Nothing
R/utils_S3_methods.R
In FielDHub: A Shiny App for Design of Experiments in Life Sciences
Defines functions
plot.FielDHub
print.fieldLayout
print.summary.FielDHub
summary.FielDHub
print.FielDHub
Documented in
plot.FielDHub
print.FielDHub
print.fieldLayout
print.summary.FielDHub
summary.FielDHub
#-----------------------------------------------------------------------
# Print
#-----------------------------------------------------------------------
#' @rdname print.FielDHub
#' @method print FielDHub
#' @title Print a \code{FielDHub} object
#' @usage \method{print}{FielDHub}(x, n, ...)
#' @aliases print.FielDHub
#' @description Prints information about any \code{FielDHub} function.
#' @return an object inheriting from class \code{FielDHub}
#' @param x an object inheriting from class
#' @param n a single integer. If positive or zero, size for the
#' resulting object: number of elements for a vector (including
#' lists), rows for a matrix or data frame or lines for a function. If
#' negative, all but the n last/first number of elements of x.
#'
#' @param ... further arguments passed to \code{\link{head}}.
#' @author Thiago de Paula Oliveira,
#' \email{thiago.paula.oliveira@@alumni.usp.br} [aut],
#' Didier Murillo [aut]
#' @importFrom utils head str
#' @examples
#' # Example 1: Generates a CRD design with 5 treatments and 5 reps each.
#' crd1 <- CRD(t = 5, reps = 5, plotNumber = 101,
#' seed = 1985, locationName = "Fargo")
#' crd1$infoDesign
#' print(crd1)
#'
#' @export
print.FielDHub <- function(x, n=10, ...){
#---------------------------------------------------------------------
# Parameters
#---------------------------------------------------------------------
if (x$infoDesign$id_design == 1) {
cat("Completely Randomized Design (CRD)", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the CRD field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 2){
cat("Randomized Complete Block Design (RCBD):", "\n\n")
#-----------------------------------------------------------
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the RCBD field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 3){
cat("Latin Square Design:", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the latin_square field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 4) {
cat("Full Factorial Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the full_factorial field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 5) {
cat("Split Plot Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the split_plot field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 6) {
cat("Split-Split Plot Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the split_split_plot field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 7) {
cat("Strip Plot Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the strip_plot field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 8) {
cat("Incomplete Blocks Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the incomplete_blocks field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 9) {
cat("Row Column Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the row_column field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 10) {
cat("Square Lattice Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the square_lattice field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 11) {
cat("Rectangular Lattice Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the rectangular_lattice field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
} else if (x$infoDesign$id_design == 12) {
cat("Alpha Lattice Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the alpha_lattice field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
} else if (x$infoDesign$id_design == 13) {
cat("Partially Replicated Design", "\n\n")
cat("\n", "Replications within location:", "\n")
print(x$reps_info)
cat("\n", "Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the partially_replicated field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
} else if (x$infoDesign$id_design == "MultiPrep") {
cat("Multi-Location Partially Replicated Design", "\n")
cat("\n", "Replications within location:", "\n")
print(x$reps_info)
cat("\n", "Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the partially_replicated field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
} else if (x$infoDesign$id_design == 14) {
cat("Augmented Randomized Complete Block Design:", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the RCBD_augmented field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 15) {
cat("Un-replicated Diagonal Arrangement Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the diagonal_arrangement field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
} else if (x$infoDesign$id_design == "Sparse") {
cat("Sparse Allocation: Un-replicated Diagonal Arrangement Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the diagonal_arrangement field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
} else if (x$infoDesign$id_design == 16) {
cat("Un-replicated Optimized Arrangement Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the optimized_arrangement field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 17) {
cat("Split families:", "\n\n")
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
cat("\n", "Data frame with the summary of cases by location:",
"\n")
print(x$rowsEachlist)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$data_locations)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the entries for each location:",
"\n")
print(head(x$data_locations, n=nhead_print, ...))
}
}
#-----------------------------------------------------------------------
# Summary
#-----------------------------------------------------------------------
#' @rdname summary.FielDHub
#' @method summary FielDHub
#' @title Summary a \code{FielDHub} object
#' @usage \method{summary}{FielDHub}(object, ...)
