HW2 (resubmitted)

README.md

@@ -84,12 +84,12 @@ Students will have the opportunity to work in small teams to create data visuali
 Your assignments will be submitted as pull requests to the class repository on github! Suppose you saved changes on your own `gh-pages` branch and would like to submit a ‘clean’ pull request with only your files and the commits you want. This is pretty easy.
 
 ### Option 1: Basic way with file checkouts (losing history):
-	git checkout upstream/gh-pages #you will be on a ‘detached HEAD’  
+	git checkout upstream/master #you will be on a ‘detached HEAD’  
 	git checkout -b hw1 #checkout a new branch called 'hw1'  
 	git checkout <branch> <folder/filename> #pluck a folder/file from another branch but stay on the current branch (in this case 'hw1').  
 	git add <folder/filename>
 	git commit -m "add only the right files on new clean branch"
-	git push -u hw1 #push commits to a new branch called hw1.
+	git push -u origin hw1 #push commits to a new branch called hw1.
 
 Your new `hw1` branch now has a copy of the folder/file(s) your plucked from elsewhere. Your working tree is still on the 'hw1' branch and you can continue to work on the files and commit+push further changes as frequently as you like.
 

ebola/2015-03-02-MinSangHee-HW2.Rmd

@@ -0,0 +1,84 @@
+---
+title: "20150302-SangheeMin-HW2"
+author: "Sang-Hee Min"
+date: "March 2, 2015"
+output: html_document
+---
+
+This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+
+When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
+
+```{r}
+getwd()
+setwd("~/data-viz/ebola")
+getwd()
+library(ggplot2)
+library(scales)
+
+##Read in data:
+germs <- read.csv(file="Microbe-scope-bugs.csv", header=TRUE)
+
+# assign descriptive column names where absent
+names(germs)[1]<-"germ"
+
+# how could you do this more carefully???
+# names(germs)[10]<-"yearly.fatalities.rounded"
+# names(germs)[11]<-"yearly.fatalities.raw"
+
+# keep only data columns, exclude notes/links
+notes <- germs[1, ] # save the notes?
+germs <- germs[-1, ] # remove **row** of notes
+# germs <- germs[, c(2, 4:7, 9:11)] # keep data **columns** only
+# how could you do this more carefully??? e.g. remove the columns you intend to remove.
+
+# how about something like this?
+notes <- grep(pattern="note", x=names(germs), ignore.case=TRUE)
+names(germs)[notes] # double check we got the right columns```
+
+germs <- subset(germs, select = -notes) # apply filter.
+
+# any more columns we want to omit?
+
+# remove percent signs
+dropPct<-function(germs, case.fatality.rate){
+        dropPct<-strsplit(as.character(germs[[case.fatality.rate]]), split="%")
+        germs[[case.fatality.rate]]<-as.numeric(dropPct)
+        return(germs[[case.fatality.rate]])}
+
+# remove % signs, leaving a numeric value.
+germs[["case.fatality.rate"]]<-dropPct(germs, "case.fatality.rate")
+
+# Convert basic reproductive rate from factor to numeric
+germs$average.basic.reproductive.rate <- as.numeric(as.character(germs$average.basic.reproductive.rate))
+
+germs <- subset(germs, primary.mode.of.transmission != "")
+
+germs <- germs[,c(1:4)]
+
+germs <- germs[complete.cases(germs),]
+
+plot <- ggplot(germs,aes(x=average.basic.reproductive.rate,y=case.fatality.rate,group =primary.mode.of.transmission,colour=primary.mode.of.transmission)) + geom_point(size=6)
+print(plot)
+
+plot <- ggplot(germs,aes(x=average.basic.reproductive.rate,y=case.fatality.rate,group =primary.mode.of.transmission,colour=primary.mode.of.transmission)) + geom_point(size=1)
+print(plot)
+
+plot <- ggplot(germs,aes(x=average.basic.reproductive.rate,y=case.fatality.rate,group =primary.mode.of.transmission,colour=primary.mode.of.transmission)) + geom_point(size=3)
+print(plot)
+
+germs <- subset(germs, germ != "Malaria (P. falciparum)")
+
+plot <- ggplot(germs,aes(x=average.basic.reproductive.rate,y=case.fatality.rate,group =primary.mode.of.transmission,colour=primary.mode.of.transmission)) + geom_point(size=2)
+print(plot)
+
+plot <- plot + 
+  scale_color_discrete(name="Primary Mode of Transmission") + 
+  ggtitle("The Microbe-scope") + 
+  scale_x_continuous("CONTAGIOUSNESS: average basic reproduction rate (R0), # people one person will likely infect", limits=c(0, 20), breaks=c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20), labels=c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20), expand = c(0,0)) + 
+  scale_y_log10("DEADLINESS: case fatality rate (%)", limits=c(.01, 150), breaks=c(0.1, 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200), labels=c(0.1, 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200), expand=c(0,0)) + 
+  theme_bw(base_size=12) + 
+  geom_text(aes(label=germ, hjust = 0.15, vjust=-0.75, angle = 10), size=2)
+print(plot)
+
+#having problems with the annotation...