, ncol=3)+scale_colour_manual(values=c("#3366CC","#CC66CC","#FF9900"))+scale_fill_manual(values=c("#3366CC","#CC66CC","#FF9900"))
ggplot(fidsize, aes(x=Length.mm))+geom_density(aes(group=Tray_1, colour=Tray_1),alpha=0.3)+facet_wrap(~Date, ncol=3)+scale_colour_manual(values=c("#3366CC","#CC66CC","#FF9900"))+scale_fill_manual(values=c("#3366CC","#CC66CC","#FF9900"))
outoys<-subset(outplant1, Site=="Oyster Bay")
ggplot(outoys, aes(x=Size))+geom_density(aes(group=Tray_1, colour=Tray_1, fill=Tray_1),alpha=0.3)+scale_colour_manual(values=c("#3366CC","#CC66CC","#FF9900"))+scale_fill_manual(values=c("#3366CC","#CC66CC","#FF9900"))+ggtitle("Outplant\nOyster Bay Size Distribution")+labs(x="Length.mm")
outfid<-subset(outplant1, Site=="Fidalgo")
ggplot(outfid, aes(x=Size))+geom_density(aes(group=Tray_1, colour=Tray_1, fill=Tray_1),alpha=0.3)+scale_colour_manual(values=c("#3366CC","#CC66CC","#FF9900"))+scale_fill_manual(values=c("#3366CC","#CC66CC","#FF9900"))+ggtitle("Outplant\nFidalgo Size Distribution")+labs(x="Length.mm")
outman<-subset(outplant1, Site=="Manchester")
ggplot(outman, aes(x=Size))+geom_density(aes(group=Tray_1, colour=Tray_1, fill=Tray_1),alpha=0.3)+scale_colour_manual(values=c("#3366CC","#CC66CC","#FF9900"))+scale_fill_manual(values=c("#3366CC","#CC66CC","#FF9900"))+ggtitle("Outplant\nManchester Size Distribution")+labs(x="Length.mm")
outendoys<-merge(endoys, outoys, by="Site")
ggplot(aes(endoys,x=Length.mm)+(outoys,x=Size))+geom_density(aes(group=Tray_1, colour=Tray_1),alpha=0.3)+facet_wrap(~Tray_1, ncol=1)+scale_colour_manual(values=c("#3366CC","#CC66CC","#FF9900"))+scale_fill_manual(values=c("#3366CC","#CC66CC","#FF9900"))
ggplot()+geom_density(data=outoys, aes(x=Length.mm, group=Tray_1, colour=Tray_1, fill=Tray_1),alpha=0.3)+geom_density(data=endoys, aes(x=Length.mm, group=Tray_1, colour=Tray_1, fill=Tray_1),alpha=0.3)+scale_colour_manual(values=c("#3366CC","#CC66CC","#FF9900"))+scale_fill_manual(values=c("#3366CC","#CC66CC","#FF9900"))+ggtitle("Size Comparison\nAugust 2013 vs. August 2014")
ggplot(mansize, aes(Date,Length.mm, group=Tray_1, color=Tray_1))+geom_point()+geom_smooth(method=lm)+scale_colour_manual(values=c("#3366CC","#CC66CC","#FF9900"))
endoys$Date<-as.Date(endoys$Date, "%m/%d/%Y")
outoys$Date<-as.Date(outoys$Date, "%m/%d/%Y")
mansize$Date<-as.Date(mansize$Date, "%m/%d/%Y")