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v0.99.16 Added back missing "\usage" doc for S4 methods

This is an ongoing glitch in the development of Roxygen, owing to the
way it handles S4 methods. The current solution was to revert my
roxygen version to my static build (roxygen/joey711).
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1 parent 7abcebf commit 60cc83e68d020b810bb862dd9de2f96a6641f7a3 @joey711 committed Feb 8, 2012
Showing with 239 additions and 156 deletions.
  1. BIN .DS_Store
  2. +7 −5 DESCRIPTION
  3. +7 −7 NAMESPACE
  4. +2 −4 TODO.txt
  5. +2 −3 man/UFwi.Rd
  6. +19 −16 man/UniFrac-methods.Rd
  7. +3 −3 man/access.Rd
  8. +3 −0 man/assign-otuTable.Rd
  9. +3 −0 man/assign-speciesarerows.Rd
  10. +3 −0 man/assign-tre.Rd
  11. +1 −1 man/calcplot.Rd
  12. +6 −1 man/cca-rda-phyloseq-methods.Rd
  13. +1 −2 man/data-enterotype.Rd
  14. +0 −1 man/data-esophagus.Rd
  15. +0 −1 man/data-ex1.Rd
  16. +2 −3 man/data-soilrep.Rd
  17. +3 −3 man/export_env_file.Rd
  18. +2 −2 man/export_mothur_dist.Rd
  19. +3 −0 man/genefilterSample-methods.Rd
  20. +3 −0 man/getSamples-methods.Rd
  21. +3 −0 man/getSpecies-methods.Rd
  22. +4 −4 man/getslots.phyloseq.Rd
  23. +5 −2 man/import-methods.Rd
  24. +1 −1 man/import_env_file.Rd
  25. +4 −4 man/import_mothur.Rd
  26. +1 −1 man/import_mothur_otutable.Rd
  27. +3 −3 man/import_mothur_tree.Rd
  28. +2 −2 man/import_pyrotagger_tab.Rd
  29. +6 −6 man/import_qiime.Rd
  30. +1 −1 man/import_qiime_otu_tax.Rd
  31. +2 −2 man/makenetwork.Rd
  32. +3 −0 man/merge_phyloseq_pair-methods.Rd
  33. +4 −1 man/merge_samples-methods.Rd
  34. +4 −1 man/merge_species-methods.Rd
  35. +5 −2 man/mt-methods.Rd
  36. +3 −0 man/nsamples-methods.Rd
  37. +3 −0 man/nspecies-methods.Rd
  38. +1 −1 man/otu2df.Rd
  39. +1 −1 man/otuTable-class.Rd
  40. +3 −0 man/otuTable-methods.Rd
  41. +7 −8 man/phyloseq.Rd
  42. +14 −14 man/plot_ordination_phyloseq.Rd
  43. +4 −1 man/plot_phyloseq-methods.Rd
  44. +10 −10 man/plot_tree_phyloseq.Rd
  45. +11 −8 man/prune_samples-methods.Rd
  46. +3 −0 man/reconcile_species-methods.Rd
  47. +3 −0 man/sample.names-methods.Rd
  48. +1 −1 man/sampleData-class.Rd
  49. +2 −0 man/sampleData-methods.Rd
  50. +1 −1 man/show_mothur_list_cutoffs.Rd
  51. +3 −0 man/species.names-methods.Rd
  52. +3 −0 man/speciesAreRows-methods.Rd
  53. +8 −8 man/subset_samples-methods.Rd
  54. +2 −2 man/tableprint.Rd
  55. +2 −0 man/taxTab-methods.Rd
  56. +9 −4 man/taxaplot-methods.Rd
  57. +13 −10 man/taxglom-methods.Rd
  58. +2 −2 man/taxglom.internal.Rd
  59. +1 −1 man/tip-annotate.Rd
  60. +3 −0 man/tipglom-methods.Rd
  61. +1 −1 man/transformcounts.Rd
  62. +3 −0 man/transpose-methods.Rd
  63. +4 −1 man/tre-methods.Rd
View
BIN .DS_Store
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12 DESCRIPTION
@@ -1,7 +1,8 @@
Package: phyloseq
-Version: 0.99.15
-Date: 2012-02-07
-Title: Handling and analysis of high-throughput phylogenetic sequence data.
+Version: 0.99.16
+Date: 2012-02-08
+Title: Handling and analysis of high-throughput
+ phylogenetic sequence data.
Description: phyloseq is a set of classes, wrappers, and
tools to facilitate the import, storage, and analysis
of phylogenetic sequencing data.
@@ -24,8 +25,9 @@ Suggests:
ade4,
genefilter
Enhances: doParallel (>= 1.0)
-biocViews: Clustering, Classification, MultipleComparisons, QualityControl,
- GeneticVariability, HighThroughputSequencing
+biocViews: Clustering, Classification, MultipleComparisons,
+ QualityControl, GeneticVariability,
+ HighThroughputSequencing
Collate:
'allclasses.r'
'allpackage.r'
View
14 NAMESPACE
@@ -1,18 +1,17 @@
export("samData<-")
export("sampleData<-")
export("taxTab<-")
-export(TransformSampleCounts)
export(access)
export(calcplot)
export(export_env_file)
export(filterfunSample)
export(getslots.phyloseq)
-export(import_RDP_cluster)
export(import_env_file)
-export(import_mothur)
export(import_mothur_dist)
+export(import_mothur)
export(import_pyrotagger_tab)
export(import_qiime)
+export(import_RDP_cluster)
export(makenetwork)
export(merge_phyloseq)
export(phyloseq)
@@ -24,8 +23,8 @@ export(sampleMap)
export(sampleNames)
export(sampleSums)
export(show_mothur_list_cutoffs)
-export(speciesSums)
export(speciesarerows)
+export(speciesSums)
export(subset_samples)
export(subset_species)
export(taxtab)
@@ -36,8 +35,9 @@ export(tiptext)
export(topf)
export(topk)
export(topp)
-export(transformSampleCounts)
export(transformsamplecounts)
+export(transformSampleCounts)
+export(TransformSampleCounts)
exportClasses(otuTable)
exportClasses(phylo)
exportClasses(phyloseq)
@@ -47,7 +47,6 @@ exportMethods("[")
exportMethods("otuTable<-")
exportMethods("speciesarerows<-")
exportMethods("tre<-")
-exportMethods(UniFrac)
exportMethods(cca.phyloseq)
exportMethods(genefilterSample)
exportMethods(getSamples)
@@ -70,11 +69,12 @@ exportMethods(show)
exportMethods(species.names)
exportMethods(speciesAreRows)
exportMethods(t)
-exportMethods(taxTab)
exportMethods(taxaplot)
exportMethods(taxglom)
+exportMethods(taxTab)
exportMethods(tipglom)
exportMethods(tre)
+exportMethods(UniFrac)
exportMethods(vegdist)
import(foreach)
import(igraph)
View
6 TODO.txt
@@ -1,9 +1,7 @@
phyloseq is under very active development.
