############# ###Statistics ############# ###### #ANOVA require(car) lm.data <- lm(sum ~ trt, data=data) Anova(lm.data, type=3) summary(lm.data) #or data.aov <- aov(sum ~ trt, data) ############################ #Tukey multiple comparisons TukeyHSD(data) ######### #pairwise #method= "bonferroni", "fdr" pairwise.t.test(data$var1, data$var2, p.adjust.method="none") ########## #PERMANOVA #requires a reference data.frame with year, treatment, plot #... (of the same length as spp. cover matrix) require(vegan) perm <- adonis(spp_matrix ~ treatment*year, data=enviro_info, perm=200) summary(perm) ####### #SIMPER #requires a reference data.frame with year, treatment, plot #... (of the same length as spp. cover matrix) require(vegan) spp_matrx.sim <- with(enviro_info, simper(spp_matrix, enviroVariable)) summary(spp_matrix.sim, ordered=TRUE, digits=max(3))