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--- rworkshop8 [2014/11/02 20:54]
johannabradie
+++ rworkshop8 [2014/11/03 11:18] (current)
johannabradie
@@ Line 11: / Line 11: @@
 Download the R script and data for this lesson:
--- NEED TO PUT R SCRIPT AND DATA HERE
+[[http://qcbs.ca/wiki/_media/co2_good.csv|CO2 Dataset]]
@@ Line 25: / Line 26: @@
 ===== Flow Control =====
-. Execute statements **conditionally** using:
+Flow control allows you to run the same series of commands multiple times and subject to specified conditions.  In this section, you will learn how to:
-  * if
-  * if/else
+  - Execute statements **conditionally** using: if, if/else
-. Execute statements **multiple times** using:
+  - Execute statements **multiple times** using: for loops, while loops, repeat loops
-  * for loops
+  - **Modify loop** execution using: break statements, next statements
-  * while loops
-  * repeat loops
-. **Modify loop execution** using:
-  * break statements
-  * next statements
 ==== if and if/else statements ====
@@ Line 55: / Line 52: @@
 </code>
-Curly brackets are used so that R knows that your command is not complete with the first line of code.
+For example,
-For example, try:
+<code rsplus>
+if (2+2)==4 {
+print("Arithmetic works.") }
+if (2+1)==4 {
+print("Arithmetic works.") }
+</code>
+Curly brackets { } are used so that R knows to expect more input.  When using brackets, R waits to evaluate the command until the brackets have been closed.  If the curly brackets are not used, R may not behave as you are expecting.  For example, try:
 <code rsplus>
-if (2+2)==4 print("Arithmetic works.")
+if (2+1)==4 print("Arithmetic works.")
 else print("Houston, we have a problem.")
 </code>
@@ Line 70: / Line 75: @@
 <code rsplus>
 if (2+2)==4 {
-print("Arithmetic works.")
+print("Arithmetic works.")  # R does not evaluate this expression yet because the bracket isn't closed.
 } else {
 print("Houston, we have a problem.")
+}  # Since all brackets are now closed, R will evaluate the commands.
+</code>
+Note that if and if/else test a single condition.  If you want to test a vector of conditions (and get a vector of results), you can use ifelse:
+For example,
+<code rsplus>
+a<-1:10
+ifelse(a>5,"yes","no")
+</code>
+You can also use ifelse in a function to apply a function only under certain conditions:
+For example,
+<code rsplus>
+a<-(-4):5
+sqrt(ifelse(a>=0,a,NA))
+</code>
+**Exercise**
+<code rsplus>
+Paws<-"cat"
+Scruffy<-"dog"
+Sassy<-cat
+animals<-c(Paws,Scruffy,Sassy)
+</code>
+. Use an if statement to print "meow" if Paws is a "cat".
+<hidden>
+<code rsplus>
+if(Paws=="cat") {
+  print("meow")}
+</code>
+</hidden>
+. Use an if/else statement to print "woof" if you supply an object that is a "dog" and "meow" if it is not.  Try it out with Paws and Scruffy.
+<hidden>
+<code rsplus>
+if(Scruffy=="dog") {
+  print("woof")
+} else {
+  print ("meow")
 }
+if(Paws=="dog") {
+  print("woof")
+} else {
+  print ("meow")
+}
+</code>
+</hidden>
+. Use an ifelse statement to display "woof" for animals that are dogs and "meow" for animals that are cats.
+<hidden>
+<code rsplus>
+ifelse(animals=="dog","woof","meow")
 </code>
+</hidden>
-When using brackets, R waits to evaluate the command until the brackets have been closed.
 ==== Loops ====
@@ Line 87: / Line 153: @@
   * iterating a calculation until it converges
-**Syntax**
+===for loops===
-<file rsplus>
-for(variable in sequence) {
-expression }
-while(condition) {
+The //for loop// is the most common type of loop.  Use a //for loop// to execute a block of code a known number of times.
-expression }
-repeat(expression)
+**Syntax**
+<file rsplus>
+for (variable in sequence) {
+expression
+}
 </file>
-===for loops===
+Each time the series of commands in a loop are executed, it is known as an iteration.
-The most common loop is the 'for loop'.  Use a 'for loop' to execute a block of code a known number of times.
+For example:
-**Syntax**
 <file rsplus>
 for (i in 1:5) {
-expression
+print(i)
 }
 </file>
-The example above would cause R to evaluate the expression 5 times.  In the first iteration, R would replace every instance of i with 1.  In the second iteration i would be replaced with 2, and so on.
+In this example, R will evaluate the expression 5 times.  In the first iteration, R will replace each instance of i with 1.  In the second iteration i would be replaced with 2, and so on.
