spell checking docs

Author: zachary-foster

R/calculations.R

@@ -77,7 +77,7 @@ calc_obs_props <- function(obj, dataset, cols = NULL, other_cols = FALSE,
 #' Replace low counts with zero
 #'
 #' For a given table in a \code{\link[taxa]{taxmap}} object, convert all counts
-#' below a minimum numer to zero. This is useful for effectivly removing
+#' below a minimum number to zero. This is useful for effectively removing
 #' "singletons", "doubletons", or other low abundance counts.
 #'
 #' @param obj A \code{\link[taxa]{taxmap}} object
@@ -88,7 +88,7 @@ calc_obs_props <- function(obj, dataset, cols = NULL, other_cols = FALSE,
 #' @param use_total If \code{TRUE}, the \code{min_count} applies to the total
 #'   count for each row (e.g. OTU counts for all samples), rather than each cell
 #'   in the table. For example \code{use_total = TRUE, min_count = 10} would
-#'   convert all counts of any row to zero if the totol for all counts in that
+#'   convert all counts of any row to zero if the total for all counts in that
 #'   row was less than 10.
 #' @param cols The names/indexes of columns in \code{dataset} to use. By
 #'   default, all numeric columns are used. Takes one of the following inputs:
@@ -294,7 +294,7 @@ 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 
-#'   recieve the data for each treatment, passed a two character vecotors.
+#'   receive the data for each treatment, passed a 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
 #'   results of a fixed length. If named, the names will be used in the output.

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 coordinates
+#' Given a position, size, rotation, and justification of a label, calculate the bounding box coordinates
 #' 
 #' @param x Horizontal position of center of text grob
 #' @param y Vertical position of center of text grob
@@ -195,7 +195,7 @@ check_element_length <- function(args) {
 
 #' Transformation functions
 #' 
-#' Functions used by plotting funtions to transform data.
+#' Functions used by plotting functions to transform data.
 #' Calling the function with no parameters returns available function names.
 #' Calling with just the function name returns the transformation function
 #' 

R/heat_tree--shape_generators.R

@@ -1,5 +1,5 @@
 #===================================================================================================
-#' Makes coordinates for a regualr polygon
+#' Makes coordinates for a regular polygon
 #' 
 #' Generates an n x 2 matrix containing x and y coordinates between 1 and 0 for the points of a 
 #' regular polygon. 

R/heat_tree--vertex_size.R

@@ -58,9 +58,9 @@ inter_circle_gap <- function(x, y, r) {
 #' 
 #' Finds optimal max and min value using an optimality criterion.
 #' 
-#' @param max_range (\code{numeric} of length 2) The min and max boundries to the search space for
+#' @param max_range (\code{numeric} of length 2) The min and max boundaries to the search space for
 #' the optimal maximum value.
-#' @param min_range (\code{numeric} of length 2) The min and max boundries to the search space for
+#' @param min_range (\code{numeric} of length 2) The min and max boundaries to the search space for
 #' the optimal minimum value.
 #' @param resolution (\code{numeric} of length 2) The number of increments in each dimension.
 #' @param opt_crit (\code{function}) A function that takes two arguments, the max and min, and

