5.2.3: Nested Model in R
- Page ID
- 33641
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- Load the Exercise Hours data.
- Obtain the ANOVA table for the nested treatment design.
- Obtain estimators and CIs for means for each region and city.
- Obtain means plot for region and city within the region.
- Obtain Tukey’s multiple comparisons CIs.
1. Load the Exercise Hours data by using the following commands:
setwd("~/path-to-folder/")
ex_hours_data <- read.table("ex_hours_data.txt",header=T)
attach(ex_hours_data)
2. Obtain the ANOVA table for the nested treatment design by using the following commands:
nested<-aov(Ex_hours ~ Region+Region/City,data=ex_hours_data)
summary(nested)
# Df Sum Sq Mean Sq F value Pr(>F)
# Region 2 424.7 212.33 65.33 8.46e-05 ***
# Region:City 3 496.8 165.58 50.95 0.000116 ***
# Residuals 6 19.5 3.25
# ---
# Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
3. Obtain estimators and CIs for means for each region and city by using the following commands:
library(lsmeans) lsmeans(nested,"Region") # Region lsmean SE df lower.CL upper.CL # MW 15.2 0.901 6 13.04 17.5 # NE 25.8 0.901 6 23.54 28.0 # W 11.8 0.901 6 9.54 14.0 #Results are averaged over the levels of: City #Confidence level used: 0.95 lsmeans(nested,"City") #City Region lsmean SE df lower.CL upper.CL # Chicago MW 9.5 1.27 6 6.38 12.62 # Detroit MW 21.0 1.27 6 17.88 24.12 # NY NE 32.5 1.27 6 29.38 35.62 # Pittsburgh NE 19.0 1.27 6 15.88 22.12 # LA W 18.5 1.27 6 15.38 21.62 # Seattle W 5.0 1.27 6 1.88 8.12 #Confidence level used: 0.95
4. Obtain means plot for region and city within region by using the following commands:
library(plotrix) region_means<-as.data.frame(lsmeans(nested,"Region")) plotCI(x = region_means$lsmean,y = NULL ,li = region_means$lower.CL, ui = region_means$upper.CL, xaxt = "n", xlab="Region",ylab="ExHours") axis(1, at=1:3, labels=region_means$Region)
city_means<-as.data.frame(lsmeans(nested,"City")) City_Region<-paste(city_means$City,city_means$Region) plotCI(x = city_means$lsmean,y = NULL ,li = city_means$lower.CL, ui = city_means$upper.CL, xaxt = "n", xlab="City(Region)",ylab="ExHours") axis(1, at=1:6, labels=City_Region)
5. Obtain Tukey’s multiple comparisons CIs by using the following commands:
library(multcomp)
library(multcompView)
tukey_multiple_comparisons_region<-TukeyHSD(nested,"Region",conf.level=0.95,ordered=TRUE)
tukey_multiple_comparisons_region
Tukey multiple comparisons of means
95% family-wise confidence level
factor levels have been ordered
Fit: aov(formula = Ex_hours ~ Region + Region/City, data = ex_hours_data)
# $Region
# diff lwr upr p adj
#MW-W 3.5 -0.4112978 7.411298 0.0747598
#NE-W 14.0 10.0887022 17.911298 0.0000836
plot(tukey_multiple_comparisons_region)
tukey_multiple_comparisons_city<-TukeyHSD(nested,"Region:City",conf.level=0.95,ordered=TRUE)
cities<-as.data.frame(na.omit(tukey_multiple_comparisons_city$"Region:City"))
cities
# diff lwr upr p adj
# MW:Chicago-W:Seattle 4.5 -4.96579743 13.965797 0.5867601138
# W:LA-W:Seattle 13.5 4.03420257 22.965797 0.0087623039
# NE:Pittsburgh-W:Seattle 14.0 4.53420257 23.465797 0.0072411812
# MW:Detroit-W:Seattle 16.0 6.53420257 25.465797 0.0035459602
# NE:NY-W:Seattle 27.5 18.03420257 36.965797 0.0001761692
# W:LA-MW:Chicago 9.0 -0.46579743 18.465797 0.0626471065
# NE:Pittsburgh-MW:Chicago 9.5 0.03420257 18.965797 0.0491884424
# MW:Detroit-MW:Chicago 11.5 2.03420257 20.965797 0.0198221594
# NE:NY-MW:Chicago 23.0 13.53420257 32.465797 0.0004610102
# NE:Pittsburgh-W:LA 0.5 -8.96579743 9.965797 1.0000000000
# MW:Detroit-W:LA 2.5 -6.96579743 11.965797 0.9752059356
# NE:NY-W:LA 14.0 4.53420257 23.465797 0.0072411812
# MW:Detroit-NE:Pittsburgh 2.0 -7.46579743 11.465797 0.9960158169
# NE:NY-NE:Pittsburgh 13.5 4.03420257 22.965797 0.0087623039
# NE:NY-MW:Detroit 11.5 2.03420257 20.965797 0.0198221594
library(plotrix)
city_diff<-as.character(c("
MW:Chicago-W:Seattle","W:LA-W:Seattle", "NE:Pittsburgh-W:Seattle","MW:Detroit-W:Seattle","NE:NY-W:Seattle ","W:LA-MW:Chicago ","NE:Pittsburgh-MW:Chicago","MW:Detroit-MW:Chicago","NE:NY-MW:Chicago ","NE:Pittsburgh-W:LA ","MW:Detroit-W:LA","NE:NY-W:LA ", "MW:Detroit-NE:Pittsburgh", "NE:NY-NE:Pittsburgh","NE:NY-MW:Detroit"))
par(mar=c(8, 4, 2, 2) + 0.1)
plotCI(x = cities$diff,y = NULL ,li = cities$lwr, ui = cities$upr, xaxt = "
n",ylab="Differences of Means",xlab="")
abline(h=0)
axis(1, at=1:15, labels=city_diff,las = 2, cex.axis = 0.8)