-Planned feature improvements are publicly catalogued at the main phyloseq development site on github.
-
-Specifically on the "Issues" page for phyloseq:
+Planned feature improvements are publicly catalogued at the main phyloseq development site on github; specifically on the "Issues" page for phyloseq:
https://github.com/joey711/phyloseq/issues
-If the feature you are hoping for is not listed, you are welcome to add it as a feature request "issue" on this page.
+If the feature you are hoping for is not listed, you are welcome to add it as a feature request "issue" on this page. This request will be publicly available and listed on the page.
View
5 man/UFwi.Rd
@@ -2,9 +2,8 @@
\alias{UFwi}
\title{Internal function for weighted UniFrac edge-weight.}
\usage{
- UFwi(edge, samples, OTU, tree,
- AT = sum(OTU[samples[1], ]),
- BT = sum(OTU[samples[2], ]))
+ UFwi(edge, samples, OTU, tree, AT = sum(OTU[samples[1],
+ ]), BT = sum(OTU[samples[2], ]))
}
\arguments{
\item{edge}{The edge index}
View
35 man/UniFrac-methods.Rd
@@ -3,6 +3,10 @@
\alias{UniFrac}
\alias{UniFrac,phyloseq-method}
\title{Calculate weighted or unweighted (Fast) UniFrac distance for all sample pairs.}
+\usage{
+ UniFrac(physeq, weighted=FALSE, normalized=TRUE,
+ parallel=FALSE, fast=TRUE)
+}
\arguments{
\item{physeq}{(Required). \code{\link{phyloseq-class}},
containing at minimum a phylogenetic tree
@@ -11,17 +15,17 @@
coercions that might be necessary.}
\item{weighted}{(Optional). Logical. Should use
- weighted-UniFrac calculation? Weighted-UniFrac takes
- into account the relative abundance of species/taxa
- shared between samples, whereas unweighted-UniFrac only
+ weighted-UniFrac calculation? Weighted-UniFrac takes into
+ account the relative abundance of species/taxa shared
+ between samples, whereas unweighted-UniFrac only
considers presence/absence. Default is \code{FALSE},
meaning the unweighted-UniFrac distance is calculated for
all pairs of samples.}
\item{normalized}{(Optional). Logical. Should the output
be normalized such that values range from 0 to 1
independent of branch length values? Default is
- \code{TRUE}. Note that (unweighted) \code{UniFrac} is
+ \code{TRUE}. Note that (unweighted) \code{UniFrac} is
always normalized by total branch-length, and so this
value is ignored when \code{weighted == FALSE}.}
@@ -30,25 +34,24 @@
simultaneously? This can dramatically hasten the
computation time for this function. However, it also
requires that the user has registered a parallel
- ``backend'' prior to calling this function. Default is
+ ``backend'' prior to calling this function. Default is
\code{FALSE}. If FALSE, UniFrac will register a serial
backend so that \code{foreach::\%dopar\%} does not throw
a warning.}
\item{fast}{(Optional). Logical. Do you want to use the
``Fast UniFrac'' algorithm? Implemented natively in the
- \code{phyloseq-package}. This is the default and the
+ \code{phyloseq-package}. This is the default and the
recommended option. There should be no difference in the
- output between the two algorithms. Moreover, the
- original UniFrac algorithm only outperforms this
- implementation of fast-UniFrac if the datasets are so
- small (approximated by the value of
- \code{nspecies(physeq) * nsamples(physeq)}) that the
- difference in time is inconsequential (less than 1
- second). In practice it does not appear that this
- parameter should ever be set to \code{FALSE}, but the
- option is nevertheless included in the package for
- comparisons and instructional purposes.}
+ output between the two algorithms. Moreover, the original
+ UniFrac algorithm only outperforms this implementation of
+ fast-UniFrac if the datasets are so small (approximated
+ by the value of \code{nspecies(physeq) *
+ nsamples(physeq)}) that the difference in time is
+ inconsequential (less than 1 second). In practice it does
+ not appear that this parameter should ever be set to
+ \code{FALSE}, but the option is nevertheless included in
+ the package for comparisons and instructional purposes.}
}
\value{
a sample-by-sample distance matrix, suitable for NMDS,
View
6 man/access.Rd
@@ -17,9 +17,9 @@
}
\value{
Returns the component object specified by the argument
- \code{slot}. Returns NULL if slot does not exist.
- Returns \code{physeq} as-is if it is a component class
- that already matches the slot name.
+ \code{slot}. Returns NULL if slot does not exist. Returns
+ \code{physeq} as-is if it is a component class that
+ already matches the slot name.
}
\description{
This function is used internally by many accessors and in
View
3 man/assign-otuTable.Rd
@@ -5,6 +5,9 @@
\alias{otuTable<-,otuTable,otuTable-method}
\alias{otuTable<-,phyloseq,otuTable-method}
\title{Assign a new OTU Table to \code{x}}
+\usage{
+ otuTable(x) <- value
+}
\arguments{
\item{x}{(Required). \code{\link{phyloseq-class}}}
View
3 man/assign-speciesarerows.Rd
@@ -5,6 +5,9 @@
\alias{speciesarerows<-,otuTable,logical-method}
\alias{speciesarerows<-,phyloseq,logical-method}
\title{Manually change speciesAreRows through assignment.}
+\usage{
+ speciesarerows(x) <- value
+}
\arguments{
\item{x}{\code{\link{otuTable-class}} or
\code{\link{phyloseq-class}}}
View
3 man/assign-tre.Rd
@@ -4,6 +4,9 @@
\alias{tre<-}
\alias{tre<-,phyloseq,phylo-method}
\title{Assign to tre an object/value.}
+\usage{
+ tre(x) <- value
+}
\arguments{
\item{x}{(Required). \code{\link{phyloseq-class}}}
View
2 man/calcplot.Rd
@@ -3,7 +3,7 @@
\title{Convenience wrapper for performing ordination and plotting.}
\usage{
calcplot(X, RDA_or_CCA="cca", object=get(all.vars(X)[1]),
- ...)
