Feature #6384 ยป Metric_Statistics.R
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###Statistics
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######
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#ANOVA
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require(car) |
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lm.data <- lm(sum ~ trt, data=data) |
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Anova(lm.data, type=3) |
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summary(lm.data) |
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#or
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data.aov <- aov(sum ~ trt, data) |
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############################
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#Tukey multiple comparisons
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TukeyHSD(data) |
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#########
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#pairwise
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#method= "bonferroni", "fdr"
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pairwise.t.test(data$var1, data$var2, p.adjust.method="none") |
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#PERMANOVA
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#requires a reference data.frame with year, treatment, plot #... (of the same length as spp. cover matrix)
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require(vegan) |
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perm <- adonis(spp_matrix ~ treatment*year, data=enviro_info, perm=200) |
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summary(perm) |
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#######
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#SIMPER
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#requires a reference data.frame with year, treatment, plot #... (of the same length as spp. cover matrix)
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require(vegan) |
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spp_matrx.sim <- with(enviro_info, simper(spp_matrix, enviroVariable)) |
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summary(spp_matrix.sim, ordered=TRUE, digits=max(3)) |