diff --git a/R/rotl-package.R b/R/rotl-package.R index 2544c2d..7deabcb 100644 --- a/R/rotl-package.R +++ b/R/rotl-package.R @@ -15,15 +15,15 @@ ##' All functions that use API end points can take 2 arguments to ##' customize the API call and are passed as \code{...} arguments. ##' -##' \itemize{ +##' \describe{ ##' -##' \item{ \code{otl_v} } { This argument controls which version +##' \item{ \code{otl_v}}{This argument controls which version ##' of the API your call is using. The default value for this ##' argument is a call to the non-exported function ##' \code{otl_version()} which returns the current version of the ##' Open Tree of Life APIs (v2).} ##' -##' \item{ \code{dev_url} } { This argument controls whether to use +##' \item{ \code{dev_url}}{This argument controls whether to use ##' the development version of the API. By default, \code{dev_url} ##' is set to \code{FALSE}, using \code{dev_url = TRUE} in your ##' function calls will use the development version.} @@ -44,6 +44,5 @@ ##' Interoperability Phylogenetic group, and Arbor. ##' ##' @name rotl -##' @docType package ##' @import ape NULL diff --git a/R/studies-methods.R b/R/studies-methods.R index dad8630..62bea76 100644 --- a/R/studies-methods.R +++ b/R/studies-methods.R @@ -3,7 +3,7 @@ ##' List trees ids in objects returned by ##' \code{\link{studies_find_studies}} and -##' \code{\link{studies_find_trees}}. +##' \code{\link{studies_find_trees}} ##' ##' \code{list_trees} returns all trees associated with a particular ##' study when used on an object returned by diff --git a/R/studies.R b/R/studies.R index d5c2891..86d36af 100644 --- a/R/studies.R +++ b/R/studies.R @@ -372,28 +372,26 @@ get_study_tree <- function(study_id = NULL, tree_id = NULL, object_format = c("p res } -##' Retrieve metadata about a study in the Open Tree of Life datastore. +##' Retrieve metadata about a study in the Open Tree of Life datastore ##' ##' \code{get_study_meta} returns a long list of attributes for the ##' studies that are contributing to the synthetic tree. To help with ##' the extraction of relevant information from this list, several -##' helper functions exists: \itemize{ +##' helper functions exists: \describe{ ##' -##' \item {get_tree_ids} { The identifiers of the trees -##' associated with the study } +##' \item{get_tree_ids}{The identifiers of the trees +##' associated with the study.} ##' -##' \item {get_publication} { The citation information of the +##' \item{get_publication}{The citation information of the ##' publication for the study. The DOI (or URL) for the study is ##' available as an attribute to the returned object (i.e., -##' \code{attr(object, "DOI")} ) }. +##' \code{attr(object, "DOI")} ).} ##' -##' \item {candidate_for_synth} { The identifier of the tree(s) from +##' \item{candidate_for_synth}{The identifier of the tree(s) from ##' the study used in the synthetic tree. This is a subset of the -##' result of \code{get_tree_ids}. +##' result of \code{get_tree_ids}.} ##' -##' \item {get_study_year} { The year of publication of the study. } -##' -##' } +##' \item{get_study_year}{The year of publication of the study.} ##' } ##' ##' @title Study Metadata diff --git a/R/taxonomy.R b/R/taxonomy.R index 1e5d9f5..5836ab0 100644 --- a/R/taxonomy.R +++ b/R/taxonomy.R @@ -9,19 +9,19 @@ ##' @param ... additional arguments to customize the API request (see ##' \code{\link{rotl}} package documentation). ##' @return A list with the following properties: -##' \itemize{ +##' \describe{ ##' -##' \item {weburl} {String. The release page for this version +##' \item{weburl}{String. The release page for this version ##' of the taxonomy.} ##' -##' \item {author} {String. The author string.} +##' \item{author}{String. The author string.} ##' -##' \item {name} {String. The name of the taxonomy.} +##' \item{name}{String. The name of the taxonomy.} ##' -##' \item {source} {String. The full identifying information for +##' \item{source}{String. The full identifying information for ##' this version of the taxonomy.} ##' -##' \item {version} {String. The version number of the taxonomy.} +##' \item{version}{String. The version number of the taxonomy.