{
    "contents" : "#Name: Jake Heare\n#Assignment 2\n\n#Q1\n#q1a\nrequire(plyr)\nhead(beaver1)\n?beaver1\nbeavmeanin<-ddply(beaver1,.(activ),summarise, mean_temp=mean(temp,na.rm=T))\n#q1b\nrequire(ggplot2)\nrequire(scales)\nbeaver1$obs<-1:nrow(beaver1)\nggplot(data=beaver1, aes(x=obs,y=temp))+\n  geom_line()+\n  geom_point(aes(obs[activ==1],temp[activ==1]),color=\"Green\",size=5)+\n  theme_bw()+\n  theme(axis.text.x=element_text(size=20),\n                   axis.text.y=element_text(angle=90, size=20,hjust=0.5))+\n  scale_y_continuous(breaks=c(36.4,36.6,36.8,37.0,37.2,37.4))+\n  scale_x_continuous(breaks=c(1,20,40,60,80,100,114))+\n  theme(plot.background=element_blank(),\n        panel.grid.major=element_blank(),\n        panel.grid.minor=element_blank(),\n        plot.title=element_text(size=25,vjust=2,lineheight=0.6,face=\"bold\"),\n        axis.title.x=element_text(size=20,vjust=-0.5),\n        axis.title.y=element_text(size=20,vjust=2))+\n  labs(x=\"observation #\",y=\"temperature\")+\n  ggtitle(\"Beaver 1 body temperature\")+\n  geom_hline(aes(yintercept=36.84213,linetype=\"inside mean temperature\"),\n             color=\"gray\",show_guide=TRUE)+\n  geom_hline(aes(yintercept=37.22333,linetype=\"ouside mean temperature\"),\n             color=\"gray\",show_guide=TRUE)+\n  scale_linetype_manual(name=NULL,\n                        labels=c(\"inside mean temperature\",\"ouside mean temperature\"),\n                        values=c(\"inside mean temperature\"=2,\"ouside mean temperature\"=3),\n                        guide=guide_legend(title=NULL,))+\n  theme(legend.position=c(0.25,0.93),legend.text=element_text(size=20))+\n  annotate(geom=\"text\",x=95,y=36.3,label=\"Plotted by the hands of Jake Heare\", size=5)\n#q1c\nbeaver1b<-rbind(beaver1[1:82,],c(346,2220,37.3,1,83),beaver1[83:nrow(beaver1),])\nbeaver1b$obs<-1:nrow(beaver1b)\n#q1d\nbeavbmeanin<-ddply(beaver1b,.(activ),summarise, mean_temp=mean(temp,na.rm=T))\noutdiff<-beavmeanin$mean_temp[beavmeanin$activ==1]-beavbmeanin$mean_temp[beavbmeanin$activ==1]\noutdiff\n\n#Q2\n#q2a\nlibrary(MASS)\nhead(crabs)\nmeanlobecrab<-ddply(crabs,.(sp),summarise, mean_size=mean(FL,na.rm=T))\nsdlobecrab<-ddply(crabs,.(sp),summarise, sd_size=sd(FL,na.rm=T))\nmeanlobecrab\nsdlobecrab\n#q2b\nspsex<-crabs$sp:crabs$sex\n#this shows the combination of specie and sex for every entry in the data frame. \n#q2c\nlevels(spsex)[1:4]<-c(\"B:F\"=\"Blue Female\", \"B:M\"=\"Blue Male\", \"O:F\"=\"Orange Female\",\"O:M\"=\"Orange Male\")\nspsex\n#q2d\nmeanlobecrab2<-ddply(crabs,.(spsex),summarise, mean_size=mean(FL,na.rm=T))\nmeanlobecrab2\n#q2e\ncrab.counts<-table(spsex)\n#q2f\nggplot()+geom_bar(data=meanlobecrab2,aes(x=spsex,y=mean_size,color=spsex,fill=spsex),\n                  stat=\"identity\")+\n  ggtitle(\"Frontal Lobe Size\\nby Species/Sex\")+\n  labs(x=\"Species/Sex\",y=\"Average Size of Frontal Lobe\")+\n  theme_bw()+\n  theme(legend.position=c(0.1,0.85))\n \n",
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