Commit bbb62381 authored by Eric Coissac's avatar Eric Coissac

documentation correction

parent 83351cf7
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/read_obifasta.R
\name{.build_key_value_pattern}
\alias{.build_key_value_pattern}
\title{Builds a regex pattern matching key=value; patterns}
\usage{
.build_key_value_pattern(keys = NULL)
}
\arguments{
\item{keys}{the \code{NULL} value or a character vector indicating the list
of tags to extract from the fasta header.}
}
\value{
a regular pattern from the \code{ore} library
}
\description{
The pattern is usable to parse the key=value; patterns
included in the obifasta sequence header lines.
}
\examples{
ROBITools2:::.build_key_value_pattern(c("taxid","species"))
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/taxonomy_methods.R, R/taxonomy_robi.R
\name{full_taxonomy}
\alias{full_taxonomy}
\alias{full_taxonomy.robitaxonomy}
\title{Converts a partial toxonomy to a full taxonomy.}
\usage{
full_taxonomy(taxonomy)
\method{full_taxonomy}{robitaxonomy}(taxonomy)
}
\arguments{
\item{taxonomy}{}
}
\value{
a full taxonomy instance.
}
\description{
By looking into its reference taxonomy the partial
taxonomy is completed with the minimum set of taxa
allowing to respect the completude constraint asking
that parent taxa of every taxa are described in the
taxonomy.
}
\author{
Eric Coissac
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/robitaxid.R
% Please edit documentation in R/type_robitaxid.R
\name{is_robitaxid}
\alias{is_robitaxid}
\title{Test if an object belongs \code{robitaxid} class}
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/read_obifasta.R
\name{read_obifasta}
\alias{read_obifasta}
\title{Reads OBITools extended version of fasta files.}
\usage{
read_obifasta(file, keys = NULL, verbose = is_robi_verbose())
}
\arguments{
\item{file}{a character string containing the filename to read}
\item{keys}{the \code{NULL} value or a character vector indicating the list
of tags to extract from the fasta header.}
\item{verbose}{}
}
\description{
Reads OBITools extended version of fasta files.
}
\examples{
filename <- system.file("extdata", "B5.fasta.gz",
package = "ROBITools2")
read_obifasta(filename)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/robitaxid.R, R/taxonomy_methods.R,
% R/taxonomy_robi.R
\name{reference_taxonomy.robitaxid}
\alias{reference_taxonomy.robitaxid}
% Please edit documentation in R/method_reference_taxonomy.R
\name{reference_taxonomy}
\alias{reference_taxonomy}
\alias{reference_taxonomy.robitaxonomy}
\alias{reference_taxonomy.robitaxid}
\title{Returns the reference taxonomy of an object}
\usage{
\method{reference_taxonomy}{robitaxid}(object)
reference_taxonomy(object)
\method{reference_taxonomy}{robitaxonomy}(object)
\method{reference_taxonomy}{robitaxid}(object)
}
\arguments{
\item{object}{the interrogated object.}
......@@ -24,13 +23,13 @@ robiobjects including taxonomy can be linked to a reference taxonomy.
This method return this taxonomy.
}
\details{
For \code{\link[ROBITools2]{robitaxid}}, is no reference taxonomy
For \code{\link[ROBITools2]{robitaxid}}, if no reference taxonomy
are attached to an instance, then the ROBITools2 default taxonomy
is returned.
}
\examples{
x <- robitaxid(c(1,2,2759))
x <- as_robitaxid(c(1,2,2759))
reference_taxonomy(x)
}
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/robiatomic.R, R/robicategory.R
% Please edit documentation in R/type_robiatomic.R, R/robicategory.R
\name{robiatomic}
\alias{robiatomic}
\alias{new_robiatomic}
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils.R
\name{robimessage}
\alias{robimessage}
\title{Writes a message on the console in verbose mode}
\usage{
robimessage(message, ..., .envir = parent.frame())
}
\arguments{
\item{message}{a string template sent to the \code{glue::glue} preprocessor.}
\item{...}{other values to be concatenated to the end of the message}
\item{.envir}{the environment passed to the \code{glue::glue} preprocessor}
}
\description{
The message is written to the console if the code
is executed in the verbose mode. The verbose mode
can be specified by declaring a \code{verbose} logical
value to \code{TRUE}. If no \code{verbose} variable is defined,
the result of the \code{ROBITools2::is_robi_verbose}
function is used to decide of the verbose status.
}
\examples{
verbose = TRUE
robimessage("Hello world !")
verbose = FALSE
robimessage("Hello world !")
rm(verbose)
v_mode = is_robi_verbose()
v_mode
robimessage("Hello world !")
options(ROBITools2.verbose = FALSE)
robimessage("Hello world !")
options(ROBITools2.verbose = TRUE)
robimessage("Hello world !")
options(ROBITools2.verbose = v_mode)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/robitag.R
% Please edit documentation in R/type_robitag.R
\name{robitag}
\alias{robitag}
\alias{new_robitag}
......@@ -126,6 +126,8 @@ distinction no difference exists with \code{robitag}.
