fixing r cmd check warning messeges

Author: zachary-foster

DESCRIPTION

@@ -50,7 +50,8 @@ Suggests:
     phyloseq,
     phylotate,
     traits,
-    biomformat
+    biomformat,
+    DESeq2
 VignetteBuilder: knitr
 RoxygenNote: 7.2.3
 Date: 2021-06-23

R/calculations--differential_abundance.R

@@ -1,17 +1,17 @@
 #' Differential abundance with DESeq2
 #'
 #' EXPERIMENTAL: This function is still being tested and developed; use with caution. Uses the
-#' \code{\link{DESeq2}} package to conduct differential abundance analysis of count data. Counts can
+#' \code{\link[DESeq2]{DESeq2-package}} package to conduct differential abundance analysis of count data. Counts can
 #' be of OTUs/ASVs or taxa. The plotting function \code{\link{heat_tree_matrix}} is useful for
 #' visualizing these results. See details section below for considerations on preparing data for
 #' this analysis.
 #'
 #' Data should be raw read counts, not rarefied, converted to proportions, or modified with any
-#' other technique designed to correct for sample size since \code{\link{DESeq2}} is designed to be
-#' used with count data and takes into accoutn unequal sample size when determining differential
+#' other technique designed to correct for sample size since \code{\link[DESeq2]{DESeq2-package}} is designed to be
+#' used with count data and takes into account unequal sample size when determining differential
 #' abundance. Warnings will be given if the data is not integers or all sample sizes are equal.
 #'
-#' @param obj A \code{\link[taxa]{taxmap}} object
+#' @param obj A \code{\link[metacoder]{taxmap}} object
 #' @param data The name of a table in \code{obj} that contains data for each sample in columns.
 #' @param cols The names/indexes of columns in \code{data} to use. By default, all numeric columns
 #'   are used. Takes one of the following inputs: \describe{ \item{TRUE/FALSE:}{All/No columns will
@@ -28,7 +28,7 @@
 #' \describe{
 #'   \item{'none'}{No log fold change adjustments.}
 #'   \item{'normal'}{The original DESeq2 shrinkage estimator}
-#'   \item{'ashr'}{Adaptive shrinkage estimator from the \code{\link{ashr}} package, using a fitted mixture of normals prior.}
+#'   \item{'ashr'}{Adaptive shrinkage estimator from the \code{ashr} package, using a fitted mixture of normals prior.}
 #' }
 #' @param ... Passed to \code{\link[DESeq2]{results}} if the \code{lfc_shrinkage} option is "none"
 #'   and to \code{\link[DESeq2]{lfcShrink}} otherwise.

R/calculations.R

@@ -641,7 +641,7 @@ compare_groups <- function(obj, data, cols, groups,
   # Get every combination of groups to compare
   if (is.null(combinations)) {
     if (is.ordered(groups)) {
-      group_order <- factor(levels(groups), levels = levels(groups), order = TRUE)
+      group_order <- factor(levels(groups), levels = levels(groups), ordered = TRUE)
     } else {
       group_order <- unique(groups)
     }

R/old_taxa--taxmap--class.R

@@ -914,7 +914,7 @@ Taxmap <- R6::R6Class(
                               dataset_name, '", so there are no taxon IDs.'))
           return(NULL)
         }
-      } else if (class(data) == "list" || is.vector(data) || can_be_used_in_taxmap(data)) {
+      } else if (inherits(data, "list") || is.vector(data) || can_be_used_in_taxmap(data)) {
         if (! is.null(names(data))) {
           is_valid <- private$ids_are_valid(names(data))
           if (all(is_valid)) {

R/old_taxa--taxmap--parsers.R

@@ -1066,18 +1066,18 @@ extract_tax_data <- function(tax_data, key, regex, class_key = "taxon_name",
   class_key <- validate_regex_key_pair(class_regex, class_key, multiple_allowed = "info")
 
   # classification sep
-  if (!is.null(class_sep) && (class(class_sep) != "character" | length(class_sep) != 1)) {
+  if (!is.null(class_sep) && (! inherits(class_sep, "character") | length(class_sep) != 1)) {
     stop('"class_sep" must be a character vector of length 1 or NULL')
   }
 
   # Boolean options
-  if (class(class_rev) != "logical" | length(class_rev) != 1) {
+  if (! inherits(class_rev, "logical") | length(class_rev) != 1) {
     stop('"class_rev" must be TRUE/FALSE')
   }
-  if (class(include_match) != "logical" | length(include_match) != 1) {
+  if (! inherits(include_match, "logical") | length(include_match) != 1) {
     stop('"include_match" must be TRUE/FALSE')
   }
-  if (class(include_tax_data) != "logical" | length(include_tax_data) != 1) {
+  if (! inherits(include_tax_data, "logical") | length(include_tax_data) != 1) {
     stop('"include_tax_data" must be TRUE/FALSE')
   }
 

R/option_parsers.R

@@ -342,11 +342,11 @@ parse_seq_input <- function(input = NULL, file = NULL, output_format = "characte
   if (output_format == "character") {
     if (! is.null(file)) {
       result <- read_fasta(file)
-    } else if (length(input) == 0 || class(input) == "character") {
+    } else if (length(input) == 0 || inherits(input, "character")) {
       result <- input
-    } else if (class(input) == "DNAbin") {
+    } else if (inherits(input,"DNAbin")) {
       result <- toupper(vapply(as.character(input), paste, character(1), collapse = ""))
-    } else if (class(input[[1]]) == "SeqFastadna" || class(input) == "list") {
+    } else if (inherits(input[[1]], "SeqFastadna") || inherits(input, "list")) {
       result <- vapply(input, paste, character(1), collapse = "")
     } else {
       stop(paste0('Could not parse sequence information of class "', class(input), '".'),
@@ -366,17 +366,17 @@ parse_seq_input <- function(input = NULL, file = NULL, output_format = "characte
         file <- make_fasta_with_u_replaced(file)
       }
       result <- ape::read.FASTA(file)
-    } else if (length(input) == 0 || class(input) == "character") {
+    } else if (length(input) == 0 || inherits(input, "character")) {
       if (u_to_t) {
         input <- vapply(input, FUN = gsub, FUN.VALUE = character(1),
                         pattern = "U", replacement = "T", fixed = TRUE)
         input <- vapply(input, FUN = gsub, FUN.VALUE = character(1),
                         pattern = "u", replacement = "t", fixed = TRUE)
       }
       result <- ape::as.DNAbin(strsplit(input, split = ""))
-    } else if (class(input) == "DNAbin") {
+    } else if (inherits(input,  "DNAbin")) {
       result <- input
-    } else if (class(input[[1]]) == "SeqFastadna" || class(input) == "list") {
+    } else if (inherits(input[[1]], "SeqFastadna") || inherits(input, "list")) {
       input <- lapply(input, function(x) {
         attributes(x) <- NULL
         return(x)