miga-base 0.4.3.0 → 0.5.0.0

data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd

@@ -1,83 +1,111 @@
-\name{plot.enve.RecPlot2}
-\alias{plot.enve.RecPlot2}
-\title{plot enve RecPlot2}
-\description{Plots an `enve.RecPlot2` object.}
-\usage{\method{plot}{enve.RecPlot2}(x, layout = matrix(c(5, 5, 2, 1, 4, 3), nrow = 2), 
-    panel.fun = list(), widths = c(1, 7, 2), heights = c(1, 2), 
-    palette = grey((100:0)/100), underlay.group = TRUE, peaks.col = "darkred", 
-    use.peaks, id.lim = range(x$id.breaks), pos.lim = range(x$pos.breaks), 
-    pos.units = c("Mbp", "Kbp", "bp"), mar = list(`1` = c(5, 
-        4, 1, 1) + 0.1, `2` = c(ifelse(any(layout == 1), 1, 5), 
-        4, 4, 1) + 0.1, `3` = c(5, ifelse(any(layout == 1), 1, 
-        4), 1, 2) + 0.1, `4` = c(ifelse(any(layout == 1), 1, 
-        5), ifelse(any(layout == 2), 1, 4), 4, 2) + 0.1, `5` = c(5, 
-        3, 4, 1) + 0.1, `6` = c(5, 4, 4, 2) + 0.1), pos.splines = 0, 
-    id.splines = 1/2, in.lwd = ifelse(is.null(pos.splines) || 
-        pos.splines > 0, 1/2, 2), out.lwd = ifelse(is.null(pos.splines) || 
-        pos.splines > 0, 1/2, 2), id.lwd = ifelse(is.null(id.splines) || 
-        id.splines > 0, 1/2, 2), in.col = "darkblue", out.col = "lightblue", 
-    id.col = "black", breaks.col = "#AAAAAA40", peaks.opts = list(), 
-    ...)}
-\arguments{
-  \item{x}{`enve.RecPlot2` object to plot.}
-  \item{layout}{Matrix indicating the position of the different panels in the layout,
-where:
-0: Empty space,
-1: Counts matrix,
-2: position histogram (sequencing depth),
-3: identity histogram,
-4: Populations histogram (histogram of sequencing depths),
-5: Color scale for the counts matrix (vertical),
-6: Color scale of the counts matrix (horizontal)
-Only panels indicated here will be plotted. To plot only one panel
-simply set this to the number of the panel you want to plot.}
-  \item{panel.fun}{List of functions to be executed after drawing each panel. Use the
-indices in `layout` (as characters) as keys. Functions for indices
-missing in `layout` are ignored. For example, to add a vertical line
-at the 3Mbp mark in both the position histogram and the counts matrix:
-`list('1'=function() abline(v=3), '2'=function() abline(v=3))`.
-Note that the X-axis in both panels is in Mbp by default. To change
-this behavior, set `pos.units` accordingly.}
-  \item{widths}{Relative widths of the columns of `layout`.}
-  \item{heights}{Relative heights of the rows of `layout`.}
-  \item{palette}{Colors to be used to represent the counts matrix, sorted from no hits
-to the maximum sequencing depth.}
-  \item{underlay.group}{If TRUE, it indicates the in-group and out-group areas couloured based
-on `in.col` and `out.col`. Requires support for semi-transparency.}
-  \item{peaks.col}{If not NA, it attempts to represent peaks in the population histogram
-in the specified color. Set to NA to avoid peak-finding.}
-  \item{use.peaks}{A list of `enve.RecPlot2.Peak` objects, as returned by
-`enve.recplot2.findPeaks`. If passed, `peaks.opts` is ignored.}
