STA02B2_Practical 4.pdf

Mathematical Statistics 2B Practical 4: Parametric vs. Non-Parametric Tests Department of Statistics - University of Johannesburg 1. Introduction Parametric statistics are based on assumptions about the distribution of t...

Mathematical Statistics 2B Practical 4: Parametric vs. Non-Parametric Tests Department of Statistics - University of Johannesburg 1. Introduction Parametric statistics are based on assumptions about the distribution of the population from which the sample was taken. For parametric tests, the data must meet the following requirements:  Continuous variable of interest (interval or ratio)  A random sample of data from the population  Independent observations  Normal distribution (approximately) of the sample and population on the variable of interest  Homogeneity of variances (for two or more independent groups)  No outliers If the parametric assumptions are not met, we can use the corresponding nonparametric tests that do not rely on assumptions about the shape or parameters of the underlying population distribution. Nonparametric tests are typically used when the sample is not normally distributed, or the sample size is small, or the variables are measured on nominal or ordinal scales. It can sometimes be difficult to decide whether to use a parametric or nonparametric procedure. Nonparametric procedures generally have less power for the same sample size than the corresponding parametric procedure if the data truly are normal. Interpretation of nonparametric procedures can also be more difficult than for parametric procedures. For this module we will look at how to perform and interpret parametric vs. non-parametric tests in R for one sample, paired samples, two independent samples, multiple independent samples, and correlation. The one- sample and two-sample hypothesis formulation in the notes are all given for two-sided tests. The form of the alternative hypothesis can be adjusted in the built-in functions to reflect a left-sided or a right-sided test, depending on the problem statement. 2. Datasets For Examples The following datasets are used in this practical. Create the following vectors/data frames in R data1=c(84,86,90,97,98,98,99,102,102,103,108,111) data2=c(91,95,96,96,96,97,98,101,103,105,106,123,130,143,145) test_data=cbind(1:8,c(59,68,60,60,59,62,58,76),c(61,78,65,56,55,62,60,68)) colnames(test_data)=c("Student","Test1","Test2") Create the growth dataset A researcher wants to know if three different fertilizers lead to different levels of plant growth. A sample of 30 plants are randomly divided into three groups of 10 and a different fertilizer applied to each group. The height of each plant was measured at the end of one month. Use the following code to construct the dataset in R: growth=data.frame(group=rep(c('A', 'B', 'C'), each=10), height=c(7, 14, 14, 13, 12, 9, 6, 14, 12, 8, 15, 17, 13, 15, 15, 13, 9, 12, 10, 8, 6, 8, 8, 9, 5, 14, 13, 8, 10, 9)) The cars dataset is available in R The data give the speed of 50 cars and the distances taken to stop. speed Speed (mph) dist Stopping distance (ft) The mtcars dataset is available in R The data give fuel consumption and 10 aspects of automobile design and performance for 32 cars. mpg Miles/(US) gallon qsec 1/4 mile time cyl Number of cylinders vs Engine (0 = V-shaped, 1 = straight) disp Displacement (cu.in.) am Transmission (0 = automatic, 1 = manual) hp Gross horsepower gear Number of forward gears drat Rear axle ratio carb Number of carburetors wt Weight (1000 lbs) 3. One-Sample Tests The one-sample t-test examines whether the mean of a population is statistically different from a known or hypothesized value. It is a parametric test, commonly used to test the statistical difference between a mean and a known or hypothesized value of the mean in the population, or the statistical difference between a change (difference) score and zero. It tests the hypothesis H 0 :   0 vs. H1 :   0. The t.test() function in R is used to test if the mean is different from a specific value. The non-parametric equivalent is called the one-sample Wilcoxon signed rank test, which tests hypotheses about the median of the population instead of the mean (as in the parametric test), namely H 0 : m  m0 vs. H1 : m  m0. The wilcox.test() function in R is used to test if the median is different from a specific value. For both the parametric and non-parametric test functions we will use the arguments x (variable of interest), y (second variable for paired data), alternative (to define the form), mu (if this is a number different from 0) and paired (to indicate a paired test). By default the wilcox.test() calculates an exact p-value if the samples contain less than 50 finite values and there are no ties. If there are ties in the data, you will see the warning message “cannot compute exact p-value with ties” as R adjusts the p-value by the continuity correction. In such a case we can use the option correct=FALSE to turn off the continuity correction, or the option exact=FALSE. Example 1: One-sample (test_data) The lecturer wants to test if the average/median mark for test 1 is significantly better than the average/median mark of last year, namely: mean = 56 and median = 55. #check assumptions > shapiro.test(test1) p-value = 0.009245 #One-sample t-test > t.test(test1,mu=56,alternative = "greater") p-value = 0.008946 # Wilcoxon signed rank test >wilcox.test(test1,mu=55,alternative = "greater", exact=FALSE) p-value = 0.007015 Example: Paired sample (test_data) The lecturer wants to know if there is a significant difference in students’ marks for test 1 compared to test 2. #Dependent samples t-test (test1 mark minus test2 mark) > t.test(test1,test2,paired = T) p-value = 0.8578 mean difference: -0.375 # Wilcoxon signed rank test > wilcox.test(test1,test2,paired = T,exact=FALSE) p-value = 0.9324 I will leave it up to you to check the summary statistics and any other assumptions tests not included in the above. 