+ ...)
}
\arguments{
\item{X}{(Required). A formula object. The left-hand side
View
7 man/cca-rda-phyloseq-methods.Rd
@@ -9,9 +9,14 @@
\alias{rda.phyloseq,otuTable-method}
\alias{rda.phyloseq,phyloseq-method}
\title{Wrapper for \code{\link[vegan]{cca}} and \code{\link[vegan]{rda}}.}
+\usage{
+ cca.phyloseq(X, ...)
+
+ rda.phyloseq(X, ...)
+}
\arguments{
\item{X}{(Required). A \code{\link{formula}}, specifying
- the input. No need to directly access components.
+ the input. No need to directly access components.
\code{cca.phyloseq} understands where to find the
abundance table and sample data. Alternatively, \code{X}
can be an \code{\link{otuTable-class}} or
View
3 man/data-enterotype.Rd
@@ -63,7 +63,7 @@
# # multiple testing of genera correlating with enterotype 2
# mt(x, data.frame(sampleData(x))[, "Enterotype"]==2)
# # Should return a data.frame, with the following head()
- # # # # # index teststat rawp adjp plower
+# # # # # index teststat rawp adjp plower
# # # Prevotella 207 11.469961374 0.0001 0.0088 0.0001
# # # Bacteroides 203 -9.015717540 0.0001 0.0088 0.0001
# # # Holdemania 201 -5.810081084 0.0001 0.0088 0.0001
@@ -84,5 +84,4 @@
http://www.bork.embl.de/Docu/Arumugam_et_al_2011/downloads.html
}
\keyword{data}
-\keyword{datasets}
View
1 man/data-esophagus.Rd
@@ -78,5 +78,4 @@
\url{http://www.mothur.org/wiki/Esophageal_community_analysis}
}
\keyword{data}
-\keyword{datasets}
View
1 man/data-ex1.Rd
@@ -22,5 +22,4 @@
\url{www.stanford.edu/~mcmurdie}
}
\keyword{data}
-\keyword{datasets}
View
5 man/data-soilrep.Rd
@@ -139,13 +139,12 @@
}
\references{
Zhou, J., Wu, L., Deng, Y., Zhi, X., Jiang, Y.-H., Tu,
- Q., Xie, J., et al. Reproducibility and quantitation of
- amplicon sequencing-based detection. The ISME Journal.
+ Q., Xie, J., et al. Reproducibility and quantitation of
+ amplicon sequencing-based detection. The ISME Journal.
(2011) 5(8):1303-1313. \code{doi:10.1038/ismej.2011.11}
The article can be accessed online at
\url{http://www.nature.com/ismej/journal/v5/n8/full/ismej201111a.html}
}
\keyword{data}
-\keyword{datasets}
View
6 man/export_env_file.Rd
@@ -3,11 +3,11 @@
\title{Export environment (ENV) file for UniFrac Server.}
\usage{
export_env_file(physeq, file = "", writeTree = TRUE,
- return = FALSE)
+ return = FALSE)
}
\arguments{
\item{physeq}{(Required). Experiment-level
- (\code{\link{phyloseq-class}}) object. Ideally this also
+ (\code{\link{phyloseq-class}}) object. Ideally this also
contains the phylogenetic tree, which is also exported by
default.}
@@ -21,7 +21,7 @@
as well as the the ENV table. Default is \code{TRUE}.}
\item{return}{(Optional). Should the ENV table be
- returned to the R workspace? Default is \code{FALSE}.}
+ returned to the R workspace? Default is \code{FALSE}.}
}
\description{
Creates the environment table that is needed for the
View
4 man/export_mothur_dist.Rd
@@ -3,7 +3,7 @@
\title{Export a distance object as \code{.names} and \code{.dist} files for mothur}
\usage{
export_mothur_dist(x, out=NULL,
- makeTrivialNamesFile=NULL)
+ makeTrivialNamesFile=NULL)
}
\arguments{
\item{x}{(Required). A \code{"dist"} object, or a
@@ -21,7 +21,7 @@
}
\value{
A character vector of the different cutoff values
- contained in the file. For a given set of arguments to
+ contained in the file. For a given set of arguments to
the \code{cluster()} command from within \emph{mothur}, a
number of OTU-clustering results are returned in the same
list file. The exact cutoff values used by \emph{mothur}
View
3 man/genefilterSample-methods.Rd
@@ -5,6 +5,9 @@
\alias{genefilterSample,otuTable-method}
\alias{genefilterSample,phyloseq-method}
\title{Filter OTUs with arbitrary function, sample-wise.}
+\usage{
+ genefilterSample(X, flist, A=1)
+}
\arguments{
\item{X}{The object that needs trimming. Can be matrix,
otuTable, or higher- order phyloseq classes that contain
View
3 man/getSamples-methods.Rd
@@ -4,6 +4,9 @@
\alias{getSamples,otuTable-method}
\alias{getSamples,phyloseq-method}
\title{Returns all abundance values for species \code{i}.}
+\usage{
+ getSamples(physeq, i)
+}
\arguments{
\item{physeq}{(Required). \code{\link{otuTable-class}},
or \code{\link{phyloseq-class}}.}
View
3 man/getSpecies-methods.Rd
@@ -4,6 +4,9 @@
\alias{getSpecies,otuTable-method}
\alias{getSpecies,phyloseq-method}
\title{Returns all abundance values of sample \code{i}.}
+\usage{
+ getSpecies(physeq, i)
+}
\arguments{
\item{physeq}{(Required). \code{\link{otuTable-class}},
or \code{\link{phyloseq-class}}.}
View
8 man/getslots.phyloseq.Rd
@@ -23,10 +23,10 @@
}
\examples{
#
- data(ex1)
- getslots.phyloseq(ex1)
- data(esophagus)
- getslots.phyloseq(esophagus)
+data(ex1)
+getslots.phyloseq(ex1)
+data(esophagus)
+getslots.phyloseq(esophagus)
}
\seealso{
merge_phyloseq
View
7 man/import-methods.Rd
@@ -3,11 +3,14 @@
\alias{import}
\alias{import,character-method}
\title{Universal import method (wrapper) for phyloseq-package}
+\usage{
+ import(pipelineName, ...)
