One-Stop-shop Forward point and confidence-interval estimation of a monotone response (y) as a function of dose (x), using centered-isotonic-regression (CIR, default) or isotonic regression. Input format is rather flexible.
This function calls cirPAVA, oldPAVA, iterCIR (speculatively), or a user-written function, for the point estimate, then isotInterval for the confidence interval. Vector input is allowed, but the preferred input format is a doseResponse object.
An analogous function for dose-finding (inverse estimation) is quickInverse.
quickIsotone(
y,
x = NULL,
wt = NULL,
outx = NULL,
dec = FALSE,
estfun = cirPAVA,
intfun = morrisCI,
conf = 0.9,
adaptiveShrink = FALSE,
parabola = FALSE,
...
)can be either of the following: y values (response rates), a 2-column matrix with positive/negative response counts by dose, a DRtrace object or a doseResponse object.
dose levels (if not included in y). Note that the PAV algorithm doesn't really use them.
weights (if not included in y).
vector of x values for which predictions will be made. If NULL (default), this will be set to the set of unique values in the x argument (or equivalently in y$x).
logical, is the true function assumed to be monotone decreasing rather than increasing? Default FALSE.
the function to be used for point estimation. Default cirPAVA.
the function to be used for interval estimation. Default wilsonCI (see help on that function for additional options).
numeric, the interval's confidence level as a fraction in (0,1). Default 0.9.
logical, should the y-values be pre-shrunk towards an experiment's target? Recommended if data were obtained via an adaptive dose-finding design. If TRUE, then must also provide a target argument that will be passed via ....
logical, should interpolated interval boundaries between observations be parabolically curved outwards to allow for more uncertainty? Default FALSE
arguments passed on to other functions (constructor, point estimate and interval estimate).
A data frame with 4 variables:
x either the input x values, or outx of specified;
y The point estimates of x
lowerPPconf,upperPPconf the interval-boundary estimates for a 'PP'=100*conf confidence interval
# NOT RUN {
# Interesting run (#664) from a simulated up-and-down ensemble:
# (x will be auto-generated as dose levels 1:5)
dat=doseResponse(y=c(1/7,1/8,1/2,1/4,4/17),wt=c(7,24,20,12,17))
# CIR, using the default 'quick' function that also provides CIs (default 90%).
quick1=quickIsotone(dat)
quick1
# Use 'estfun' argument to operate the same function with old PAVA as the estimator
quick0=quickIsotone(dat,estfun=oldPAVA)
quick0
### Showing the data and the fits
par(mar=c(3,3,1,1),mgp=c(2,.5,0),tcl=-0.25)
plot(dat,ylim=c(0.05,0.55),refsize=1,las=1) # uses plot.doseResponse()
# The IR fit: a straightforward interpolation
lines(quick0$y,lty=2)
# With CIR, 'quickIsotone' cannot show us the true underlying interpolation;
# it only provides the estimates at requested points. Interpolation should be done between
# shrinkage points, not the original design points. So we must call the full 'cirPAVA' function:
slow1=cirPAVA(dat,full=TRUE)
# Now, compare these 3 (the first one is wrong, b/c it interpolates from design points):
midpts=1:4+0.5
approx(1:5,quick1$y,xout=midpts)$y
quickIsotone(dat,outx=midpts) # instead, you can just call 'quickIsotone' and specify 'outx'
approx(slow1$shrinkage$x,slow1$shrinkage$y,xout=midpts)$y # Or use 'cirPAVA'
# Ok... finally plotting the CIR curve
# Both flat intervals are shrunk, because neither are at y=0 or y=1
lines(slow1$shrinkage$x,slow1$shrinkage$y)
# Last but not least, here's the true response function
lines(seq(1,5,0.1),pweibull(seq(1,5,0.1),shape=1.1615,scale=8.4839),col=2)
legend('topleft',pch=c(NA,'X',NA,NA),lty=c(1,NA,2,1),col=c(2,1,1,1),
legend=c('True Curve','Observations','IR','CIR'),bty='n')
# }
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