} ##' } ##' @examples ##' \dontrun{ @@ -112,21 +112,21 @@ taxonomy_taxon_info <- function(ott_ids, include_children = FALSE, ##' @param file the file name where to save the output of the ##' function. Ignored unless \code{output_format} is set to ##' \dQuote{\code{phylo}}. -##' @return If the \code{file} argument is missing: \itemize{ +##' @return If the \code{file} argument is missing: \describe{ ##' -##' \item{\dQuote{\code{taxa}}} { a list of the taxa names +##' \item{\dQuote{\code{taxa}}}{ a list of the taxa names ##' (species) in slot \code{tip_label}, and higher-level taxonomy ##' (e.g., families, genera) in slot \code{edge_label}, descending ##' from the taxa corresponding to the \code{ott_id} provided. } ##' -##' \item{\dQuote{\code{newick}}} { a character vector containing +##' \item{\dQuote{\code{newick}}}{ a character vector containing ##' the newick formatted string corresponding to the taxonomic ##' subtree for the \code{ott_id} provided. } ##' -##' \item{\dQuote{\code{phylo}}} { an object of the class +##' \item{\dQuote{\code{phylo}}}{ an object of the class ##' \code{phylo} from the \code{ape} package. } ##' -##' \item{\dQuote{\code{raw}}} { the direct output from the API, +##' \item{\dQuote{\code{raw}}}{ the direct output from the API, ##' i.e., a list with an element named \sQuote{newick} that ##' contains the subtree as a newick formatted string. } ##' @@ -183,19 +183,19 @@ taxonomy_subtree <- function(ott_id = NULL, ##' function ##' @param ... additional arguments to customize the API request (see ##' \code{\link{rotl}} package documentation). -##' @return \itemize{ +##' @return \describe{ ##' -##' \item{\code{taxonomy_mrca}} { returns a list about the +##' \item{\code{taxonomy_mrca}}{ returns a list about the ##' taxonomic information relating to the MRCA for the ott_ids ##' provided. } ##' -##' \item{\code{tax_rank}} { returns a character vector of the +##' \item{\code{tax_rank}}{ returns a character vector of the ##' taxonomic rank for the MRCA. } ##' -##' \item{\code{tax_name}} { returns a character vector the +##' \item{\code{tax_name}}{ returns a character vector the ##' Open Tree Taxonomy name for the MRCA. } ##' -##' \item{\code{ott_id}} { returns a numeric vector of the ott id +##' \item{\code{ott_id}}{ returns a numeric vector of the ott id ##' for the MRCA. } ##' ##' } diff --git a/R/tol.R b/R/tol.R index 26abdd1..3255010 100644 --- a/R/tol.R +++ b/R/tol.R @@ -38,68 +38,68 @@ ##' ##' @return An invisible list of synthetic tree summary statistics: ##' -##' \itemize{ +##' \describe{ ##' -##' \item {date_created} {String. The creation date of the tree.} +##' \item{date_created}{String. The creation date of the tree.} ##' -##' \item {num_source_studies} {Integer. The number of studies +##' \item{num_source_studies}{Integer. The number of studies ##' (publications)used as sources.} ##' -##' \item {num_source_trees} {The number of trees used as sources +##' \item{num_source_trees}{The number of trees used as sources ##' (may be >1 tree per study).} ##' -##' \item {taxonomy_version} {The Open Tree Taxonomy version used +##' \item{taxonomy_version}{The Open Tree Taxonomy version used ##' as a source.} ##' -##' \item {filtered_flags} {List. Taxa with these taxonomy flags were +##' \item{filtered_flags}{List. Taxa with these taxonomy flags were ##' not used in construction of the tree.} ##' -##' \item {root} {List. Describes the root node:} -##' \itemize{ -##' \item {node_id} {String. The canonical identifier of the node.} +##' \item{root}{List. Describes the root node:} +##' \describe{ +##' \item{node_id}{String. The canonical identifier of the node.} ##' -##' \item {num_tips} {Numeric. The number of descendant tips.} +##' \item{num_tips}{Numeric. The number of descendant tips.} ##' -##' \item {taxon} {A list of taxonomic properties:} -##' \itemize{ -##' \item {ott_id} {Numeric. The OpenTree Taxonomy ID (ott_id).} +##' \item{taxon}{A list of taxonomic properties:} +##' \describe{ +##' \item{ott_id}{Numeric. The OpenTree Taxonomy ID (ott_id).} ##' -##' \item {name} {String. The taxonomic name of the queried node.} +##' \item{name}{String. The taxonomic name of the queried node.} ##' -##' \item {unique_name} {String. The string that uniquely +##' \item{unique_name}{String. The string that uniquely ##' identifies the taxon in OTT.} ##' -##' \item {rank} {String. The taxonomic rank of the taxon in OTT.} +##' \item{rank}{String. The taxonomic rank of the taxon in OTT.} ##' -##' \item {tax_sources} {List. A list of identifiers for taxonomic +##' \item{tax_sources}{List. A list of identifiers for taxonomic ##' sources, such as other taxonomies, that define taxa judged ##' equivalent to this taxon.