Merge reduced_data-patch to the dev-master.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MicrobiomeR
 Title: Analyze Microbiome Data
-Version: 0.0.9
+Version: 0.0.9.1
 Authors@R: c(
     person("Robert", "Gilmore", email = "[email protected]", role = "cre"),
     person("Shaurita", "Hutchins", email = "[email protected]", role = "aut"))
@@ -10,7 +10,7 @@ Description: An R package for microbiome analysis combining functions from phylo
     and microbiome into an easy to use and full featured microbiome analysis package.
 Roxygen: list(markdown = TRUE)
 Depends:
-    R (>= 3.5.0)
+    R (>= 3.3.0)
 Remotes: 
     github::ropensci/taxa,
     github::grunwaldlab/metacoder,

R/correlation-plot.R

@@ -11,6 +11,8 @@
 #' @examples
 #' \dontrun{
 #' if(interactive()){
+#' # This example uses data that are no longer available in the MicrobiomeR package,
+#' # however, they can be easily generated with \code{\link{MicrobiomeR}{as_analyzed_format}}.
 #' library(MicrobiomeR)
 #' correlation_plot(MicrobiomeR::analyzed_silva, primary_rank = "Class", secondary_rank = "Phylum")
 #'  }
@@ -129,6 +131,8 @@ correlation_plot <- function(obj, primary_rank, secondary_rank = TRUE,
 #' @examples
 #' \dontrun{
 #' if(interactive()){
+#' # This example uses data that are no longer available in the MicrobiomeR package,
+#' # however, they can be easily generated with \code{\link{MicrobiomeR}{as_analyzed_format}}.
 #' library(MicrobiomeR)
 #' corr_plots <- get_correlation_plots(MicrobiomeR::analyzed_silva, primary_ranks = c("Phylum", "Class", "Order"),
 #'                       secondary_ranks = c("Phylum", "Class", "Order", "Family", "Genus"), pairwise = TRUE)
@@ -198,6 +202,8 @@ get_correlation_plots <- function(obj, primary_ranks, secondary_ranks = TRUE, pa
 #' @examples
 #' \dontrun{
 #' if(interactive()){
+#' # This example uses data that are no longer available in the MicrobiomeR package,
+#' # however, they can be easily generated with \code{\link{MicrobiomeR}{as_analyzed_silva}}.
 #' library(MicrobiomeR)
 #' corr_plot <- correlation_plot(MicrobiomeR::analyzed_silva, primary_rank = "Class", secondary_rank = "Phylum")
 #' # Save to \emph{./output/corr_plot} folder.

