This function evaluates, the performance metrics for fitting dose-response models (using asymptotic approximations or simulations). Note that some metrics are available via the print method and others only via the summary method applied to planMod objects. The implemented metrics are
Root of the mean-squared error to estimate the placebo-adjusted
dose-response averaged over the used dose-levels, i.e. a rather discrete set
(dRMSE). Available via the print method of planMod objects.
Root of the mean-squared error to estimate the placebo-adjusted
dose-response (cRMSE) averaged over fine (almost continuous) grid at
101 equally spaced values between placebo and the maximum dose. NOTE:
Available via the summary method applied to planMod objects.
Ratio of
the placebo-adjusted mean-squared error (at the observed doses) of
model-based vs ANOVA approach (Eff-vs-ANOVA). This can be interpreted
on the sample size scale. NOTE: Available via the summary method applied to
planMod objects.
Power that the (unadjusted) one-sided 1-alpha
confidence interval comparing the dose with maximum effect vs placebo is
larger than tau. By default alpha = 0.025 and tau = 0
(Pow(maxDose)). Available via the print method of planMod objects.
Probability that the EDp estimate is within the true [EDpLB, EDpUB]
(by default p=0.5, pLB=0.25 and pUB=0.75). This metric
gives an idea on the ability to characterize the increasing part of the
dose-response curve (P(EDp)). Available via the print method of
planMod objects.
Length of the quantile range for a target dose (TD
or EDp). This is calculated by taking the difference of the dUB and dLB
quantile of the empirical distribution of the dose estimates.
(lengthTDCI and lengthEDpCI). It is NOT calculated by
calculating confidence interval lengths in each simulated data-set and
taking the mean. NOTE: Available via the summary method of planMod objects.
planMod(
model,
altModels,
n,
sigma,
S,
doses,
asyApprox = TRUE,
simulation = FALSE,
alpha = 0.025,
tau = 0,
p = 0.5,
pLB = 0.25,
pUB = 0.75,
nSim = 100,
cores = 1,
showSimProgress = TRUE,
bnds,
addArgs = NULL
)# S3 method for planMod
summary(
object,
digits = 3,
len = 101,
Delta = NULL,
p = NULL,
dLB = 0.05,
dUB = 0.95,
...
)
# S3 method for planMod
plot(
x,
type = c("dose-response", "ED", "TD"),
p,
Delta,
placAdj = FALSE,
xlab = "Dose",
ylab = "",
...
)
Character vector determining the dose-response model(s) to be used for fitting the data. When more than one dose-response model is provided the best fitting model is chosen using the AIC. Built-in models are "linlog", "linear", "quadratic", "emax", "exponential", "sigEmax", "betaMod" and "logistic" (see drmodels).
An object of class Mods, defining the true mean vectors under which operating characteristics should be calculated.
Either a vector n and sigma or S need to be specified. When n and
sigma are specified it is assumed computations are made for a normal homoscedastic ANOVA model with group
sample sizes given by n and residual standard deviation sigma, i.e. the covariance matrix used for
the estimates is thus sigma^2*diag(1/n) and the degrees of freedom are calculated as
sum(n)-nrow(contMat). When a single number is specified for n it is assumed this is the sample size
per group and balanced allocations are used.
When S is specified this will be used as covariance matrix for the estimates.
Doses to use
Logicals determining, whether asymptotic approximations or simulations should be calculated. If multiple models are specified in model asymptotic approximations are not available.
Significance level for the one-sided confidence interval for model-based contrast of best dose vs placebo. Tau is the threshold to compare the confidence interval limit to. CI(MaxDCont) gives the percentage that the bound of the confidence interval was larger than tau.
p determines the type of EDp to estimate. pLB and pUB define the bounds for the EDp estimate. The performance metric Pr(Id-ED) gives the percentage that the estimated EDp was within the true EDpLB and EDpUB.
Number of simulations
Number of cores to use for simulations. By default 1 cores is used, note that cores > 1 will have no effect Windows, as the mclapply function is used internally.
In case of simulations show the progress using a progress-bar.
Bounds for non-linear parameters. This needs to be a list with list entries corresponding to the selected
bounds. The names of the list entries need to correspond to the model names. The defBnds function
provides the default selection.
See the corresponding argument in function fitMod. This argument is directly passed to
fitMod.
object: A planMod object. digits: Digits in summary output
Number of equally spaced points to determine the mean-squared error on a grid (cRMSE).
Additional arguments determining what dose estimate to plot, when type = "ED" or type = "TD"
Which quantiles to use for calculation of lengthTDCI and lengthEDpCI. By default dLB =
0.05 and dUB = 0.95, so that this corresponds to a 90% interval.
Additional arguments (currently ignored)
An object of class planMod
Type of plot to produce
When type = "dose-response", this determines whether dose-response estimates are shown on placebo-adjusted or original scale
Labels for the plot (ylab only applies for type = "dose-response")
Bjoern Bornkamp
A plot method exists to summarize dose-response and dose estimations graphically.
TBD
fitMod
if (FALSE) {
doses <- c(0,10,25,50,100,150)
fmodels <- Mods(linear = NULL, emax = 25,
logistic = c(50, 10.88111), exponential= 85,
betaMod=rbind(c(0.33,2.31),c(1.39,1.39)),
doses = doses, addArgs=list(scal = 200),
placEff = 0, maxEff = 0.4)
sigma <- 1
n <- rep(62, 6)*2
model <- "quadratic"
pObj <- planMod(model, fmodels, n, sigma, doses=doses,
simulation = TRUE,
alpha = 0.025, nSim = 200,
p = 0.5, pLB = 0.25, pUB = 0.75)
print(pObj)
## to get additional metrics (e.g. Eff-vs-ANOVA, cRMSE, lengthTDCI, ...)
summary(pObj, p = 0.5, Delta = 0.3)
plot(pObj)
plot(pObj, type = "TD", Delta=0.3)
plot(pObj, type = "ED", p = 0.5)
}
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