1. 1 Peter Fox Data Analytics – ITWS-4963/ITWS-6965 Week 2a, February 2, 2016, LALLY 102 Data and Information Resources, Role of Hypothesis, Exploration and Distributions

2. Contents Data sources –Cyber –Human “Munging” Exploring –Distributions… –Summaries –Visualization Testing and evaluating the results (beginning) 2

3. Lower layers in the Analytics Stack 3

4. “Cyber Data” … 4

5. “Human Data” … 5

6. Data Prepared for Analysis = Munging Missing values, null values, etc. E.g. in the EPI_data – they use “--” –Most data applications provide built ins for these higher- order functions – in R “NA” is used and functions such as is.na(var), etc. provide powerful filtering options (we’ll cover these on Friday) Of course, different variables often are missing “different” values In R – higher-order functions such as: Reduce, Filter, Map, Find, Position and Negate will become your enemies and then your friends: http://www.johnmyleswhite.com/notebook/2010/09/2 3/higher-order-functions-in-r/ http://www.johnmyleswhite.com/notebook/2010/09/2 3/higher-order-functions-in-r/ 6

7. Getting started – summarize data Summary statistic –Ranges, “hinges” –Tukey’s five numbers Look for a distribution match Tests…for… –Normality – shapiro-wilks – returns a statistic (W!) and a p-value – what is the null hypothesis here? > shapiro.test(EPI_data$EPI) Shapiro-Wilk normality test data: EPI_data$EPI W = 0.9866, p-value = 0.1188 7

8. Accept or Reject? Reject the null hypothesis if the p-value is less than the level of significance. You will fail to reject the null hypothesis if the p-value is greater than or equal to the level of significance. Typical significance 0.05 (!) 8

9. Another variable in EPI > shapiro.test(EPI_data$DALY) Shapiro-Wilk normality test data: EPI_data$DALY W = 0.9365, p-value = 1.891e-07 Accept or reject? 9

10. Distribution tests Binomial, …. most distributions have tests Wilcoxon (Mann-Whitney) –Comparing populations – versus to a distribution Kolmogorov-Smirnov (KS) … It got out of control when people realized they can name the test after themselves, v. someone else… 10

11. Getting started – look at the data Visually –What is the improvement in the understanding of the data as compared to the situation without visualization? –Which visualization techniques are suitable for one's data? Scatter plot diagrams Box plots (min, 1 st quartile, median, 3 rd quartile, max) Stem and leaf plots Frequency plots Group Frequency Distributions plot Cumulative Frequency plots Distribution plots 11

12. Why visualization? Reducing amount of data, quantization Patterns Features Events Trends Irregularities Leading to presentation of data, i.e. information products Exit points for analysis 12

13. Exploring the distribution > summary(EPI) # stats Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 32.10 48.60 59.20 58.37 67.60 93.50 68 > boxplot(EPI) > fivenum(EPI,na.rm=TRUE) [1] 32.1 48.6 59.2 67.6 93.5 Tukey: min, lower hinge, median, upper hinge, max 13

14. Stem and leaf plot > stem(EPI)# like-a histogram The decimal point is 1 digit(s) to the right of the | - but the scale of the stem is 10… watch carefully.. 3 | 234 3 | 66889 4 | 00011112222223344444 4 | 5555677788888999 5 | 0000111111111244444 5 | 55666677778888999999 6 | 000001111111222333344444 6 | 5555666666677778888889999999 7 | 000111233333334 7 | 5567888 8 | 11 8 | 669 9 | 4 14

15. Grouped Frequency Distribution aka binning > hist(EPI)#defaults 15

16. Distributions Shape Character Parameter(s) Which one fits? 16

17. 17 > hist(EPI, seq(30., 95., 1.0), prob=TRUE) > lines (density(EPI,na.rm=TR UE,bw=1.)) > rug(EPI) or > lines (density(EPI,na.rm=TR UE,bw=“SJ”))

18. 18 > hist(EPI, seq(30., 95., 1.0), prob=TRUE) > lines (density(EPI,na.rm=TR UE,bw=“SJ”))

