R: Compare Groups of Growth Curves

growthcurve {statmod} | R Documentation

## Compare Groups of Growth Curves

### Description

Do all pairwise comparisons between groups of growth curves using a permutation test.

### Usage

    compareGrowthCurves(group, y, levels=NULL, nsim=100, fun=meanT, times=NULL,
                        verbose=TRUE, adjust="holm")
    compareTwoGrowthCurves(group, y, nsim=100, fun=meanT)
    plotGrowthCurves(group, y, levels=sort(unique(group)), times=NULL, col=NULL,...)

### Arguments

`group` | vector or factor indicating group membership. Missing values are allowed in `compareGrowthCurves` but not in `compareTwoGrowthCurves`.
`y` | matrix of response values with rows for individuals and columns for times. The number of rows must agree with the length of `group`. Missing values are allowed.
`levels` | a character vector containing the identifiers of the groups to be compared. By default all groups with two more more members will be compared.
`nsim` | number of permutations to estimated p-values.
`fun` | a function defining the statistic used to measure the distance between two groups of growth curves. Defaults to `meanT`.
`times` | a numeric vector containing the column numbers on which the groups should be compared. By default all the columns are used.
`verbose` | should progress results be printed?
`adjust` | method used to adjust for multiple testing, see `p.adjust`.
`col` | vector of colors corresponding to distinct groups
`...` | other arguments passed to `plot()`

### Details

`compareTwoGrowthCurves` performs a permutation test of the difference between two groups of growth curves. `compareGrowthCurves` does all pairwise comparisons between two or more groups of growth curves. Accurate p-values can be obtained by setting `nsim` to some large value, `nsim=10000` say.

### Value

`compareTwoGrowthCurves` returns a list with two components, `stat` and `p.value`, containing the observed statistics and the estimated p-value. `compareGrowthCurves` returns a data frame with components

`Group1` | name of first group in a comparison
`Group2` | name of second group in a comparison
`Stat` | observed value of the statistic
`P.Value` | estimated p-value
`adj.P.Value` | p-value adjusted for multiple testing

### Author(s)

Gordon Smyth

### References

Elso, C. M., Roberts, L. J., Smyth, G. K., Thomson, R. J., Baldwin, T. M., Foote, S. J., and Handman, E. (2004). Leishmaniasis host response loci (lmr13) modify disease severity through a Th1/Th2-independent pathway. Genes and Immunity 5, 93-100.

Baldwin, T., Sakthianandeswaren, A., Curtis, J., Kumar, B., Smyth, G. K., Foote, S., and Handman, E. (2007). Wound healing response is a major contributor to the severity of cutaneous leishmaniasis in the ear model of infection. Parasite Immunology 29, 501-513.

### See Also

`meanT`, `compareGrowthCurves`, `compareTwoGrowthCurves`

### Examples

    # A example with only one time
    data(PlantGrowth)
    compareGrowthCurves(PlantGrowth$group,as.matrix(PlantGrowth$weight))
    # Can make p-values more accurate by nsim=10000

[Package statmod version 1.4.36 Index]