Fix typos and update doc

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 = "[email protected]")
-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

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)

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

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