#' @aliases summary.FielDHub
#' @description Summarise information on the design parameters, and data
#' frame structure
#' @return an object inheriting from class \code{summary.FielDHub}
#' @param object an object inheriting from class
#' \code{FielDHub}
#'
#' @param ... Unused, for extensibility
#' @author Thiago de Paula Oliveira,
#' \email{thiago.paula.oliveira@@alumni.usp.br}
#'
#' @examples
#' # Example 1: Generates a CRD design with 5 treatments and 5 reps each.
#' crd1 <- CRD(t = 5, reps = 5, plotNumber = 101,
#' seed = 1985, locationName = "Fargo")
#' crd1$infoDesign
#' summary(crd1)
#'
#' @export
summary.FielDHub <- function(object, ...) {
structure(object, oClass=class(object),
class = "summary.FielDHub")
}
#-----------------------------------------------------------------------
# Print summary
#-----------------------------------------------------------------------
#' @rdname print.summary.FielDHub
#' @method print summary.FielDHub
#' @title Print the summary of a \code{FielDHub} object
#' @usage \method{print}{summary.FielDHub}(x, ...)
#' @aliases print.summary.FielDHub
#' @description Print summary information on the design parameters, and
#' data frame structure
#' @return an object inheriting from class \code{FielDHub}
#' @param x an object inheriting from class \code{FielDHub}
#'
#' @param ... Unused, for extensibility
#' @author Thiago de Paula Oliveira,
#' \email{thiago.paula.oliveira@@alumni.usp.br} [aut],
#' Didier Murillo [aut]
#' @importFrom utils str
#' @importFrom dplyr glimpse
#' @export
print.summary.FielDHub <- function(x, ...) {
if (x$infoDesign$id_design == 1) {
cat("Completely Randomized Design (CRD):", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the CRD field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 2) {
cat("Randomized Complete Block Design (RCBD):", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Layout randomization for each location:", "\n")
print(x$layoutRandom)
cat("\n")
#---------------------------------------------------------------------
cat("3. Plot numbers layout:", "\n")
print(x$plotNumber)
cat("\n")
#---------------------------------------------------------------------
cat("4. Structure of the data frame with the RCBD field book:", "\n\n")
str(x$fieldBook)
#---------------------------------------------------------------------
}else if (x$infoDesign$id_design == 3) {
cat("Latin Square Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Squares:", "\n")
print(x$squares)
cat("\n")
#---------------------------------------------------------------------
cat("3. Plot squares:", "\n")
print(x$plotSquares)
cat("\n")
#---------------------------------------------------------------------
cat("4. Structure of the data frame with the latin_square field book:", "\n\n")
str(x$fieldBook)
#---------------------------------------------------------------------
}else if (x$infoDesign$id_design == 4) {
cat("Full Factorial Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the full_factorial field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 5) {
cat("Split Plot Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
cat("2. Layout randomization for each location:", "\n")
print(x$layoutlocations)
cat("\n")
#---------------------------------------------------------------------
cat("3. Structure of the data frame with the split_plot field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 6) {
cat("Split-Split Plot Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the split_split_plot field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 7) {
cat("Strip Plot Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#----------------------------------------------------------------------
cat("2. Layout randomization for each location:", "\n")
print(x$stripsBlockLoc)
cat("\n")
#----------------------------------------------------------------------
cat("3. Plot number layout for each location:", "\n")
print(x$plotLayouts)
cat("\n")
#---------------------------------------------------------------------
cat("4. Structure of the data frame with the strip_plot field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 8) {
cat("Incomplete Blocks Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the incomplete_blocks field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 9) {
cat("Row Column Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#----------------------------------------------------------------------
cat("2. Resolvable row column blocks", "\n")
print(x$resolvableBlocks)
cat("\n")
#----------------------------------------------------------------------
cat("3. Concurrence matrix:", "\n")
print(x$concurrence)
cat("\n")
#---------------------------------------------------------------------
cat("4. Structure of the data frame with the row_column field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 10) {
cat("Square Lattice:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the square_lattice field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 11) {
