04 reports

If you’re using a laptop, start
installing latex, from the
instructions on the website

Thursday, 2 September 2010

Ofﬁce hours: before class.

Lab access: you should now
have it


Stat405 Statistical reports

Hadley Wickham

1. More subsetting.
2. Missing values.
3. Statistical reports: data, code,
graphics & written report


Saving results
# Prints to screen
diamonds[diamonds$x > 10, ]

# Saves to new data frame
big <- diamonds[diamonds$x > 10, ]

# Overwrites existing data frame. Dangerous!
diamonds <- diamonds[diamonds$x < 10,]


diamonds <- diamonds[1, 1]
diamonds

# Uh oh!

rm(diamonds)
str(diamonds)

# Phew!


Your turn
Create a logical vector that selects
diamonds with equal x & y. Create a new
dataset that only contains these values.
Create a logical vector that selects
diamonds with incorrect/unusual x, y, or z
values. Create a new dataset that omits
these values. (Hint: do this one variable
at a time)


equal_dim <- diamonds$x == diamonds$y
equal <- diamonds[equal_dim, ]

y_big <- diamonds$y > 10
z_big <- diamonds$z > 6

x_zero <- diamonds$x == 0
y_zero <- diamonds$y == 0
z_zero <- diamonds$z == 0
zeros <- x_zero | y_zero | z_zero

bad <- y_big | z_big | zeros
good <- diamonds[!bad, ]


Missing
values

Data errors

Typically removing the entire row because
of one error is overkill. Better to
selectively replace problem values with
missing values.
In R, missing values are indicated by NA


Expression Guess Actual
5 + NA
NA / 2
sum(c(5, NA))
mean(c(5, NA)
NA < 3
NA == 3
NA == NA


NA behaviour

Missing values propagate
Use is.na() to check for missing values
Many functions (e.g. sum and mean) have
na.rm argument to remove missing values
prior to computation.


# Can use subsetting + <- to change individual
# values

diamonds$x[diamonds$x == 0] <- NA
diamonds$y[diamonds$y == 0] <- NA
diamonds$z[diamonds$z == 0] <- NA

y_big <- !is.na(diamonds$y) & diamonds$y > 10
diamonds$y[y_big] <- diamonds$y[y_big] / 10
z_big <- !is.na(diamonds$z) & diamonds$z > 6
diamonds$z[z_big] <- diamonds$z[z_big] / 10


Your turn

What happens if you don’t remove
missing values? Why?


Statistical
reports

Statistical reports

Regardless of whether you go into academia
or industry, you need to be able to present
your ﬁndings.
And you should be able to do more than just
present them, you should be able to
reproduce them.


In
Data (.csv)

on
e
di
re
+

ct
o
ry
Code (.r)
+
Graphics (.png, .pdf)
+
Written report (.tex)

Working directory
Set your working directory to specify
where ﬁles will be saved by default.
From the terminal (linux or mac): the
working directory is the directory you’re in
when you start R
On windows: File | Change dir.
On the mac: ⌘-D


Data
So far we’ve just used built in datasets
Next week we’ll learn how to use external data


Code


Workﬂow
At the end of each interactive session, you
want a summary of everything you did
Two options:
Save everything that you did with
savehistory(filename.r) then remove the
unimportant bits
Build up the important bits as you go
Up to you - I prefer the second


R editor

Linux: gedit
(copy and paste - see website)

Windows: File | New Script
(press F5 to send line)

Mac: File | New document
(press command-enter to send)


Code is
communication!


Code presentation
Use comments (#) to describe what you are
doing and to create scannable headings in
your code
Every comma should be followed by a space,
and every mathematical operator (+, -, =, *, /
etc) should be surrounded by spaces.
Parentheses do not need spaces
Lines should be at most 80 characters. If you
have to break up a line, indent the following
piece

qplot(table,depth,data=diamonds)
qplot(table,depth,data=diamonds)+xlim
(50,70)+ylim(50,70)
qplot(table-depth,data=diamonds,geom="histo
gram")
qplot(table/depth,data=diamonds,geom="histo
gram",binwidth=0.01)+xlim(0.8,1.2)


# Table and depth -------------------------

qplot(table, depth, data = diamonds)
qplot(table, depth, data = diamonds) +
xlim(50, 70) + ylim(50, 70)

# Is there a linear relationship?
qplot(table - depth, data = diamonds,
geom = "histogram")

# This bin width seems the most revealing
qplot(table / depth, data = diamonds,
geom = "histogram", binwidth = 0.01) +
xlim(0.8, 1.2)
# Also tried: 0.05, 0.005, 0.002


Graphics


Saving graphics
# Uses size on screen:
ggsave("my-plot.pdf")
ggsave("my-plot.png")

# Specify size
ggsave("my-plot.pdf",
width = 6, height = 6)

# Saves file in working directory
# (where you started R from)


PDF PNG

Vector based Raster based
(can zoom in inﬁnitely) (made up of pixels)

Good for plots
Good for most
with thousands of
plots
points


Your turn

Recreate some of the graphics from
previous lectures and save them.
Experiment with the scale and height and
width settings.
Modify the template to include them.


Written
report

Latex
We are going to use the open source
document typesetting system called latex to
produce our reports.
This is widespread in statistics - if you ever
write a journal article, you will probably write
it in latex.
(Not so useful if you’re not in grad school)


Edit-Compile-Preview
Edit: a text document with special
formatting
Compile: to produce a pdf
Preview: with a pdf viewer

See web page for system speciﬁcs.


Latex
Template
Sections
Images
Figures and cross-references
Verbatim input (for code)


Your turn
# Get the sample report
wget http://had.co.nz/stat405/
resources/sample-report.zip
unzip sample-report.zip

cd sample-report
gedit template.tex &
pdflatex template.tex
evince template.pdf
# Experiment!


Your turn

If not on linux, follow the instructions on
the class website.
If you feel comfortable, start on
homework 2.


Homework


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