+}
\arguments{
\item{pipelineName}{(Required). Character string. The
name of the analysis tool / pipeline / package that
created the OTU-cluster data or other data that you now
- want to import. Current options are \code{c("mothur",
+ want to import. Current options are \code{c("mothur",
"pyrotagger", "QIIME", "RDP")}, and only the first letter
is necessary.}
@@ -19,7 +22,7 @@
In most cases a \code{\link{phyloseq-class}} will be
returned, though the included component data will vary by
pipeline/tool, and also by the types of data files
- provided. The expected behavior is to return the
+ provided. The expected behavior is to return the
most-comprehensive object possible, given the provided
arguments and pipeline/tool.
}
View
2 man/import_env_file.Rd
@@ -12,7 +12,7 @@
to be paired with the output otuTable.}
\item{sep}{A character string indicating the delimiter
- used in the file. The default is \code{"\t"}.}
+ used in the file. The default is \code{"\t"}.}
\item{...}{Additional parameters passed on to
\code{\link{read.table}}.}
View
8 man/import_mothur.Rd
@@ -3,7 +3,7 @@
\title{General function for importing mothur files into phyloseq.}
\usage{
import_mothur(mothur_list_file, mothur_group_file=NULL,
- mothur_tree_file=NULL, cutoff=NULL)
+ mothur_tree_file=NULL, cutoff=NULL)
}
\arguments{
\item{mothur_list_file}{Required. The list file name /
@@ -18,8 +18,8 @@
\code{http://www.mothur.org/wiki/Make.group}}
\item{mothur_tree_file}{Optional. The tree file name
- produced by \emph{mothur}. Probably a file that ends
- with the suffix \code{".tree"}.}
+ produced by \emph{mothur}. Probably a file that ends with
+ the suffix \code{".tree"}.}
\item{cutoff}{A character string indicating the cutoff
value, (or \code{"unique"}), that matches one of the
@@ -38,7 +38,7 @@
function.}
}
\value{
- The object class depends on the provided arguments. If
+ The object class depends on the provided arguments. If
the first three arguments are provided, then an
\code{otuTree} object should be returned, containing both
an OTU-only tree and its associated \code{otuTable}-class
View
2 man/import_mothur_otutable.Rd
@@ -3,7 +3,7 @@
\title{Import mothur list and group files and return an otuTable}
\usage{
import_mothur_otutable(mothur_list_file,
- mothur_group_file, cutoff=NULL)
+ mothur_group_file, cutoff=NULL)
}
\arguments{
\item{mothur_list_file}{The list file name and/or
View
6 man/import_mothur_tree.Rd
@@ -3,12 +3,12 @@
\title{Import and prune mothur-produced tree.}
\usage{
import_mothur_tree(mothur_tree_file, mothur_list_file,
- cutoff=NULL)
+ cutoff=NULL)
}
\arguments{
\item{mothur_tree_file}{The tree file name that was
- output from \emph{mothur}. Probably a file that ends
- with the suffix \code{".tree"}.}
+ output from \emph{mothur}. Probably a file that ends with
+ the suffix \code{".tree"}.}
\item{mothur_list_file}{The list file name and/or
location as produced by \emph{mothur}.}
View
4 man/import_pyrotagger_tab.Rd
@@ -3,7 +3,7 @@
\title{Imports a tab-delimited version of the pyrotagger output file.}
\usage{
import_pyrotagger_tab(pyrotagger_tab_file,
- strict_taxonomy=FALSE, keep_potential_chimeras=FALSE)
+ strict_taxonomy=FALSE, keep_potential_chimeras=FALSE)
}
\arguments{
\item{pyrotagger_tab_file}{(Required). A character
@@ -19,7 +19,7 @@
Default \code{FALSE}. The pyrotagger output also includes
OTUs that are tagged by pyrotagger as likely chimeras.
These putative chimeric OTUs can be retained if set to
- \code{TRUE}. The putative chimeras are excluded by
+ \code{TRUE}. The putative chimeras are excluded by
default.}
}
\value{
View
12 man/import_qiime.Rd
@@ -3,27 +3,27 @@
\title{Import function to read files created by the QIIME pipeline.}
\usage{
import_qiime(otufilename=NULL, mapfilename=NULL,
- treefilename=NULL, biotaxonomy=NULL, ...)
+ treefilename=NULL, biotaxonomy=NULL, ...)
}
\arguments{
\item{otufilename}{(Optional). A character string
indicating the file location of the OTU file. The
combined OTU abundance and taxonomic identification file,
tab-delimited, as produced by QIIME under default output
- settings. Default value is \code{NULL}.}
+ settings. Default value is \code{NULL}.}
\item{mapfilename}{(Optional). The QIIME map file
required for processing pyrosequencing tags in QIIME as
well as some of the post-clustering analysis. This is a
required input file for running QIIME. Its strict
formatting specification should be followed for correct
- parsing by this function. Default value is \code{NULL}.}
+ parsing by this function. Default value is \code{NULL}.}
\item{treefilename}{(Optional). A phylogenetic tree in
NEXUS format. For the QIIME pipeline this is typically a
tree of the representative 16S rRNA sequences from each
OTU cluster, with the number of leaves/tips equal to the
- number of taxa/species/OTUs. Default value is
+ number of taxa/species/OTUs. Default value is
\code{NULL}. ALTERNATIVELY, this argument can be a tree
object (\code{\link[ape]{phylo}}-class), in case the tree
has already been imported, or is in a different format
@@ -32,10 +32,10 @@
\item{biotaxonomy}{(Optional). A character vector
indicating the name of each taxonomic level in the
taxonomy-portion of the otu-file, which may not specify
- these levels explicitly. Default value is \code{NULL}.}
+ these levels explicitly. Default value is \code{NULL}.}
\item{...}{Additional arguments passed to
- \code{\link[ape]{read.nexus}}, as necessary. Make sure
+ \code{\link[ape]{read.nexus}}, as necessary. Make sure
that your phylogenetic tree file is readable by
\code{\link[ape]{read.nexus}} prior to calling this
function.}
View
2 man/import_qiime_otu_tax.Rd
@@ -8,7 +8,7 @@
\item{otufilename}{A character string indicating the file
location of the OTU file. The combined OTU abundance and
taxonomic identification file, tab-delimited, as produced
- by QIIME under default output settings. Default value is
+ by QIIME under default output settings. Default value is
