fixed spelling errors

zachary-foster · zachary-foster · commit 34f2d18dac5d · 2017-05-22T19:22:49.000-07:00
diff --git a/R/dataset_documentation.R b/R/dataset_documentation.R
@@ -21,7 +21,7 @@
 "genbank_ex_data"
 
 
-#' Example dataset of comtamination
+#' Example dataset of contamination
 #'
 #' A dataset containing information from 97 NCBI accession numbers representing possible contamination:
 #' 
diff --git a/R/extract_taxonomy--internal.R b/R/extract_taxonomy--internal.R
@@ -56,7 +56,7 @@ validate_regex_match <- function(input, regex, max_print = 10) {
 #' Check a regex-key pair
 #' 
 #' Checks that the number of capture groups in the regex matches the length of the key.
-#' Checks that only certian values of \code{key} can appear more that once.
+#' Checks that only certain values of \code{key} can appear more that once.
 #' Adds names to keys that will be used for column names in the output of \code{extract_taxonomy}.
 #' Uses non-standard evaluation to get the name of input variables.
 #'
diff --git a/R/extract_taxonomy--parsers.R b/R/extract_taxonomy--parsers.R
@@ -60,7 +60,7 @@ class_from_obs_id <- function(obs_id, database = c("ncbi", "none"), batch_size =
 #' Any names added to the terms will be used as column names in the output.
 #' At least \code{"taxon_id"} or \code{"name"} must be specified.
 #' Only \code{"taxon_info"} can be used multiple times.
-#' Each term must be one of those decribed below:
+#' Each term must be one of those described below:
 #'  \describe{
 #'    \item{\code{taxon_id}}{A unique numeric id for a taxon for a particular \code{database} (e.g. ncbi accession number).
 #'          Requires an internet connection.}
@@ -76,7 +76,7 @@ class_from_obs_id <- function(obs_id, database = c("ncbi", "none"), batch_size =
 #' The character(s) used to separate individual taxa within a classification.
 #' @param class_rev (\code{logical} of length 1)
 #' Used with the \code{class} term in the \code{key} argument.
-#' If \code{TRUE}, the order of taxon data in a classfication is reversed to be specific to broad.
+#' If \code{TRUE}, the order of taxon data in a classification is reversed to be specific to broad.
 #' @param database (\code{character} of length 1) The name of the database that patterns given in 
 #'  \code{parser} will apply to. Valid databases include "ncbi", "itis", "eol", "col", "tropicos",
 #'  "nbn", and "none". \code{"none"} will cause no database to be quired; use this if you want to not use the
diff --git a/R/extract_taxonomy--wrappers.R b/R/extract_taxonomy--wrappers.R
@@ -1,6 +1,6 @@
 #' Parse HMP QIIME results
 #' 
-#' NOTE: Not extensivley tested
+#' NOTE: Not extensively tested
 #' Parses the results of the Human Microbiome Project QIIME analysis of the 16S metagenomic data.
 #' This is mostly a wrapper for \code{\link{extract_taxonomy}}.
 #' 
diff --git a/R/extract_taxonomy.R b/R/extract_taxonomy.R
@@ -20,7 +20,7 @@
 #'    \item{\code{name}}{The name of a taxon. Not necessarily unique, but are interpretable
