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Introduction to R. Jiang Du Jan 17th 2008. What is R?. A software package for data analysis and graphical representation Scripting language Flexible and customizable Free… Weaknesses Not particularly efficient in handling large data sets Slow in executing big loops. Where to get R?.
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Introduction to R Jiang Du Jan 17th 2008
What is R? • A software package for data analysis and graphical representation • Scripting language • Flexible and customizable • Free… • Weaknesses • Not particularly efficient in handling large data sets • Slow in executing big loops
Where to get R? • http://www.r-project.org/
Basic operations > 1+2*3 [1] 7 > log(10) [1] 2.302585 > 4^2 [1] 16 > sqrt(16) [1] 4 > pi [1] 3.141593
Basic operations > x = pi * 2 > x [1] 6.283185 > floor(x) [1] 6 > ceiling(x) [1] 7
Data type: vector > x = c(1,2,3,5,4) > x [1] 1 2 3 5 4 > y = 1:5 > y [1] 1 2 3 4 5 > x + 2 [1] 3 4 5 7 6 > x+y [1] 2 4 6 9 9 > length(x) [1] 5 > sorted_x = sort(x) > sorted_x [1] 1 2 3 4 5
Data type: vector > x [1] 1 2 3 5 4 > x[3] [1] 3 > x[1:2] [1] 1 2 > x[-3] [1] 1 2 5 4 > x[x > 3] [1] 5 4 > x > 3 [1] FALSE FALSE FALSE TRUE TRUE > which(x > 3) [1] 4 5
Data type: matrix > m = matrix(1:9, nrow = 3, ncol = 3, byrow = TRUE) > m [,1] [,2] [,3] [1,] 1 2 3 [2,] 4 5 6 [3,] 7 8 9 > m[1, 2] [1] 2 > m[1:2, 2:3] [,1] [,2] [1,] 2 3 [2,] 5 6
Data type: matrix > m2 = matrix(c(2,0,0,0,2,0,0,0,2), nrow = 3, byrow = TRUE) > m2 [,1] [,2] [,3] [1,] 2 0 0 [2,] 0 2 0 [3,] 0 0 2 > m * m2 [,1] [,2] [,3] [1,] 2 0 0 [2,] 0 10 0 [3,] 0 0 18 > m %*% m2 [,1] [,2] [,3] [1,] 2 4 6 [2,] 8 10 12 [3,] 14 16 18
Date type: data frame > a = c(1:5) > b = a^2 > df = data.frame(a,b) > df a b 1 1 1 2 2 4 3 3 9 4 4 16 5 5 25 > df$b [1] 1 4 9 16 25 > df[3, 2] [1] 9
Data type: data frame > dim(df) [1] 5 2 > subset(df, a > 2) a b 3 3 9 4 4 16 5 5 25 > subset(df, a > 2 & b < 10) a b 3 3 9
Visualization of data > x = 1:10 > y = x^2 > plot(x, y) > z = c(rep(1, 3), rep(5:6, 10), 1:10) > hist(z)
Visualization of data > x = seq(-10, 10, length= 30) > y = x > f = function(x,y) { r <- sqrt(x^2+y^2); 10 * sin(r)/r } > z = outer(x, y, f) > persp(x, y, z, theta = 30, phi = 30, expand = 0.5, col = "lightblue")
Loops, functions, etc. > x = c(1, 2, 3, 4, 5) > y = x > for (i in 1:length(x)) {y[i] = x[i]^2} > y [1] 1 4 9 16 25 > apply(as.array(x), 1, "^", 2) [1] 1 4 9 16 25 > x^2 [1] 1 4 9 16 25
Loops, functions, etc. > x = 1:5 > f3 = function(x) {return(x^3)} > apply(as.array(x), 1, f3) [1] 1 8 27 64 125 > source("~/test.r") [1] -1 -1 9 16 25
One of the most useful commands ? > ?apply
Practice: on Bordeaux wines • Problem • Bordeaux wine vintage quality and the weather • Bordeaux wines in different vintage years have different qualities (reflected in prices) • The older the better? • Weather is an important factor • Hot, dry summer preferred
Practice: the data WRAIN Winter (Oct.-March) Rain ML DEGREES Average Temperature (Deg Cent.) April-Sept. HRAIN Harvest (August and Sept.) ML TIME_SV Time since Vintage (Years)
Practice: load the data > wine_data = read.table("~/wine.data", header = TRUE, na.strings = ".");
Practice: visualization > plot(wine_data$TIME_SV, wine_data$LPRICE2);
Practice: visualization avg_price = median(wine_data$LPRICE2, na.rm = TRUE); plot(wine_data$DEGREES, wine_data$HRAIN, type = "n", xlab = "Temperature", ylab = "Harvest rain"); points(wine_data$DEGREES[wine_data$LPRICE2 >= avg_price], wine_data$HRAIN[wine_data$LPRICE2 >= avg_price], pch = 19, col = "blue"); points(wine_data$DEGREES[wine_data$LPRICE2 < avg_price], wine_data$HRAIN[wine_data$LPRICE2 < avg_price], pch = 19, col = "red"); legend(15, 250, c(">= avg price", "< avg price"), pch = 19, col = c("blue", "red"));
Practice: linear regression • Find a set of parameters a, …, e, such that: • LPRICE2 ~ a * WRAIN + b * DEGREES + c * HRAIN + d * TIME_SV + e + error_term • The overall error should be minimized • In this case, the sum/average of squared errors • Sum((prediction - actual_price)^2)
Practice: linear regression > lmfit = lm(LPRICE2 ~ WRAIN + DEGREES + HRAIN + TIME_SV, wine_data); > lmfit … Coefficients: (Intercept) WRAIN DEGREES HRAIN TIME_SV -12.145334 0.001167 0.616392 -0.003861 0.023847 > cat("RMS: ", sqrt(sum(lmfit$residuals^2)/length(lmfit$residuals)), "\n"); RMS: 0.2586167
Practice: linear regression plot(wine_data$VINT, wine_data$LPRICE2, xlab = "Vintage year", ylab = "log2 rel. price”, pch = 19, col = "black"); points(wine_data$VINT[30:38], predict(lmfit, wine_data[30:38,]), pch = 19, col = "red"); legend(1965, -0.2, c("old data", "prediction"), pch = 19, col = c("black", "red"));
Practice: linear regression • Using fewer parameters in the model? • LPRICE2 ~ b * DEGREES + c * HRAIN + d + error_term • lmfit2 = lm(LPRICE2 ~ DEGREES + HRAIN, wine_data); • RMS: 0.349513
Links • Classesv2: http://classesv2.yale.edu/ • Course wiki: http://lab.zoo.cs.yale.edu/cs445-wiki/ • R: http://www.r-project.org/ • Bordeaux wine analysis: http://www.liquidasset.com/orley.htm