| mcpHill {simboot} | R Documentation |
Multiplicity-adjusted p-values for comparing biodiversity via simultaneous inference of a user-defined selection of diversity indices
Description
The function mcpHill allows for comparing biological diversities of two or more groups. It simultaneously tests a user-defined selection of Hill numbers of orders q, which are considered appropriate and useful indices for measuring diversity (Jost 2008). As an output mcpHill gives p-values adjusted for multiplicity according to the method of Westfall & Young (1993).
Usage
mcpHill(dataf, fact, align = FALSE, block, boots = 5000, udmat
= FALSE, usermat, mattype = "Dunnett", dunbase = 1, qval = seq(-1, 3),
opt = "two.sided") Arguments
dataf |
Data frame containing numerical values (e.g. species counts or relative abundances). Rows represent repeated observations of the (two or more) groups, columns represent taxonomic units (usually species, or phyla, classes etc.). |
fact |
Vector assigning (two or more) factor levels to the observations, i.e. the groups to be compared. The length of fact must equal the number of rows in dataf. |
align |
Logical indicating whether a block alignment should be carried out. If TRUE, the blocks must be specified as a vector in block. Default is FALSE. |
block |
Vector assigning which block an observation belongs to. Only required if align=TRUE. The length of block must equal the number of rows in dataf. |
boots |
Number of bootstrap replications. Values lower than 999 are rejected. Default is 5000. |
udmat |
Logical indicating whether used-defined contrasts are applied for multiple testing. If TRUE, a contrast matrix has to be specified via usermat. Default is FALSE, meaning that the contrast matrix is specified by a catchword (e.g. "Tukey", "Dunnett" etc.). |
usermat |
Matrix specifying user-defined multiple testing contrasts. Only required if udmat=TRUE. The row sums in the matrix must equal zero. |
mattype |
Type of
contrast matrix for multiple comparisons of
groups. Hence only required for comparisons of more than
two groups. Can be specified by the catchwords used in
function |
dunbase |
Integer determining the factor group (in alphanumerical order) to be considered the baseline or control and therefore only needed for Dunnett-type multiple contrasts. Default is 1. |
qval |
Vector containing the requested selection of q-values in order to specify the Hill numbers of orders q to be investigated. Default is seq(-1,3). |
opt |
"greater" performs an upper-tailed test, "less" a lower-tailed test and "two.sided" a two-tailed test. Default is "two.sided". |
Value
The output of mcpHill is a matrix containing the chosen selection of Hill numbers (their orders q) in the first column. The multiplicity-adjusted p-values for each hypothesis tested are in the second column. The names of the rows denote which groups are being compared.
Author(s)
Philip Pallmann
References
Pallmann, P. et al. (2012) Assessing group differences in biodiversity by simultaneously testing a user-defined selection of diversity indices. Molecular ecology resources 12, 1068–78.
Jost, L. (2008) G(ST) and its relatives do not measure differentiation. Molecular Ecology, 17, 4015–4026.
Westfall, P.H. and Young S.S. (1993) Resampling-based multiple testing: examples and methods for p-value adjustment. New York: Wiley.
Examples
### Multiple testing with user-defined contrasts after block alignment
data(predatGM)
mymat <- rbind( "GM - S1" = c(1,-1,0,0), "GM - S2" = c(1,0,-1,0), "GM -
S3" = c(1,0,0,-1), "S1 - S2" = c(0,1,-1,0), "S1 - S3" = c(0,1,0,-1) )
# example runs with only 100 bootstrap steps. For estimation use 2000 or more.
mcpHill(dataf=predatGM[,3:35], fact=predatGM[,2], align=TRUE,
block=predatGM[,1], boots=100, udmat=TRUE, usermat=mymat, qval=seq(-1,
3, by=0.5))
# with Dunnett-type contrast matrix
mcpHill(dataf=predatGM[,3:35], fact=predatGM[,2], align=TRUE,
block=predatGM[,1], boots=100, udmat=FALSE, mattype = "Dunnett", qval=seq(-1,
3, by=0.5))