R/data.R

@@ -77,119 +77,3 @@
 #'
 #' @source \href{https://nephele.niaid.nih.gov/user_guide_pipes/#amplicon_pipes}{Nephele-16S Qiime Pipeline}
 "raw_greengenes"
-
-#' Stress Microbiome "basic_format" Data (Silva)
-#'
-#' Data from the Nephele-16S-Qiime-Silva microbiome pipeline
-#' in the form of a taxmap object.  This taxmap object has been
-#' formatted into the MicrobiomeR "basic_format".
-#'
-#' @docType data
-#' @usage data(basic_silva)
-#' @format An object of class \code{"Taxmap"} with customized observation tables:
-#' \describe{
-#' \item{otu_abundance}{An abundance table with otu_id, taxon_id, and Sample_* columns.}
-#' \item{otu_annotations}{A taxonomy annotations table with otu_id, taxon_id, and multiple rank columns.}
-#' \item{otu_proportions}{A proportion table derived from the otu_abundance table.}
-#' \item{sample_data}{A metadata table with SampleID, BarcodeSequence, LinkerPrimerSequence,
-#' ForwardFastqFile, ReverseFastqFile, TreatmentGroup, SampleName, Description}
-#' \item{phy_tree}{A phylogenetic tree.}
-#' \item{taxa_abundance}{A taxonomy table interpolated from the otu_abundance table with taxon_id,
-#' and Sample_* columns.}
-#' \item{taxa_proportions}{A taxonomy table derived from the taxa_abundance table.}
-#' }
-#' @keywords datasets
-#'
-#' @references Zhang et al. (2019)
-#' (\href{https://www.ncbi.nlm.nih.gov/pubmed/}{PubMed})
-#'
-#' @source \href{https://nephele.niaid.nih.gov/user_guide_pipes/#amplicon_pipes}{Nephele-16S Qiime Pipeline}
-"basic_silva"
-
-#' Stress Microbiome "basic_format" Data (Greengenes)
-#'
-#' Data from the Nephele-16S-Qiime-Greengenes microbiome pipeline
-#' in the form of a taxmap object.  This taxmap object has been
-#' formatted into the MicrobiomeR "basic_format".
-#'
-#' @docType data
-#' @usage data(basic_greengenes)
-#' @format An object of class \code{"Taxmap"} with customized observation tables:
-#' \describe{
-#' \item{otu_abundance}{An abundance table with otu_id, taxon_id, and Sample_* columns.}
-#' \item{otu_annotations}{A taxonomy annotations table with otu_id, taxon_id, and multiple rank columns.}
-#' \item{otu_proportions}{A proportion table derived from the otu_abundance table.}
-#' \item{sample_data}{A metadata table with SampleID, BarcodeSequence, LinkerPrimerSequence,
-#' ForwardFastqFile, ReverseFastqFile, TreatmentGroup, SampleName, Description}
-#' \item{phy_tree}{A phylogenetic tree.}
-#' \item{taxa_abundance}{A taxonomy table interpolated from the otu_abundance table with taxon_id,
-#' and Sample_* columns.}
-#' \item{taxa_proportions}{A taxonomy table derived from the taxa_abundance table.}
-#' }
-#' @keywords datasets
-#'
-#' @references Zhang et al. (2019)
-#' (\href{https://www.ncbi.nlm.nih.gov/pubmed/}{PubMed})
-#'
-#' @source \href{https://nephele.niaid.nih.gov/user_guide_pipes/#amplicon_pipes}{Nephele-16S Qiime Pipeline}
-"basic_greengenes"
-
-#' Stress Microbiome "analyzed_format" Data (Silva)
-#'
-#' Data from the Nephele-16S-Qiime-Silva microbiome pipeline
-#' in the form of a taxmap object.  This taxmap object has been
-#' formatted into the MicrobiomeR "analyzed_format".
-#'
-#' @docType data
-#' @usage data(analyzed_silva)
-#' @format An object of class \code{"Taxmap"} with customized observation tables:
-#' \describe{
-#' \item{otu_abundance}{An abundance table with otu_id, taxon_id, and Sample_* columns.}
-#' \item{otu_annotations}{A taxonomy annotations table with otu_id, taxon_id, and multiple rank columns.}
-#' \item{otu_proportions}{A proportion table derived from the otu_abundance table.}
-#' \item{sample_data}{A metadata table with SampleID, BarcodeSequence, LinkerPrimerSequence,
-#' ForwardFastqFile, ReverseFastqFile, TreatmentGroup, SampleName, Description}
-#' \item{phy_tree}{A phylogenetic tree.}
-#' \item{taxa_abundance}{A taxonomy table interpolated from the otu_abundance table with taxon_id,
-#' and Sample_* columns.}
-#' \item{taxa_proportions}{A taxonomy table derived from the taxa_abundance table.}
-#' \item{statistical_data}{A data table that contains statistical analysis comparing treatment groups.}
-#' \item{stats_tax_data}{A data table that combines taxa and statistical datasets for plotting.}
-#' }
-#' @keywords datasets
-#'
-#' @references Zhang et al. (2019)
-#' (\href{https://www.ncbi.nlm.nih.gov/pubmed/}{PubMed})
-#'
-#' @source \href{https://nephele.niaid.nih.gov/user_guide_pipes/#amplicon_pipes}{Nephele-16S Qiime Pipeline}
-"analyzed_silva"
-
-#' Stress Microbiome "analyzed_format" Data (Greengenes)
-#'
-#' Data from the Nephele-16S-Qiime-Greengenes microbiome pipeline
-#' in the form of a taxmap object.  This taxmap object has been
-#' formatted into the MicrobiomeR "analyzed_format".
-#'
-#' @docType data
-#' @usage data(analyzed_greengenes)
-#' @format An object of class \code{"Taxmap"} with customized observation tables:
-#' \describe{
-#' \item{otu_abundance}{An abundance table with otu_id, taxon_id, and Sample_* columns.}
-#' \item{otu_annotations}{A taxonomy annotations table with otu_id, taxon_id, and multiple rank columns.}
-#' \item{otu_proportions}{A proportion table derived from the otu_abundance table.}
-#' \item{sample_data}{A metadata table with SampleID, BarcodeSequence, LinkerPrimerSequence,
-#' ForwardFastqFile, ReverseFastqFile, TreatmentGroup, SampleName, Description}
-#' \item{phy_tree}{A phylogenetic tree.}
-#' \item{taxa_abundance}{A taxonomy table interpolated from the otu_abundance table with taxon_id,
-#' and Sample_* columns.}
-#' \item{taxa_proportions}{A taxonomy table derived from the taxa_abundance table.}
-#' \item{statistical_data}{A data table that contains statistical analysis comparing treatment groups.}
-#' \item{stats_tax_data}{A data table that combines taxa and statistical datasets for plotting.}
-#' }
-#' @keywords datasets
-#'
-#' @references Zhang et al. (2019)
-#' (\href{https://www.ncbi.nlm.nih.gov/pubmed/}{PubMed})
-#'
-#' @source \href{https://nephele.niaid.nih.gov/user_guide_pipes/#amplicon_pipes}{Nephele-16S Qiime Pipeline}
-"analyzed_greengenes"