cat("Rectangular Lattice Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the rectangular_lattice field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 12) {
cat("Alpha Lattice Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the alpha_lattice field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 13) {
cat("Partially Replicated Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#----------------------------------------------------------------------
cat("2. Layout randomization:", "\n")
print(x$layoutRandom)
cat("\n")
#----------------------------------------------------------------------
cat("3. Plot number layout:", "\n")
print(x$plotNumber)
cat("\n")
#---------------------------------------------------------------------
cat("4. Structure of the data frame with the data input:", "\n\n")
str(x$data_entry)
#---------------------------------------------------------------------
cat("5. Structure of the data frame with the partially_replicated field book:", "\n\n")
str(x$fieldBook)
} else if (x$infoDesign$id_design == 14) {
cat("Augmented Randomized Complete Block Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#----------------------------------------------------------------------
cat("2. Layout randomization:", "\n")
print(x$layoutRandom)
cat("\n")
#----------------------------------------------------------------------
cat("3. Plot number layout:", "\n")
print(x$plotNumber)
cat("\n")
#----------------------------------------------------------------------
cat("4. Experiments name layout:", "\n")
print(x$exptNames)
cat("\n")
#---------------------------------------------------------------------
cat("5. Structure of the data frame with the data input:", "\n\n")
str(x$data_entry)
#---------------------------------------------------------------------
cat("6. Structure of the data frame with the RCBD_augmented field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 15) {
cat("Un-replicated Diagonal Arrangement Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#----------------------------------------------------------------------
cat("2. Layout randomization:", "\n")
print(x$layoutRandom)
cat("\n")
#----------------------------------------------------------------------
cat("3. Plot number layout:", "\n")
print(x$plotsNumber)
cat("\n")
#---------------------------------------------------------------------
cat("4. Structure of the data frame with the data input:", "\n\n")
str(x$data_entry)
#---------------------------------------------------------------------
cat("5. Structure of the data frame with the diagonal_arrangement field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 16) {
cat("Un-replicated Optimized Arrangement Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
cat("\n")
#----------------------------------------------------------------------
cat("2. Layout randomization:", "\n")
print(x$layoutRandom)
cat("\n")
#----------------------------------------------------------------------
cat("3. Plot number layout:", "\n")
print(x$plotNumber)
cat("\n")
#---------------------------------------------------------------------
cat("4. Structure of the data frame with the data input:", "\n\n")
str(x$data_entry)
#---------------------------------------------------------------------
cat("5. Structure of the data frame with the optimized_arrangement field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 17) {
cat("Split families:", "\n\n")
#---------------------------------------------------------------------
cat("1. Structure of the data frame with the summary of entries by location:", "\n\n")
str(x$rowsEachlist)
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the entries for each location:", "\n\n")
str(x$data_locations)
}
}
#-----------------------------------------------------------------------
# Print plot
#-----------------------------------------------------------------------
#' @rdname print.fieldLayout
#' @method print fieldLayout
#' @title Print a \code{fieldLayout} plot object
#' @usage \method{print}{fieldLayout}(x, ...)
#' @aliases print.fieldLayout
#' @description Prints a plot object of class \code{fieldLayout}.
#' @return a plot object inheriting from class \code{fieldLayout}.
#' @param x a plot object inheriting from class fieldLayout.
#' @param ... unused, for extensibility.
#' @author Didier Murillo [aut]
#'
#' @export
print.fieldLayout <- function(x, ...) {
if (!missing(x)) {
if (is.null(x)) stop("x must be a fieldLayout object!")
if (!inherits(x,"fieldLayout")) {
stop("x must be a fieldLayout object!")
}
return(print(x$layout))
} else stop("x is missing!")
}
#-----------------------------------------------------------------------
# Plot
#-----------------------------------------------------------------------
#' @rdname plot.FielDHub
#' @method plot FielDHub
#' @title Plot a \code{FielDHub} object
#' @usage \method{plot}{FielDHub}(x, ...)
#' @aliases plot.FielDHub
#' @description Draw a field layout plot for a \code{FielDHub} object.
