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First commit adding support for Poisson outcomes
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‎DESCRIPTION

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Package: multiarm
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Type: Package
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Title: Design of single- and multi-stage multi-arm clinical trials
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Version: 0.11.3
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Version: 0.12.0
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Authors@R: c(person(given = "Michael J", family = "Grayling",
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email = "[email protected]",
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role = c("aut", "cre")))
@@ -42,6 +42,6 @@ Imports:
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tibble,
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tidyr,
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xml2
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Date: 2020-09-16
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Date: 2020-12-15
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URL: http://github.com/mjg211/multiarm
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BugReports: http://github.com/mjg211/multiarm/issues

‎NAMESPACE

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S3method(plot,multiarm_des_dtl_bern)
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S3method(plot,multiarm_des_dtl_norm)
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S3method(plot,multiarm_des_dtl_pois)
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S3method(plot,multiarm_des_gs_bern)
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S3method(plot,multiarm_des_gs_norm)
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S3method(plot,multiarm_des_gs_pois)
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S3method(plot,multiarm_des_ss_bern)
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S3method(plot,multiarm_des_ss_norm)
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S3method(plot,multiarm_des_ss_pois)
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export(build_dtl_bern)
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export(build_dtl_norm)
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export(build_dtl_pois)
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export(build_gs_bern)
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export(build_gs_norm)
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export(build_gs_pois)
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export(build_ss_bern)
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export(build_ss_norm)
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export(build_ss_pois)
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export(des_dtl_bern)
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export(des_dtl_norm)
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export(des_dtl_pois)
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export(des_gs_bern)
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export(des_gs_norm)
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export(des_gs_pois)
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export(des_ss_bern)
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export(des_ss_norm)
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export(des_ss_pois)
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export(gui)
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export(opchar_dtl_bern)
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export(opchar_dtl_norm)
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export(opchar_dtl_pois)
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export(opchar_gs_bern)
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export(opchar_gs_norm)
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export(opchar_gs_pois)
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export(opchar_ss_bern)
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export(opchar_ss_norm)
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export(opchar_ss_pois)
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export(sim_dtl_bern)
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export(sim_dtl_norm)
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export(sim_dtl_pois)
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export(sim_gs_bern)
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export(sim_gs_norm)
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export(sim_gs_pois)
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export(sim_ss_bern)
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export(sim_ss_norm)
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export(sim_ss_pois)

‎NEWS.md

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# multiarm 0.12
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* Support added for clinical trials with Poisson distributed outcomes
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(`build_dtl_pois()`, `build_gs_pois()`, `build_ss_pois()`, `des_dtl_pois()`,
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`des_gs_pois()`, `des_ss_pois()`, `opchar_dtl_pois()`, `opchar_gs_pois()`,
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`opchar_ss_pois()`, `plot.multiarm_des_dtl_pois()`,
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`plot.multiarm_des_gs_pois()`, `plot.multiarm_des_ss_pois()`, `sim_dtl_pois()`,
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`sim_gs_pois()`, `sim_ss_pois()`).
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# multiarm 0.11
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* Analysis functions removed; focus purely on design for now.

