SimSolve | R Documentation |
This function provides a stochastic optimization approach to solving
specific quantities in simulation experiments (e.g., solving for a specific
sample size to meet a target power rate) using the
Probablistic Bisection Algorithm with Bolstering and Interpolations
(ProBABLI; Chalmers, in review). The structure follows the
steps outlined in runSimulation
, however portions of
the design
input are taken as variables to be estimated rather than
fixed, and the constant b
is required in order to
solve the root equation f(x) - b = 0
.
SimSolve(
design,
interval,
b,
generate,
analyse,
summarise,
replications = list(burnin = 15L, burnin.reps = 100L, max.reps = 500L, increase.by =
10L),
integer = TRUE,
formula = y ~ poly(x, 2),
family = "binomial",
parallel = FALSE,
cl = NULL,
save = TRUE,
ncores = parallel::detectCores() - 1L,
type = ifelse(.Platform$OS.type == "windows", "PSOCK", "FORK"),
maxiter = 100L,
verbose = TRUE,
control = list(),
...
)
## S3 method for class 'SimSolve'
summary(object, tab.only = FALSE, reps.cutoff = 300, ...)
## S3 method for class 'SimSolve'
plot(x, y, ...)
design |
a |
interval |
a vector of length two, or matrix with |
b |
a single constant used to solve the root equation |
generate |
generate function. See |
analyse |
analysis function. See |
summarise |
summary function that returns a single number corresponding
to a function evaluation |
replications |
a named list or vector indicating the number of replication to
use for each design condition per PBA iteration. By default the input is a
Vector inputs can specify the exact replications for each iterations. As a general rule, early iterations should be relatively low for initial searches to avoid unnecessary computations for locating the approximate root, though the number of replications should gradually increase to reduce the sampling variability as the PBA approaches the root. |
integer |
logical; should the values of the root be considered integer
or numeric? If |
formula |
regression formula to use when |
family |
Note that if individual results from the |
parallel |
for parallel computing for slower simulation experiments
(see |
cl |
see |
save |
logical; store temporary file in case of crashes. If detected
in the working directory will automatically be loaded to resume (see
|
ncores |
see |
type |
type of cluster object to define. If |
maxiter |
the maximum number of iterations (default 100) |
verbose |
logical; print information to the console? |
control |
a
|
... |
additional arguments to be pasted to |
object |
object of class |
tab.only |
logical; print only the (reduce) table of estimates? |
reps.cutoff |
integer indicating the rows to omit from output if the number of replications do no reach this value |
x |
object of class |
y |
design row to plot. If omitted defaults to 1 |
Optimization is performed using the probabilistic bisection algorithm
(PBA
) to find the associated root given the noisy simulation
objective function evaluations. Information is also collected throughout
the iterations in order to make more aggressive predictions about the
associated root via interpolation and extrapolation.
the filled-in design
object containing the associated lower and upper interval
estimates from the stochastic optimization
Phil Chalmers rphilip.chalmers@gmail.com
Chalmers, R. P., & Adkins, M. C. (2020). Writing Effective and Reliable Monte Carlo Simulations
with the SimDesign Package. The Quantitative Methods for Psychology, 16
(4), 248-280.