-  \item{id.lim}{Limits of identities to represent.}
-  \item{pos.lim}{Limits of positions to represent (in bp, regardless of `pos.units`).}
-  \item{pos.units}{Units in which the positions should be represented (powers of 1,000
-base pairs).}
-  \item{mar}{
-}
-  \item{pos.splines}{Smoothing parameter for the splines in the position histogram. Zero
-(0) for no splines. Use NULL to automatically detect by leave-one-out
-cross-validation.}
-  \item{id.splines}{Smoothing parameter for the splines in the identity histogram. Zero
-(0) for no splines. Use NULL to automatically detect by leave-one-out
-cross-validation.}
-  \item{in.lwd}{Line width for the sequencing depth of in-group matches.}
-  \item{out.lwd}{Line width for the sequencing depth of out-group matches.}
-  \item{id.lwd}{Line width for the identity histogram.}
-  \item{in.col}{Color associated to in-group matches.}
-  \item{out.col}{Color associated to out-group matches.}
-  \item{id.col}{Color for the identity histogram.}
-  \item{breaks.col}{Color of the vertical lines indicating sequence breaks.}
-  \item{peaks.opts}{Options passed to `enve.recplot2.findPeaks`, if `peaks.col` is not NA.}
-  \item{\dots}{Any other graphic parameters (currently ignored).}
-}
-
-\value{Returns a list of `enve.RecPlot2.Peak` objects (see
-`enve.recplot2.findPeaks`). If `peaks.col`=NA or `layout` doesn't include
-4, returns NA.}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{plot.enve.RecPlot2}
+\alias{plot.enve.RecPlot2}
+\title{Enveomics: Recruitment Plot (2)}
+\usage{
+\method{plot}{enve.RecPlot2}(x, layout = matrix(c(5, 5, 2, 1, 4, 3), nrow
+  = 2), panel.fun = list(), widths = c(1, 7, 2), heights = c(1, 2),
+  palette = grey((100:0)/100), underlay.group = TRUE,
+  peaks.col = "darkred", use.peaks, id.lim = range(x$id.breaks),
+  pos.lim = range(x$pos.breaks), pos.units = c("Mbp", "Kbp", "bp"),
+  mar = list(`1` = c(5, 4, 1, 1) + 0.1, `2` = c(ifelse(any(layout == 1),
+  1, 5), 4, 4, 1) + 0.1, `3` = c(5, ifelse(any(layout == 1), 1, 4), 1, 2) +
+  0.1, `4` = c(ifelse(any(layout == 1), 1, 5), ifelse(any(layout == 2), 1,
+  4), 4, 2) + 0.1, `5` = c(5, 3, 4, 1) + 0.1, `6` = c(5, 4, 4, 2) + 0.1),
+  pos.splines = 0, id.splines = 1/2,
+  in.lwd = ifelse(is.null(pos.splines) || pos.splines > 0, 1/2, 2),
+  out.lwd = ifelse(is.null(pos.splines) || pos.splines > 0, 1/2, 2),
+  id.lwd = ifelse(is.null(id.splines) || id.splines > 0, 1/2, 2),
+  in.col = "darkblue", out.col = "lightblue", id.col = "black",
+  breaks.col = "#AAAAAA40", peaks.opts = list(), ...)
+}
+\arguments{
+\item{x}{\code{\link{enve.RecPlot2}} object to plot.}
+
+\item{layout}{Matrix indicating the position of the different panels in the layout,
+where:
+\itemize{
+  \item 0: Empty space
+  \item 1: Counts matrix
+  \item 2: position histogram (sequencing depth)
+  \item 3: identity histogram
+  \item 4: Populations histogram (histogram of sequencing depths)
+  \item 5: Color scale for the counts matrix (vertical)
+  \item 6: Color scale of the counts matrix (horizontal)
+}
+Only panels indicated here will be plotted. To plot only one panel