‎R/build_dtl_pois.R

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#' Build a multi-stage drop-the-losers multi-arm clinical trial for a Poisson
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#' distributed primary outcome
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#'
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#' \code{build_dtl_pois()} builds a multi-stage drop-the-losers multi-arm
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#' clinical trial design object assuming the primary outcome variable is
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#' Poisson distributed, like those returned by \code{\link{des_dtl_pois}}.
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#'
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#' @param n1 A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>n</i><sub>1</sub>}}{\eqn{n_1}}, the total sample size
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#' required in stage one of the trial. Defaults to \code{147}.
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#' @param n10 A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>n</i><sub>10</sub>}}{\eqn{n_{10}}}, the sample size
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#' required in the control arm in stage one of the trial. Defaults to \code{49}.
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#' @param e A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>e</i>}}{\eqn{e}}, the critical rejection boundary for
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#' the final analysis. Defaults to \code{2.17}.
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#' @param Kv A \code{\link{numeric}} \code{\link{vector}} of strictly decreasing
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#' values, indicating the chosen value for
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#' \ifelse{html}{\out{<b><i>K</i></b>}}{\eqn{\bold{K}}}, the number of
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#' experimental treatment arms present in each stage. Defaults to
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#' \code{c(2, 1)}.
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#' @param alpha A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>&alpha;</i>}}{\eqn{\alpha}}, the significance level
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#' (family-wise error-rate). Defaults to \code{0.025}.
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#' @param beta A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>&beta;</i>}}{\eqn{\beta}}, used in the definition of
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#' the desired power. Defaults to \code{0.1}.
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#' @param lambda0 A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>&lambda;</i><sub>0</sub>}}{\eqn{\lambda_0}}, the
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#' event rate in the control arm. Defaults to \code{5}.
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#' @param delta1 A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>&delta;</i><sub>1</sub>}}{\eqn{\delta_1}}, the
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#' 'interesting' treatment effect. Defaults to \code{1}.
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#' @param delta0 A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>&delta;</i><sub>0</sub>}}{\eqn{\delta_0}}, the
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#' 'uninteresting' treatment effect. Defaults to \code{0}.
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#' @param ratio A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>r</i>}}{\eqn{r}}, the stage-wise allocation ratio to
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#' present experimental arms. Defaults to \code{1}.
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#' @param power A \code{\link{character}} string indicating the chosen type of
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#' power to design the trial for. Can be \code{"disjunctive"} or
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#' \code{"marginal"}. Defaults to \code{"marginal"}.
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#' @param type A \code{\link{character}} string indicating the choice for the
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#' stage-wise sample size. Can be \code{"variable"} or \code{"fixed"}. Defaults
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#' to \code{"variable"}.
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#' @param summary A \code{\link{logical}} variable indicating whether a summary
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#' of the function's progress should be printed to the console. Defaults to
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#' \code{FALSE}.
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#' @return A \code{\link{list}}, with additional class
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#' \code{"multiarm_des_dtl_pois"}, containing the following elements:
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#' \itemize{
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#' \item A \code{\link{tibble}} in the slot \code{$opchar} summarising the
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#' operating characteristics of the identified design.
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#' \item A \code{\link{numeric}} in the slot \code{$maxN} specifying
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#' \ifelse{html}{\out{<i>N</i>}}{\eqn{N}}, the trial's total required sample
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#' size.
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#' \item A \code{\link{numeric}} in the slot \code{$n_factor}, for internal use
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#' in other functions.
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#' \item Each of the input variables.
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#' }
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#' @examples
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#' # The design for the default parameters
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#' des <- build_dtl_pois()
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#' @seealso \code{\link{des_dtl_pois}}, \code{\link{gui}},
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#' \code{\link{opchar_dtl_pois}}, \code{\link{plot.multiarm_des_dtl_pois}},
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#' \code{\link{sim_dtl_pois}}.
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#' @export
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build_dtl_pois <- function(n1 = 210, n10 = 70, e = 2.17, Kv = c(2, 1),
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alpha = 0.025, beta = 0.1, lambda0 = 5, delta1 = 1,
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delta0 = 0, ratio = 1, power = "marginal",
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type = "variable", summary = FALSE) {
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##### Check input variables ##################################################
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#check_n1_n10(n1, n10, "n1", "n10", int = F)
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check_real_range_strict(e, "e", c(-Inf, Inf), 1)
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Kv <- check_Kv(Kv, "Kv")
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J <- length(Kv)
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check_real_range_strict(alpha, "alpha", c(0, 1), 1)
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check_real_range_strict(beta, "beta", c(0, 1), 1)
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check_real_range_strict(lambda0, "lambda0", c(0, Inf), 1)
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check_delta0_delta1(delta0, delta1, "delta0", "delta1", lambda0 = lambda0,
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name_lambda0 = "lambda0")
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check_real_range_strict(ratio, "ratio", c(0, Inf), 1)
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check_belong(power, "power", c("disjunctive", "marginal"), 1)
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check_belong(type, "type", c("fixed", "variable"), 1)
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check_logical(summary, "summary")
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##### Print summary ##########################################################
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if (summary) {
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#summary_build_dtl_pois(n1, n10, e, Kv, alpha, beta, lambda0, delta1, delta0,
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# ratio, power, stopping, type)
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message("")
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}
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##### Perform main computations ##############################################
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if (summary) {
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message(" Building outputs..")
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}
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integer <- all(c(n1, n10)%%1 == 0)
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if (type == "variable") {
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n_factor <- n10
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} else {
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n_factor <- n1
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}
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comp <- components_dtl_init(alpha, beta, delta0, delta1, integer, Kv,
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power, ratio, summary, type,
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lambda0 = lambda0, n_factor = n_factor,
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e = e)
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tau <- rbind(numeric(Kv[1]), rep(delta1, Kv[1]),
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matrix(delta0, Kv[1], Kv[1]) +
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(delta1 - delta0)*diag(Kv[1]))
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comp <- components_dtl_update(comp, tau,
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lambda = cbind(lambda0, tau + lambda0))
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comp <- opchar_dtl_internal(comp)
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##### Outputting #############################################################
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if (summary) {
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message("..outputting.")
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}
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output <- list(alpha = alpha,
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beta = beta,
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delta0 = delta0,
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delta1 = delta1,
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e = e,
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integer = integer,
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Kv = Kv,
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lambda0 = lambda0,
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maxN = comp$opchar$maxN[1],
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n_factor = n_factor,
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n1 = n1,
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n10 = n10,
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opchar = comp$opchar,
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power = power,
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ratio = ratio,
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summary = summary,
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type = type)
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class(output) <- c("multiarm_des_dtl_pois", class(output))
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output
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}