+The letter 'i' can be replaced with any letter and the sequence can be almost anything.
 Try:
 <file rsplus>
-for (m in 1:10) {
+for (m in 4:10) {
 print(m*2)
+}
+for (a in c("Hello","R","Programmers")) {
+print(a)
+}
+for (z in 1:30) {
+a<-rnorm(n=1,mean=5,sd=2) # draw a value from a normal distribution with mean 5 and sd 2
+print(a)
 }
 </file>
+Loops are often used to loop over a dataset.  We will use loops to perform functions on a CO2 dataset.
+<file rsplus>
+CO2<-read.csv("co2_data.csv")
+for (i in 1:length(CO2[,1])) { # for each row in the CO2 dataset
+  print(CO2$conc[i]) #print the CO2 concentration
+}
+for (i in 1:length(CO2[,1])) { # for each row in the CO2 dataset
+  if(CO2$Type[i]=="Quebec") { # if the type is "Quebec"
+    print(CO2$conc[i]) #print the CO2 concentration }
+    }
+}
+</file>
+The expression part of the loop can be almost anything and is usually a compound statement containing many commands.
+<file rsplus>
+for (i in 4:5) { # for i in 4 to 5
+  print(colnames(CO2[i]))
+  print(mean(CO2[,i])) #print the mean of that column from the CO2 dataset
+}
+</file>
+Note that this could be done more quickly using apply(), but that wouldn't teach you about loops.
+//while loops// and //repeat loops// operate similarly to //for loops//.  Once you understand how //for loops// work, you should be able to use any type of loop.  You will see some examples of //while loops// and //repeat loops// in the next section.
+**Exercise**
+NEED TO WRITE IN AN EXERCISE
+==== Loop Modifications ====
+Normally, loops iterate over and over until they finish.  To change this behavior, you can use **break** which breaks out of the loops execution entirely, or **next**, which stops executing the current iteration and jumps to the next iteration.
+For example,
+<file rsplus>
+# Print the CO2 concentrations for "chilled" treatments and keep count of how many replications there were.
+count=0
+for (i in 1:length(CO2[,1])) {
+  if (CO2$Treatment[i]=="nonchilled") next #Skip to next iteration if treatment is nonchilled
+  count=count+1
+  print(CO2$conc[i])
+}
+print(count) # The count and print command were performed 42 times.
+# This could be equivalently written using a repeat loop:
+count=0
+i=0
+repeat {
+      i <- i + 1
+      if (CO2$Treatment[i]=="nonchilled") next  # skip this loop
+      count=count+1
+      print(CO2$conc[i])
+      if (i == length(CO2[,1])) break     # stop looping
+    }
+print(count)
+### This could also be written using a while loop:
+i <- 0
+count=0
+while (i < length(CO2[,1]))
+{
+  i <- i + 1
+  if (CO2$Treatment[i]=="nonchilled") next  # skip this loop
+  count=count+1
+  print(CO2$conc[i])
+}
+print(count)
+</file>
+**Exercise**
+NEED TO WRITE IN AN EXERCISE
+**Using flow control to make a complex plot**
+The idea here is that we have a dataset we want to plot, with concentration and uptake values, but each point has a type (Quebec or Mississippi) and a treatment ("chilled" or "nonchilled") and we want to plot the points differently for these cases.
+You can read more about mathematical typesetting with ?plotmath, and more about the way # that different colors, sizes, rotations, etc. are used in ?par.
+<file rsplus>
+head(CO2) # Look at the dataset
+unique(CO2$Type)
+unique(CO2$Treatment)
+# plot the dataset, showing each type and treatment as a different colour
+plot(x=CO2$conc, y=CO2$uptake, type="n", cex.lab=1.4,xlab="CO2 concentration", ylab="CO2 uptake") # Type "n" tells R to not actually plot the points.
+for (i in 1:length(CO2[,1]))
+{
+  if (CO2$Type[i]=="Quebec"&CO2$Treatment[i]=="nonchilled") {
+    points(CO2$conc[i],CO2$uptake[i],col="red",type="p") }
+  if (CO2$Type[i]=="Quebec"&CO2$Treatment[i]=="chilled") {
+    points(CO2$conc[i],CO2$uptake[i],col="blue") }
+  if (CO2$Type[i]=="Mississippi"&CO2$Treatment[i]=="nonchilled") {
+    points(CO2$conc[i],CO2$uptake[i],col="orange") }
+  if (CO2$Type[i]=="Mississippi"&CO2$Treatment[i]=="chilled") {
+    points(CO2$conc[i],CO2$uptake[i],col="green") }
+}
+</file>
+**Exercise**
+NEED TO WRITE IN AN EXERCISE
 <file rsplus>
 </file>