#' @return
#' \itemize{
#' \item a plot object inheriting from class \code{fieldLayout}
#' \item \code{field_book} a data frame with the fieldbook that includes the coordinates ROW and COLUMN.
#' }
#' @param x a object inheriting from class \code{FielDHub}
#' @param ... further arguments passed to utility function \code{plot_layout()}.
#' \itemize{
#' \item \code{layout} a integer. Options available depend on the
#' type of design and its characteristics
#' \item \code{l} a integer to specify the location to plot.
#' \item \code{planter} it can be \code{serpentine} or \code{cartesian}.
#' \item \code{stacked} it can be \code{vertical} or \code{horizontal} stacked layout.
#' }
#' @author Didier Murillo [aut]
#' @examples
#' \dontrun{
#' # Example 1: Plot a RCBD design with 24 treatments and 3 reps.
#' s <- RCBD(t = 24, reps = 3, plotNumber = 101, seed = 12)
#' plot(s)
#' }
#'
#' @export
plot.FielDHub <- function(x, ...) {
if (!missing(x)) {
if (is.null(x)) stop("x must be a FielDHub object!")
if (!inherits(x,"FielDHub")) {
stop("x is not a FielDHub class")
}
p <- plot_layout(x = x, ...)
if (is.null(p)) {
img <- ggplot2::ggplot() + ggplot2::theme_minimal()
class(img) <- "fieldLayout"
print(x = img)
} else {
out <- list(
field_book = p$allSitesFieldbook,
layout = p$out_layout
)
class(out) <- "fieldLayout"
print(x = out)
return(invisible(list(field_book = out$field_book)))
}
} else stop("x is missing!")
}
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FielDHub documentation built on Oct. 20, 2023, 1:07 a.m.
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Defines functions plot.FielDHub print.fieldLayout print.summary.FielDHub summary.FielDHub print.FielDHub
Documented in plot.FielDHub print.FielDHub print.fieldLayout print.summary.FielDHub summary.FielDHub
#-----------------------------------------------------------------------
# Print
#-----------------------------------------------------------------------
#' @rdname print.FielDHub
#' @method print FielDHub
#' @title Print a \code{FielDHub} object
#' @usage \method{print}{FielDHub}(x, n, ...)
#' @aliases print.FielDHub
#' @description Prints information about any \code{FielDHub} function.
#' @return an object inheriting from class \code{FielDHub}
#' @param x an object inheriting from class
#' @param n a single integer. If positive or zero, size for the
#' resulting object: number of elements for a vector (including
#' lists), rows for a matrix or data frame or lines for a function. If
#' negative, all but the n last/first number of elements of x.
#'
#' @param ... further arguments passed to \code{\link{head}}.
#' @author Thiago de Paula Oliveira,
#' \email{thiago.paula.oliveira@@alumni.usp.br} [aut],
#' Didier Murillo [aut]
#' @importFrom utils head str
#' @examples
#' # Example 1: Generates a CRD design with 5 treatments and 5 reps each.