} ##' } ##' } ##' -##' \item {source_list} {List. Present only if +##' \item{source_list}{List. Present only if ##' \code{include_source_list} is \code{TRUE}. The sourceid ##' ordering is the precedence order for synthesis, with ##' relationships from earlier trees in the list having priority ##' over those from later trees in the list. See ##' \code{source_id_map} below for study details.} ##' -##' \item {source_id_map} {Named list of lists. Present only if +##' \item{source_id_map}{Named list of lists. Present only if ##' \code{include_source_list} is \code{TRUE}. Names correspond to ##' the \sQuote{sourceids} used in \code{source_list} ##' above. Source trees will have the following properties:} ##' -##' \itemize{ -##' \item {git_sha} {String. The git SHA identifying a particular source +##' \describe{ +##' \item{git_sha}{String. The git SHA identifying a particular source ##' version.} #' -##' \item {tree_id} {String. The tree id associated with the study id used.} +##' \item{tree_id}{String. The tree id associated with the study id used.} ##' -##' \item {study_id} {String. The study identifier. Will typically include +##' \item{study_id}{String. The study identifier. Will typically include ##' a prefix ("pg_" or "ot_").} ##' } ##' -##' \item {synth_id} {The unique string for this version of the tree.} +##' \item{synth_id}{The unique string for this version of the tree.} ##' } ##' @seealso \code{\link{source_list}} to explore the list of studies ##' used in the synthetic tree (see example). @@ -198,30 +198,30 @@ source_list.tol_summary <- .source_list ##' ##' @return An invisible list of the MRCA node properties: ##' -##' \itemize{ +##' \describe{ ##' -##' \item {mrca} {List of node properties.} +##' \item{mrca}{List of node properties.} ##' -##' \itemize{ -##' \item {node_id} {String. The canonical identifier of the node.} +##' \describe{ +##' \item{node_id}{String. The canonical identifier of the node.} ##' -##' \item {num_tips} {Numeric. The number of descendant tips.} +##' \item{num_tips}{Numeric. The number of descendant tips.} ##' -##' \item {taxon} {A list of taxonomic properties. Only returned if +##' \item{taxon}{A list of taxonomic properties. Only returned if ##' the queried node is a taxon. (If the node is not a taxon, a ##' \code{nearest_taxon} list is returned (see below)).} ##' -##' \itemize{ -##' \item {ott_id} {Numeric. The OpenTree Taxonomy ID (ottID).} +##' \describe{ +##' \item{ott_id}{Numeric. The OpenTree Taxonomy ID (ottID).} ##' -##' \item {name} {String. The taxonomic name of the queried node.} +##' \item{name}{String. The taxonomic name of the queried node.} ##' -##' \item {unique_name} {String. The string that uniquely +##' \item{unique_name}{String. The string that uniquely ##' identifies the taxon in OTT.} ##' -##' \item {rank} {String. The taxonomic rank of the taxon in OTT.} +##' \item{rank}{String. The taxonomic rank of the taxon in OTT.} ##' -##' \item {tax_sources} {List. A list of identifiers for taxonomic +##' \item{tax_sources}{List. A list of identifiers for taxonomic ##' sources, such as other taxonomies, that define taxa judged ##' equivalent to this taxon.} ##' } @@ -231,54 +231,54 @@ source_list.tol_summary <- .source_list ##' nodeid values (see \code{source_id_map} below) Not all properties are ##' are present for every node. ##' -##' \item {partial_path_of} {List. The edge below this synthetic tree node +##' \item{partial_path_of}{List. The edge below this synthetic tree node ##' is compatible with the edge below each of these input tree nodes (one ##' per tree). Each returned element is reported as sourceid:nodeid.} ##' -##' \item {supported_by} {List. Input tree nodes (one per tree) that support +##' \item{supported_by}{List. Input tree nodes (one per tree) that support ##' this synthetic tree node. Each returned element is reported as ##' sourceid:nodeid.} ##' -##' \item {terminal} {List. Input tree nodes (one per tree) that are equivalent +##' \item{terminal}{List. Input tree nodes (one per tree) that are equivalent ##' to this synthetic tree node (via an exact mapping, or the input tree ##' terminal may be the only terminal descended from this synthetic tree node. ##' Each returned element is reported as sourceid:nodeid.} ##' -##' \item {conflicts_with} {Named list of lists. Names correspond to +##' \item{conflicts_with}{Named list of lists. Names correspond to ##' sourceid keys. Each list contains input tree node ids (one or more per tree) ##' that conflict with this synthetic node.