+simply set this to the number of the panel you want to plot.}
+
+\item{panel.fun}{List of functions to be executed after drawing each panel. Use the
+indices in \code{layout} (as characters) as keys. Functions for indices
+missing in \code{layout} are ignored. For example, to add a vertical line
+at the 3Mbp mark in both the position histogram and the counts matrix:
+\code{list('1'=function() abline(v=3), '2'=function() abline(v=3))}.
+Note that the X-axis in both panels is in Mbp by default. To change
+this behavior, set \code{pos.units} accordingly.}
+
+\item{widths}{Relative widths of the columns of \code{layout}.}
+
+\item{heights}{Relative heights of the rows of \code{layout}.}
+
+\item{palette}{Colors to be used to represent the counts matrix, sorted from no hits
+to the maximum sequencing depth.}
+
+\item{underlay.group}{If TRUE, it indicates the in-group and out-group areas couloured based
+on \code{in.col} and \code{out.col}. Requires support for semi-transparency.}
+
+\item{peaks.col}{If not \code{NA}, it attempts to represent peaks in the population histogram
+in the specified color. Set to \code{NA} to avoid peak-finding.}
+
+\item{use.peaks}{A list of \code{\link{enve.RecPlot2.Peak}} objects, as returned by
+\code{\link{enve.recplot2.findPeaks}}. If passed, \code{peaks.opts} is ignored.}
+
+\item{id.lim}{Limits of identities to represent.}
+
+\item{pos.lim}{Limits of positions to represent (in bp, regardless of \code{pos.units}).}
+
+\item{pos.units}{Units in which the positions should be represented (powers of 1,000
+base pairs).}
+
+\item{mar}{Margins of the panels as a list, with the character representation of
+the number of the panel as index (see \code{layout}).}
+
+\item{pos.splines}{Smoothing parameter for the splines in the position histogram. Zero
+(0) for no splines. Use \code{NULL} to automatically detect by leave-one-out
+cross-validation.}
+
+\item{id.splines}{Smoothing parameter for the splines in the identity histogram. Zero
+(0) for no splines. Use \code{NULL} to automatically detect by leave-one-out
+cross-validation.}
+
+\item{in.lwd}{Line width for the sequencing depth of in-group matches.}
+
+\item{out.lwd}{Line width for the sequencing depth of out-group matches.}
+
+\item{id.lwd}{Line width for the identity histogram.}
+
+\item{in.col}{Color associated to in-group matches.}
+
+\item{out.col}{Color associated to out-group matches.}
+
+\item{id.col}{Color for the identity histogram.}
+
+\item{breaks.col}{Color of the vertical lines indicating sequence breaks.}
+
+\item{peaks.opts}{Options passed to \code{\link{enve.recplot2.findPeaks}},
+if \code{peaks.col} is not \code{NA}.}
+
+\item{...}{Any other graphic parameters (currently ignored).}
+}
+\value{
+Returns a list of \code{\link{enve.RecPlot2.Peak}} objects (see
+\code{\link{enve.recplot2.findPeaks}}). If \code{peaks.col=NA} or
+\code{layout} doesn't include 4, returns \code{NA}.
+}
+\description{
+Plots an \code{\link{enve.RecPlot2}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd

@@ -1,18 +1,19 @@
-\name{summary.enve.GrowthCurve}
-\alias{summary.enve.GrowthCurve}
-\title{summary enve GrowthCurve}
-\description{Summary of an `enve.GrowthCurve` object.}
-\usage{\method{summary}{enve.GrowthCurve}(object, ...)}
-\arguments{
-  \item{object}{`enve.GrowthCurve` object.}
-  \item{\dots}{No additional parameters are currently supported.}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/growthcurve.R
+\name{summary.enve.GrowthCurve}
+\alias{summary.enve.GrowthCurve}
+\title{Enveomics: Summary of Growth Curve}
+\usage{
+\method{summary}{enve.GrowthCurve}(object, ...)
+}
+\arguments{
+\item{object}{An \code{\link{enve.GrowthCurve}} object.}
+
+\item{...}{No additional parameters are currently supported.}
+}
+\description{
+Summary of an \code{\link{enve.GrowthCurve}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd

@@ -1,18 +1,19 @@
-\name{summary.enve.TRIBS}
-\alias{summary.enve.TRIBS}
-\title{summary enve TRIBS}
-\description{Summary of an `enve.TRIBS` object.}
-\usage{\method{summary}{enve.TRIBS}(object, ...)}
-\arguments{
-  \item{object}{`enve.TRIBS` object.}
-  \item{\dots}{No additional parameters are currently supported.}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{summary.enve.TRIBS}
+\alias{summary.enve.TRIBS}
+\title{Enveomics: TRIBS Summary}
+\usage{
+\method{summary}{enve.TRIBS}(object, ...)
+}
+\arguments{
+\item{object}{\code{\link{enve.TRIBS}} object.}
+
+\item{...}{No additional parameters are currently supported.}
+}
+\description{
+Summary of an \code{\link{enve.TRIBS}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd

@@ -1,18 +1,19 @@
-\name{summary.enve.TRIBStest}
-\alias{summary.enve.TRIBStest}
-\title{summary enve TRIBStest}
-\description{Summary of an `enve.TRIBStest` object.}
-\usage{\method{summary}{enve.TRIBStest}(object, ...)}
-\arguments{
-  \item{object}{`enve.TRIBStest` object.}
-  \item{\dots}{No additional parameters are currently supported.}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{summary.enve.TRIBStest}
+\alias{summary.enve.TRIBStest}
+\title{Enveomics: TRIBS Summary Test}
+\usage{
+\method{summary}{enve.TRIBStest}(object, ...)
+}
+\arguments{
+\item{object}{\code{\link{enve.TRIBStest}} object.}
+
+\item{...}{No additional parameters are currently supported.}
+}
+\description{
+Summary of an \code{\link{enve.TRIBStest}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/find-medoid.R

@@ -5,12 +5,12 @@
 #
 
 #= Load stuff
-argv <- commandArgs(trailingOnly=T)
+argv <- commandArgs(trailingOnly = T)
 suppressPackageStartupMessages(library(ape))
 suppressPackageStartupMessages(library(enveomics.R))
 
 find_medoids <- function(ani.df, out, clades) {
-  if(nrow(ani.df)==0) return(NULL)
+  if(nrow(ani.df) == 0) return(NULL)
   ani.df$d <- 1 - (ani.df$value/100)
   dist <- enve.df2dist(ani.df, 'a', 'b', 'd', default.d = max(ani.df$d)*1.2)
   dist <- as.matrix(dist)
@@ -31,5 +31,6 @@ find_medoids <- function(ani.df, out, clades) {
 
 #= Main
 load(argv[1])
+if(! exists('ani')) ani <- aai
 find_medoids(ani.df = ani, out = argv[2], clades = argv[3])
 

data/utils/representatives.rb

@@ -9,9 +9,11 @@ proj_path = ARGV.shift or raise "Usage: #{$0} path/to/project"
 p = MiGA::Project.load(proj_path) or
   raise "Cannot load project: #{proj_path}"
 pr = p.result(:clade_finding) or
-  raise "Unavailable result: clade_finding"
-pf = pr.file_path(:clades_ani95) or
-  raise "Unavailable result file: clades_ani95"
+  raise 'Unavailable result: clade_finding'
+if (pf = pr.file_path(:clades_gsp)).nil?
+  pf = pr.file_path(:clades_ani95) or
+    raise 'Unavailable result files: clades_gsp and clades_ani95'
+end
 
