Description Usage Arguments Value Author(s) References See Also Examples
Derives power in a two arm clinical trial under a group sequential design. Allows for arbitrary number of interim analyses, arbitrary specification of arm-0/arm-1 time to event distributions (via survival or hazard), arm-0/arm-1 censoring distribution, provisions for two types of continuous time non-compliance according to arm-0/arm-1 rate followed by switch to new hazard rate. Allows for analyses using (I) weighted log-rank statistic, with weighting function (a) a member of the Flemming-Harrington G-Rho class, or (b) a stopped version thereof, or (c) the ramp-plateau deterministic weights, or (II) the integrated survival distance (currently under method=="S" without futility only). Stopping boundaries are computed via the Lan-Demets method, Haybittle method, or converted from the stochastic curtailment procedure. The Lan-Demets boundaries can be constructed usign either O'Brien-Flemming, Pocock or Wang-Tsiatis power alpha-spending. The C kernel is readily extensible, and further options will become available in the near future.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | PwrGSD(EfficacyBoundary = LanDemets(alpha = 0.05, spending = ObrienFleming),
FutilityBoundary = LanDemets(alpha = 0.1, spending = ObrienFleming),
NonBindingFutility = TRUE, sided = c("2>", "2<", "1>", "1<"),
method = c("S", "A"), accru, accrat, tlook,
tcut0 = NULL, h0 = NULL, s0 = NULL, tcut1 = NULL,
rhaz = NULL, h1 = NULL, s1 = NULL, tcutc0 = NULL, hc0 = NULL,
sc0 = NULL, tcutc1 = NULL, hc1 = NULL, sc1 = NULL, tcutd0A = NULL,
hd0A = NULL, sd0A = NULL, tcutd0B = NULL, hd0B = NULL, sd0B = NULL,
tcutd1A = NULL, hd1A = NULL, sd1A = NULL, tcutd1B = NULL,
hd1B = NULL, sd1B = NULL, tcutx0A = NULL, hx0A = NULL, sx0A = NULL,
tcutx0B = NULL, hx0B = NULL, sx0B = NULL, tcutx1A = NULL,
hx1A = NULL, sx1A = NULL, tcutx1B = NULL, hx1B = NULL, sx1B = NULL,
noncompliance = c("none", "crossover", "mixed", "user"),
gradual = FALSE, WtFun = c("FH", "SFH", "Ramp"), ppar = cbind(c(0, 0)),
Spend.Info = c("Variance", "Events", "Hybrid(k)", "Calendar"), RR.Futility = NULL,
qProp.one.or.Q = c("one", "Q"), Nsim = NULL, detail = FALSE, StatType = c("WLR",
"ISD"))
|
EfficacyBoundary |
This specifies the method used to construct the efficacy boundary. The available choices are: (i) (ii) (iii) (iv) User supplied boundary points in the form |
FutilityBoundary |
This specifies the method used to construct the futility boundary. The available choices are: (i) (ii) (iii) (iv) User supplied boundary points in the form |
NonBindingFutility |
When using a futility boundary and this is set to 'TRUE', the efficacy boundary will be constructed in the absence of the futility boundary, and then the futility boundary will be constructed given the resulting efficacy boundary. This results in a more conservative efficacy boundary with true type I error less than the nominal level. This is recommended due to the fact that futility crossings are viewed by DSMB's with much less gravity than an efficacy crossing and as such, the consensus is that efficacy bounds should not be discounted towards the null hypothesis because of paths which cross a futility boundary. Default value is 'TRUE'. |
sided |
Set to “2>” (quoted) for two sided tests of the null hypothesis when a positive drift corresponds to
efficacy. Set to “2<” (quoted) for two sided tests of the null hypothesis when a negative drift corresponds to
efficacy. Set to “1>” or “1<” for one sided tests of H0 when efficacy corresponds to a positive or negative drift,
respectively. If |
method |
Determines how to calculate the power. Set to “A” (Asymptotic method, the default) or “S” (Simulation method) |
accru |
The upper endpoint of the accrual period beginning with time 0. |
accrat |
The rate of accrual per unit of time. |
tlook |
The times of planned interim analyses. |
tcut0 |
Left hand endpoints for intervals upon which the arm-0 specific mortality is constant. The last given component is the left hand endpoint of the interval having right hand endpoint infinity. |
h0 |
A vector of the same length as |
s0 |
Alternatively, the arm-0 mortality distribution can be supplied via this argument, in terms of of the corresponding
survival function values at the times given in the vector |
tcut1 |
Left hand endpoints for intervals upon which the arm-1 specific mortality is constant. The last given component is the left hand endpoint of the interval having right hand endpoint infinity. |