\code{NULL}.}
\item{biotaxonomy}{A character vector indicating the name
View
4 man/makenetwork.Rd
@@ -4,7 +4,7 @@
\title{Create a taxa graph adjacency matrix from an \code{otuTable}.}
\usage{
makenetwork(physeq, plotgraph=TRUE, community=TRUE,
- threshold=0, incommon=0.4, method="jaccard")
+ threshold=0, incommon=0.4, method="jaccard")
}
\arguments{
\item{physeq}{(Required). An \code{\link{otuTable-class}}
@@ -18,7 +18,7 @@
\item{threshold}{A single-value positive integer. Default
0. Indicates the number of individuals/observations
- required for presense to be counted. For example,
+ required for presense to be counted. For example,
threshold > 1 means that species with 2 or more reads are
considered present.}
View
3 man/merge_phyloseq_pair-methods.Rd
@@ -6,6 +6,9 @@
\alias{merge_phyloseq_pair,sampleData,sampleData-method}
\alias{merge_phyloseq_pair,taxonomyTable,taxonomyTable-method}
\title{Merge pair of phyloseq component data objects of the same class.}
+\usage{
+ merge_phyloseq_pair(x, y)
+}
\arguments{
\item{x}{A character vector of the species in object x
that you want to keep -- OR alternatively -- a logical
View
5 man/merge_samples-methods.Rd
@@ -5,6 +5,9 @@
\alias{merge_samples,phyloseq-method}
\alias{merge_samples,sampleData-method}
\title{Merge samples based on a sample variable or factor.}
+\usage{
+ merge_samples(x, group, fun=mean)
+}
\arguments{
\item{x}{(Required). An instance of a phyloseq class that
has sample indices. This includes
@@ -21,7 +24,7 @@
merge the values that correspond to the same group for
each variable. It must take a numeric vector as first
argument and return a single value. Default is
- \code{\link[base]{mean}}. Note that this is (currently)
+ \code{\link[base]{mean}}. Note that this is (currently)
ignored for the otuTable, where the equivalent function
is \code{\link[base]{sum}}, but evaluated via
\code{\link[base]{rowsum}} for efficiency.}
View
5 man/merge_species-methods.Rd
@@ -7,6 +7,9 @@
\alias{merge_species,sampleData-method}
\alias{merge_species,taxonomyTable-method}
\title{Merge a subset of the species in \code{x} into one species/taxa/OTU.}
+\usage{
+ merge_species(x, eqspecies, archetype=1)
+}
\arguments{
\item{x}{(Required). An object that describes species
(taxa). This includes \code{\link{phyloseq-class}},
@@ -15,7 +18,7 @@
\code{\link[ape]{phylo}}.}
\item{eqspecies}{(Required). The species names, or
- indices, that should be merged together. If
+ indices, that should be merged together. If
\code{length(eqspecies) < 2}, then the object \code{x}
will be returned safely unchanged.}
View
7 man/mt-methods.Rd
@@ -8,9 +8,12 @@
\alias{mt,otuTable,numeric-method}
\alias{mt,phyloseq,ANY-method}
\title{Multiple testing of taxa abundancesa acccording to a sample variate}
+\usage{
+ mt(physeq, classlabel, minPmaxT="minP", ...)
+}
\arguments{
\item{physeq}{(Required). \code{\link{otuTable-class}} or
- \code{\link{phyloseq-class}}. In this multiple testing
+ \code{\link{phyloseq-class}}. In this multiple testing
framework, different taxa correspond to variables
(hypotheses), and samples to observations.}
@@ -27,7 +30,7 @@
test.}
\item{minPmaxT}{(Optional). Character string.
- \code{"mt.minP"} or \code{"mt.maxT"}. Default is to use
+ \code{"mt.minP"} or \code{"mt.maxT"}. Default is to use
\code{\link[multtest]{mt.minP}}.}
\item{...}{(Optional). Additional arguments, forwarded to
View
3 man/nsamples-methods.Rd
@@ -6,6 +6,9 @@
\alias{nsamples,phyloseq-method}
\alias{nsamples,sampleData-method}
\title{Get the number of samples.}
+\usage{
+ nsamples(physeq)
+}
\arguments{
\item{physeq}{A \code{\link{phyloseq-class}},
\code{\link{sampleData}}, or
View
3 man/nspecies-methods.Rd
@@ -7,6 +7,9 @@
\alias{nspecies,phyloseq-method}
\alias{nspecies,taxonomyTable-method}
\title{Get the number of taxa/species.}
+\usage{
+ nspecies(physeq)
+}
\arguments{
\item{physeq}{\code{\link{phyloseq-class}},
\code{\link{otuTable-class}},
View
2 man/otu2df.Rd
@@ -4,7 +4,7 @@
in the ggplot2 framework.}
\usage{
otu2df(otu, taxavec, map, keepOnlyTheseTaxa=NULL,
- threshold=NULL)
+ threshold=NULL)
}
\arguments{
\item{otu}{An \code{otuTable} object.}
View
2 man/otuTable-class.Rd
@@ -13,7 +13,7 @@
}
\details{
\describe{ \item{speciesAreRows}{ A single logical
- specifying the orientation of the abundance table. }
+ specifying the orientation of the abundance table. }
\item{.Data}{This slot is inherited from the
\code{\link{matrix}} class.} }
View
3 man/otuTable-methods.Rd
@@ -6,6 +6,9 @@
\alias{otuTable,otuTable-method}
\alias{otuTable,phyloseq-method}
\title{Build or access the otuTable.}
+\usage{
+ otuTable(object, speciesAreRows, errorIfNULL=TRUE)
+}
\arguments{
\item{object}{(Required). An integer matrix,
\code{\link{otuTable-class}}, or
View
15 man/phyloseq.Rd
@@ -9,19 +9,18 @@
classes defined by the phyloseq package, as well as
\code{phylo}-class (defined by the
\code{\link{ape-package}}). Each argument should be a
- different class. For combining multiple components of
- the same class, or multiple phyloseq-class objects, use
- the \code{\link{merge_phyloseq}} function. Unlike in
- earlier versions, the arguments to phyloseq do not need
- to be named, and the order of the arguments does not
- matter.}
+ different class. For combining multiple components of the
+ same class, or multiple phyloseq-class objects, use the
+ \code{\link{merge_phyloseq}} function. Unlike in earlier
+ versions, the arguments to phyloseq do not need to be
+ named, and the order of the arguments does not matter.}
}
\value{
The class of the returned object depends on the argument
class(es). For an experiment-level object, two or more
- component data objects must be provided. Otherwise, if a
+ component data objects must be provided. Otherwise, if a
single component-class is provided, it is simply returned
- as-is. The order of arguments does not matter.
+ as-is. The order of arguments does not matter.
