# Exercise 6.2 # Statistical Methods in Biology: Design and Analysis of Experiments and Regression # by S.J. Welham, S.A. Gezan, S.J. Clark & A. Mead (2014) # Chapman & Hall/CRC Press, Boca Raton, Florida. ISBN: 978-1-4398-0878-8 # Data from Rothamsted Research (A. Karp) # Version 1, 13/08/2014 # Set working directory - use setwd() function or from Session menu in RStudio # e.g. setwd("d:/stats4biol/data) # load external packages - availabel from CRAN library(ggplot2) library(lsmeans) # tables of predicted means & contrasts # Read data & assign factors transect <- read.table('transect.dat', sep="", header=TRUE) transect$fDist <- as.factor(transect$fDist) summary(transect) # Plot data qplot(data=transect, y=Count, x=Distance) # One-way ANOVA of raw data transect.aov <- aov(Count ~ fDist, data=transect) summary(transect.aov) # Residual plots plot(transect.aov, ask=FALSE) hist(residuals(transect.aov)) # Take log10-transformation transect$logCount <- log10(transect$Count) summary(transect) # One-way ANOVA of log10-transformed data transect.aov.2 <- aov(logCount ~ fDist, data=transect) summary(transect.aov.2) # Residual plots plot(transect.aov.2, ask=FALSE) hist(residuals(transect.aov.2)) # Get table of predcited means with back-transform transect.lsm <- lsmeans(transect.aov.2, ~fDist) transect.lsm.df <- summary(transect.lsm) transect.lsm.df$bt <- 10^(transect.lsm.df$lsmean) transect.lsm.df # End of file