‎R/build_gs_pois.R

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#' Build a multi-stage group-sequential multi-arm clinical trial for a Poisson
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#' distributed primary outcome
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#'
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#' \code{build_gs_pois()} builds a multi-stage group-sequential multi-arm
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#' clinical trial design object assuming the primary outcome variable is
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#' Poisson distributed, like those returned by \code{\link{des_gs_pois}}.
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#'
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#' @param n1 A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>n</i><sub>1</sub>}}{\eqn{n_1}}, the total sample size
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#' required in stage one of the trial. Defaults to \code{162}.
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#' @param n10 A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>n</i><sub>10</sub>}}{\eqn{n_{10}}}, the sample size
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#' required in the control arm in stage one of the trial. Defaults to \code{54}.
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#' @param e A \code{\link{numeric}} \code{\link{vector}} indicating the chosen
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#' value for \ifelse{html}{\out{<b><i>e</i></b>}}{\eqn{\bold{e}}}, the efficacy
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#' (upper) stopping boundaries. Defaults to \code{c(2.42, 2.42)}.
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#' @param f A \code{\link{numeric}} \code{\link{vector}} indicating the chosen
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#' value for \ifelse{html}{\out{<b><i>f</i></b>}}{\eqn{\bold{f}}}, the futility
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#' (lower) stopping boundaries. Defaults to \code{c(-2.42, 2.42)}.
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#' @param K A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>K</i>}}{\eqn{\bold{K}}}, the (initial) number of
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#' experimental treatment arms. Defaults to \code{2}.
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#' @param alpha A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>&alpha;</i>}}{\eqn{\alpha}}, the significance level
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#' (family-wise error-rate). Defaults to \code{0.025}.
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#' @param beta A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>&beta;</i>}}{\eqn{\beta}}, used in the definition of
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#' the desired power. Defaults to \code{0.1}.
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#' @param lambda0 A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>&lambda;</i><sub>0</sub>}}{\eqn{\lambda_0}}, the
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#' event rate in the control arm. Defaults to \code{5}.
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#' @param delta1 A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>&delta;</i><sub>1</sub>}}{\eqn{\delta_1}}, the
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#' 'interesting' treatment effect. Defaults to \code{1}.
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#' @param delta0 A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>&delta;</i><sub>0</sub>}}{\eqn{\delta_0}}, the
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#' 'uninteresting' treatment effect. Defaults to \code{0}.
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#' @param ratio A \code{\link{numeric}} indicating the chosen value for
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#' \ifelse{html}{\out{<i>r</i>}}{\eqn{r}}, the stage-wise allocation ratio to
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#' present experimental arms. Defaults to \code{1}.
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#' @param power A \code{\link{character}} string indicating the chosen type of
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#' power to design the trial for. Can be \code{"disjunctive"} or
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#' \code{"marginal"}. Defaults to \code{"marginal"}.
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#' @param stopping A \code{\link{character}} string indicating the chosen type
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#' of stopping rule. Can be \code{"separate"} or \code{"simultaneous"}. Defaults
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#' to \code{"simultaneous"}.
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#' @param type A \code{\link{character}} string indicating the choice for the
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#' stage-wise sample size. Can be \code{"variable"} or \code{"fixed"}. Defaults
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#' to \code{"variable"}.
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#' @param summary A \code{\link{logical}} variable indicating whether a summary
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#' of the function's progress should be printed to the console. Defaults to
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#' \code{FALSE}.
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#' @return A \code{\link{list}}, with additional class
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#' \code{"multiarm_des_gs_pois"}, containing the following elements:
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#' \itemize{
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#' \item A \code{\link{tibble}} in the slot \code{$opchar} summarising the
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#' operating characteristics of the identified design.
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#' \item A \code{\link{tibble}} in the slot \code{$pmf_N} summarising the
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#' probability mass function of the random required sample size under key
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#' scenarios.
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#' \item A \code{\link{numeric}} in the slot \code{$maxN} specifying
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#' \ifelse{html}{\out{max <i>N</i>}}{max \eqn{N}}, the trial's maximum required
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#' sample size.
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#' \item A \code{\link{numeric}} in the slot \code{$n_factor}, for internal use
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#' in other functions.
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#' \item Each of the input variables.
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#' }
