cps.ma.binary: Simulation-based power estimation for binary outcome...

In clusterPower: Power Calculations for Cluster-Randomized and Cluster-Randomized Crossover Trials

Description

This function uses iterative simulations to determine approximate power for multi-arm cluster-randomized controlled trials with binary outcomes of interest. Users can modify a variety of parameters to suit the simulations to their desired experimental situation. This function validates the user's input and passes the necessary arguments to an internal function, which performs the simulations. This function returns the summary power values for each treatment arm.

Usage

cps.ma.binary(
  nsim = 1000,
  nsubjects = NULL,
  narms = NULL,
  nclusters = NULL,
  probs = NULL,
  sigma_b_sq = NULL,
  alpha = 0.05,
  quiet = FALSE,
  method = "glmm",
  multi_p_method = "bonferroni",
  allSimData = FALSE,
  seed = NULL,
  cores = NA,
  tdist = FALSE,
  poorFitOverride = FALSE,
  lowPowerOverride = FALSE,
  timelimitOverride = TRUE,
  nofit = FALSE,
  optmethod = "Nelder-Mead",
  return.all.models = FALSE
)

Arguments

nsim	Number of datasets to simulate; accepts integer (required).
nsubjects	Number of subjects per cluster (required); accepts an integer if all are equal and narms and nclusters are provided. Alternately, the user can supply a list with one entry per arm if the cluster sizes are the same within the arm, or, if they are not the same within the arms, the user can supply a list of vectors where each vector represents an arm and each entry in the vector is the number of subjects per cluster.
narms	Integer value representing the number of trial arms.
nclusters	An integer or vector of integers representing the number of clusters in each arm.
probs	Expected absolute treatment effect probabilities for each arm; accepts a scalar or a vector of length narms (required).
sigma_b_sq	Between-cluster variance; accepts a vector of length narms (required).
alpha	Significance level; default = 0.05.
quiet	When set to FALSE, displays simulation progress and estimated completion time; default is FALSE.
method	Analytical method, either Generalized Linear Mixed Effects Model (GLMM) or Generalized Estimating Equation (GEE). Accepts c('glmm', 'gee') (required); default = 'glmm'.
multi_p_method	A string indicating the method to use for adjusting p-values for multiple comparisons. Choose one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". The default is "bonferroni". See ?p.adjust for additional details.
allSimData	Option to output list of all simulated datasets; default = FALSE.
seed	Option to set.seed. Default is NULL.
cores	String ("all"), NA, or scalar value indicating the number of cores to be used for parallel computing. Default = NA (no parallel computing).
tdist	Logical value indicating whether simulated data should be drawn from a t-distribution rather than the normal distribution. Default = FALSE.
poorFitOverride	Option to override stop() if more than 25% of fits fail to converge or power<0.5 after 50 iterations; default = FALSE.
lowPowerOverride	Option to override stop() if the power is less than 0.5 after the first 50 simulations and every ten simulations thereafter. On function execution stop, the actual power is printed in the stop message. Default = FALSE. When TRUE, this check is ignored and the calculated power is returned regardless of value.
timelimitOverride	Logical. When FALSE, stops execution if the estimated completion time is more than 2 minutes. Defaults to TRUE.
nofit	Option to skip model fitting and analysis and return the simulated data. Defaults to FALSE.
optmethod	User-specified optimizer method. Accepts bobyqa, Nelder_Mead (default), and optimizers wrapped in the optimx package.
return.all.models	Logical; Returns all of the fitted models and the simulated data. Defaults to FALSE.

Details

Users must specify the desired number of simulations, number of subjects per cluster, number of clusters per treatment arm, group probabilities, and the between-cluster variance. Significance level, analytic method, progress updates, poor/singular fit override, and whether or not to return the simulated data may also be specified. The internal function can be called directly by the user to return the fitted models rather than the power summaries (see ?cps.ma.normal.internal for details).

Because the model for binary outcomes may be slower to fit than those for other distributions, this function may be slower than its normal or count-distributed counterparts. Users can spread the simulated data generation and model fitting tasks across multiple cores using the cores argument. Users should expect that parallel computing may make model fitting faster than using a single core for more complicated models. For simpler models, users may prefer to use single thread computing (cores=1), as the processes involved in allocating memory and copying data across cores also may take some time. For time-savings, this function stops execution early if estimated power < 0.5 or more than 25% of models produce a singular fit or non-convergence warning message, unless poorFitOverride = TRUE.

Non-convergent models are not included in the calculation of exact confidence intervals.

Value

A list with the following components:

power

Data frame with columns "power" (Estimated statistical power), "lower.95.ci" (Lower 95% confidence interval bound), "upper.95.ci" (Upper 95% confidence interval bound).

model.estimates

Data frame with columns corresponding to each arm with descriptive suffixes as follows: ".Estimate" (Estimate of treatment effect for a given simulation), "Std.Err" (Standard error for treatment effect estimate), ".zval" (for GLMM) | ".wald" (for GEE), and ".pval" (the p-value estimate).

overall.power

Table of F-test (when method="glmm") or chi^2 (when method="gee") significance test results.

overall.power.summary

Summary overall power of treatment model compared to the null model.

sim.data

Produced when allSimData==TRUE. List of nsim data frames, each containing: "y" (simulated response value), "trt" (indicator for treatment group or arm), and "clust" (indicator for cluster).

model.fit.warning.percent

Character string containing the percent of nsim in which the glmm fit was singular or failed to converge, produced only when method = "glmm" & allSimData = FALSE.

model.fit.warning.incidence

Vector of length nsim denoting whether or not a simulation glmm fit triggered a "singular fit" or "non-convergence" error, produced only when method = "glmm" & allSimData=TRUE.

If nofit = T, a data frame of the simulated data sets, containing:

• "arm" (Indicator for treatment arm)

• "cluster" (Indicator for cluster)

• "y1" ... "yn" (Simulated response value for each of the nsim data sets).

Testing details

This function has been verified, where possible, against reference values from the NIH's GRT Sample Size Calculator, PASS11, CRTsize::n4prop, clusterPower::cps.binary, and clusterPower::cpa.binary.

Author(s)

Alexandria C. Sakrejda ([e-mail]), Alexander R. Bogdan, and Ken Kleinman ([e-mail])

Examples

## Not run: 
bin.ma.rct.unbal <- cps.ma.binary(nsim = 12,
                            nsubjects = list(rep(20, times=15),
                            rep(15, times=15),
                            rep(17, times=15)),
                            narms = 3,
                            nclusters = 15,
                            probs = c(0.35, 0.43, 0.50),
                            sigma_b_sq = c(0.1, 0.1, 0.1),
                            alpha = 0.05, allSimData = TRUE,
                            seed = 123, cores="all")

bin.ma.rct.bal <- cps.ma.binary(nsim = 100, nsubjects = 50, narms=3,
                            nclusters=8,
                            probs = c(0.35, 0.4, 0.5),
                            sigma_b_sq = 0.1, alpha = 0.05,
                            quiet = FALSE, method = 'glmm',
                            allSimData = FALSE,
                            multi_p_method="none",
                            seed = 123, cores="all",
                            poorFitOverride = FALSE)

## End(Not run)

clusterPower documentation built on Jan. 29, 2021, 1:06 a.m.