 #'          by a particular \code{database}. Requires an internet connection.}
 #'    \item{\code{taxon_info}}{Arbitrary taxon info you want included in the output. Can be used more than once.}
-#'    \item{\code{class}}{A list of taxa information that consitutes the full taxonomic classification
+#'    \item{\code{class}}{A list of taxa information that constitutes the full taxonomic classification
 #'          from broad to specific (see \code{class_rev}) for a particular \code{database}. Individual taxa
 #'          are separated by the \code{class_sep} argument and the information is parsed by the
 #'          \code{class_regex} and \code{class_key} arguments.}
@@ -313,7 +313,7 @@ extract_taxonomy.list <- function(input, ...) {
 #'          Requires an internet connection.}
 #'    \item{\code{name}}{The name of a taxon. Not necessarily unique, but are interpretable
 #'          by a particular \code{database}. Requires an internet connection.}
-#'    \item{\code{class}}{A list of taxa information that consitutes the full taxonomic classification
+#'    \item{\code{class}}{A list of taxa information that constitutes the full taxonomic classification
 #'          from broad to specific (see \code{class_rev}) for a particular \code{database}. Individual taxa
 #'          are separated by the \code{class_sep} argument and the information is parsed by the
 #'          \code{class_regex} and \code{class_key} arguments.}
diff --git a/R/heat_tree--internal.R b/R/heat_tree--internal.R
@@ -1,6 +1,6 @@
 #' Bounding box coords for labels
 #' 
-#' Given a position, size, rotation, and justification of a lable, calculate the bounding box coordinants
+#' Given a position, size, rotation, and justification of a lable, calculate the bounding box coordinates
 #' 
 #' @param x Horizontal position of center of text grob
 #' @param y Vertical position of center of text grob
diff --git a/R/heat_tree--layouts.R b/R/heat_tree--layouts.R
@@ -8,7 +8,7 @@
 #' @param name (\code{character} of length 1 OR NULL) name of algorithm. Leave \code{NULL} to 
 #' see all options. 
 #' @param graph (\code{igraph}) The graph to generate the layout for.
-#' @param intitial_coords (\code{matrix}) Initial node layout to bawse new layout off of.
+#' @param intitial_coords (\code{matrix}) Initial node layout to base new layout off of.
 #' @param effort  (\code{numeric} of length 1) The amount of effort to put into layouts. Typically
 #' determines the the number of iterations. 
 #' @param ... (other arguments) Passed to igraph layout function used.
diff --git a/R/heat_tree--mapping.R b/R/heat_tree--mapping.R
@@ -1,6 +1,6 @@
 #' Rescale numeric vector to have specified minimum and maximum.
 #' 
-#' Rescale numeric vector to have specified minimum and maximum, but allow for hard boundries.
+#' Rescale numeric vector to have specified minimum and maximum, but allow for hard boundaries.
 #' Light wrapper for scales::rescale
 #' 
 #' @param x values to rescale
@@ -53,7 +53,7 @@ apply_color_scale <- function(values, color_series, interval = NULL, no_color_in
 