rhaz |
A vector of piecewise constant arm-1 versus arm-0 mortality rate ratios. If |
h1 |
Alternatively, the arm-1 mortality distribution can be supplied via this argument by specifying the piecewise constant arm-1 mortality rate. See the comments above. |
s1 |
Alternatively, the arm-1 mortality distribution can be supplied via this argument, in terms of of the corresponding
survival function values at the times given in the vector |
tcutc0 |
Left hand endpoints for intervals upon which the arm-0 specific censoring distribution hazard function is constant. The last given component is the left hand endpoint of the interval having right hand endpoint infinity. |
hc0 |
A vector of the same length as |
sc0 |
Alternatively, the arm-0 censoring distribution can be supplied via this argument, in terms of of the corresponding
survival function values at the times given in the vector |
tcutc1 |
Left hand endpoints for intervals upon which the arm-1 specific censoring distribution hazard function is constant. The last given component is the left hand endpoint of the interval having right hand endpoint infinity. |
hc1 |
A vector of the same length as |
sc1 |
Alternatively, the arm-1 censoring distribution can be supplied via this argument, in terms of of the
corresponding survival function values at the times given in the vector |
noncompliance |
(i) Seting |
tcutd0A |
Left hand endpoints for intervals upon which the arm-0 specific cause-A delay distribution hazard
function is constant. The last given component is the left hand endpoint of the interval having right hand endpoint
infinity. Required only when |
hd0A |
A vector of the same length as |
sd0A |
When required, the arm-0 cause-A-delay distribution is alternately specified via a survival function. A
vector of the same length as |
tcutd0B |
Left hand endpoints for intervals upon which the arm-0 specific cause-B delay distribution hazard
function is constant. The last given component is the left hand endpoint of the interval having right hand endpoint
infinity. Always required when |
hd0B |
A vector of the same length as |
sd0B |
When required, the arm-0 cause-B-delay distribution is alternately specified via a
survival function. A vector of the same length as |
tcutd1A |
Left hand endpoints for intervals upon which the arm-1 specific cause-A delay distribution hazard
function is constant. The last given component is the left hand endpoint of the interval having right hand endpoint
infinity. Required only when |
hd1A |
A vector of the same length as |
sd1A |
When required, the arm-1 cause-A-delay distribution is alternately specified via a survival function. A
vector of the same length as |
tcutd1B |
Left hand endpoints for intervals upon which the arm-1 specific cause-B delay distribution hazard
function is constant. The last given component is the left hand endpoint of the interval having right hand endpoint
infinity. Always required when |
hd1B |
A vector of the same length as |
sd1B |
When required, the arm-1 cause-A-delay distribution is alternately specified via a survival function. A
vector of the same length as |
tcutx0A |
Left hand endpoints for intervals upon which the arm-0 specific post-cause-A-delay-mortality rate is
constant. The last given component is the left hand endpoint of the interval having right hand endpoint infinity. Required
only when |
hx0A |
A vector of the same length as |
sx0A |
When required, the arm-0 post-cause-A-delay mortality distribution is alternately specified via a
survival function. A vector of the same length as |
tcutx0B |
Left hand endpoints for intervals upon which the arm-0 specific post-cause-B-delay-mortality rate is
constant. The last given component is the left hand endpoint of the interval having right hand endpoint infinity. Always
required when |
hx0B |
A vector of the same length as |
sx0B |
When required, the arm-0 post-cause-B-delay mortality distribution is alternately specified via a
survival function. A vector of the same length as |
tcutx1A |
Left hand endpoints for intervals upon which the arm-1 specific post-cause-A-delay-mortality rate is
constant. The last given component is the left hand endpoint of the interval having right hand endpoint infinity. Required
only when |
hx1A |
A vector of the same length as |
sx1A |
When required, the arm-1 post-cause-A-delay mortality distribution is alternately specified via a
survival function. A vector of the same length as |