} ##' } ##' -##' \item {nearest_taxon} {A list of taxonomic properties of the nearest rootward +##' \item{nearest_taxon}{A list of taxonomic properties of the nearest rootward ##' taxon node to the MRCA node. Only returned if the MRCA node is a not taxon ##' (otherwise the \code{taxon} list above is returned).} ##' -##' \itemize{ -##' \item {ott_id} {Numeric. The OpenTree Taxonomy ID (ottID).} +##' \describe{ +##' \item{ott_id}{Numeric. The OpenTree Taxonomy ID (ottID).} ##' -##' \item {name} {String. The taxonomic name of the queried node.} +##' \item{name}{String. The taxonomic name of the queried node.} ##' -##' \item {unique_name} {String. The string that uniquely +##' \item{unique_name}{String. The string that uniquely ##' identifies the taxon in OTT.} ##' -##' \item {rank} {String. The taxonomic rank of the taxon in OTT.} +##' \item{rank}{String. The taxonomic rank of the taxon in OTT.} ##' -##' \item {tax_sources} {List. A list of identifiers for taxonomic +##' \item{tax_sources}{List. A list of identifiers for taxonomic ##' sources, such as other taxonomies, that define taxa judged ##' equivalent to this taxon.} ##' } ##' -##' \item {source_id_map} {Named list of lists. Names correspond to the +##' \item{source_id_map}{Named list of lists. Names correspond to the ##' sourceid keys used in the support/conflict properties of the \code{mrca} ##' list above. Source trees will have the following properties:} ##' -##' \itemize{ -##' \item {git_sha} {The git SHA identifying a particular source +##' \describe{ +##' \item{git_sha}{The git SHA identifying a particular source ##' version.} ##' -##' \item {tree_id} {The tree id associated with the study id used.} +##' \item{tree_id}{The tree id associated with the study id used.} ##' -##' \item {study_id} {The study identifier. Will typically include +##' \item{study_id}{The study identifier. Will typically include ##' a prefix ("pg_" or "ot_").} ##' } ##' The only sourceid that does not correspond to a source tree is the taxonomy, @@ -523,33 +523,33 @@ strip_ott_ids <- function(tip_labels, remove_underscores = FALSE) { ##' @return \code{tol_node_info} returns an invisible list of summary ##' information about the queried node: ##' -##' \itemize{ +##' \describe{ ##' -##' \item {node_id} {String. The canonical identifier of the node.} +##' \item{node_id}{String. The canonical identifier of the node.} ##' -##' \item {num_tips} {Numeric. The number of descendant tips.} +##' \item{num_tips}{Numeric. The number of descendant tips.} ##' -##' \item {partial_path_of} {List. The edge below this synthetic tree node +##' \item{partial_path_of}{List. The edge below this synthetic tree node ##' is compatible with the edge below each of these input tree nodes (one ##' per tree). Each returned element is reported as sourceid:nodeid.} ##' -##' \item {query} { The node id that resolved to this node. This can differ +##' \item{query}{ The node id that resolved to this node. This can differ ##' from the node_id field if the query id is not canonical. } ##' -##' \item {taxon} {A list of taxonomic properties. Only returned if +##' \item{taxon}{A list of taxonomic properties. Only returned if ##' the queried node is a taxon. Each source has:} ##' -##' \itemize{ -##' \item {ott_id} {Numeric. The OpenTree Taxonomy ID (ottID).} +##' \describe{ +##' \item{ott_id}{Numeric. The OpenTree Taxonomy ID (ottID).} ##' -##' \item {name} {String. The taxonomic name of the queried node.} +##' \item{name}{String. The taxonomic name of the queried node.} ##' -##' \item {unique_name} {String. The string that uniquely +##' \item{unique_name}{String. The string that uniquely ##' identifies the taxon in OTT.} ##' -##' \item {rank} {String. The taxonomic rank of the taxon in OTT.} +##' \item{rank}{String. The taxonomic rank of the taxon in OTT.} ##' -##' \item {tax_sources} {List. A list of identifiers for taxonomic +##' \item{tax_sources}{List. A list of identifiers for taxonomic ##' sources, such as other taxonomies, that define taxa judged ##' equivalent to this taxon.} ##' } @@ -558,17 +558,17 @@ strip_ott_ids <- function(tip_labels, remove_underscores = FALSE) { ##' synthesis source trees. All properties involve sourceid keys and ##' nodeid values (see \code{source_id_map} below). ##' -##' \item {supported_by} {List. Input tree nodes (one per tree) that support +##' \item{supported_by}{List. Input tree nodes (one per tree) that support ##' this synthetic tree node. Each returned element is reported as ##' sourceid:nodeid.