#' Automatic report for a Completely Randomized Design (CRD)
#'
#' Produces an automatic report for selected traits in an experiment with a CRD.
#' @param traits The traits to analize.
#' @param trt The treatments.
#' @param trt.lab The labels for treatments.
#' @param eu The experimental unit. Must be defined in case of subsamples.
#' @param dfr The name of the data frame.
#' @param mc Logical. If \code{"mc = TRUE"} multiple comparison tests are included
#' even if the factor effect is not significat. Default to \code{"mc = FALSE"}.
#' @param title Report title.
#' @param subtitle Report subtitle.
#' @param author Report author.
#' @param format The output file format for the report, \code{"html"} by default.
#' Other options are \code{"word"} and \code{"pdf"}.
#' @details It fits a linear model for a CRD and explains the results.
#'
#' Under the assumption of fixed effects an ANOVA table is computed.
#' In case of subsampling the ANOVA table is computed over the means for each
#' experimental unit, and a second ANOVA table is computed considering subsampling.
#' If the ANOVA results in a significant value then the Tukey HSD method for pairwise
#' differences is applied. Assumptions of the model are evaluated with residual plots.
#'
#' Under the assumption of random effects the model is estimated using REML and the
#' variance components are shown.
#' @return It returns an explanation about the CRD fitted model.
#' @author Raul Eyzaguirre.
#' @examples
#' repo.crd(c("trw", "vw"), "geno", "genotype", dfr = pjpz09)
#' # With a small data set
#' temp <- pjpz09[1:18, ]
#' repo.crd(c("trw", "vw", "crw"), "geno", "genotypes", dfr = temp)
#' @import st4gi
#' @importFrom utils browseURL
#' @export
repo.crd <- function(traits, trt, trt.lab = "treatment", eu = NULL, dfr, mc = FALSE,
title = "Automatic report for a Completely Randomized Design (CRD)",
subtitle = NULL,
author = "International Potato Center",
format = c("html", "word", "pdf")) {
format <- paste0(match.arg(format), "_document")
dirfiles <- system.file(package = "pepa")
fileRmd <- paste0(dirfiles, "/rmd/crd.Rmd")
fileURL <- paste0(dirfiles, "/rmd/crd.html")
fileDOCX <- paste0(dirfiles, "/rmd/crd.docx")
filePDF <- paste0(dirfiles, "/rmd/crd.pdf")
rmarkdown::render(fileRmd, output_format = format,
params = list(traits = traits,
trt = trt,
trt.lab = trt.lab,
eu = eu,
dfr = dfr,
mc = mc,
title = title,
subtitle = subtitle,
author = author))
if (format == "html_document")
try(browseURL(fileURL))
if (format == "word_document")
try(system(paste("open", fileDOCX)))
if (format == "pdf_document")
try(system(paste("open", filePDF)))
}
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