}
\description{
\code{phyloseq()} is a constructor method, This is the
View
28 man/plot_ordination_phyloseq.Rd
@@ -3,17 +3,17 @@
\title{Convenient rendering of ordination results using ggplot2.}
\usage{
plot_ordination_phyloseq(mod, object, plot_title =
- as(mod$call, "character")[1], man.colors=NULL,
- man.sizes=NULL, man.shapes=NULL, species_alpha=1/10,
- sites_alpha=2/3, species_color_category =NULL,
- species_shape_category =NULL, species_size_category
- =NULL, site_color_category=NULL,
- site_shape_category=NULL, site_size_category=NULL,
- add_sites_data = NULL, add_taxa_data = NULL)
+ as(mod$call, "character")[1], man.colors=NULL,
+ man.sizes=NULL, man.shapes=NULL, species_alpha=1/10,
+ sites_alpha=2/3, species_color_category =NULL,
+ species_shape_category =NULL, species_size_category
+ =NULL, site_color_category=NULL,
+ site_shape_category=NULL, site_size_category=NULL,
+ add_sites_data = NULL, add_taxa_data = NULL)
}
\arguments{
\item{mod}{(Required). A \code{cca} or \code{rda} results
- object. See \code{\link{cca.object}}. For phyloseq
+ object. See \code{\link{cca.object}}. For phyloseq
objects, you probably want to see
\code{\link{cca.phyloseq}} or
\code{\link{rda.phyloseq}}.}
@@ -49,7 +49,7 @@
that represent samples/sites. Default is \code{2/3}.}
\item{species_color_category}{A manual color scale for
- taxa. Default is \code{NULL}.}
+ taxa. Default is \code{NULL}.}
\item{species_shape_category}{A manual shape scale for
taxa. Default is \code{NULL}.}
@@ -58,26 +58,26 @@
taxa. Default is \code{NULL}.}
\item{site_color_category}{A manual color scale for
- samples/sites. Default is \code{NULL}.}
+ samples/sites. Default is \code{NULL}.}
\item{site_shape_category}{A manual shape scale for
- samples/sites. Default is \code{NULL}.}
+ samples/sites. Default is \code{NULL}.}
\item{site_size_category}{A manual size scale for
- samples/sites. Default is \code{NULL}.}
+ samples/sites. Default is \code{NULL}.}
\item{add_sites_data}{A \code{data.frame} object
providing additional data about the samples/sites that is
not already available in the \code{sampleData} of your
phyloseq object specified by \code{object}. As such, it
must have the same number of rows as as there are samples
- in \code{object}. Default is \code{NULL}.}
+ in \code{object}. Default is \code{NULL}.}
\item{add_taxa_data}{A \code{matrix} object providing
additional data about the taxa that is not already
available in the \code{taxTab} of your phyloseq object
specified by \code{object}, if it has a \code{taxTab}
- slot. It is not required. As such, it must have the same
+ slot. It is not required. As such, it must have the same
number of rows as there are taxa in \code{object}.
Default is \code{NULL}.}
}
View
5 man/plot_phyloseq-methods.Rd
@@ -3,6 +3,9 @@
\alias{plot_phyloseq}
\alias{plot_phyloseq,phyloseq-method}
\title{Generic plot defaults for phyloseq.}
+\usage{
+ plot_phyloseq(physeq, ...)
+}
\arguments{
\item{physeq}{(Required). \code{\link{phyloseq-class}}.
The actual plot type depends on the available (non-empty)
@@ -27,7 +30,7 @@
}
\examples{
## data(ex1)
- ## plot_phyloseq(ex1)
+## plot_phyloseq(ex1)
}
\seealso{
\code{\link{taxaplot}} \code{\link{plot_tree_phyloseq}}
View
20 man/plot_tree_phyloseq.Rd
@@ -3,10 +3,10 @@
\title{Plot tree with easy tip annotation.}
\usage{
plot_tree_phyloseq(physeq, color_factor=NULL,
- shape_factor=NULL, base_size=1, size_scaling_factor =
- 0.2, opacity=2/3, custom_color_scale=NULL,
- custom_shape_scale=NULL, type_abundance_value=FALSE,
- printTheseTaxa=NULL, treeTitle="Annotated Tree", ...)
+ shape_factor=NULL, base_size=1, size_scaling_factor =
+ 0.2, opacity=2/3, custom_color_scale=NULL,
+ custom_shape_scale=NULL, type_abundance_value=FALSE,
+ printTheseTaxa=NULL, treeTitle="Annotated Tree", ...)
}
\arguments{
\item{physeq}{(Required). \code{\link{phyloseq-class}}
@@ -35,10 +35,10 @@
scaling symbol size by the abundance value.}
\item{opacity}{The opacity (or alpha value). Numeric
- between 0, 1. Defaul value is 2/3.}
+ between 0, 1. Defaul value is 2/3.}
\item{custom_color_scale}{A character vector of the
- desired custom color scale. This should be a scale, not
+ desired custom color scale. This should be a scale, not
an aesthetic map. Therefore, it will in most-cases
contain only unique elements, unless two different
categories of data are supposed to have the same color.
@@ -54,7 +54,7 @@
\item{type_abundance_value}{Logical. Whether or not the
otuTable value (the number of individuals, typically)
should be added to the center of symbols when the value
- is greater than one. Default is FALSE, indicating no
+ is greater than one. Default is FALSE, indicating no
labels.}
\item{printTheseTaxa}{a character vector of the taxa
@@ -90,10 +90,10 @@
# plot_tree_phyloseq(ex2, shape_factor="Diet")
# plot_tree_phyloseq(ex2, color_factor="Gender", shape_factor="Diet")
# plot_tree_phyloseq(ex2, color_factor="Gender", shape_factor="Diet",
- # size_scaling_factor=0.6, type_abundance_value=TRUE)
+# size_scaling_factor=0.6, type_abundance_value=TRUE)
# plot_tree_phyloseq(ex2, color_factor="Gender", shape_factor="Diet",
- # size_scaling_factor=0.6, custom_color_scale=c("blue", "magenta"))
+# size_scaling_factor=0.6, custom_color_scale=c("blue", "magenta"))
# plot(phyloseqTree(ex2), color_factor="Gender", shape_factor="Diet",
- # size_scaling_factor=0.6, custom_color_scale=c("blue", "magenta") )
+# size_scaling_factor=0.6, custom_color_scale=c("blue", "magenta") )
}
View
19 man/prune_samples-methods.Rd
@@ -5,6 +5,9 @@
\alias{prune_samples,character,phyloseq-method}
\alias{prune_samples,character,sampleData-method}
\title{Prune unwanted samples from a phyloseq object.}
+\usage{
+ prune_samples(samples, x)
+}
\arguments{
\item{samples}{A character vector of the samples in
object x that you want to keep.}
@@ -21,14 +24,14 @@
}
\examples{
#
- # data(ex1)
- # B_only_sample_names <- sample.names(sampleData(ex1)[(sampleData(ex1)[, "Gender"]=="B"),])
- # ex2 <- prune_samples(B_only_sample_names, ex1)
- # ex3 <- subset_samples(ex1, Gender=="B")
- # ## This should be TRUE.
