Compare Groups of Growth Curves
Do all pairwise comparisons between groups of growth curves using a permutation test.
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,...)group |
vector or factor indicating group membership. Missing values are allowed in |
y |
matrix of response values with rows for individuals and columns for times. The number of rows must agree with the length of |
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 |
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 |
col |
vector of colors corresponding to distinct groups |
... |
other arguments passed to |
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.
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 |
Gordon Smyth
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.
# A example with only one time data(PlantGrowth) compareGrowthCurves(PlantGrowth$group,as.matrix(PlantGrowth$weight)) # Can make p-values more accurate by nsim=10000
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