final check of function documentation

Author: zachary-foster

R/calculations.R

@@ -294,9 +294,9 @@ rarefy_obs <- function(obj, dataset, sample_size = NULL, cols = NULL,
 #'   order and length as \code{cols}.
 #' @param func The function to apply for each comparison. For each row in 
 #'   \code{dataset}, for each combination of groups, this function will 
-#'   receive the data for each treatment, passed a two character vectors.
+#'   receive the data for each treatment, passed as two character vectors.
 #'   Therefore the function must take at least 2 arguments corresponding to the
-#'   two groups compared. The function should return a vector or list or
+#'   two groups compared. The function should return a vector or list of
 #'   results of a fixed length. If named, the names will be used in the output.
 #'   The names should be consistent as well. A simple example is
 #'   \code{function(x, y) mean(x) - mean(y)}. By default, the following function

R/dataset_documentation.R

@@ -4,7 +4,7 @@
 #' It contains OTU ids, taxonomic lineages, and the read counts for 50 samples.
 #' See \code{\link{hmp_samples}} for the matching dataset of sample information.
 #' 
-#' The 50 samples were randomly elected such that there were 10 in each of 5
+#' The 50 samples were randomly selected such that there were 10 in each of 5
 #' treatments: "Saliva", "Throat", "Stool", "Right_Antecubital_fossa",
 #' "Anterior_nares". For each treatment, there were 5 samples from men and 5
 #' from women. 
@@ -24,7 +24,7 @@ NULL
 #' matrix stored in \code{\link{hmp_otus}}. The "sample_id" column corresponds
 #' to the column names of \code{\link{hmp_otus}}.
 #'
-#' The 50 samples were randomly elected such that there were 10 in each of 5
+#' The 50 samples were randomly selected such that there were 10 in each of 5
 #' treatments: "Saliva", "Throat", "Stool", "Right_Antecubital_fossa",
 #' "Anterior_nares". For each treatment, there were 5 samples from men and 5
 #' from women. "Right_Antecubital_fossa" was renamed to "Skin" and

R/metacoder-package.R

@@ -9,7 +9,7 @@
 #'   \item Standardized parsing of taxonomic information from diverse resources.
 #'   \item Visualization of statistics distributed over taxonomic classifications.
 #'   \item Evaluating potential metabarcoding primers for taxonomic specificity.
-#'   \item Provide flexible functions for analyzing taxonomic and abundance data.
+#'   \item Providing flexible functions for analyzing taxonomic and abundance data.
 #' }
 #' 
 #' To accomplish these goals, \code{metacoder} leverages resources from other R packages, interfaces with
@@ -79,7 +79,7 @@
 #'   \item \code{\link{ncbi_taxon_sample}}
 #' }
 #' 
-#' @author Zachary Foster
+#' @author Zachary Foster and Niklaus Grunwald
 #' @name metacoder
 #' @docType package
 #' @useDynLib metacoder

R/parsers.R

@@ -423,7 +423,7 @@ parse_unite_general <- function(input = NULL, file = NULL, include_seqs = TRUE)
 #' Parse RDP FASTA release
 #' 
 #' Parses an RDP reference FASTA file that can be found at
-#' https://rdp.cme.msu.edu/misc/resources.jsp.
+#' \url{https://rdp.cme.msu.edu/misc/resources.jsp}.
 #' 
 #' The input file has a format like:
 #' 
@@ -493,7 +493,7 @@ parse_rdp <- function(input = NULL, file = NULL, include_seqs = TRUE, add_specie
 #' Parse SILVA FASTA release
 #'
 #' Parses an SILVA FASTA file that can be found at
-#' https://www.arb-silva.de/no_cache/download/archive/release_128/Exports/.
+#' \url{https://www.arb-silva.de/no_cache/download/archive/release_128/Exports/}.
 #'
 #' The input file has a format like:
 #'

R/remove_ambiguous.R

@@ -62,11 +62,12 @@ ambiguous_patterns <- function(unknown = TRUE, uncultured = TRUE,
 