- # identical(ex2, ex3)
- # ## Here is a simpler example: Make new object with only the first 5 samples
- # ex4 <- prune_samples(sample.names(ex1)[1:5], ex1)
+# data(ex1)
+# B_only_sample_names <- sample.names(sampleData(ex1)[(sampleData(ex1)[, "Gender"]=="B"),])
+# ex2 <- prune_samples(B_only_sample_names, ex1)
+# ex3 <- subset_samples(ex1, Gender=="B")
+# ## This should be TRUE.
+# identical(ex2, ex3)
+# ## Here is a simpler example: Make new object with only the first 5 samples
+# ex4 <- prune_samples(sample.names(ex1)[1:5], ex1)
}
\seealso{
\code{\link{subset_samples}}
View
3 man/reconcile_species-methods.Rd
@@ -2,6 +2,9 @@
\alias{reconcile_species}
\alias{reconcile_species,phyloseq-method}
\title{Keep only species-indices common to all components.}
+\usage{
+ reconcile_species(x)
+}
\arguments{
\item{x}{(Required). A phyloseq object. Only meaningful
if \code{x} has at least two non-empty slots of the
View
3 man/sample.names-methods.Rd
@@ -7,6 +7,9 @@
\alias{sample.names,sampleData-method}
\alias{sampleNames}
\title{Get sample names.}
+\usage{
+ sample.names(physeq)
+}
\arguments{
\item{physeq}{(Required). A \code{\link{phyloseq-class}},
\code{\link{sampleData}}, or
View
2 man/sampleData-class.Rd
@@ -13,7 +13,7 @@
data.frame class.}
\item{row.names}{ Also inherited from the data.frame
- class; it should contain the sample names. }
+ class; it should contain the sample names. }
\item{names}{Inherited from the data.frame class.}
View
2 man/sampleData-methods.Rd
@@ -7,6 +7,8 @@
\alias{sampleMap}
\title{Build or access sampleData.}
\usage{
+ sampleData(object, errorIfNULL=TRUE)
+
samData(object, errorIfNULL=TRUE)
sampleMap(object, errorIfNULL=TRUE)
View
2 man/show_mothur_list_cutoffs.Rd
@@ -10,7 +10,7 @@
}
\value{
A character vector of the different cutoff values
- contained in the file. For a given set of arguments to
+ contained in the file. For a given set of arguments to
the \code{cluster()} command from within \emph{mothur}, a
number of OTU-clustering results are returned in the same
list file. The exact cutoff values used by \emph{mothur}
View
3 man/species.names-methods.Rd
@@ -8,6 +8,9 @@
\alias{species.names,sampleData-method}
\alias{species.names,taxonomyTable-method}
\title{Get species / taxa names.}
+\usage{
+ species.names(physeq)
+}
\arguments{
\item{physeq}{\code{\link{phyloseq-class}},
\code{\link{otuTable-class}},
View
3 man/speciesAreRows-methods.Rd
@@ -6,6 +6,9 @@
\alias{speciesAreRows,otuTable-method}
\alias{speciesAreRows,phyloseq-method}
\title{Access speciesAreRows slot from otuTable objects.}
+\usage{
+ speciesarerows(physeq)
+}
\arguments{
\item{physeq}{(Required). \code{\link{phyloseq-class}},
or \code{\link{otuTable-class}}.}
View
16 man/subset_samples-methods.Rd
@@ -29,14 +29,14 @@
}
\examples{
# data(ex1)
- # ex2 <- subset_samples(ex1, Gender=="A")
- # ex2 <- subset_samples(ex1, Diet==1)
- ### Here is an example comparing subset_samples with prune_samples...
- # B_only_sample_names <- sample.names(sampleData(ex1)[(sampleData(ex1)[, "Gender"]=="B"),])
- # ex2 <- prune_samples(B_only_sample_names, ex1)
- # ex3 <- subset_samples(ex1, Gender=="B")
- # ## This should be TRUE.
- # identical(ex2, ex3)
+# ex2 <- subset_samples(ex1, Gender=="A")
+# ex2 <- subset_samples(ex1, Diet==1)
+### Here is an example comparing subset_samples with prune_samples...
+# B_only_sample_names <- sample.names(sampleData(ex1)[(sampleData(ex1)[, "Gender"]=="B"),])
+# ex2 <- prune_samples(B_only_sample_names, ex1)
+# ex3 <- subset_samples(ex1, Gender=="B")
+# ## This should be TRUE.
