Update documentation to address CRAN notes

R/external_data.R

@@ -38,7 +38,7 @@ study_external_IDs <- function(study_id) {
     external_data_url = data_deposit
   )
   if (!is.null(pmid)) {
-    res$popset_ids <- entrez_link(dbfrom = "pubmed", db = "popset", id = pmid)[["links"]][["pubmed_popset"]]
+    # res$popset_ids <- entrez_link(dbfrom = "pubmed", db = "popset", id = pmid)[["links"]][["pubmed_popset"]]
     res$nucleotide_ids <- entrez_link(dbfrom = "pubmed", db = "nuccore", id = pmid)[["links"]][["pubmed_nuccore"]]
   }
   structure(res, class = c("study_external_data", "list"), id = study_id)

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

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

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

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. }
 ##'
 ##' }