## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL ## Related to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html ) ## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE---------------- ## Track time spent on making the vignette startTime <- Sys.time() ## Bib setup library("RefManageR") ## Write bibliography information bib <- c( R = citation(), BiocStyle = citation("BiocStyle")[1], knitr = citation("knitr")[1], RefManageR = citation("RefManageR")[1], rmarkdown = citation("rmarkdown")[1], sessioninfo = citation("sessioninfo")[1], testthat = citation("testthat")[1], phyloseq = citation("phyloseq")[1], treesummarizedexperiment = citation("TreeSummarizedExperiment")[1], tidyverse = citation("tidyverse")[1], mixtools = citation("mixtools")[1], fitdistrplus = citation("fitdistrplus")[1], CBEA = citation("CBEA")[1], broom = citation("broom")[1], BiocParallel = citation("BiocParallel")[1] ) ## ----"install", eval = FALSE-------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("CBEA") # # ## Check that you have a valid Bioconductor installation # BiocManager::valid() ## ----"start", message=FALSE--------------------------------------------------- library("CBEA") library(BiocSet) library(tidyverse) set.seed(1020) ## ----load_data---------------------------------------------------------------- data("hmp_gingival") abun <- hmp_gingival$data metab_sets <- hmp_gingival$set abun # this is a TreeSummarizedExperiment object ## ----load_sets---------------------------------------------------------------- metab_sets ## ----run_cbea, eval = TRUE---------------------------------------------------- results <- cbea(abun, set = metab_sets, abund_values = "16SrRNA", output = "cdf", distr = "mnorm", adj = TRUE, thresh = 0.05, n_perm = 10) results ## ----results_obj, eval = TRUE------------------------------------------------- names(results) ## ----results_obj_2, eval = TRUE----------------------------------------------- str(results$R) ## ----tidy_functions, eval = TRUE---------------------------------------------- tidy(results) glance(results, "fit_comparison") glance(results, "fit_diagnostic") ## ----check_backend, eval= TRUE------------------------------------------------ BiocParallel::registered() ## ----parallel_computing, eval=FALSE------------------------------------------- # cbea(abun, set = metab_sets, abund_values = "16SrRNA", # output = "cdf", distr = "mnorm", adj = TRUE, thresh = 0.05, n_perm = 10, # parallel_backend = MulticoreParam(workers = 2)) ## ----"citation"--------------------------------------------------------------- ## Citation info citation("CBEA") ## ----createVignette, eval=FALSE----------------------------------------------- # ## Create the vignette # library("rmarkdown") # system.time(render("basic_usage.Rmd", "BiocStyle::html_document")) # # ## Extract the R code # library("knitr") # knit("basic_usage.Rmd", tangle = TRUE) ## ----reproduce1, echo=FALSE--------------------------------------------------- ## Date the vignette was generated Sys.time() ## ----reproduce2, echo=FALSE--------------------------------------------------- ## Processing time in seconds totalTime <- diff(c(startTime, Sys.time())) round(totalTime, digits = 3) ## ----reproduce3, echo=FALSE------------------------------------------------------------------------------------------- ## Session info library("sessioninfo") options(width = 120) session_info() ## ----vignetteBiblio, results = "asis", echo = FALSE, warning = FALSE, message = FALSE--------------------------------- ## Print bibliography PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))