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Adding p.adjust.method argument for TBI #41

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Merged
sdray merged 1 commit into from
Feb 23, 2026
+9 −6
Merged

Adding p.adjust.method argument for TBI #41

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15 changes: 9 additions & 6 deletions R/TBI.R
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,9 @@
#' temporal beta indices and the permutation test of the B-C difference. Use
#' \code{nperm} = 999 or 9999 in real studies.
#'
#' @param p.adjust.method a string indicating a method for multiple adjustment,
#' see \code{p.adjust.methods} for possible choices.
#'
#' @param BCD If \code{BCD=TRUE}, the B and C components of the
#' percentage difference (\code{method="\%difference"}) and Ruzicka
#' (\code{method"ruzicka"}) indices are computed and presented in an output
Expand Down Expand Up @@ -181,9 +184,9 @@
#' their species composition.
#'
#' \item \code{p.adj} The p-values are corrected for multiple testing using
#' function p.adjust of \code{stats}. The adjustment is done using
#' \code{method="holm"}, which is the default option of the \code{p.adjust}
#' function.
#' function p.adjust of \code{stats}. The adjustment is done by default using
#' \code{method="holm"}. User can change the correction type via the argument
#' \code{pa.adjust.method}, see \code{p.adjust.methods} for possible choices.
#'
#' \item \code{BCD.mat} An output table with four columns: B/den, C/den,
#' D=(B+C)/den, and Change. The value den is the denominator of the index,
Expand Down Expand Up @@ -311,8 +314,8 @@
#' @export TBI
#'

TBI <- function(mat1, mat2, method = "%difference", pa.tr = FALSE, nperm = 99, BCD = TRUE, replace = FALSE,
test.BC = TRUE, test.t.perm = FALSE, save.BC = FALSE, seed. = NULL, clock = FALSE) {
TBI <- function(mat1, mat2, method = "%difference", pa.tr = FALSE, nperm = 99, p.adjust.method = "holm", BCD = TRUE,
replace = FALSE, test.BC = TRUE, test.t.perm = FALSE, save.BC = FALSE, seed. = NULL, clock = FALSE) {

### Internal functions --

Expand Down Expand Up @@ -562,7 +565,7 @@ TBI <- function(mat1, mat2, method = "%difference", pa.tr = FALSE, nperm = 99, B
} else
p.dist <- NA # if nperm=0

p.adj <- p.adjust(p.dist,"holm")
p.adj <- p.adjust(p.dist, method = p.adjust.method)
})
A[3] <- sprintf("%2f",A[3])
if (clock) cat("Computation time =", A[3]," sec",'\n')
Expand Down
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