} ##' -##' \item {terminal} {List. Input tree nodes (one per tree) that are +##' \item{terminal}{List. Input tree nodes (one per tree) that are ##' equivalent to this synthetic tree node (via an exact mapping, or the ##' input tree terminal may be the only terminal descended from this ##' synthetic tree node. Each returned element is reported as ##' sourceid:nodeid.} ##' -##' \item {conflicts_with} {Named list of lists. Names correspond to +##' \item{conflicts_with}{Named list of lists. Names correspond to ##' sourceid keys. Each list contains input tree node ids (one or more per ##' tree) that conflict with this synthetic node.} ##' } diff --git a/man/get_study_meta.Rd b/man/get_study_meta.Rd index fccfbd7..2d80dac 100644 --- a/man/get_study_meta.Rd +++ b/man/get_study_meta.Rd @@ -43,29 +43,27 @@ named-list containing the metadata associated with the study requested } \description{ -Retrieve metadata about a study in the Open Tree of Life datastore. +Retrieve metadata about a study in the Open Tree of Life datastore } \details{ \code{get_study_meta} returns a long list of attributes for the studies that are contributing to the synthetic tree. To help with the extraction of relevant information from this list, several -helper functions exists: \itemize{ +helper functions exists: \describe{ - \item {get_tree_ids} { The identifiers of the trees - associated with the study } + \item{get_tree_ids}{The identifiers of the trees + associated with the study.} - \item {get_publication} { The citation information of the + \item{get_publication}{The citation information of the publication for the study. The DOI (or URL) for the study is available as an attribute to the returned object (i.e., - \code{attr(object, "DOI")} ) }. + \code{attr(object, "DOI")} ).} - \item {candidate_for_synth} { The identifier of the tree(s) from + \item{candidate_for_synth}{The identifier of the tree(s) from the study used in the synthetic tree. This is a subset of the - result of \code{get_tree_ids}. + result of \code{get_tree_ids}.} - \item {get_study_year} { The year of publication of the study. } - - } + \item{get_study_year}{The year of publication of the study.} } } \examples{ diff --git a/man/list_trees.Rd b/man/list_trees.Rd index d7ffa93..d8bd0e0 100644 --- a/man/list_trees.Rd +++ b/man/list_trees.Rd @@ -5,7 +5,7 @@ \alias{list_trees.matched_studies} \title{List trees ids in objects returned by \code{\link{studies_find_studies}} and -\code{\link{studies_find_trees}}.} +\code{\link{studies_find_trees}}} \usage{ list_trees(matched_studies, ...) diff --git a/man/rotl.Rd b/man/rotl.Rd index af369b9..f4daaf9 100644 --- a/man/rotl.Rd +++ b/man/rotl.Rd @@ -1,6 +1,5 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/rotl-package.R -\docType{package} \name{rotl} \alias{rotl} \title{An Interface to the Open Tree of Life API} @@ -22,15 +21,15 @@ provides. The documentation of the API is available at: All functions that use API end points can take 2 arguments to customize the API call and are passed as \code{...} arguments. - \itemize{ + \describe{ - \item{ \code{otl_v} } { This argument controls which version + \item{ \code{otl_v}}{This argument controls which version of the API your call is using. The default value for this argument is a call to the non-exported function \code{otl_version()} which returns the current version of the Open Tree of Life APIs (v2).} - \item{ \code{dev_url} } { This argument controls whether to use + \item{ \code{dev_url}}{This argument controls whether to use the development version of the API. By default, \code{dev_url} is set to \code{FALSE}, using \code{dev_url = TRUE} in your function calls will use the development version.} diff --git a/man/taxonomy_about.Rd b/man/taxonomy_about.Rd index 8dc34bc..8ccd8ac 100644 --- a/man/taxonomy_about.Rd +++ b/man/taxonomy_about.Rd @@ -12,19 +12,19 @@ taxonomy_about(...) } \value{ A list with the following properties: -\itemize{ +\describe{ - \item {weburl} {String. The release page for this version + \item{weburl}{String. The release page for this version of the taxonomy.} - \item {author} {String. The author string.} + \item{author}{String. The author string.} - \item {name} {String. The name of the taxonomy.} + \item{name}{String. The name of the taxonomy.} - \item {source} {String. The full identifying information for + \item{source}{String. The full identifying information for this version of the taxonomy.} - \item {version} {String. The version number of the taxonomy.} + \item{version}{String. The version number of the taxonomy.