course edits from Dec 2015

Author: markdunning

day1.Rmd

@@ -1332,23 +1332,23 @@ plot(patients$Age,patients$Weight,main="Relationship between Weight and Age")
 
 - Adding the x-axis label
 ```{r,fig.height=5}
-plot(patients$Age,patients$Weight,xlab="Weight")
+plot(patients$Age,patients$Weight,xlab="Age")
 ```
 
 ## Simple customisations
 - Adding the y-axis label
 
 ```{r,fig.height=5}
-plot(patients$Age,patients$Weight,ylab="Age")
+plot(patients$Age,patients$Weight,ylab="Weight")
 ```
 
 ## Simple customisations
 - We can specifiy multiple arguments at once
     + here `ylim` and `xlim` are used to specify axis limits
 ```{r,fig.height=5}
 plot(patients$Age,patients$Weight,
-     ylab="Age",
-     xlab="Weight",
+     ylab="Weight",
+     xlab="Age",
      main="Relationship between Weight and Age",
      xlim=c(10,70),
      ylim=c(60,80))
@@ -1508,18 +1508,6 @@ display.brewer.all()
 boxplot(weather$Ozone~weather$Month,col=brewer.pal(5,"Set1"))
 ```
 
-## And finally..
-
-```{r eval=FALSE}
-library(palettetown)
-boxplot(weather$Ozone~weather$Month,col=pokepal("Pikachu",5))
-```
-
-```{r echo=FALSE, message=FALSE,fig.height=5}
-if(!require(palettetown)) install.packages("palettetown")
-library(palettetown)
-boxplot(weather$Ozone~weather$Month,col=pokepal("Pikachu",5))
-```
 
 
 

day1.html

@@ -259,6 +259,7 @@ dev.off()
 ```
 
 - pdf is a good choice for publication as they can be imported into photoshop, inkscape etc
+    - sometimes it is easier to edit in these tools than R!
 
 ## Exporting graphs from RStudio
 
@@ -469,15 +470,15 @@ points(80, dnorm(80, mean=tempMean,sd=tempSD),col="red",pch=16)
     ```{r eval=FALSE}
 xs <- c(50,60,70,80,90,100)
 ys <- dnorm(xs, mean=tempMean,sd=tempSD)
-lines(xs,ys,col="red",pch=16)
+lines(xs,ys,col="red")
 ```
 
 ```{r fig.height=4,echo=FALSE}
 hist(weather$Temp,col="purple",xlab="Temperature",
      main="Distribution of Temperature",breaks = 50:100,freq=FALSE)
 xs <- c(50,60,70,80,90,100)
 ys <- dnorm(xs, mean=tempMean,sd=tempSD)
-lines(xs,ys,col="red",pch=16)
+lines(xs,ys,col="red")
 ```
 
 
@@ -490,7 +491,7 @@ lines(xs,ys,col="red",pch=16)
 ```{r eval=FALSE}
 xs <- seq(50,100,length.out = 10000)
 ys <- dnorm(xs, mean=tempMean,sd=tempSD)
-lines(xs,ys,col="red",pch=16)
+lines(xs,ys,col="red")
 ```
 
 
@@ -500,7 +501,7 @@ hist(weather$Temp,col="purple",xlab="Temperature",
      main="Distribution of Temperature",breaks = 50:100,freq=FALSE)
 xs <- seq(50,100,length.out = 10000)
 ys <- dnorm(xs, mean=tempMean,sd=tempSD)
-lines(xs,ys,col="red",pch=16)
+lines(xs,ys,col="red")
 ```
 
 ## Simple testing
@@ -706,6 +707,12 @@ plot(weather$Temp, weather$Ozone,pch=16)
 abline(mod1,col="red",lty=2)
 ```
 
+## Word of caution
+
+***Correlation != Causation***
+![spurious](images/spurious.png)
+
+http://tylervigen.com/spurious-correlations
 
 # 3. Data Manipulation Techniques