#' crd1 <- CRD(t = 5, reps = 5, plotNumber = 101,
#' seed = 1985, locationName = "Fargo")
#' crd1$infoDesign
#' print(crd1)
#'
#' @export
print.FielDHub <- function(x, n=10, ...){
#---------------------------------------------------------------------
# Parameters
#---------------------------------------------------------------------
if (x$infoDesign$id_design == 1) {
cat("Completely Randomized Design (CRD)", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the CRD field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 2){
cat("Randomized Complete Block Design (RCBD):", "\n\n")
#-----------------------------------------------------------
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the RCBD field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 3){
cat("Latin Square Design:", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the latin_square field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 4) {
cat("Full Factorial Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the full_factorial field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 5) {
cat("Split Plot Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the split_plot field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 6) {
cat("Split-Split Plot Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the split_split_plot field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 7) {
cat("Strip Plot Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the strip_plot field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 8) {
cat("Incomplete Blocks Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the incomplete_blocks field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 9) {
cat("Row Column Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the row_column field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 10) {
cat("Square Lattice Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the square_lattice field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 11) {
cat("Rectangular Lattice Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the rectangular_lattice field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
} else if (x$infoDesign$id_design == 12) {
cat("Alpha Lattice Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the alpha_lattice field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
} else if (x$infoDesign$id_design == 13) {
cat("Partially Replicated Design", "\n\n")
cat("\n", "Replications within location:", "\n")
print(x$reps_info)
cat("\n", "Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the partially_replicated field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
} else if (x$infoDesign$id_design == "MultiPrep") {
cat("Multi-Location Partially Replicated Design", "\n")
cat("\n", "Replications within location:", "\n")
print(x$reps_info)
cat("\n", "Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the partially_replicated field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
} else if (x$infoDesign$id_design == 14) {
cat("Augmented Randomized Complete Block Design:", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the RCBD_augmented field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 15) {
cat("Un-replicated Diagonal Arrangement Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the diagonal_arrangement field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
} else if (x$infoDesign$id_design == "Sparse") {
cat("Sparse Allocation: Un-replicated Diagonal Arrangement Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the diagonal_arrangement field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
} else if (x$infoDesign$id_design == 16) {
cat("Un-replicated Optimized Arrangement Design", "\n\n")
cat("Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
# str(x$infoDesign)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$fieldBook)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the optimized_arrangement field book:",
"\n")
print(head(x$fieldBook, n=nhead_print, ...))
}else if (x$infoDesign$id_design == 17) {
cat("Split families:", "\n\n")
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
cat("\n", "Data frame with the summary of cases by location:",
"\n")
print(x$rowsEachlist)
#---------------------------------------------------------------------
# Head
#---------------------------------------------------------------------
nr <- nrow(x$data_locations)
nhead_print <- infoPrint(n, nr)
cat("\n", nhead_print,
"First observations of the data frame with the entries for each location:",
"\n")
print(head(x$data_locations, n=nhead_print, ...))
}
}
#-----------------------------------------------------------------------
# Summary
#-----------------------------------------------------------------------
#' @rdname summary.FielDHub
#' @method summary FielDHub
#' @title Summary a \code{FielDHub} object
#' @usage \method{summary}{FielDHub}(object, ...)
#' @aliases summary.FielDHub
#' @description Summarise information on the design parameters, and data
#' frame structure
#' @return an object inheriting from class \code{summary.FielDHub}
#' @param object an object inheriting from class
#' \code{FielDHub}
#'
#' @param ... Unused, for extensibility
#' @author Thiago de Paula Oliveira,
#' \email{thiago.paula.oliveira@@alumni.usp.br}
#'
#' @examples
#' # Example 1: Generates a CRD design with 5 treatments and 5 reps each.
#' crd1 <- CRD(t = 5, reps = 5, plotNumber = 101,
#' seed = 1985, locationName = "Fargo")
#' crd1$infoDesign
#' summary(crd1)
#'
#' @export
summary.FielDHub <- function(object, ...) {
structure(object, oClass=class(object),
class = "summary.FielDHub")
}
#-----------------------------------------------------------------------
# Print summary
#-----------------------------------------------------------------------
#' @rdname print.summary.FielDHub
#' @method print summary.FielDHub
#' @title Print the summary of a \code{FielDHub} object
#' @usage \method{print}{summary.FielDHub}(x, ...)