19. Why are histograms so unsatisfying? 19

20. > xn<-seq(30,95,1) > qn<- dnorm(xn,mean=63, sd=5,log=FALSE) > lines(xn,qn) > lines(xn,.4*qn) > ln<-dnorm(xn,mean=44, sd=5,log=FALSE) > lines(xn,.26*ln) 20

21. Exploring the distribution > summary(DALY) # stats Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.00 37.19 60.35 53.94 71.97 91.50 39 > fivenum(DALY,na.rm=TRUE) [1] 0.000 36.955 60.350 72.320 91.500 21 EPIDALY

22. Stem and leaf plot > stem(DALY) # The decimal point is 1 digit(s) to the right of the | 0 | 0000111244 0 | 567899 1 | 0234 1 | 56688 2 | 000123 2 | 5667889 3 | 00001134 3 | 5678899 4 | 00011223444 4 | 555799 5 | 12223344 5 | 556667788999999 6 | 0000011111222233334444 6 | 6666666677788889999 7 | 00000000223333444 7 | 66888999 8 | 1113333333 8 | 555557777777777799999 9 | 22 22

23. Beyond histograms Cumulative distribution function: probability that a real-valued random variable X with a given probability distribution will be found at a value less than or equal to x. > plot(ecdf(EPI), do.points=FALSE, verticals=TRUE) 23

24. Beyond histograms Quantile ~ inverse cumulative density function – points taken at regular intervals from the CDF, e.g. 2-quantiles=median, 4-quantiles=quartiles Quantile-Quantile (versus default=normal dist.) > par(pty="s") > qqnorm(EPI); qqline(EPI) 24

25. Beyond histograms Simulated data from t-distribution (random): > x <- rt(250, df = 5) > qqnorm(x); qqline(x) 25

26. Beyond histograms Q-Q plot against the generating distribution: x<- seq(30,95,1) > qqplot(qt(ppoints(250), df = 5), x, xlab = "Q-Q plot for t dsn") > qqline(x) 26

27. But if you are not sure it is normal > wilcox.test(EPI,DALY) Wilcoxon rank sum test with continuity correction data: EPI and DALY W = 15970, p-value = 0.7386 alternative hypothesis: true location shift is not equal to 0 27

28. Comparing the CDFs > plot(ecdf(EPI), do.points=FALSE, verticals=TRUE) > plot(ecdf(DALY), do.points=FALSE, verticals=TRUE, add=TRUE) 28

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33. More munging Bad values, outliers, corrupted entries, thresholds … Noise reduction – low-pass filtering, binning Modal filtering REMEMBER: when you munge you MUST record what you did (and why) and save copies of pre- and post- operations… 33

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36. Populations within populations In the EPI example: –Geographic regions (GEO_subregion) –EPI_regions –Eco-regions (EDC v. LEDC – know what that is?) –Primary industry(ies) –Climate region What would you do to start exploring? 36

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38. 38 Or, a twist – n=1 but many attributes? The item of interest in relation to its attributes

39. Summary: explore Going from preliminary to initial analysis… Determining if there is one or more common distributions involved – i.e. parametric statistics (assumes or asserts a probability distribution) Fitting that distribution -> provides a model! Or NOT –A hybrid or –Non-parametric (statistics) approaches are needed – more on this to come 39

40. Goodness of fit And, we cannot take the models at face value, we must assess how fit they may be: –Chi-Square –One-sided and two-sided Kolmogorov-Smirnov tests –Lilliefors tests –Ansari-Bradley tests –Jarque-Bera tests Just a preview… 40

41. 41 Summary Cyber and Human data; quality, uncertainty and bias – you will often spend a lot of time with the data Distributions – the common and not-so common ones and how cyber and human data can have distinct distributions How simple statistical distributions can mislead us Populations and samples and how inferential statistics will lead us to model choices (no we have not actually done that yet in detail) Munging toward exploratory analysis Toward models!

42. How are the software installs going? R Data exercises? –You can try some of the examples from today on the EPI dataset More on Friday… and other datasets. 42