ctmaPower {CoTiMA}R Documentation

ctmaPower

Description

Fits a full invariant model to a list of primary studies and performs analyses of expected (post hoc) power and required sample sizes.

Usage

ctmaPower(
  ctmaInitFit = NULL,
  activeDirectory = NULL,
  statisticalPower = c(),
  failSafeN = NULL,
  failSafeP = NULL,
  timeRange = NULL,
  useMBESS = FALSE,
  coresToUse = 1,
  digits = 4,
  indVarying = FALSE,
  activateRPB = FALSE,
  silentOverwrite = FALSE,
  loadAllInvFit = c(),
  saveAllInvFit = c(),
  loadAllInvWOSingFit = c(),
  saveAllInvWOSingFit = c(),
  skipScaling = TRUE,
  useSampleFraction = NULL,
  optimize = TRUE,
  nopriors = TRUE,
  finishsamples = NULL,
  iter = NULL,
  chains = NULL,
  verbose = NULL,
  customPar = FALSE
)

Arguments

ctmaInitFit

object to which all single 'ctsem' fits of primary studies has been assigned to (i.e., what has been returned by ctmaInit)

activeDirectory

defines another active directory than the one used in ctmaInit

statisticalPower

vector of requested statistical power values

failSafeN

sample size used to determine across which time intervals effects become non-significant

failSafeP

p-value used to determine across which time intervals effects become non-significant

timeRange

vector describing the time range for x-axis as sequence from/to/stepSize (e.g., c(1, 144, 1))

useMBESS

use 'MBESS' package to calculate statistical power (slower)

coresToUse

vector describing the time range for x-axis as sequence from/to/stepSize (e.g., c(1, 144, 1))

digits

number of digits used for rounding (in outputs)

indVarying

Allows continuous time intercepts to vary at the individual level (random effects model, accounts for unobserved heterogeneity)

activateRPB

set to TRUE to receive push messages with 'CoTiMA' notifications on your phone

silentOverwrite

overwrite old files without asking

loadAllInvFit

load the fit of fully constrained 'CoTiMA' model

saveAllInvFit

save the fit of fully constrained 'CoTiMA' model

loadAllInvWOSingFit

load series of fits of fully constrained 'CoTiMA' model with single cross effects excluded, respectively

saveAllInvWOSingFit

save series of fits of fully constrained 'CoTiMA' model with single cross effects excluded, respectively

skipScaling

does not (re-)scale raw data (re-scaling of imported pseudo raw data achieves correlations = 1)

useSampleFraction

to speed up debugging. Provided as fraction (e.g., 1/10)

optimize

if set to FALSE, Stan’s Hamiltonian Monte Carlo sampler is used (default = TRUE = maximum a posteriori / importance sampling) .

nopriors

if TRUE, any priors are disabled – sometimes desirable for optimization

finishsamples

number of samples to draw (either from hessian based covariance or posterior distribution) for final results computation (default = 1000).

iter

number of iterations (defaul = 1000). Sometimes larger values could be required fom Bayesian estimation

chains

number of chains to sample, during HMC or post-optimization importance sampling.

verbose

integer from 0 to 2. Higher values print more information during model fit – for debugging

customPar

logical. Leverages the first pass using priors and ensure that the drift diagonal cannot easily go too negative (could help with ctsem > 3.4)

Value

ctmaPower returns a list containing some arguments supplied, a fitted model with all (!) parameters invariant across primary studies, different elements summarizing the main results, model type, and the type of plot that could be performed with the returned object. The arguments in the returned object are activeDirectory, coresToUse, n.latent, n.manifest, and primaryStudyList. A further result returned is n.studies = 1 (required for proper plotting). Further arguments, which are just copied from the init-fit object supplied, are, n.latent, studyList, and the statisticsList. The fitted model is found in studyFitList, which is a large list with many elements (e.g., the ctsem model specified by CoTiMA, the rstan model created by ctsem, the fitted rstan model etc.). Further results returned are a list with modelResults (i.e., DRIFT=DRIFT, DIFFUSION=DIFFUSION, T0VAR=T0VAR, CINT=NULL) and the paramter names internally used. The summary list, which is printed if the summary function is applied to the returned object, contains "estimates", which is itself a list comprising "Estimates of Model with all Effects Invariant", "Requested Statistical Power" (which just returns the argument statisticalPower), "Power (post hoc) for Drift Effects", "Required Sample Sizes" "Effect Sizes (based on discrete-time calcs; used for power calcs.)", and "Range of significant effects" (across which intervals effects were significant). Plot type is plot.type=c("power") and model.type="stanct" ("omx" was deprecated).

Examples

## Not run: 
CoTiMAInitFit_D_BO$activeDirectory <- "/Users/tmp/" # adapt!
CoTiMAPower_D_BO <- ctmaPower(ctmaInitFit=CoTiMAInitFit_D_BO,
                              statisticalPower = c(.50, .80, .95),
                              finishsamples = 10000)
summary(CoTiMAPower_D_BO)

## End(Not run)


[Package CoTiMA version 0.4.0 Index]