 
 
-#' The defualt quantative color palette
+#' The default quantative color palette
 #' 
 #' Returns the default color palette for quantative data.
 #' 
@@ -68,7 +68,7 @@ quantative_palette <- function() {
 }
 
 
-#' The defualt qualitative color palette
+#' The default qualitative color palette
 #' 
 #' Returns the default color palette for qualitative data
 #' 
@@ -82,7 +82,7 @@ qualitative_palette <- function() {
   return(c(RColorBrewer::brewer.pal(9, "Set1"), RColorBrewer::brewer.pal(9, "Pastel1")))
 }
 
-#' The defualt diverging color palette
+#' The default diverging color palette
 #' 
 #' Returns the default color palette for diverging data
 #' 
diff --git a/R/heat_tree--vertex_size.R b/R/heat_tree--vertex_size.R
@@ -1,7 +1,7 @@
 #===================================================================================================
-#' Get all distances beween points
+#' Get all distances between points
 #' 
-#' Returns the distances bewteen every possible combination of two points.
+#' Returns the distances between every possible combination of two points.
 #' 
 #' @param x (\code{numeric} of length 1) x coordinate
 #' @param y (\code{numeric} of length 1) y coordinate
diff --git a/R/heat_tree.R b/R/heat_tree.R
@@ -44,7 +44,7 @@ heat_tree.taxmap <- function(.input, ...) {
 #' Taxonomic classifications can have multiple roots, resulting in multiple trees on the same plot.
 #' Sizes and colors of nodes, edges, labels, and individual trees can be displayed relative to
 #' numbers (e.g. taxon statistics, such as abundance).
-#' The displayed range of colors and sizes can be explicitly defined or automatically genereated.
+#' The displayed range of colors and sizes can be explicitly defined or automatically generated.
 #' Various transforamtions can be applied to numbers sizes/colors are mapped to.
 #' Several types of tree layout algorithms from \code{\link{igraph}} can be used. 
 #' 
@@ -70,7 +70,7 @@ heat_tree.taxmap <- function(.input, ...) {
 # #' Default: Not used. 
 #' 
 #' @param node_label_size See details on size.
-#' Default: relative to veterx size.
+#' Default: relative to vertex size.
 #' @param edge_label_size See details on size.
 #' Default: relative to edge size.
 #' @param tree_label_size See details on size.
@@ -167,7 +167,7 @@ heat_tree.taxmap <- function(.input, ...) {
 #' 
 #' @param overlap_avoidance (\code{numeric})
 #' The relative importance of avoiding overlaps vs maximizing size range.
-#' Higher numbers will cause node size optimazation to avoid overlaps more.
+#' Higher numbers will cause node size optimization to avoid overlaps more.
 #' Default: \code{1}.
 #' 
 #' @param margin_size (\code{numeric} of length 2)
@@ -183,7 +183,7 @@ heat_tree.taxmap <- function(.input, ...) {
 #' Default: Not used.
 #' @param make_legend if TRUE...
 #' @param title Name to print above the graph.
-#' @param title_size The size of the title realtive to the rest of the graph. 
+#' @param title_size The size of the title relative to the rest of the graph. 
 #' 
 #' @param node_color_axis_label The label on the scale axis corresponding to \code{node_color}.
 #' Default: The expression given to \code{node_color}.
@@ -257,7 +257,7 @@ heat_tree.taxmap <- function(.input, ...) {
 #' 
 #' @section ranges:
 #' 
-#' The displayed range of colors and sizes can be explicitly defined or automatically genereated.
+#' The displayed range of colors and sizes can be explicitly defined or automatically generated.
 #' Size ranges are specified by supplying a \code{numeric} vector with two values: the minimum and maximum.
 #' The units used should be between 0 and 1, representing the proportion of a dimension of the graph.
 #' Since the dimensions of the graph are determined by layout, and not always square, the value
@@ -282,7 +282,7 @@ heat_tree.taxmap <- function(.input, ...) {
 #'   \item{"graphopt"}{Use \code{\link[igraph]{with_graphopt}}. A force-directed layout.}
 #'   \item{"mds"}{Use \code{\link[igraph]{with_mds}}. Multidimensional scaling.}
 #'   \item{"fruchterman-reingold"}{Use \code{\link[igraph]{with_fr}}. A force-directed layout.}
-#'   \item{"kamada-kawai"}{Use \code{\link[igraph]{with_kk}}. A layout based on a phyisical model of springs.}
+#'   \item{"kamada-kawai"}{Use \code{\link[igraph]{with_kk}}. A layout based on a physical model of springs.}
 #'   \item{"large-graph"}{Use \code{\link[igraph]{with_lgl}}. Meant for larger graphs.}
 #'   \item{"drl"}{Use \code{\link[igraph]{with_drl}}. A force-directed layout.}
 #' }
@@ -295,7 +295,7 @@ heat_tree.taxmap <- function(.input, ...) {
 #' These are defined in the same units as element size/color.
 #' By default, the minimum and maximum equals the range of the values used to infer size/color.
 #' Setting a custom interval is useful for making size/color in multiple graphs correspond to the same statistics,
-#' or setting logical bounderies (such as \code{c(0,1)} for proportions.
+#' or setting logical boundaries (such as \code{c(0,1)} for proportions.
 #' Note that this is different from the "range" options, which determine the range of graphed sizes/colors.
 #'  
 #' @examples 
diff --git a/R/in_silico_pcr.R b/R/in_silico_pcr.R
@@ -201,7 +201,7 @@ primersearch.character <- function(input, forward, reverse, mismatch = 5, ...) {
 #' 
 #' @param sequence_col (\code{character} of length 1) The name of the column in \code{obs_data} that has the input sequences.
 #' @param result_cols (\code{character}) The names of columns to include in the output.
-#' By defualt, all output columns are included.
+#' By default, all output columns are included.
 #' 
 #' @rdname primersearch
 #' @export
diff --git a/R/internal.R b/R/internal.R
@@ -89,7 +89,7 @@ can_be_num <- function(input) {
 
