diff --git a/R/testNhoods.R b/R/testNhoods.R index 239595c..38f5202 100644 --- a/R/testNhoods.R +++ b/R/testNhoods.R @@ -71,11 +71,18 @@ #' function \code{fitGLMM} can be used to fit a mixed effect model to each #' nhood (see \code{fitGLMM} docs for details). #' -#' Parallelisation is currently only enabled for the NB-LMM and uses the BiocParallel paradigm. In -#' general the GLM implementation in \code{glmQLFit} is sufficiently fast that it does not require +#' Parallelisation is currently only enabled for the NB-GLMM and uses the BiocParallel paradigm at +#' the level of R, and OpenMP to allow multi-threading of RCpp code. In general the GLM implementation +#' in \code{glmQLFit} is sufficiently fast that it does not require #' parallelisation. Parallelisation requires the user to pass a \linkS4class{BiocParallelParam} object -#' with the parallelisation arguments contained therein. This relies on the user to specify how -#' parallelisation - for details see the \code{BiocParallel} package. +#' with the parallelisation arguments contained therein. This relies on the user specifying how to +#' parallelise - for details see the \code{BiocParallel} package. +#' +#' \code{model.contrasts} are used to define specific comparisons for DA testing. Currently, +#' \code{testNhoods} will take the last formula variable for comparisons, however, contrasts +#' need this to be the first variable. A future update will harmonise these behaviours for +#' consistency. While it is strictly feasible to compute multiple contrasts at once, the +#' recommendation, for ease of interpretability, is to compute one at a time. #' #' @return A \code{data.frame} of model results, which contain: #' \describe{