diff --git a/DESCRIPTION b/DESCRIPTION index bbb49e5..72ce24c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,10 +3,10 @@ Title: PhyloseqExtended Version: 0.1.0.9000 Authors@R: person(given = "Mahendra", - family = "Mahendra", + family = "Mariadassou", role = c("aut", "cre"), email = "mahendra.mariadassou@inra.fr") -Description: Adds severals additional functions to phyloseq, mainly used for training. +Description: Adds severals additional functions to phyloseq (rarefaction curves, phylogenetic diversities, specificity and prevalence indices, nice composition plots, etc). Mostly used during training sessions. License: GPL-3 Encoding: UTF-8 LazyData: true diff --git a/NAMESPACE b/NAMESPACE index 22a6078..f7aa0b6 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -2,6 +2,7 @@ export(estimate_local_specificity) export(estimate_prevalence) +export(fast_tax_glom) export(ggformat) export(ggpdrare) export(ggrare) @@ -24,5 +25,6 @@ importFrom(biomformat,biom_data) importFrom(biomformat,read_biom) importFrom(biomformat,sample_metadata) importFrom(plyr,rbind.fill.matrix) +importFrom(tibble,column_to_rownames) importFrom(vegan,ordilabel) importFrom(vegan,specnumber) diff --git a/R/richness.R b/R/richness.R index e17816f..2918d49 100644 --- a/R/richness.R +++ b/R/richness.R @@ -1,6 +1,3 @@ -require(parallel) -options(mc.cores= 2) - #' Phylogenetic diversity #' #' @param physeq phyloseq class object, from which phylogeny and abundance data are extracted @@ -46,7 +43,6 @@ phylodiv <- function(physeq, theta = 0) { return(pd) } - #' Rarefaction curves for phylogenetic diversity, ggplot-style #' #' @inheritParams ggrare diff --git a/R/specificity_methods.R b/R/specificity_methods.R index 20c3719..4d4dff5 100644 --- a/R/specificity_methods.R +++ b/R/specificity_methods.R @@ -3,6 +3,7 @@ ## Compute specificity of a vector ## x represents (possibly not normalised) distribution of quantity ## of interest across conditions +#' @keywords internal specificity <- function(x, index = c("shannon", "simpson", "yanai", "indspec"), groupfrac = NULL) { ## Args: ## - x: matrix (vectors are automatically coerced to 1-row matrices), specificity @@ -54,6 +55,7 @@ specificity <- function(x, index = c("shannon", "simpson", "yanai", "indspec"), ## Compute local specificity of a vector ## x represents (possibly not normalised) distribution of quantity ## of interest across conditions +#' @keywords internal local_specificity <- function(x, index = c("fraction", "indspec"), groupfrac = NULL) { ## Args: ## - x: matrix (vectors are automatically coerced to 1-row matrices), specificity diff --git a/man/top_taxa.Rd b/man/top_taxa.Rd index 40998d7..7a785e5 100644 --- a/man/top_taxa.Rd +++ b/man/top_taxa.Rd @@ -14,7 +14,7 @@ top_taxa(physeq, taxaRank = NULL, numberOfTaxa = 9) \item{numberOfTaxa}{Number of top taxa to return} } \value{ -A character vector the the `numberOfTaxa` most abundant `taxaRank`-level taxa +A matrix corresponding to the `numberOfTaxa` most abundant taxa at level `taxaRank`-level } \description{ Find the most abundant taxa at a given taxonomic rank