nEffRatio: Effective Sample Size Ratio

In csoneson/compcodeR: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

Effective Sample Size Ratio

Description

Ratio between the tree sample size and the sample size of the equivalent problem with independent measures. A result larger than one indicates a problem that is made "easier" by the tree structure. Note that it strongly depends on the tip conditions (see examples).

Usage

nEffRatio(tree, id.condition, model, selection.strength)

Arguments

tree	A phylogenetic tree. If NULL, samples are assumed to be iid.
id.condition	A named vector giving the state of each tip (sample).
model	The trait evolution model. One of "BM" or "OU".
selection.strength	If model="OU", the selection strength parameter.

Value

The ratio of sample sizes.

Examples

set.seed(1289)
## Ballanced tree
ntips <- 2^5
tree <- ape::compute.brlen(ape::stree(ntips, "balanced"))
## Alt cond : nEff greater than 1
id_cond <- rep(rep(0:1, each = 2), ntips / 4)
names(id_cond) <- tree$tip.label
plot(tree); ape::tiplabels(pch = 21, col = id_cond, bg = id_cond)
compcodeR:::nEffRatio(tree, id_cond, "BM", 0)
## Bloc cond : nEff smaller than 1
id_cond <- rep(0:1, each = ntips / 2)
names(id_cond) <- tree$tip.label
plot(tree); ape::tiplabels(pch = 21, col = id_cond, bg = id_cond)
compcodeR:::nEffRatio(tree, id_cond, "BM", 0)

csoneson/compcodeR documentation built on Nov. 3, 2024, 6:05 a.m.