#' @aliases print.summary.FielDHub
#' @description Print summary information on the design parameters, and
#' data frame structure
#' @return an object inheriting from class \code{FielDHub}
#' @param x an object inheriting from class \code{FielDHub}
#'
#' @param ... Unused, for extensibility
#' @author Thiago de Paula Oliveira,
#' \email{thiago.paula.oliveira@@alumni.usp.br} [aut],
#' Didier Murillo [aut]
#' @importFrom utils str
#' @importFrom dplyr glimpse
#' @export
print.summary.FielDHub <- function(x, ...) {
if (x$infoDesign$id_design == 1) {
cat("Completely Randomized Design (CRD):", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the CRD field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 2) {
cat("Randomized Complete Block Design (RCBD):", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Layout randomization for each location:", "\n")
print(x$layoutRandom)
cat("\n")
#---------------------------------------------------------------------
cat("3. Plot numbers layout:", "\n")
print(x$plotNumber)
cat("\n")
#---------------------------------------------------------------------
cat("4. Structure of the data frame with the RCBD field book:", "\n\n")
str(x$fieldBook)
#---------------------------------------------------------------------
}else if (x$infoDesign$id_design == 3) {
cat("Latin Square Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Squares:", "\n")
print(x$squares)
cat("\n")
#---------------------------------------------------------------------
cat("3. Plot squares:", "\n")
print(x$plotSquares)
cat("\n")
#---------------------------------------------------------------------
cat("4. Structure of the data frame with the latin_square field book:", "\n\n")
str(x$fieldBook)
#---------------------------------------------------------------------
}else if (x$infoDesign$id_design == 4) {
cat("Full Factorial Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the full_factorial field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 5) {
cat("Split Plot Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
cat("2. Layout randomization for each location:", "\n")
print(x$layoutlocations)
cat("\n")
#---------------------------------------------------------------------
cat("3. Structure of the data frame with the split_plot field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 6) {
cat("Split-Split Plot Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the split_split_plot field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 7) {
cat("Strip Plot Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#----------------------------------------------------------------------
cat("2. Layout randomization for each location:", "\n")
print(x$stripsBlockLoc)
cat("\n")
#----------------------------------------------------------------------
cat("3. Plot number layout for each location:", "\n")
print(x$plotLayouts)
cat("\n")
#---------------------------------------------------------------------
cat("4. Structure of the data frame with the strip_plot field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 8) {
cat("Incomplete Blocks Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the incomplete_blocks field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 9) {
cat("Row Column Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#----------------------------------------------------------------------
cat("2. Resolvable row column blocks", "\n")
print(x$resolvableBlocks)
cat("\n")
#----------------------------------------------------------------------
cat("3. Concurrence matrix:", "\n")
print(x$concurrence)
cat("\n")
#---------------------------------------------------------------------
cat("4. Structure of the data frame with the row_column field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 10) {
cat("Square Lattice:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the square_lattice field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 11) {
cat("Rectangular Lattice Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the rectangular_lattice field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 12) {
cat("Alpha Lattice Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the alpha_lattice field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 13) {
cat("Partially Replicated Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#----------------------------------------------------------------------
cat("2. Layout randomization:", "\n")
print(x$layoutRandom)
cat("\n")
#----------------------------------------------------------------------
cat("3. Plot number layout:", "\n")
print(x$plotNumber)
cat("\n")
#---------------------------------------------------------------------
cat("4. Structure of the data frame with the data input:", "\n\n")
str(x$data_entry)
#---------------------------------------------------------------------
cat("5. Structure of the data frame with the partially_replicated field book:", "\n\n")
str(x$fieldBook)
} else if (x$infoDesign$id_design == 14) {
cat("Augmented Randomized Complete Block Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#----------------------------------------------------------------------
cat("2. Layout randomization:", "\n")
print(x$layoutRandom)
cat("\n")
#----------------------------------------------------------------------