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#' @examples
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#' # The design for the default parameters
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#' des <- build_gs_pois()
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#' @seealso \code{\link{des_gs_pois}}, \code{\link{gui}},
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#' \code{\link{opchar_gs_pois}}, \code{\link{plot.multiarm_des_gs_pois}},
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#' \code{\link{sim_gs_pois}}.
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#' @export
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build_gs_pois <- function(n1 = 231, n10 = 77, e = c(2.42, 2.42),
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f = c(-2.42, 2.42), K = 2, alpha = 0.025, beta = 0.1,
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lambda0 = 5, delta1 = 1, delta0 = 0, ratio = 1,
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power = "marginal", stopping = "simultaneous",
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type = "variable", summary = F) {
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##### Check input variables ##################################################
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#check_n1_n10(n1, n10, "n1", "n10", int = F)
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#check_ef(e, f, "e", "f")
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J <- length(e)
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K <- check_integer_range(K, "K", c(1, Inf), 1)
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check_real_range_strict(alpha, "alpha", c(0, 1), 1)
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check_real_range_strict(beta, "beta", c(0, 1), 1)
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check_real_range_strict(lambda0, "lambda0", c(0, Inf), 1)
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check_delta0_delta1(delta0, delta1, "delta0", "delta1", lambda0 = lambda0,
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name_lambda0 = "lambda0")
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check_real_range_strict(ratio, "ratio", c(0, Inf), 1)
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check_belong(power, "power", c("conjunctive", "disjunctive", "marginal"), 1)
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check_belong(stopping, "stopping", c("simultaneous", "separate"), 1)
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check_belong(type, "type", c("fixed", "variable"), 1)
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check_logical(summary, "summary")
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##### Print summary ##########################################################
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if (summary) {
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#summary_build_gs_pois(n1, n10, e, f, K, alpha, beta, lambda0, delta1,
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# delta0, ratio, power, stopping, type)
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message("")
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}
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##### Perform main computations ##############################################
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if (summary) {
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message(" Building outputs..")
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}
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integer <- all(c(n1, n10)%%1 == 0)
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if (type == "variable") {
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n_factor <- n10
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} else {
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n_factor <- n1
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}
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comp <- components_gs_init(alpha, beta, delta0, delta1, NA, NA, NA, NA,
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integer, J, K, power, ratio, stopping,
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summary, type, lambda0 = lambda0,
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n_factor = n_factor, f = f, e = e)
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tau <- rbind(numeric(K), rep(delta1, K),
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matrix(delta0, K, K) + (delta1 - delta0)*diag(K))
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comp <- components_gs_update(comp, tau,
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lambda = cbind(lambda0, tau + lambda0))
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comp <- opchar_gs_internal(comp)
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##### Outputting #############################################################
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if (summary) {
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message("..outputting.")
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}
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output <- list(alpha = alpha,
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beta = beta,
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delta0 = delta0,
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delta1 = delta1,
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e = comp$e,
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efix = NA,
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eshape = NA,
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f = comp$f,
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ffix = NA,
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fshape = NA,
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integer = integer,
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J = J,
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K = K,
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lambda0 = lambda0,
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n_factor = comp$n_factor,
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n10 = n10,
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n1 = n1,
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opchar = comp$opchar,
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pmf_N = comp$pmf_N,
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power = power,
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ratio = ratio,
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stopping = stopping,
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summary = summary,
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type = type)
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class(output) <- c("multiarm_des_gs_pois", class(output))
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output
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}

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