statmod (version 1.4.2)

growthcurve: 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

the statistic used to measure the distance between two groups of growth curves. Default to a mean t-statistic.

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()

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

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.

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. http://www.nature.com/gene/journal/v5/n2/full/6364042a.html 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. http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-3024.2007.00969.x

See Also

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