It plays the same role than `robitag_forward` but for the reverse
tag located at the three prime end of the PCR product.
\code{is_robitag_reverse} tests if an object belongs the \code{is_robitag_reverse} class
\code{as_robitag} converts an object to a \code{robitag} instance.
}
\examples{
......@@ -150,7 +152,7 @@ rf <- new_robitag_forward(c("AGT","GGT","CGT","GTA","CCC"))
is_robitag_forward(rf)
is_robitag_forward("toto")
x <- c("A","B","C")
x <- c("AA","CC","CG")
as_robitag_forward(x)
......@@ -160,7 +162,7 @@ rr <- new_robitag_reverse(c("AGT","GGT","CGT","GTA","CCC"))
is_robitag_reverse(rr)
is_robitag_reverse("toto")
x <- c("A","B","C")
x <- c("AA","CC","CG")
as_robitag_reverse(x)
}
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/robitaxid.R
% Please edit documentation in R/type_robitaxid.R
\name{robitaxid}
\alias{robitaxid}
\alias{new_robitaxid}
\alias{as_robitaxid}
\alias{robitaxid_master}
\alias{new_robitaxid_master}
\alias{as_robitaxid_master}
\alias{as_robitaxid_master.default}
\alias{robipath}
\alias{new_robipath}
\alias{robilca}
\alias{new_robilca}
\title{Build a \code{robitaxid} instance}
\usage{
robitaxid(x = 0)
robitaxid(length = 0)
robitaxid_master(x = 0)
new_robitaxid(
object,
reference = NULL,
...,
verbose = is_robi_verbose(),
class = character()
)
robipath(x = 0)
as_robitaxid(object)
robilca(x = 0)
robitaxid_master(length = 0)
new_robitaxid_master(
object,
reference = NULL,
...,
verbose = is_robi_verbose(),
class = character()
)
as_robitaxid_master(object)
\method{as_robitaxid_master}{default}(object)
robipath(length = 0)
new_robipath(
object,
reference = NULL,
...,
verbose = is_robi_verbose(),
class = character()
)
robilca(length = 0)
new_robilca(
object,
reference = NULL,
...,
verbose = is_robi_verbose(),
class = character()
)
}
\arguments{
\item{x}{an object coercible to an \code{integer}}
\item{length}{A non-negative integer specifying the desired length. Double
values will be coerced to integer: supplying an argument of length other
than one is an error.}
\item{object}{the object to convert.}
\item{verbose}{if `TRUE` warnings are emitted if the constructor takes
some decision because of missing values and estimates
\item{...}{Passed on to [`base::structure()`]. It allows for defining
attributes, specified in tag = value form, which will be attached to data
(see [`robiatomic`]).}
\item{verbose}{if `TRUE` warnings and messages are emitted when the
constructor takes some decision because of missing values and estimates
default values these missing data.}
\item{class}{Subclasses to assign to the new object, default: none}
}
\value{
a \code{robitaxid} instance
the \code{as_robitaxid()} funtion returns a \code{robitaxid} value.
the \code{as_robitaxid_master()} funtion returns a \code{robitaxid_master} value.
}
\description{
a \code{robitaxid} is an integer vector that is for storing numerical taxonomic
identifiers. They are normally used to store NCBI taxids. They have to be positive
and not null.
identifiers. They are usually used to store NCBI taxids. They have to be strictly
positive.
}
\details{
\code{as_robitaxid} converts an object to a \code{robitaxid} instance.
}
\examples{
robitaxid(1:10)
new_robitaxid(1:10)
x <- c(1,10,33)
rt <- as_robitaxid(x)
x <- c(1,10,33)
rt <- as_robitaxid_master(x)
}
\author{
Eric Coissac <eric.coissac@metabarcoding.org>
Eric Coissac <eric.coissac@metabarcoding.org>
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/robiobject.R, R/robiatomic.R, R/alignment.R,
% R/robidata.R, R/robitaxid.R, R/robitag.R, R/robiuniqueid.R, R/robimotu.R,
% R/robicategory.R, R/robisample.R, R/robimetabar.R, R/robimutation.R
% Please edit documentation in R/robiobject.R, R/type_robiatomic.R,
% R/alignment.R, R/robidata.R, R/type_robitaxid.R, R/type_robitag.R,
% R/robiuniqueid.R, R/robimotu.R, R/robicategory.R, R/robisample.R,
% R/robimetabar.R, R/robimutation.R
\name{validate_object}
\alias{validate_object}
\alias{validate_object.default}
......@@ -117,7 +118,6 @@ validate_object(rt)
rt <- new_robitag(c("AGT","GGT","CGT","GTA","CCC"))
validate_object(rt)
# For robimotu instance
......
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