R/heat_tree.R

@@ -44,7 +44,7 @@ heat_tree.Taxmap <- function(.input, ...) {
 #' 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 generated.
-#' Various transforamtions can be applied to numbers sizes/colors are mapped to.
+#' Various transformations can be applied to numbers sizes/colors are mapped to.
 #' Several types of tree layout algorithms from \code{\link{igraph}} can be used. 
 #' 
 #' @param taxon_id The unique ids of taxa.
@@ -200,9 +200,9 @@ heat_tree.Taxmap <- function(.input, ...) {
 #' Default: Do not save plot.
 #' 
 #' @param aspect_ratio The aspect_ratio of the plot.
-#' @param repel_labels If \code{TRUE} (Defualt), use the ggrepel pacakge to spread out labels.
-#' @param repel_force The force of which overlapping labels will be repeled from eachother. 
-#' @param repel_iter The number of iterations used whe repeling labels
+#' @param repel_labels If \code{TRUE} (Defualt), use the ggrepel package to spread out labels.
+#' @param repel_force The force of which overlapping labels will be repelled from eachother. 
+#' @param repel_iter The number of iterations used when repelling labels
 #' @param verbose If \code{TRUE} print progress reports as the function runs.
 #' 
 #' @param ... (other named arguments)
@@ -214,7 +214,7 @@ heat_tree.Taxmap <- function(.input, ...) {
 #' 
 #' The size of nodes, edges, labels, and trees can be mapped to arbitrary numbers.
 #' This is useful for displaying statistics for taxa, such as abundance.
-#' Only the relative size of numbers is used, not the values themeselves.
+#' Only the relative size of numbers is used, not the values themselves.
 #' They can be transformed to make the mapping non-linear using the transformation options.
 #' The range of actual sizes displayed on the graph can be set using the range options.
 #' 
@@ -225,7 +225,7 @@ heat_tree.Taxmap <- function(.input, ...) {
 #' 
 #' The colors of nodes, edges, labels, and trees can be mapped to arbitrary numbers.
 #' This is useful for highlighting groups of taxa.
-#' Only the relative size of numbers is used, not the values themeselves.
+#' Only the relative size of numbers is used, not the values themselves.
 #' They can be transformed to make the mapping non-linear using the transformation options.
 #' The range of actual colors displayed on the graph can be set using the range options.
 #' 
@@ -307,7 +307,7 @@ heat_tree.Taxmap <- function(.input, ...) {
 #' 
 #' This package includes code from the R package ggrepel to handle label overlap
 #' avoidance with permission from the author of ggrepel Kamil Slowikowski. We
-#' included the code instead of depending on ggrepel becacuse we are using
+#' included the code instead of depending on ggrepel because we are using
 #' internal functions to ggrepel that might change in the future. We thank Kamil
 #' Slowikowski for letting us use his code and would like to acknowledge his
 #' implementation of the label overlap avoidance used in metacoder.
@@ -388,7 +388,7 @@ heat_tree.Taxmap <- function(.input, ...) {
 #'           node_size_trans = "log10 area")
 #' 
 #' # Setting the interval displayed:
-#' #  By defualt, the whole range of the statistic provided will be displayed.
+#' #  By default, the whole range of the statistic provided will be displayed.
 #' #  You can set what range of values are displayed using options ending in `_interval`.
 #' heat_tree(x, node_label = taxon_names, node_size = n_obs, node_color = n_obs,
 #'           node_size_interval = c(10, 100))
@@ -742,10 +742,10 @@ heat_tree.default <- function(taxon_id, supertaxon_id,
   #|
   #| #### Infer edge size range -------------------------------------------------------------------
   #|
-  infer_size_range <- function(specified_range, reference_range, defualt_scale) {
+  infer_size_range <- function(specified_range, reference_range, default_scale) {
     result <- specified_range * square_side_length
     if (is.na(result[1]) && is.na(result[2])) { # If the user has not set range
-      result <- reference_range * defualt_scale
+      result <- reference_range * default_scale
     } else if (is.na(result[1])) { # If the user has set a maximum but not a minimum
       result[1] <- result[2] * reference_range[1] / reference_range[2]
     } else if (is.na(result[2])) { # If the user has set a minimum but not a maximum
@@ -754,7 +754,7 @@ heat_tree.default <- function(taxon_id, supertaxon_id,
     return(result)
   }
 
-  esr_plot <- infer_size_range(edge_size_range, vsr_plot, defualt_scale = 0.5)
+  esr_plot <- infer_size_range(edge_size_range, vsr_plot, default_scale = 0.5)
   data$es_plot <- rescale(data$es_t, to = esr_plot, from = edge_size_interval_trans)
   #|
   #| #### Infer tree size range -------------------------------------------------------------------
@@ -777,9 +777,9 @@ heat_tree.default <- function(taxon_id, supertaxon_id,
     data$tls_user <- sqrt(data$tree_area)
     data$tls_trans <- apply_trans("tls_user") 
   }
-  vlsr_plot <- infer_size_range(node_label_size_range, vsr_plot, defualt_scale = 0.8)
-  elsr_plot <- infer_size_range(edge_label_size_range, esr_plot, defualt_scale = 0.8)
-  tlsr_plot <- infer_size_range(tree_label_size_range, tsr_plot, defualt_scale = 0.1)
+  vlsr_plot <- infer_size_range(node_label_size_range, vsr_plot, default_scale = 0.8)
+  elsr_plot <- infer_size_range(edge_label_size_range, esr_plot, default_scale = 0.8)
+  tlsr_plot <- infer_size_range(tree_label_size_range, tsr_plot, default_scale = 0.1)
   data$vls_plot <- rescale(data$vls_trans, to = vlsr_plot)
   data$els_plot <- rescale(data$els_trans, to = elsr_plot)
   data$tls_plot <- rescale(data$tls_trans, to = tlsr_plot)

