R: Multiple comparisons, "Least significant difference" and...

LSD.test {agricolae} | R Documentation

## Multiple comparisons, "Least significant difference" and Adjust P-values

### Description

Multiple comparisons of treatments by means of LSD and a grouping of treatments. The level by alpha default is 0.05. Returns p-values adjusted using one of several methods

### Usage

    LSD.test(y, trt, DFerror, MSerror, alpha = 0.05, p.adj=c("none","holm","hommel",
    "hochberg", "bonferroni", "BH", "BY", "fdr"), group=TRUE, main = NULL,console=FALSE)

### Arguments

`y` | model(aov or lm) or answer of the experimental unit
`trt` | Constant( only y=model) or vector treatment applied to each experimental unit
`DFerror` | Degrees of freedom of the experimental error
`MSerror` | Means square error of the experimental
`alpha` | Level of risk for the test
`p.adj` | Method for adjusting p values (see p.adjust)
`group` | TRUE or FALSE
`main` | title of the study
`console` | logical, print output

### Details

For equal or different repetition. p.adj = "holm", "hommel", "hochberg", "bonferroni", "BH", "BY", "fdr". see p.adjust() p-adj ="none" is t-student. p-adj ="hommel" is not applied in this test.

### Value

`y` | class (aov or lm) or vector numeric
`trt` | constant (only y=model) or vector alfanumeric
`DFerror` | Numeric
`MSerror` | Numeric
`alpha` | Numeric
`p.adj` | text, see p.adjust
`group` | Logic
`main` | Numeric

### Author(s)

Felipe de Mendiburu

### References

Steel, R.; Torri,J; Dickey, D.(1997) Principles and Procedures of Statistics A Biometrical Approach. pp178.

### See Also

`HSD.test`, `waller.test`, `SNK.test` , `bar.err`, `bar.group`,`duncan.test`

### Examples

    library(agricolae)
    data(sweetpotato)
    model<-aov(yield~virus, data=sweetpotato)
    out <- LSD.test(model,"virus", p.adj="bonferroni")
    #stargraph
    bar.group(out$groups,ylim=c(0,45),density=4,border="blue")
    #endgraph
    # Old version LSD.test()
    df<-df.residual(model)
    MSerror<-deviance(model)/df
    out <- with(sweetpotato,LSD.test(yield,virus,df,MSerror, p.adj="bonferroni",
    group=FALSE))
    #stargraph
    # Variation range: Max - Min
    bar.err(out$means,variation="range",ylim=c(0,44),bar=FALSE,col=0)
    #endgraph
    LSD.test(model,"virus",p.adj="bon",console=TRUE)

[Package agricolae version 1.2-6 Index]