tcutx1B |
Left hand endpoints for intervals upon which the arm-1 specific post-cause-B-delay-mortality rate is
constant. The last given component is the left hand endpoint of the interval having right hand endpoint infinity. Always
required when |
hx1B |
A vector of the same length as |
sx1B |
When required, the arm-1 post-cause-B-delay mortality distribution is alternately specified via a
survival function. A vector of the same length as |
gradual |
Should the conversion to post-noncompliance mortality be gradual. Under the default behavior,
|
WtFun |
Specifies the name of a weighting function (of time) for assigning relative weights to events according to the
times at which they occur. The default, “FH”, a two parameter weight function, specifies the
‘Fleming-Harrington’ |
ppar |
A vector containing all the weight function parameters, in the order determined by that of “WtFun”. For
example, if |
RR.Futility |
The relative risk corresponding to the alternative alternative hypothesis that is required in the
construction of the futility boundary. Required if |
Spend.Info |
When the test statistic is something other than the unweighted log-rank statistic, the variance
information, i.e. the ratio of variance at interim analysis to variance at the end of trial, is something other than the
ratio of events at interim analysis to the events at trial end. The problem is that in practice one doesn't necessarily
have a good idea what the end of trial variance should be. In this case the user may wish to spend the type I and type II
error probabilities according to a different time scale. Possible choices are “Variance”, (default), which just uses
the variance ratio scale, “Events”, which uses the events ratio scale, “Hybrid(k)”, which makes a linear
transition from the “Variance” scale to the “Events” scale beginning with analysis number |
qProp.one.or.Q |
If a futility boundary is specified, what assumption should be made about the drift function (the mean
value of the weighted log-rank statistic at analysis |
Nsim |
If you specify |
detail |
If you specify |
StatType |
If you specify |
Returns a value of class PwrGSD
which has components listed below. Note that the print method will display a
summary table of estimated powers and type I errors as a nstat
by 2 matrix. The summary method returns the same
object invisibly, but after computing the summary table mentioned above, and it is included in the returned value as a
commponent TBL
. See examples below.
dPower |
A |
dErrorI |
A |
detail |
A list with components equal to the arguments of the C-call, which correspond in a natural way to the
arguments specified in the R call, along with the computed results in |
call |
the call |
Grant Izmirlian izmirlian@nih.gov
Gu, M.-G. and Lai, T.-L. “Determination of power and sample size in the design of clinical trials with failure-time endpoints and interim analyses.” Controlled Clinical Trials 20 (5): 423-438. 1999
Izmirlian, G. “The PwrGSD package.” NCI Div. of Cancer Prevention Technical Report. 2004
Jennison, C. and Turnbull, B.W. (1999) Group Sequential Methods: Applications to Clinical Trials Chapman & Hall/Crc, Boca Raton FL
Proschan, M.A., Lan, K.K.G., Wittes, J.T. (2006), corr 2nd printing (2008) Statistical Monitoring of Clinical Trials A Unified Approach Springer Verlag, New York
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | library(PwrGSD)
test.example <-
PwrGSD(EfficacyBoundary = LanDemets(alpha = 0.05, spending = ObrienFleming),
FutilityBoundary = LanDemets(alpha = 0.1, spending = ObrienFleming),
RR.Futility = 0.82, sided="1<",method="A",accru =7.73, accrat =9818.65,
tlook =c(7.14, 8.14, 9.14, 10.14, 10.64, 11.15, 12.14, 13.14,
14.14, 15.14, 16.14, 17.14, 18.14, 19.14, 20.14),
tcut0 =0:19, h0 =c(rep(3.73e-04, 2), rep(7.45e-04, 3),
rep(1.49e-03, 15)),
tcut1 =0:19, rhaz =c(1, 0.9125, 0.8688, 0.7814, 0.6941,
0.6943, 0.6072, 0.5202, 0.4332, 0.6520,
0.6524, 0.6527, 0.6530, 0.6534, 0.6537,
0.6541, 0.6544, 0.6547, 0.6551, 0.6554),
tcutc0 =0:19, hc0 =c(rep(1.05e-02, 2), rep(2.09e-02, 3),
rep(4.19e-02, 15)),
tcutc1 =0:19, hc1 =c(rep(1.05e-02, 2), rep(2.09e-02, 3),
rep(4.19e-02, 15)),
tcutd0B =c(0, 13), hd0B =c(0.04777, 0),
tcutd1B =0:6, hd1B =c(0.1109, 0.1381, 0.1485, 0.1637, 0.2446,
0.2497, 0),
noncompliance =crossover, gradual =TRUE,
WtFun =c("FH", "SFH", "Ramp"),
ppar =c(0, 1, 0, 1, 10, 10))
|
Loading required package: survival
PwrGSD 2.3.1
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