4. Two Independent Sample Tests The independent samples t-test is a parametric test used to test for mean differences between two independent groups. It tests the hypothesis H 0 : 1   2 vs. H1 : 1   2. The t.test() function in R is used to compare the mean of a numerical variable of interest (dependent variable) between two independent groups (independent variable). The first argument of the function identifies the dependent and independent variables in the formula format, namely dependent ~ independent. The dataset is then defined using the data argument. The test assumes equality of variance and computes a pooled variance. If this assumption is not met, the test statistic calculation is adjusted for unequal variances, and the var.equal argument is set as FALSE (default var.equal = FALSE), otherwise it is set to TRUE for equal variances assumed. The non-parametric equivalent is called the Mann-Whitney U test, also referred to as the Mann Whitney Wilcoxon test or the Wilcoxon rank sum test, and is used to test whether there is a difference with respect to central tendency, specifically the median, between the two groups, namely H 0 : m1  m2 vs. H1 : m1  m2. The wilcox.test() function in R is used for the Mann-Whitney U test. The measurements for the two groups can be defined in the x and y arguments, or in formula notation in the x argument. In the latter case, we also define the dataset using the data argument. Example: Two independent samples (data1 and data2) #summary statistics data_summary=rbind(c(mean(data1),mean(data2)),c(median(data1),median(data2)),c(sd(data1),sd(data2))) colnames(data_summary)=c("Data1","Data2") row.names(data_summary)=c("Mean","Median","Standard deviation") > data_summary Data1 Data2 Mean 98.166667 108.3333 Median 98.500000 101.0000 Standard deviation 8.155682 17.9271 #check assumptions > shapiro.test(data1) p-value = 0.6122 > shapiro.test(data2) p-value = 0.002517 > var.test(data1,data2) p-value = 0.0125 #box-and-whisker plot > boxplot(data1,data2) 140 120 100 90 1 2 #Independent samples t-test > t.test(data1,data2,var.equal = F) p-value = 0.06406 #Mann-Whitney U test > wilcox.test(data1,data2,exact=FALSE ) p-value = 0.3924 5. Multiple Independent Sample Tests The independent one-way analysis of variance (ANOVA) is a parametric test used to test for mean differences for three or more independent groups. It tests the hypothesis H0: all group means are equal vs. H1: at least one group has a different mean value. The aov() function in R is used to compare the mean of a numerical variable of interest (dependent variable) for three or more independent groups (independent variable). The first argument of the function identifies the dependent and independent variables in the formula format, namely dependent ~ independent. The dataset is then defined using the data argument. The non-parametric equivalent is called the Kruskal-Wallis test, and is used to test whether there is a difference in medians of the independent groups, namely H0: all group medians are equal vs. H1: at least one group has a different median value. The kruskal.test() function in R is used for the Kruskal-Wallis test. The dependent and independent variables are identified in formula notation. Example: Three independent samples (growth data) #box-and-whisker plot boxplot(height~group,data=growth) 16 14 12 height 10 8 6 A B C group #check assumptions > shapiro.test(growth$height[growth$group=="A"]) p-value = 0.08727 > shapiro.test(growth$height[growth$group=="B"]) p-value = 0.5756 > shapiro.test(growth$height[growth$group=="C"]) p-value = 0.4242 > bartlett.test(height~group,data=growth) p-value = 0.9512 > fligner.test(height~group,data=growth) p-value = 0.838 #ANOVA > anova_out=aov(height~group,data=growth) > summary(anova_out) p-value = 0.0317 #Kruskal-Wallis > KW_out=kruskal.test(height~group,data=growth) > KW_out p-value = 0.04311 6. Correlation The most common correlation coefficient is Pearson’s product moment correlation coefficient (or simply Pearson’s correlation), denoted with r, which measures the strength of the linear relationship between two numerical variables. For Pearson’s correlation, both variables should be normally distributed, have a linear relationship, be equally distributed about the regression line (homoscedasticity) and have no outliers. Rank correlation methods such as Kendall’s Tau and Spearman’s Rho are non-parametric alternatives to Pearson’s correlation and are based on the ranks of the data, rather than the observed values. While Pearson measures the linear relationship between two variables, Kendall and Spearman both measure the monotonic relationship. In a linear relationship the two variables move together at a constant rate (straight line). A monotonic relationship measures how likely it is for two variables to move in the same direction, but not necessarily at a constant rate. For example, the upward exponential curve y  x 2 , x  0 has a strictly positive monotonicity because as x increases y also increases, but the curved line is not linear since the rate changes in y vary at different values of x. Kendall and Spearman can be used with ordinal data. If the Pearson and Spearman coefficients are not much different, the data tend to not have extreme values (outliers), but if they are very different, it is likely that outliers are present. The Kendall correlation is more robust and shows consistent values whether there are outliers or not. All three correlation measures will return a value between −1 and +1 and are interpreted in the same way. The cor.test() function in R is used to calculate Pearson, Kendal and Spearman correlation coefficients. The x and y arguments identify the two variables, and the specific coefficient is selected in the method argument (default method = “pearson”. Example: Correlation (cars data) plot(cars$speed,cars$dist) 100 120 80 cars$dist 60 40 20 0 5 10 15 20 25 cars$speed > cor(cars$speed,cars$dist) #Pearson’s correlation 0.8068949 > cor(cars$speed,cars$dist,method = "spearman") #Spearmans’s Rho 0.8303568 > cor(cars$speed,cars$dist,method = "kendall") #Kendall’s Tau 0.6689901 Example: Correlation (mtcars data) plot(mtcars$wt, mtcars$mpg) 30 mtcars$mpg 25 20 15 10 2 3 4 5 mtcars$wt > cor(mtcars$wt, mtcars$mpg) #Pearson’s correlation -0.8676594 > cor(mtcars$wt, mtcars$mpg,method = "spearman") #Spearmans’s Rho -0.886422 > cor(mtcars$wt, mtcars$mpg,method = "kendall") #Kendall’s Tau -0.7278321