Beginners workshop. Chris Knight

Transcription

1 Beginners workshop Chris Knight

2 Sta%s%cs package What is R? Data visualisa%on and analysis tool General modelling tool Programming language Glorified pocket calculator h?p://r4stats.com/ar%cles/popularity/ Environment for sta%s%cal compu%ng and graphics

3 Why use R? Free CuLng edge and growing func%onality Increasingly used for doing science Jobs! If you learn only one new piece of compu%ng sonware aner Excel, learn R Big user base Lots of help available

4 What s in this workshop Basic interac%on with R Moving rapidly to more complex analyses Where to learn more Where to turn for help

5 What s not in this workshop Advanced programming See e.g.?control,?"function" and resources (later) The fundamentals of sta%s%cs See resources given later, esp. Crawley books How do I analyse X? Google (e.g. %me series R ) and resources (later) Working in R environments other than Rstudio ( Default Windows GUI Default Mac GUI R commander Command line

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7 > [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] R as a calculator

8 R help documenta>on > log(5) [1] Check what the log() func%on is doing (e.g. which base?) >?log Package What s covered General informa%on Arguments and defaults What those arguments need to be

9 R help documenta>on > log(5) [1] Check what the log() func%on is doing (e.g. which base?) >?log If you really care What you get back Some%mes very useful, some%mes not Run from here or use example(log) Where it s come from Useful link

10 R help documenta>on > log(5) [1] Check what the log() func%on is doing (e.g. which base?) >?log

11 R as a calculator > log(5) [1] Check what the log() func%on is doing (e.g. which base?) >?log > log(5, base=10) [1] > log10(5) [1] 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

12 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

13 Keeping track of what you re doing Navigate history using arrows Store code in a text file (.R) 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 Write in comments #like this

14 Keeping track of what you re doing Use R as a web browser to see the file containing this workshop s code: url.show("h?p://is.gd/rwkshp15") Copy it to a new R script file (.R) Try running the first 32 lines one at a %me or in one go Try saving the file somewhere useful Try wri%ng some more commented and uncommented lines

15 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)

16 Places to go for more informa>on Sta%s%cs Crawley Books Courses Masters lectures now! h?ps:// 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:// Task views h?p://cran.r- project.org/web/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

17 Packages to consider Manipula%ng data (summarising, splilng, etc.) dplyr, %dyr Work with data frames, ±intui%ve, fast vigne?e("introduc%on", package="dplyr ) 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)

18 Places to go for help R help documenta%on??? help(package="base") demo() example("func%on") vigne?e() Google stackoverflow.com (programming) crossvalidated (Stats) R help list archives h?p:// project.org/ > Mailing lists > R- help web interface > Searchable archives R support groups FLS (FLSRGROUP listerv) or jamie.soul@postgrad.manchester.ac.uk Manchester R User group h?p:// R/