R/heat_tree_matrix.R

@@ -1,14 +1,14 @@
 #' Plot a matrix of heat trees
 #' 
-#' Plot a matrix of heat trees for showing parwise comparisions. A larger,
+#' Plot a matrix of heat trees for showing parwise comparisons. A larger,
 #' labelled tree serves as a key for the matrix of smaller unlabelled trees. The
 #' data for this function is typically created with \code{\link{compare_groups}},
 #' 
 #' @param obj A \code{\link[taxa]{taxmap}} object
 #' @param dataset The name of a table in \code{obj$data} that is the output of 
 #'   \code{\link{compare_groups}} or in the same format.
 #' @param label_small_trees If \code{TRUE} add labels to small trees as well as 
-#'   the key tree. Otherwise, only the key tree will be labled.
+#'   the key tree. Otherwise, only the key tree will be labeled.
 #' @param key_size The size of the key tree relative to the whole graph. For
 #'   example, 0.5 means half the width/height of the graph.
 #' @param seed That random seed used to make the graphs.

R/internal.R

@@ -39,16 +39,6 @@ get_node_children <- function(graph, node) {
 }
 
 
-#' delete_vetices_and_children
-#' 
-#' @keywords internal
-delete_vetices_and_children <- function(graph, nodes) {
-  nodes <- unlist(sapply(nodes, function(x) get_node_children(graph, x)))
-  graph <- igraph::delete.vertices(graph, nodes)
-  return(graph)
-}
-
-
 #' add_alpha
 #' 
 #' @keywords internal

R/metacoder-package.R

@@ -12,7 +12,7 @@
 #'   \item Provide flexible functions for analyzing taxonomic and abundance data.
 #' }
 #' 
-#' To accomplish these goals, `metacoder` leverages resources from other R packages, interfaces with
+#' To accomplish these goals, \code{metacoder} leverages resources from other R packages, interfaces with
 #' external programs, and provides novel functions where needed to allow for entire analyses within R.
 #' 
 #' @section Documentation:
@@ -23,7 +23,7 @@
 #' 
 #' \code{browseVignettes(package = "metacoder")}
 #' 
-#' \strong{Plotting taxonomic distribution of data:}
+#' \strong{Plotting:}
 #' 
 #' \itemize{
 #'   \item \code{\link{heat_tree}}
@@ -73,6 +73,12 @@
 #'   \item \code{\link{write_unite_general}}
 #' }
 #' 
+#' \strong{Database querying:}
+#' 
+#' \itemize{
+#'   \item \code{\link{ncbi_taxon_sample}}
+#' }
+#' 
 #' @author Zachary Foster
 #' @name metacoder
 #' @docType package

R/mothur.R

@@ -2,7 +2,7 @@
 #' Parse summary.seqs output
 #' 
 #' Extract statistics from the command line output of mothur command \code{summary.seqs} and
-#' return the resutls in a \code{data.frame}
+#' return the results in a \code{data.frame}
 #' 
 #' @param text The text output of \code{summary.seqs}
 #' @param file The path to saved output of \code{summary.seqs}

R/parsers.R

@@ -438,7 +438,7 @@ parse_unite_general <- function(input = NULL, file = NULL, include_seqs = TRUE)
 #' @param include_seqs (\code{logical} of length 1) If \code{TRUE}, include 
 #'   sequences in the output object.
 #' @param add_species (\code{logical} of length 1) If \code{TRUE}, add the
-#'   species information to the taxonomy. In this databse, the speceis name
+#'   species information to the taxonomy. In this databse, the species name
 #'   often contains other information as well.
 #'   
 #' @return \code{\link{taxmap}}