 # Read ANIspp
 ani_spp = []

data/utils/subclade/pipeline.rb

@@ -4,7 +4,10 @@ module MiGA::SubcladeRunner::Pipeline
 
   # Run species-level clusterings using ANI > 95% / AAI > 90%
   def cluster_species
-    tasks = {ani95: [:ani_distances, 95.0], aai90: [:aai_distances, 90.0]}
+    tasks = {
+      ani95: [:ani_distances, opts[:gsp_ani], :ani],
+      aai90: [:aai_distances, opts[:gsp_aai], :aai]
+    }
     tasks.each do |k, par|
       # Final output
       ogs_file = "miga-project.#{k}-clades"
@@ -23,23 +26,31 @@ module MiGA::SubcladeRunner::Pipeline
       end
       ofh.close
       # Cluster genomes
-      `ogs.mcl.rb -o '#{ogs_file}.tmp' --abc '#{abc_path}' -t '#{opts[:thr]}'`
-      File.open(ogs_file, 'w') do |fh|
-        File.foreach("#{ogs_file}.tmp").with_index do |ln, lno|
-          fh.puts ln if lno > 0
+      if File.size? abc_path
+        `ogs.mcl.rb -o '#{ogs_file}.tmp' --abc '#{abc_path}' -t '#{opts[:thr]}'`
+        File.open(ogs_file, 'w') do |fh|
+          File.foreach("#{ogs_file}.tmp").with_index do |ln, lno|
+            fh.puts ln if lno > 0
+          end
         end
+        File.unlink "#{ogs_file}.tmp"
+      else
+        FileUtils.touch ogs_file
+      end
+      if par[2].to_s == opts[:gsp_metric]
+        FileUtils.cp(ogs_file, "miga-project.gsp-clades")
       end
-      File.unlink "#{ogs_file}.tmp"
     end
 
-    # Find species medoids
+    # Find genomospecies medoids
     src = File.expand_path('utils/find-medoid.R', MiGA::MiGA.root_path)
-    `Rscript '#{src}' ../../09.distances/03.ani/miga-project.Rdata \
-      miga-project.ani95-medoids miga-project.ani95-clades`
+    dir = opts[:gsp_metric] == 'aai' ? '02.aai' : '03.ani'
+    `Rscript '#{src}' ../../09.distances/#{dir}/miga-project.Rdata \
+      miga-project.gsp-medoids miga-project.gsp-clades`
 
     # Propose clades
     ofh = File.open('miga-project.proposed-clades', 'w')
-    File.open('miga-project.ani95-clades', 'r') do |ifh|
+    File.open('miga-project.gsp-clades', 'r') do |ifh|
       ifh.each_line do |ln|
         next if $.==1
         r = ln.chomp.split(',')
@@ -55,7 +66,7 @@ module MiGA::SubcladeRunner::Pipeline
     metric_res = project.result(step) or raise "Incomplete step #{step}"
     matrix = metric_res.file_path(:matrix)
     `Rscript '#{src}' '#{matrix}' miga-project '#{opts[:thr]}' \
-      miga-project.ani95-medoids`
+      miga-project.ani95-medoids '#{opts[:run_clades] ? 'cluster' : 'empty'}'`
     File.rename('miga-project.nwk',"miga-project.#{metric}.nwk") if
           File.exist? 'miga-project.nwk'
   end

data/utils/subclade/runner.rb

@@ -18,7 +18,11 @@ class MiGA::SubcladeRunner
     clades_dir = File.expand_path('data/10.clades', project.path)
     @home = File.expand_path(@step == :clade_finding ? '01.find' : '02.ani',
           clades_dir)
-    @opts[:thr] ||= ENV.fetch("CORES"){ 2 }.to_i
+    @opts[:thr] ||= ENV.fetch('CORES') { 2 }.to_i
+    @opts[:run_clades] = !!@project.metadata.data.fetch(:run_clades) { true }
+    @opts[:gsp_ani] = @project.metadata.data.fetch(:gsp_ani) { 95.0 }.to_f
+    @opts[:gsp_aai] = @project.metadata.data.fetch(:gsp_aai) { 90.0 }.to_f
+    @opts[:gsp_metric] = @project.metadata.data.fetch(:gsp_metric){ 'ani' }.to_s
   end
 
   # Launch the appropriate analysis

data/utils/subclades-compile.rb

@@ -46,4 +46,4 @@ max_depth = c.values.map{|i| i.count}.max
 File.open("#{out}.tsv", 'w') do |fh|
   c.each { |k,v| fh.puts ([k] + v + ["0"]*(max_depth-v.count)).join("\t") }
 end
-File.open("#{out}.nwk", 'w') { |fh| fh.puts print_tree(c) + ";" }
+File.open("#{out}.nwk", 'w') { |fh| fh.puts print_tree(c).to_s + ";" }

