update

.Rbuildignore

@@ -1,2 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+.travis.yml

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: MicEco
 Title: Various functions for microbial community data
-Version: 0.9.2
+Version: 0.9.3
 Authors@R: person("Jakob", "Russel", email = "russel2620@gmail.com", role = c("aut", "cre"))
-Description: What the title says.
+Description: Collection of functions for microbiome analyses. E.g. fitting neutral models and standardized effect sizes of phylogenetic beta diversities, and much more.
 Depends: R (>= 3.2.5)
-Imports: phyloseq, foreach, doSNOW, picante, vegan, snow, bbmle, Hmisc, abind
-License: GPL (>= 3)
+Imports: stats, utils, phyloseq, foreach, doSNOW, picante, vegan, snow, bbmle, Hmisc, abind
+License: GPL (>= 3) | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.1
 Remotes: bioc::release/phyloseq

NAMESPACE

@@ -11,7 +11,6 @@ export(rarefy_rrna)
 export(rarefy_rrna.matrix)
 export(rarefy_rrna.phyloseq)
 export(ses.UniFrac)
-export(ses.bootstrap)
 export(ses.comdist)
 export(ses.comdist2)
 export(ses.comdistnt)
@@ -26,3 +25,16 @@ import(phyloseq)
 import(picante)
 import(vegan)
 importFrom(abind,abind)
+importFrom(stats,as.dist)
+importFrom(stats,cov)
+importFrom(stats,dnorm)
+importFrom(stats,p.adjust)
+importFrom(stats,pbeta)
+importFrom(stats,quantile)
+importFrom(stats,sd)
+importFrom(stats,var)
+importFrom(stats,weighted.mean)
+importFrom(utils,combn)
+importFrom(utils,read.table)
+importFrom(utils,setTxtProgressBar)
+importFrom(utils,txtProgressBar)

R/UniFrac.multi.R

@@ -10,6 +10,8 @@
 #' @return A distance object with the average \code{UniFrac} distances 
 #' @import foreach parallel doSNOW phyloseq
 #' @importFrom abind abind
+#' @importFrom stats as.dist cov dnorm p.adjust pbeta quantile sd var weighted.mean
+#' @importFrom utils combn read.table setTxtProgressBar txtProgressBar
 #' @export
 UniFrac.multi <- function(physeq, R = 100, seed = 42, cores = 1, ...){
 
@@ -31,6 +33,7 @@ UniFrac.multi <- function(physeq, R = 100, seed = 42, cores = 1, ...){
   opts <- list(progress = progress)
 
   # UniFracs
+  i <- NULL
   UFs <- foreach(i = 1:R, .packages = "phyloseq", .options.snow = opts) %dopar% {
     set.seed(seeds[i])
     UniFrac(physeq, ...)

R/comdist.par.R

@@ -39,7 +39,8 @@ comdist.par <- function (comm, dis, abundance.weighted = FALSE, cores = 1, progr
     cl <- makeCluster(cores)
     registerDoSNOW(cl)
   }
-
+
+  l <- NULL 
   comdist <- foreach(l = 1:(N - 1),.combine = cbind, .options.snow = opts) %dopar% {
     comdist.sub <- as.numeric(rep(NA,N))
     for (k in 2:N) {

R/comdistnt.par.R

@@ -38,6 +38,7 @@ comdistnt.par <- function (comm, dis, abundance.weighted = FALSE, exclude.conspe
     registerDoSNOW(cl)
   }
 
+  i <- NULL
   comdisnt <- foreach (i = 1:(N-1),.combine = rbind, .options.snow = opts) %dopar% {
 
     comdisnt.sub <- as.numeric(rep(NA,N))

R/gg_13_5_16S.R

@@ -0,0 +1,7 @@
+#' 16S copy numbers for GreenGenes 13_5 database OTUs
+#' 
+#' Precalculated for the PICRUSt pipeline (https://picrust.github.io/picrust/picrust_precalculated_files.html)
+#' @name gg_13_5_16S
+#' @docType data
+#' @keywords data
+NULL

R/ses.UniFrac.R

@@ -71,6 +71,8 @@ ses.UniFrac <- function (physeq, method = "taxa.labels", fixedmar = "both", shuf
     cl <- makeCluster(cores)
     registerDoSNOW(cl)
   }
+
+  i <- NULL
   unifrac.rand <- foreach(i = 1:runs, .packages = "phyloseq", .options.snow = opts) %dopar% {
 
     if(method == "taxa.labels"){

R/ses.comdistnt2.R

@@ -11,6 +11,7 @@
 #' @param burnin Number of null communities discarded before proper analysis in sequential ("swap", "tswap") methods.
 #' @param thin Number of discarded permuted matrices between two evaluations in sequential ("swap", "tswap") methods.
 #' @param abundance.weighted Should mean nearest taxon distances for each species be weighted by species abundance? (default = FALSE)
+#' @param exclude.conspecifics Should conspecific taxa in different communities be exclude from MNTD calculations? (default = FALSE)
 #' @param runs Number of randomizations
 #' @param cores Number of cores to use for parallel computing
 #' @details See permat (vegan) for detailed options

README.md

@@ -1,3 +1,6 @@
+[![Travis Build
+Status](https://travis-ci.org/Russel88/MicEco.svg?branch=master)](https://travis-ci.org/Russel88/MicEco)
+
 MicEco: Various functions for analysis for microbial community data
 -------------------------------------------------------------------