 #' Return numeric values in a character
 #' 
-#' Returns just valid numeric values and igores others.
+#' Returns just valid numeric values and ignores others.
 #' 
 #' @param input
 #' 
diff --git a/R/metacoder-package.r b/R/metacoder-package.r
@@ -10,7 +10,7 @@
 #'   \item A set of functions to manipulate taxonomic data modeled after dplyr.
 #'   \item Visualization of statistics distributed over taxonomic classifications and phylogenies.
 #'   \item Evaluating potential metabarcoding primers for taxonomic specificity.
-#'   \item Evaluating potential metabarcoding loci for taxonomic discrimiation (in development).
+#'   \item Evaluating potential metabarcoding loci for taxonomic discrimination (in development).
 #' }
 #' 
 #' To accomplish these goals, `metacoder` leverages resources from other R packages, interfaces with
@@ -29,7 +29,7 @@
 #'
 #' @section Most important functions:
 #' 
-#' \strong{Parseing taxonomy information:}
+#' \strong{Parsing taxonomy information:}
 #' 
 #' \itemize{
 #'   \item \code{\link{extract_taxonomy}}
diff --git a/R/taxmap--internal.R b/R/taxmap--internal.R
@@ -40,7 +40,7 @@ format_taxon_subset <- function(obj, index) {
 
 #' Remove the redundant taxon names
 #' 
-#' Remove the names of parent taxa in the begining of their children's names in a \code{taxmap} object.
+#' Remove the names of parent taxa in the beginning of their children's names in a \code{taxmap} object.
 #' This is useful for removing genus names in binomials.
 #' 
 #' @param obj a \code{taxmap} object
diff --git a/R/taxmap--sample.R b/R/taxmap--sample.R
@@ -79,7 +79,7 @@ sample_n_obs <- function(.data, size, replace = FALSE, taxon_weight = NULL, obs_
 
 #' Sample a proportion of observations from \code{\link{taxmap}}
 #' 
-#' Randomly sample some propoortion of observations from a \code{\link{taxmap}} object. Weights can be 
+#' Randomly sample some proportion of observations from a \code{\link{taxmap}} object. Weights can be 
 #' specified for observations or the taxa they are taxmap by.
 #' See \link[dplyr]{sample_frac} for the inspiration for this function.
 #' 
@@ -185,7 +185,7 @@ sample_n_taxa <- function(.data, size, taxon_weight = NULL, obs_weight = NULL,
 
 #' Sample a proportion of taxa from \code{\link{taxmap}}
 #' 
-#' Randomly sample some propoortion of taxa from a \code{\link{taxmap}} object. Weights can be 
+#' Randomly sample some proportion of taxa from a \code{\link{taxmap}} object. Weights can be 
 #' specified for taxa or the observations assigned to them. See \link[dplyr]{sample_frac} for the
 #' inspiration for this function.
 #' 
diff --git a/R/taxmap--utilities.R b/R/taxmap--utilities.R
@@ -121,7 +121,7 @@ roots <- function(obj, subset = NULL, index = FALSE) {
 #'   queried.
 #' @param subset (\code{character}) \code{taxon_ids} or indexes of \code{taxon_data} for which
 #'   supertaxa will be returned. Default: All taxa in \code{obj} will be used.
-#' @param recursive (\code{logical}) If \code{FALSE}, only return the subtaxa one level bwlow the 
+#' @param recursive (\code{logical}) If \code{FALSE}, only return the subtaxa one level below the 
 #'   target taxa. If \code{TRUE}, return all the subtaxa of every subtaxa, etc.
 #' @param simplify (\code{logical}) If \code{TRUE}, then combine all the results into a single 
 #'   vector of unique values.
