R/ck_f.R

In reyzaguirre/st4gi: Statistical tools for genetic improvement

#' Check data for a full factorial
#'
#' This function checks the frequencies for a full factorial.
#' @param trait The name of the column for the trait to analyze.
#' @param factors The names of the columns that identify the factors.
#' @param rep The name of the column that identifies the replications, \code{NULL} for a CRD.
#' @param dfr The name of the data frame.
#' @return The number of treatments without data (\code{nt.0}), the number of
#' treatments that appear more than once in a given replication (\code{nt.mult}),
#' the number of missing values \code{nmis}, the proportion of missing values
#' (\code{pmis}), the number of factors (\code{nf}), the number of levels of each
#' factor (\code{nl}), the number of replications (\code{nrep}), a table with frequencies
#' of valid cases for each combination of the levels of the factors (\code{tf}), a table
#' with frequencies of valid cases for each combination of the levels of the factors in
#' each replication (\code{tfr}), and the number of rows in the data frame with
#' missing values for factors (\code{nmis.fac}).
#' @author Raul Eyzaguirre.
#' @examples 
#' # Create a design
#' A <- paste0("a", 1:5)
#' B <- paste0("b", 1:3)
#' dfr <- cr.f(c("A", "B"), list(A, B), "rcbd", 3, 10)
#' dfr <- dfr$book
#' # Create some random data
#' dfr$y <- rnorm(45)
#' # Delete some values
#' dfr[c(4, 5, 12), 'y'] <- NA
#' # Check the design
#' ck.f("y", c("A", "B"), "block", dfr)
#' @export

ck.f <- function(trait, factors, rep, dfr) {
  
  # Check factor structure

  out <- ck.fs(factors, rep, dfr)
  dfr <- out$dfr
  nf <- out$nf
  nl <- out$nl
  nrep <- out$nrep
  nmis.fac <- out$nmis.fac
  
  # Frequencies for factors and replications
  
  out <- ck.fq(trait, factors, rep, dfr)
  tf <- out$tf
  tfr <- out$tfr
  nmis <- out$nmis
  pmis <- out$pmis

  # Number of treatments without data
  
  nt.0 <- sum(tf == 0)
  
  # Number of treatments that appear more than once in a given replication
  
  nt.mult <- sum(tfr > 1)

  # Return
  
  list(nt.0 = nt.0, nt.mult = nt.mult, nmis = nmis, pmis = pmis, nf = nf, nl = nl,
       nrep = nrep, tf = tf, tfr = tfr, nmis.fac = nmis.fac)
  
}