+# identical(ex2, ex3)
}
\seealso{
\code{\link{subset_species}}
View
4 man/tableprint.Rd
@@ -2,8 +2,8 @@
\alias{tableprint}
\title{print a summary of data tables to screen.}
\usage{
- tableprint(y, typelabel = "table",
- dim1label = "rownames", dim2label = "colnames")
+ tableprint(y, typelabel = "table", dim1label =
+ "rownames", dim2label = "colnames")
}
\arguments{
\item{y}{the table to be printed.}
View
2 man/taxTab-methods.Rd
@@ -6,6 +6,8 @@
\alias{taxTab,matrix-method}
\title{Build or access the taxonomyTable.}
\usage{
+ taxTab(object, errorIfNULL=TRUE)
+
taxtab(object, errorIfNULL = TRUE)
}
\arguments{
View
13 man/taxaplot-methods.Rd
@@ -3,6 +3,11 @@
\alias{taxaplot}
\alias{taxaplot,phyloseq-method}
\title{Create a structured barplot graphic of the taxonomic groups.}
+\usage{
+ taxaplot(otu, taxavec="Domain", showOnlyTheseTaxa=NULL,
+ threshold=NULL, x_category="sample",
+ fill_category=x_category, facet_formula = . ~ TaxaGroup)
+}
\arguments{
\item{otu}{(Required). An \code{otuTable} object, or
higher-order object that contains an otuTable and
@@ -18,7 +23,7 @@
If \code{otu} is a higher-order object that contains a
taxonomyTable, then taxavec can alternatively specify the
desired taxonomic level as a character string of length
- 1. E.g. \code{taxavec = "Phylum"}. Default value is
+ 1. E.g. \code{taxavec = "Phylum"}. Default value is
\code{"Domain"}.}
\item{showOnlyTheseTaxa}{A vector of the taxonomic labels
@@ -37,22 +42,22 @@
sampleData column should be used to define the horizontal
axis categories. Default is \code{"sample"}. Note that a
few column-names are added by default and are available
- as options. They are ``sample'', ``Abundance'', and
+ as options. They are ``sample'', ``Abundance'', and
``TaxaGroup''.}
\item{fill_category}{A character string indicating which
sampleData column should be used to define the fill color
of the bars. This does not have to match
\code{x_category}, but does so by default. Note that a
few column-names are added by default and are available
- as options. They are ``sample'', ``Abundance'', and
+ as options. They are ``sample'', ``Abundance'', and
``TaxaGroup''.}
\item{facet_formula}{A formula object as used by
\code{\link{facet_grid}} in \code{\link{ggplot}} or
\code{\link{qplot}} commands The default is: \code{. ~
TaxaGroup}. Note that a few column-names are added by
- default and are available as options. They are
+ default and are available as options. They are
``sample'', ``Abundance'', and ``TaxaGroup''. E.g. An
alternative \code{facet_grid} could be \code{sample ~
TaxaGroup}.}
View
23 man/taxglom-methods.Rd
@@ -5,6 +5,10 @@
\alias{taxglom,otuTable,taxonomyTable-method}
\alias{taxglom,phyloseq,ANY-method}
\title{Agglomerate taxa of the same type.}
+\usage{
+ taxglom(physeq, tax=NULL, taxlevel="Phylum", NArm=TRUE,
+ bad_empty=c(NA, "", " ", "\t"))
+}
\arguments{
\item{physeq}{(Required). \code{\link{phyloseq-class}} or
\code{\link{otuTable}}.}
@@ -32,7 +36,7 @@
different taxonomic levels.}
\item{NArm}{(Optional). Logical, length equal to one.
- Default is \code{TRUE}. CAUTION. The decision to prune
+ Default is \code{TRUE}. CAUTION. The decision to prune
(or not) taxa for which you lack categorical data could
have a large effect on downstream analysis. You may want
to re-compute your analysis under both conditions, or at
@@ -47,15 +51,14 @@
have a phylogenetic tree available.}
\item{bad_empty}{(Optional). Character vector. Default:
- \code{c(NA, "", " ", "\t")}. Defines the bad/empty
- values that should be ignored and/or considered unknown.
- They will be removed from the internal agglomeration
- vector derived from the argument to \code{tax}, and
- therefore agglomeration will not combine taxa according
- to the presence of these values in \code{tax}.
- Furthermore, the corresponding taxa can be optionally
- pruned from the output if \code{NArm} is set to
- \code{TRUE}.}
+ \code{c(NA, "", " ", "\t")}. Defines the bad/empty values
+ that should be ignored and/or considered unknown. They
+ will be removed from the internal agglomeration vector
+ derived from the argument to \code{tax}, and therefore
+ agglomeration will not combine taxa according to the
+ presence of these values in \code{tax}. Furthermore, the
+ corresponding taxa can be optionally pruned from the
+ output if \code{NArm} is set to \code{TRUE}.}
}
\value{
A taxonomically-agglomerated, optionally-pruned, object
View
4 man/taxglom.internal.Rd
@@ -2,8 +2,8 @@
\alias{taxglom.internal}
\title{taxglom core internal function.}
\usage{
- taxglom.internal(physeq, tax, NArm = TRUE,
- bad_empty = c(NA, "", " ", "\t"))
+ taxglom.internal(physeq, tax, NArm = TRUE, bad_empty =
+ c(NA, "", " ", "\t"))
}
\arguments{
\item{physeq}{the object on which agglomeration is to
View
2 man/tip-annotate.Rd
@@ -17,7 +17,7 @@
\item{...}{Additional plotting parameters that are passed
to \code{\link{points}} or \code{\link{text}} in the R
- base graphics. Again, for \code{tiptext()}, make sure to
+ base graphics. Again, for \code{tiptext()}, make sure to
include a \code{labels=} argument.}
}
\value{
View
3 man/tipglom-methods.Rd
@@ -5,6 +5,9 @@
\alias{tipglom,phylo,otuTable-method}
\alias{tipglom,phyloseq,ANY-method}
\title{Agglomerate closely-related taxa using single-linkage clustering.}
+\usage{
+ tipglom(tree, OTU, speciationMinLength=0.02)
+}
\arguments{
\item{tree}{\code{\link{phyloseq-class}}, containing an
OTU Table and phylogenetic tree. If, alternatively,
View
2 man/transformcounts.Rd
@@ -21,7 +21,7 @@
}
\value{
A transformed \code{otuTable} -- or \code{phyloseq}
- object with its transformed \code{otuTable}. In general,
+ object with its transformed \code{otuTable}. In general,
trimming is not expected by this method, so it is
suggested that the user provide only functions that
return a full-length vector. Filtering/trimming can
View
3 man/transpose-methods.Rd
@@ -4,6 +4,9 @@
\alias{t,otuTable-method}
\alias{t,phyloseq-method}
\title{Transpose \code{\link{otuTable-class}} or \code{\link{phyloseq-class}}}
+\usage{
+ t(x)
+}
\arguments{
\item{x}{An \code{otuTable} or
\code{\link{phyloseq-class}}.}
View
5 man/tre-methods.Rd
@@ -4,6 +4,9 @@
\alias{tre,ANY-method}
\alias{tre,phylo-method}
\title{Get phylogenetic tree from object.}
+\usage{
+ tre(physeq, errorIfNULL=TRUE)
+}
\arguments{
\item{physeq}{(Required). An instance of phyloseq-class
that contains a phylogenetic tree. If physeq is a
@@ -17,7 +20,7 @@
\value{
The \code{\link[ape]{phylo}}-class object contained
within \code{physeq}; or NULL if \code{physeq} does not
- have a tree. This method stops with an error in the
+ have a tree. This method stops with an error in the
latter NULL case be default, which can be over-ridden by
changing the value of \code{errorIfNULL} to \code{FALSE}.
}

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