beginners’&workshop& · 2015-12-01 · what’s&in&this&workshop! •...
TRANSCRIPT
What is R? • Sta%s%cs package
• General modelling tool
• Data visualisa%on and analysis tool
• Programming language
• Glorified pocket calculator
• “Environment for sta%s%cal compu%ng and graphics” h?p://r4stats.com/ar%cles/popularity/
Why use R?
• Lots of help available
• Free
• Big user base
• Increasingly used for doing science • Jobs!
• CuLng edge and growing func%onality
• If you learn only one new piece of compu%ng soNware aNer Excel, learn R
What’s in this workshop
• Basic interac%on with R
• Where to turn for help
• Moving rapidly to more complex analyses
• Where to learn more
What’s not in this workshop • Advanced programming • See e.g. ?Control, ?"function" and resources (later)
• ‘How do I analyse X?’ • Google (e.g. ‘%me series R’) and resources (later)
• The fundamentals of sta%s%cs • See resources given later, esp. Crawley books
• Working in R environments other than Rstudio (www.rstudio.com)
Default Windows GUI Default Mac GUI R commander Command line
R as a calculator
> 9+2-‐1 [1] 10 > 5*0.5 [1] 2.5 > 27/3 [1] 9 > 9^2 [1] 81 > 9^(1/2) [1] 3 > sqrt(9) [1] 3 > log(5) [1] 1.609438
R help documenta>on
> log(5) [1] 1.609438 Check what the log() func%on is doing (e.g. which base?) > ?log
General informa%on
Package
Arguments and defaults
What those arguments need to be
What’s covered
> log(5) [1] 1.609438 Check what the log() func%on is doing (e.g. which base?) > ?log If you really care
Where it’s come from
Some%mes very useful, some%mes not Run from here or use example(log)
What you get back
Useful link
R help documenta>on
R help documenta>on
> log(5) [1] 1.609438 Check what the log() func%on is doing (e.g. which base?) > ?log
R as a calculator > log(5) [1] 1.609438 Check what the log() func%on is doing (e.g. which base?) > ?log > log(5, base=10) [1] 0.69897 > log10(5) [1] 0.69897 What happens if you get it wrong? > log("Fred") Error in log(“Fred") : non-‐numeric argument to mathema%cal func%on > log func%on (x, base = exp(1)) .Primi%ve("log") So if natural log isn’t ln(5), what is ln used for? > ?ln
R as a calculator
Comparisons > 54 > 45 Greater than [1] TRUE > 2 < 1 Less than [1] FALSE > 15 == 15 Exactly equal [1] TRUE > 50 >= 50 Greater than or equal [1] TRUE > 5 > 1 & 9 <= 15 Are both statements true? [1] TRUE > 24 == 3 | 1 == 1 Is either statement true? [1] TRUE > ?Comparison > ?Syntax
Keeping track of what you’re doing
• Store code in a text file (.R)
• Write in comments #like this
• Run commands a line at a %me • Ctl R (Windows) Ctl Return (Windows) • ⌘↵ (Mac)
• Highlight code and run in the same way
• Run a whole file using the source() func%on
• Navigate history using arrows
Keeping track of what you’re doing
• Try running the first 32 lines one at a %me or in one go
url.show("h?p://is.gd/Rwkshp15")
• Try saving the file somewhere useful
• Try wri%ng some more commented and uncommented lines
• Use R as a web browser to see the file containing this workshop’s code:
• Copy it to a new R script file (.R)
Further sec>ons • Assign values to a variable <-‐
• Create vectors c()
• Simple sta%s%cs
• Extrac%ng bits of variables []
• loop for (var in seq){}
• Data frames read.table(); write.table(); [,]
• Simple plots plot(y~x); pairs(), hist()
• Build linear models lm(y~x); anova()
• Modelling exercise rpart(y~x); randomForest(y~x)
• Sta%s%cs • Crawley Books • Courses
• Masters’ lectures now! • h?ps://www.coursera.org/course/sta%s%cs
Places to go for more informa>on
• h?p://cran.r-‐project.org/web/views/ • Task views
• Specific books • Many online with UoM access e.g. 52 in UseR! series:
h?p://link.springer.com/bookseries/6991 • Data manipula+on with R by Phil Spector very broadly useful
• R programming • R site documents (start with ‘Documents with fewer than 100 pages’) • h?p://cran.r-‐project.org/other-‐docs.html
• Courses • h?ps://www.coursera.org/course/rprog
• Manipula%ng data (summarising, spliLng, etc.) • dplyr , %dyr
• Work with data frames, ±intui%ve, fast • vigne?e("introduc%on", package="dplyr”)
Packages to consider
• Manipula%ng strings • stringr
• Consistent interface • Doesn’t get round the need to use ‘regular expressions’
• Beau%ful plots • ggplot2
• Requires familiarisa%on • Help files weak, but online resources great
• Specifics • bioconductor.org (if necessary), seqinr (bioinforma%cs) • ape (Phylogene%cs) • lmer, nlme (more advanced linear and nonlinear models) • …
Places to go for help
• R help list archives h?p://www.r-‐project.org/ > Mailing lists > R-‐help web interface > Searchable archives
• R help documenta%on ? ?? help(package="base") demo() example("func%on") vigne?e()
• R support groups • FLS (FLSRGROUP listerv) or email
[email protected] • Manchester R User group
h?p://www.meetup.com/Manchester-‐R/
• Google • stackoverflow.com (programming) crossvalidated (Stats)