 #' Find ambiguous taxon names
 #'
-#' Find taxa with ambiguous names, such as "unknown" or "uncultured". If you
-#' encounter a taxon name that represents an ambiguous taxon that is not
+#' Find taxa with ambiguous names, such as "unknown" or "uncultured".
+#' 
+#' If you encounter a taxon name that represents an ambiguous taxon that is not
 #' filtered out by this function, let us know and we will add it.
 #'
-#' @param taxon_names A taxmap object
+#' @param taxon_names A \code{\link[taxa]{taxmap}} object
 #' @inheritParams ambiguous_patterns
 #' @param ignore_case If \code{TRUE}, dont consider the case of the text when
 #'   determining a match.
@@ -97,11 +98,11 @@ is_ambiguous <- function(taxon_names, unknown = TRUE, uncultured = TRUE,
 #' If you encounter a taxon name that represents an ambiguous taxon that is not
 #' filtered out by this function, let us know and we will add it.
 #'
-#' @param obj A taxmap object
+#' @param obj A \code{\link[taxa]{taxmap}} object
 #' @inheritParams is_ambiguous
 #' @inheritParams taxa::filter_taxa
 #'
-#' @return TRUE/FALSE vector corresponding to \code{taxon_names}
+#' @return A \code{\link[taxa]{taxmap}} object
 #'
 #' @export
 filter_ambiguous_taxa <- function(obj, unknown = TRUE, uncultured = TRUE,

R/sequence_download.R

@@ -1,7 +1,7 @@
 #' Download representative sequences for a taxon
 #' 
 #' Downloads a sample of sequences meant to evenly capture the diversity of a given taxon.
-#' Can be used to get a shallow sampling of a vast groups. 
+#' Can be used to get a shallow sampling of vast groups. 
 #' \strong{CAUTION:} This function can make MANY queries to Genbank depending on arguments given and
 #' can take a very long time. 
 #' Choose your arguments carefully to avoid long waits and needlessly stressing NCBI's servers.
@@ -165,7 +165,6 @@ ncbi_taxon_sample <- function(name = NULL, id = NULL, target_rank,
         result <- traits::ncbi_searcher(id = id, seqrange = seqrange, getrelated = getrelated,
                                         fuzzy = fuzzy, limit = limit, entrez_query = entrez_query,
                                         hypothetical = hypothetical, verbose = verbose)
-        print(result)
       } else {
         child_ranks <- factor(sub_taxa$childtaxa_rank,
                               levels = levels(taxonomy_levels), ordered = TRUE) 

R/writers.R

@@ -33,8 +33,6 @@
 #' @param ids (\code{character} named by taxon ids) Sequence ids
 #' @param sequences (\code{character} named by taxon ids) Sequences
 #'   
-#' @return \code{\link{taxmap}}
-#'   
 #' @family writers
 #'   
 #' @export
@@ -113,8 +111,6 @@ write_greengenes <- function(obj, tax_file = NULL, seq_file = NULL,
 #'   "Sparassis crispa; MBUH-PIRJO&ILKKA94-1587/ss5"
 #' @param sequences (\code{character} named by taxon ids) Sequences
 #'   
-#' @return \code{\link{taxmap}}
-#'   
 #' @family writers
 #'   
 #' @export
@@ -183,8 +179,6 @@ write_rdp <- function(obj, file,
 #' @param ids (\code{character} named by taxon ids) Sequence ids
 #' @param scores TBD
 #'   
-#' @return \code{\link{taxmap}}
-#'   
 #' @family writers
 #'   
 #' @export
@@ -251,8 +245,6 @@ write_mothur_taxonomy <- function(obj, file,
 #' @param type (\code{character} named by taxon ids) What type of sequence it
 #'   is. Usually "rep" or "ref".
 #'   
-#' @return \code{\link{taxmap}}
-#'   
 #' @family writers
 #'   
 #' @export
@@ -322,10 +314,6 @@ write_unite_general <- function(obj, file,
 #' sequence.
 #' @param sequences (\code{character} named by taxon ids) Sequences
 #'   
-#' @return \code{\link{taxmap}}
-#'   
-#' @family writers
-#'   
 #' @export
 write_silva_fasta <- function(obj, file,
                               tax_names = obj$get_data("taxon_names")[[1]],