} } } \description{ diff --git a/man/taxonomy_mrca.Rd b/man/taxonomy_mrca.Rd index 07e54bc..ac001d7 100644 --- a/man/taxonomy_mrca.Rd +++ b/man/taxonomy_mrca.Rd @@ -38,19 +38,19 @@ be found (numeric).} function} } \value{ -\itemize{ +\describe{ - \item{\code{taxonomy_mrca}} { returns a list about the + \item{\code{taxonomy_mrca}}{ returns a list about the taxonomic information relating to the MRCA for the ott_ids provided. } - \item{\code{tax_rank}} { returns a character vector of the + \item{\code{tax_rank}}{ returns a character vector of the taxonomic rank for the MRCA. } - \item{\code{tax_name}} { returns a character vector the + \item{\code{tax_name}}{ returns a character vector the Open Tree Taxonomy name for the MRCA. } - \item{\code{ott_id}} { returns a numeric vector of the ott id + \item{\code{ott_id}}{ returns a numeric vector of the ott id for the MRCA. } } diff --git a/man/taxonomy_subtree.Rd b/man/taxonomy_subtree.Rd index 10d67b8..6691f64 100644 --- a/man/taxonomy_subtree.Rd +++ b/man/taxonomy_subtree.Rd @@ -30,21 +30,21 @@ function. Ignored unless \code{output_format} is set to \code{\link{rotl}} package documentation).} } \value{ -If the \code{file} argument is missing: \itemize{ +If the \code{file} argument is missing: \describe{ - \item{\dQuote{\code{taxa}}} { a list of the taxa names + \item{\dQuote{\code{taxa}}}{ a list of the taxa names (species) in slot \code{tip_label}, and higher-level taxonomy (e.g., families, genera) in slot \code{edge_label}, descending from the taxa corresponding to the \code{ott_id} provided. } - \item{\dQuote{\code{newick}}} { a character vector containing + \item{\dQuote{\code{newick}}}{ a character vector containing the newick formatted string corresponding to the taxonomic subtree for the \code{ott_id} provided. } - \item{\dQuote{\code{phylo}}} { an object of the class + \item{\dQuote{\code{phylo}}}{ an object of the class \code{phylo} from the \code{ape} package. } - \item{\dQuote{\code{raw}}} { the direct output from the API, + \item{\dQuote{\code{raw}}}{ the direct output from the API, i.e., a list with an element named \sQuote{newick} that contains the subtree as a newick formatted string. } diff --git a/man/tol_about.Rd b/man/tol_about.Rd index 49d4abc..b25e7a2 100644 --- a/man/tol_about.Rd +++ b/man/tol_about.Rd @@ -33,68 +33,68 @@ tol_about(include_source_list = FALSE, ...) \value{ An invisible list of synthetic tree summary statistics: -\itemize{ +\describe{ - \item {date_created} {String. The creation date of the tree.} + \item{date_created}{String. The creation date of the tree.} - \item {num_source_studies} {Integer. The number of studies + \item{num_source_studies}{Integer. The number of studies (publications)used as sources.} - \item {num_source_trees} {The number of trees used as sources + \item{num_source_trees}{The number of trees used as sources (may be >1 tree per study).} - \item {taxonomy_version} {The Open Tree Taxonomy version used + \item{taxonomy_version}{The Open Tree Taxonomy version used as a source.} - \item {filtered_flags} {List. Taxa with these taxonomy flags were + \item{filtered_flags}{List. Taxa with these taxonomy flags were not used in construction of the tree.} - \item {root} {List. Describes the root node:} - \itemize{ - \item {node_id} {String. The canonical identifier of the node.} + \item{root}{List. Describes the root node:} + \describe{ + \item{node_id}{String. The canonical identifier of the node.} - \item {num_tips} {Numeric. The number of descendant tips.} + \item{num_tips}{Numeric. The number of descendant tips.} - \item {taxon} {A list of taxonomic properties:} - \itemize{ - \item {ott_id} {Numeric. The OpenTree Taxonomy ID (ott_id).} + \item{taxon}{A list of taxonomic properties:} + \describe{ + \item{ott_id}{Numeric. The OpenTree Taxonomy ID (ott_id).} - \item {name} {String. The taxonomic name of the queried node.} + \item{name}{String. The taxonomic name of the queried node.} - \item {unique_name} {String. The string that uniquely + \item{unique_name}{String. The string that uniquely identifies the taxon in OTT.} - \item {rank} {String. The taxonomic rank of the taxon in OTT.} + \item{rank}{String. The taxonomic rank of the taxon in OTT.} - \item {tax_sources} {List. A list of identifiers for taxonomic + \item{tax_sources}{List. A list of identifiers for taxonomic sources, such as other taxonomies, that define taxa judged equivalent to this taxon.