R/heat-tree.R

@@ -9,6 +9,8 @@
 #' @examples
 #' \dontrun{
 #' if(interactive()){
+#' # This example uses data that are no longer available in the MicrobiomeR package,
+#' # however, they can be easily generated with \code{\link{MicrobiomeR}{as_analyzed_format}}.
 #' library(MicrobiomeR)
 #' h_trees <- get_heat_tree_plots(MicrobiomeR::analyzed_silva, rank_list = c("Phylum", "Class"))
 #' h_trees$Class
@@ -155,6 +157,8 @@ get_heat_tree_parameters <- function(obj, title, ...) {
 #' @examples
 #' \dontrun{
 #' if(interactive()){
+#' # This example uses data that are no longer available in the MicrobiomeR package,
+#' # however, they can be easily generated with \code{\link{MicrobiomeR}{as_analyzed_format}}.
 #' library(MicrobiomeR)
 #' h_trees <- get_heat_tree_plots(MicrobiomeR::analyzed_silva, rank_list = c("Phylum", "Class"))
 #' # Save to \emph{./output/heat_trees} folder.

R/metacoder-formatting.R

@@ -9,7 +9,7 @@
 #' \dontrun{
 #' if(interactive()){
 #' library(MicrobiomeR)
-#' fmt <- which fmt(MicrobiomeR::analyzed_silva)
+#' fmt <- which fmt(MicrobiomeR::raw_silva)
 #' print(fmt)
 #'  }
 #' }

R/metacoder.R

@@ -257,6 +257,8 @@ otu_id_filter <- function(obj, .f_transform = NULL, .f_filter = NULL, .f_conditi
 #' @examples
 #' \dontrun{
 #' if(interactive()){
+#' # This example uses data that are no longer available in the MicrobiomeR package,
+#' # however, they can be easily generated with \code{\link{MicrobiomeR}{as_basic_format}}.
 #' library(MicrobiomeR)
 #' phylum_obj <- agglomerate_metacoder(obj = MicrobiomeR::basic_silva, rank = "Phylum")
 #' class_obj <- agglomerate_metacoder(obj = MicrobiomeR::basic_silva, rank = "Class")

R/palettes.R

@@ -11,6 +11,8 @@
 #' @examples
 #' \dontrun{
 #' if(interactive()){
+#' # This example uses data that are no longer available in the MicrobiomeR package,
+#' # however, they can be easily generated with \code{\link{MicrobiomeR}{as_analyzed_format}}.
 #'  library(MicrobiomeR)
 #'  data <- MicrobiomeR::analyzed_silva$data$stats_tax_data$Phylum
 #'  data_len <- length(unique(data))

R/utils.R

@@ -175,6 +175,8 @@ get_output_dir <- function(start_path=NULL, experiment=NULL, plot_type=NULL, end
 #' @examples
 #' \dontrun{
 #' if(interactive()){
+#' # This example uses data that are no longer available in the MicrobiomeR package,
+#' # however, they can be easily generated with \code{\link{MicrobiomeR}{as_basic_format}}.
 #'  library(MicrobiomeR)
 #'  data <- MicrobiomeR::basic_silva$data$taxa_abundance
 #'  trans_data <- data %>%
@@ -264,6 +266,8 @@ transposer <- function(.data, ids = NULL, header_name, preserved_categories = TR
 #' @examples
 #' \dontrun{
 #' if(interactive()){
+#' # This example uses data that are no longer available in the MicrobiomeR package,
+#' # however, they can be easily generated with \code{\link{MicrobiomeR}{as_basic_format}}.
 #'  library(MicrobiomeR)
 #'  data <- MicrobiomeR::basic_silva$data$taxa_abundance
 #'  # Get proportions using the anonymous functions