cat("3. Plot number layout:", "\n")
print(x$plotNumber)
cat("\n")
#----------------------------------------------------------------------
cat("4. Experiments name layout:", "\n")
print(x$exptNames)
cat("\n")
#---------------------------------------------------------------------
cat("5. Structure of the data frame with the data input:", "\n\n")
str(x$data_entry)
#---------------------------------------------------------------------
cat("6. Structure of the data frame with the RCBD_augmented field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 15) {
cat("Un-replicated Diagonal Arrangement Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
str(x$infoDesign)
cat("\n")
#----------------------------------------------------------------------
cat("2. Layout randomization:", "\n")
print(x$layoutRandom)
cat("\n")
#----------------------------------------------------------------------
cat("3. Plot number layout:", "\n")
print(x$plotsNumber)
cat("\n")
#---------------------------------------------------------------------
cat("4. Structure of the data frame with the data input:", "\n\n")
str(x$data_entry)
#---------------------------------------------------------------------
cat("5. Structure of the data frame with the diagonal_arrangement field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 16) {
cat("Un-replicated Optimized Arrangement Design:", "\n\n")
#---------------------------------------------------------------------
cat("1. Information on the design parameters:", "\n")
len <- length(x$infoDesign)
str(x$infoDesign[1:(len-1)])
cat("\n")
#----------------------------------------------------------------------
cat("2. Layout randomization:", "\n")
print(x$layoutRandom)
cat("\n")
#----------------------------------------------------------------------
cat("3. Plot number layout:", "\n")
print(x$plotNumber)
cat("\n")
#---------------------------------------------------------------------
cat("4. Structure of the data frame with the data input:", "\n\n")
str(x$data_entry)
#---------------------------------------------------------------------
cat("5. Structure of the data frame with the optimized_arrangement field book:", "\n\n")
str(x$fieldBook)
}else if (x$infoDesign$id_design == 17) {
cat("Split families:", "\n\n")
#---------------------------------------------------------------------
cat("1. Structure of the data frame with the summary of entries by location:", "\n\n")
str(x$rowsEachlist)
#---------------------------------------------------------------------
cat("2. Structure of the data frame with the entries for each location:", "\n\n")
str(x$data_locations)
}
}
#-----------------------------------------------------------------------
# Print plot
#-----------------------------------------------------------------------
#' @rdname print.fieldLayout
#' @method print fieldLayout
#' @title Print a \code{fieldLayout} plot object
#' @usage \method{print}{fieldLayout}(x, ...)
#' @aliases print.fieldLayout
#' @description Prints a plot object of class \code{fieldLayout}.
#' @return a plot object inheriting from class \code{fieldLayout}.
#' @param x a plot object inheriting from class fieldLayout.
#' @param ... unused, for extensibility.
#' @author Didier Murillo [aut]
#'
#' @export
print.fieldLayout <- function(x, ...) {
if (!missing(x)) {
if (is.null(x)) stop("x must be a fieldLayout object!")
if (!inherits(x,"fieldLayout")) {
stop("x must be a fieldLayout object!")
}
return(print(x$layout))
} else stop("x is missing!")
}
#-----------------------------------------------------------------------
# Plot
#-----------------------------------------------------------------------
#' @rdname plot.FielDHub
#' @method plot FielDHub
#' @title Plot a \code{FielDHub} object
#' @usage \method{plot}{FielDHub}(x, ...)
#' @aliases plot.FielDHub
#' @description Draw a field layout plot for a \code{FielDHub} object.
#' @return
#' \itemize{
#' \item a plot object inheriting from class \code{fieldLayout}
#' \item \code{field_book} a data frame with the fieldbook that includes the coordinates ROW and COLUMN.
#' }
#' @param x a object inheriting from class \code{FielDHub}
#' @param ... further arguments passed to utility function \code{plot_layout()}.
#' \itemize{
#' \item \code{layout} a integer. Options available depend on the
#' type of design and its characteristics
#' \item \code{l} a integer to specify the location to plot.
#' \item \code{planter} it can be \code{serpentine} or \code{cartesian}.
#' \item \code{stacked} it can be \code{vertical} or \code{horizontal} stacked layout.
#' }
#' @author Didier Murillo [aut]
#' @examples
#' \dontrun{
#' # Example 1: Plot a RCBD design with 24 treatments and 3 reps.
#' s <- RCBD(t = 24, reps = 3, plotNumber = 101, seed = 12)
#' plot(s)
#' }
#'
#' @export
plot.FielDHub <- function(x, ...) {
if (!missing(x)) {
if (is.null(x)) stop("x must be a FielDHub object!")
if (!inherits(x,"FielDHub")) {
stop("x is not a FielDHub class")
}
p <- plot_layout(x = x, ...)
if (is.null(p)) {
img <- ggplot2::ggplot() + ggplot2::theme_minimal()
class(img) <- "fieldLayout"
print(x = img)
} else {
out <- list(
field_book = p$allSitesFieldbook,
layout = p$out_layout
)
class(out) <- "fieldLayout"
print(x = out)
return(invisible(list(field_book = out$field_book)))
}
} else stop("x is missing!")
}
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