In hsonne/blockrand2: Block Randomisation for Clinical Studies

knitr::opts_chunk$set(echo = FALSE, results = 'asis')

sectionHeader <- function(stratumInfo, n.treatments)
{
  cat(sprintf(
    "\n## Stratum: %s (%s)\n", 
    stratumInfo$stratum,
    blockrand2::toStratumString(stratumInfo[, -ncol(stratumInfo)])
  ))

  cat("Number of patients in stratum:", stratumInfo$n, "  \n")

  cat("Block length:", blocksize(stratumInfo$n, n.treatments), "  \n")  
}

Strata

noRowNameTable(
  byStratum[, seq_len(ncol(byStratum) - 2)], 
  caption = paste("All possible strata defined by the possible combinations",
                  "of stratum variable levels.")
)

Therapies

noRowNameTable(
  data.frame(
    acronym = names(treatments),
    therapy = as.character(treatments)
  ), 
  caption = "Possible therapies to be applied to the patients."
)

List of Patients with Stratum and Treatment

noRowNameTable(
  moveColumnsFirst(patientsWithTreatments, c("patient", "stratum")),
  caption = "Full list of patients with information on stratum and treatement."
)

Number of Patients within each Stratum

out <- merge(
  x = byStratum[, -ncol(byStratum)], 
  y = mergeAll(treatmentsByStratum(patientsWithTreatments, treatments))
)

noRowNameTable(
  out[order(out$stratum), ], 
  caption = paste("Number n of patients in stratum and numbers n.*therapy*",
                  "of patients that are treated with *therapy*")
)

newPageIf(newpage)

Therapies by Stratum

x <- patientsWithTreatments[, c("patient", "stratum", "treatment")]

x$therapy <- therapyString(x$treatment, treatments)

for (stratum in byStratum$stratum) {

  sectionHeader(
    stratumInfo = byStratum[byStratum$stratum == stratum, ],
    n.treatments = length(treatments)
  )

  print(noRowNameTable(
    x[x$stratum == stratum, -(2:3)],
    caption = paste0("Patiens falling into stratum '", stratum, 
                     "', with their assigned treatment.")
  ))

  newPageIf(newpage)
}