data/utils/subclades.R

@@ -248,6 +248,12 @@ ggplotColours <- function(n=6, h=c(0, 360)+15, alpha=1){
 
 #= Main
 options(warn = 1)
-subclades(ani_file = argv[1], out_base = argv[2],
-  thr = ifelse(is.na(argv[3]), 1, as.numeric(argv[3])), sel = argv[4])
-
+if(length(argv) >= 5 & argv[5] == 'empty'){
+  generate_empty_files(argv[2])
+  write.table(NULL, paste(argv[2], "medoids", sep="."))
+  write.table(NULL, paste(argv[2], "classif", sep="."))
+  write.table(date(), paste(argv[2], "ready", sep="."))
+}else{
+  subclades(ani_file = argv[1], out_base = argv[2],
+    thr = ifelse(is.na(argv[3]), 1, as.numeric(argv[3])), sel = argv[4])
+}

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.4.3.0
+  version: 0.5.0.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-09-10 00:00:00.000000000 Z
+date: 2019-11-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -101,22 +101,29 @@ files:
 - lib/miga/cli/action/about.rb
 - lib/miga/cli/action/add.rb
 - lib/miga/cli/action/add_result.rb
+- lib/miga/cli/action/classify_wf.rb
 - lib/miga/cli/action/console.rb
 - lib/miga/cli/action/daemon.rb
 - lib/miga/cli/action/date.rb
+- lib/miga/cli/action/derep_wf.rb
 - lib/miga/cli/action/doctor.rb
 - lib/miga/cli/action/edit.rb
 - lib/miga/cli/action/files.rb
 - lib/miga/cli/action/find.rb
 - lib/miga/cli/action/generic.rb
 - lib/miga/cli/action/get.rb
+- lib/miga/cli/action/get_db.rb
+- lib/miga/cli/action/index_wf.rb
 - lib/miga/cli/action/init.rb
+- lib/miga/cli/action/init/daemon_helper.rb
 - lib/miga/cli/action/ln.rb
 - lib/miga/cli/action/ls.rb
 - lib/miga/cli/action/ncbi_get.rb
 - lib/miga/cli/action/new.rb
 - lib/miga/cli/action/next_step.rb
 - lib/miga/cli/action/plugins.rb
+- lib/miga/cli/action/preproc_wf.rb
+- lib/miga/cli/action/quality_wf.rb
 - lib/miga/cli/action/rm.rb
 - lib/miga/cli/action/run.rb
 - lib/miga/cli/action/stats.rb
@@ -125,7 +132,10 @@ files:
 - lib/miga/cli/action/tax_index.rb
 - lib/miga/cli/action/tax_set.rb
 - lib/miga/cli/action/tax_test.rb
+- lib/miga/cli/action/wf.rb
 - lib/miga/cli/base.rb
+- lib/miga/cli/objects_helper.rb
+- lib/miga/cli/opt_helper.rb
 - lib/miga/common.rb
 - lib/miga/common/base.rb
 - lib/miga/common/format.rb
@@ -406,6 +416,9 @@ files:
 - utils/enveomics/enveomics.R/README.md
 - utils/enveomics/enveomics.R/data/growth.curves.rda
 - utils/enveomics/enveomics.R/data/phyla.counts.rda
+- utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd
+- utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd
+- utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd
 - utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd
 - utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd
 - utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd
@@ -449,7 +462,6 @@ files:
 - utils/enveomics/enveomics.R/man/enve.tribs.Rd
 - utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
 - utils/enveomics/enveomics.R/man/enve.truncate.Rd
-- utils/enveomics/enveomics.R/man/enveomics.R-package.Rd
 - utils/enveomics/enveomics.R/man/growth.curves.Rd
 - utils/enveomics/enveomics.R/man/phyla.counts.Rd
 - utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd
@@ -459,7 +471,6 @@ files:
 - utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd
 - utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd
 - utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd
-- utils/enveomics/enveomics.R/man/z$-methods.Rd
 - utils/enveomics/globals.mk
 - utils/enveomics/manifest.json
 - utils/find-medoid.R