# R code for chapter 45 manipulating cases/rows in r commander and r.r
# Book details:
# http://www.amazon.co.uk/Health-Science-Statistics-using-Commander/dp/190790431X
# 

group <- c(  "a","a","a","a","a","a","a","b","b","b","b","b","c","c","c","c","c")
var2<- c( 3,4,6,5,6,7,6, 5,1,1,2,3, 8,9,8,7,8)
test1 <-data.frame(group,var2)
str(test1)

# 45.1	Copying a complete dataframe 
newcopy <- test1

# 45.2	Copying a subset of rows (cases) 
a_subset <- subset(newcopy, subset=group =="a")
a_subset
### also the split command - not mentioned in chapter:
# use: newdataframe <- split(variable, factor variable)
# e.g.
newdataframe <- split(var2, group)
newdataframe
# produces:
# $a
# [1] 3 4 6 5 6 7 6
# $b
# [1] 5 1 1 2 3
# $c
# [1] 8 9 8 7 8

# str(newdataframe)
# produces
# List of 3
# $ a: num [1:7] 3 4 6 5 6 7 6
# $ b: num [1:5] 5 1 1 2 3
#  $ c: num [1:5] 8 9 8 7 8
#########
# 45.3	Obtaining summary values for a subset of rows - Aggregation

AggregatedData <- aggregate(test1[,c("var2"), drop=FALSE], by=list(group= test1$group), FUN=mean)
AggregatedData
######
# 45.4	Correlation matrices 
filename <- "http://www.robin-beaumont.co.uk/virtualclassroom/book2data/computer_s_2009_rb_reduced1.dat"
mydataframe <- read.delim(filename, header=TRUE)
mydataframe

# 45.4.1	Editing R Commander code to obtain a correlation matrix

cov_matrix <- cor(mydataframe[,c("q1","q2","q3","q4","q5","q6")], use="complete.obs")
cov_matrix 
correlations <- as.data.frame(cov_matrix)
correlations
## 
# can conbime two above steps:
correlations <- as.data.frame(cor(mydataframe[,c("q1","q2","q3","q4","q5","q6")],use="complete.obs"))
correlations
##
# can write the matrix to a file:
write.matrix(cov_matrix, file =file.choose())

###### end