} } } - \item {source_list} {List. Present only if + \item{source_list}{List. Present only if \code{include_source_list} is \code{TRUE}. The sourceid ordering is the precedence order for synthesis, with relationships from earlier trees in the list having priority over those from later trees in the list. See \code{source_id_map} below for study details.} - \item {source_id_map} {Named list of lists. Present only if + \item{source_id_map}{Named list of lists. Present only if \code{include_source_list} is \code{TRUE}. Names correspond to the \sQuote{sourceids} used in \code{source_list} above. Source trees will have the following properties:} - \itemize{ - \item {git_sha} {String. The git SHA identifying a particular source + \describe{ + \item{git_sha}{String. The git SHA identifying a particular source version.} - \item {tree_id} {String. The tree id associated with the study id used.} + \item{tree_id}{String. The tree id associated with the study id used.} - \item {study_id} {String. The study identifier. Will typically include + \item{study_id}{String. The study identifier. Will typically include a prefix ("pg_" or "ot_").} } - \item {synth_id} {The unique string for this version of the tree.} + \item{synth_id}{The unique string for this version of the tree.} } } \description{ diff --git a/man/tol_mrca.Rd b/man/tol_mrca.Rd index 1a83ccf..c0dc813 100644 --- a/man/tol_mrca.Rd +++ b/man/tol_mrca.Rd @@ -37,30 +37,30 @@ tol_mrca(ott_ids = NULL, node_ids = NULL, ...) \value{ An invisible list of the MRCA node properties: -\itemize{ +\describe{ - \item {mrca} {List of node properties.} + \item{mrca}{List of node properties.} - \itemize{ - \item {node_id} {String. The canonical identifier of the node.} + \describe{ + \item{node_id}{String. The canonical identifier of the node.} - \item {num_tips} {Numeric. The number of descendant tips.} + \item{num_tips}{Numeric. The number of descendant tips.} - \item {taxon} {A list of taxonomic properties. Only returned if + \item{taxon}{A list of taxonomic properties. Only returned if the queried node is a taxon. (If the node is not a taxon, a \code{nearest_taxon} list is returned (see below)).} - \itemize{ - \item {ott_id} {Numeric. The OpenTree Taxonomy ID (ottID).} + \describe{ + \item{ott_id}{Numeric. The OpenTree Taxonomy ID (ottID).} - \item {name} {String. The taxonomic name of the queried node.} + \item{name}{String. The taxonomic name of the queried node.} - \item {unique_name} {String. The string that uniquely + \item{unique_name}{String. The string that uniquely identifies the taxon in OTT.} - \item {rank} {String. The taxonomic rank of the taxon in OTT.} + \item{rank}{String. The taxonomic rank of the taxon in OTT.} - \item {tax_sources} {List. A list of identifiers for taxonomic + \item{tax_sources}{List. A list of identifiers for taxonomic sources, such as other taxonomies, that define taxa judged equivalent to this taxon.} } @@ -70,54 +70,54 @@ An invisible list of the MRCA node properties: nodeid values (see \code{source_id_map} below) Not all properties are are present for every node. - \item {partial_path_of} {List. The edge below this synthetic tree node + \item{partial_path_of}{List. The edge below this synthetic tree node is compatible with the edge below each of these input tree nodes (one per tree). Each returned element is reported as sourceid:nodeid.} - \item {supported_by} {List. Input tree nodes (one per tree) that support + \item{supported_by}{List. Input tree nodes (one per tree) that support this synthetic tree node. Each returned element is reported as sourceid:nodeid.} - \item {terminal} {List. Input tree nodes (one per tree) that are equivalent + \item{terminal}{List. Input tree nodes (one per tree) that are equivalent to this synthetic tree node (via an exact mapping, or the input tree terminal may be the only terminal descended from this synthetic tree node. Each returned element is reported as sourceid:nodeid.} - \item {conflicts_with} {Named list of lists. Names correspond to + \item{conflicts_with}{Named list of lists. Names correspond to sourceid keys. Each list contains input tree node ids (one or more per tree) that conflict with this synthetic node.} } - \item {nearest_taxon} {A list of taxonomic properties of the nearest rootward + \item{nearest_taxon}{A list of taxonomic properties of the nearest rootward taxon node to the MRCA node. Only returned if the MRCA node is a not taxon (otherwise the \code{taxon} list above is returned).} - \itemize{ - \item {ott_id} {Numeric. The OpenTree Taxonomy ID (ottID).