\Sexpr[results=rd]{tools:::Rd_expr_doi("10.20982/tqmp.16.4.p248")}
## Not run:
# TASK: Find specific sample size in each group for independent t-test
# corresponding to a power rate of .8
#
# For ease of the setup, assume the groups are the same size, and the mean
# difference corresponds to Cohen's d values of .2, .5, and .8
# This example can be solved numerically using the pwr package (see below),
# though the following simulation setup is far more general and can be
# used for any generate-analyse combination of interest
# SimFunctions(SimSolve=TRUE)
#### Step 1 --- Define your conditions under study and create design data.frame.
#### However, use NA placeholder for sample size as it must be solved,
#### and add desired power rate to object
Design <- createDesign(N = NA,
d = c(.2, .5, .8),
sig.level = .05)
Design # solve for NA's
#~~~~~~~~~~~~~~~~~~~~~~~~
#### Step 2 --- Define generate, analyse, and summarise functions
Generate <- function(condition, fixed_objects = NULL) {
Attach(condition)
group1 <- rnorm(N)
group2 <- rnorm(N, mean=d)
dat <- data.frame(group = gl(2, N, labels=c('G1', 'G2')),
DV = c(group1, group2))
dat
}
Analyse <- function(condition, dat, fixed_objects = NULL) {
p <- t.test(DV ~ group, dat, var.equal=TRUE)$p.value
p
}
Summarise <- function(condition, results, fixed_objects = NULL) {
# Must return a single number corresponding to f(x) in the
# root equation f(x) = b
ret <- EDR(results, alpha = condition$sig.level)
ret
}
#~~~~~~~~~~~~~~~~~~~~~~~~
#### Step 3 --- Optimize N over the rows in design
# Initial search between N = [10,500] for each row using the default
# integer solver (integer = TRUE)
# In this example, b = target power
solved <- SimSolve(design=Design, b=.8, interval=c(10, 500),
generate=Generate, analyse=Analyse,
summarise=Summarise)
solved
summary(solved)
plot(solved, 1)
plot(solved, 2)
plot(solved, 3)
# also can plot median history and estimate precision
plot(solved, 1, type = 'history')
plot(solved, 1, type = 'density')
plot(solved, 1, type = 'iterations')
# verify with true power from pwr package
library(pwr)
pwr.t.test(d=.2, power = .8, sig.level = .05)
pwr.t.test(d=.5, power = .8, sig.level = .05)
pwr.t.test(d=.8, power = .8, sig.level = .05)
# use estimated N results to see how close power was
N <- solved$N
pwr.t.test(d=.2, n=N[1], sig.level = .05)
pwr.t.test(d=.5, n=N[2], sig.level = .05)
pwr.t.test(d=.8, n=N[3], sig.level = .05)
# with rounding
N <- ceiling(solved$N)
pwr.t.test(d=.2, n=N[1], sig.level = .05)
pwr.t.test(d=.5, n=N[2], sig.level = .05)
pwr.t.test(d=.8, n=N[3], sig.level = .05)
# failing analytic formula, confirm results with more precise
# simulation via runSimulation()
csolved <- solved
csolved$N <- ceiling(solved$N)
confirm <- runSimulation(design=csolved, replications=10000, parallel=TRUE,
generate=Generate, analyse=Analyse,
summarise=Summarise)
confirm
############
# Similar setup as above, however goal is now to solve d given sample
# size and power inputs (inputs for root no longer required to be an integer)
Design <- createDesign(N = c(100, 50, 25),
d = NA,
sig.level = .05)
Design # solve for NA's
#~~~~~~~~~~~~~~~~~~~~~~~~
#### Step 2 --- Define generate, analyse, and summarise functions (same as above)
#~~~~~~~~~~~~~~~~~~~~~~~~
#### Step 3 --- Optimize d over the rows in design
# search between d = [.1, 2] for each row
# In this example, b = target power
# note that integer = FALSE to allow smooth updates of d
solved <- SimSolve(design=Design, b = .8, interval=c(.1, 2),
generate=Generate, analyse=Analyse,
summarise=Summarise, integer=FALSE)
solved
summary(solved)
plot(solved, 1)
plot(solved, 2)
plot(solved, 3)
# plot median history and estimate precision
plot(solved, 1, type = 'history')
plot(solved, 1, type = 'density')
plot(solved, 1, type = 'iterations')
# verify with true power from pwr package
library(pwr)
pwr.t.test(n=100, power = .8, sig.level = .05)
pwr.t.test(n=50, power = .8, sig.level = .05)
pwr.t.test(n=25, power = .8, sig.level = .05)
# use estimated d results to see how close power was
pwr.t.test(n=100, d = solved$d[1], sig.level = .05)
pwr.t.test(n=50, d = solved$d[2], sig.level = .05)
pwr.t.test(n=25, d = solved$d[3], sig.level = .05)
# failing analytic formula, confirm results with more precise
# simulation via runSimulation()
confirm <- runSimulation(design=solved, replications=10000, parallel=TRUE,
generate=Generate, analyse=Analyse,
summarise=Summarise)
confirm
## End(Not run)
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