} + \describe{ + \item{ott_id}{Numeric. The OpenTree Taxonomy ID (ottID).} - \item {name} {String. The taxonomic name of the queried node.} + \item{name}{String. The taxonomic name of the queried node.} - \item {unique_name} {String. The string that uniquely + \item{unique_name}{String. The string that uniquely identifies the taxon in OTT.} - \item {rank} {String. The taxonomic rank of the taxon in OTT.} + \item{rank}{String. The taxonomic rank of the taxon in OTT.} - \item {tax_sources} {List. A list of identifiers for taxonomic + \item{tax_sources}{List. A list of identifiers for taxonomic sources, such as other taxonomies, that define taxa judged equivalent to this taxon.} } - \item {source_id_map} {Named list of lists. Names correspond to the + \item{source_id_map}{Named list of lists. Names correspond to the sourceid keys used in the support/conflict properties of the \code{mrca} list above. Source trees will have the following properties:} - \itemize{ - \item {git_sha} {The git SHA identifying a particular source + \describe{ + \item{git_sha}{The git SHA identifying a particular source version.} - \item {tree_id} {The tree id associated with the study id used.} + \item{tree_id}{The tree id associated with the study id used.} - \item {study_id} {The study identifier. Will typically include + \item{study_id}{The study identifier. Will typically include a prefix ("pg_" or "ot_").} } The only sourceid that does not correspond to a source tree is the taxonomy, diff --git a/man/tol_node_info.Rd b/man/tol_node_info.Rd index 5881a03..82b2460 100644 --- a/man/tol_node_info.Rd +++ b/man/tol_node_info.Rd @@ -50,33 +50,33 @@ lineage of the node from the synthetic tree.} \code{tol_node_info} returns an invisible list of summary information about the queried node: -\itemize{ +\describe{ - \item {node_id} {String. The canonical identifier of the node.} + \item{node_id}{String. The canonical identifier of the node.} - \item {num_tips} {Numeric. The number of descendant tips.} + \item{num_tips}{Numeric. The number of descendant tips.} - \item {partial_path_of} {List. The edge below this synthetic tree node + \item{partial_path_of}{List. The edge below this synthetic tree node is compatible with the edge below each of these input tree nodes (one per tree). Each returned element is reported as sourceid:nodeid.} - \item {query} { The node id that resolved to this node. This can differ + \item{query}{ The node id that resolved to this node. This can differ from the node_id field if the query id is not canonical. } - \item {taxon} {A list of taxonomic properties. Only returned if + \item{taxon}{A list of taxonomic properties. Only returned if the queried node is a taxon. Each source has:} - \itemize{ - \item {ott_id} {Numeric. The OpenTree Taxonomy ID (ottID).} + \describe{ + \item{ott_id}{Numeric. The OpenTree Taxonomy ID (ottID).} - \item {name} {String. The taxonomic name of the queried node.} + \item{name}{String. The taxonomic name of the queried node.} - \item {unique_name} {String. The string that uniquely + \item{unique_name}{String. The string that uniquely identifies the taxon in OTT.} - \item {rank} {String. The taxonomic rank of the taxon in OTT.} + \item{rank}{String. The taxonomic rank of the taxon in OTT.} - \item {tax_sources} {List. A list of identifiers for taxonomic + \item{tax_sources}{List. A list of identifiers for taxonomic sources, such as other taxonomies, that define taxa judged equivalent to this taxon.} } @@ -85,17 +85,17 @@ lineage of the node from the synthetic tree.} synthesis source trees. All properties involve sourceid keys and nodeid values (see \code{source_id_map} below). - \item {supported_by} {List. Input tree nodes (one per tree) that support + \item{supported_by}{List. Input tree nodes (one per tree) that support this synthetic tree node. Each returned element is reported as sourceid:nodeid.} - \item {terminal} {List. Input tree nodes (one per tree) that are + \item{terminal}{List. Input tree nodes (one per tree) that are equivalent to this synthetic tree node (via an exact mapping, or the input tree terminal may be the only terminal descended from this synthetic tree node. Each returned element is reported as sourceid:nodeid.} - \item {conflicts_with} {Named list of lists. Names correspond to + \item{conflicts_with}{Named list of lists. Names correspond to sourceid keys. Each list contains input tree node ids (one or more per tree) that conflict with this synthetic node.} }