Merge branch 'cran'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: clinfun
 Title: Clinical Trial Design and Data Analysis Functions
-Version: 1.1.3.990
+Version: 1.1.5
 Depends: R (>= 3.0.0), graphics, stats
 Imports: mvtnorm
 Suggests: knitr, rmarkdown, survival

NEWS.md

@@ -1,3 +1,12 @@
+# clinfun 1.1.5 (10/19/2023)
+
+* clarified one-sided vs two-sided futility boundary for gsdesign functions
+
+# clinfun 1.1.4 (10/12/2023)
+
+* added check for n; since it is for stopping early at least two values should be given
+* addressed the warning in the example for calogrank; status had both death and transplant
+
 # clinfun 1.1.3 (07/11/2023)
 
 * fixed the bug in ph2simon/twostage.admissible when minimax is also optimal

R/toxbdry.R

@@ -113,6 +113,9 @@ bdrycross.prob <- function(n, r, ptox) {
 # P(cross bdry | low non-response rate) = cP0 -> response not promising -> 1-power
 # since size under null needs to be met priority choice should be "alt"
 futilbdry <- function(rLo, rHi, n, size=0.1, power=0.9, ngrid=3, niter=10, delta=0.5) {
+  # stop if length(n) is 1; check that values in n are increasing
+  if (length(n) == 1) stop("n should have at least two values to be able to stop early")
+  if (min(diff(n)) < 1) stop("n should be in increasing order")
   # setup toxbdry parameters
   pLo = 1-rHi
   pHi = 1-rLo
@@ -138,6 +141,9 @@ futilbdry <- function(rLo, rHi, n, size=0.1, power=0.9, ngrid=3, niter=10, delta
 
 # toxicity boundary
 toxbdry <- function(pLo, pHi, n, cP0=0.1, cP1=0.9, ngrid=6, niter=10, delta=0, priority=c("null","alt")) {
+# stop if length(n) is 1; check that values in n are increasing
+  if (length(n) == 1) stop("n should have at least two values to be able to stop early")
+  if (min(diff(n)) < 1) stop("n should be in increasing order")
 # decide whether to prioritize the type I (null) or the type II (alt) error.
   priority <- match.arg(priority)
   priorityNull= priority=="null"

man/calogrank.Rd

@@ -25,8 +25,9 @@
   pbc1 <- pbc
   pbc1$trt[pbc1$trt == -9] <- NA
   pbc1$copper[pbc1$copper == -9] <- NA
-  calogrank(pbc1$time, pbc1$status, pbc1$trt, pbc1[,c("copper")])
-  calogrank(pbc1$time, pbc1$status, pbc1$trt,
+  # only death (2) is considered; transplant(1) is censored
+  calogrank(pbc1$time, pbc1$status==2, pbc1$trt, pbc1[,c("copper")])
+  calogrank(pbc1$time, pbc1$status==2, pbc1$trt,
                                   pbc1[,c("protime", "copper")])}
 }
 \references{

man/clinfun-internal.Rd

@@ -1,8 +1,17 @@
 \name{clinfun-internal}
 \title{Internal clinfun functions}
-\alias{compareROC}
+\alias{compareROC.paired}
+\alias{compareROC.unpaired}
 \alias{exactNull}
+\alias{getBoundary}
+\alias{gsd.bdryconstant}
+\alias{gsd.drift.efficacy}
+\alias{gsd.drift.both}
 \alias{gsd.drift}
+\alias{mrcobj}
+\alias{smmrcobj}
+\alias{rocauc}
+\alias{smrocauc}
 \description{
  Internal functions used by the functions in the package.
 }

man/gsdesign.Rd

@@ -49,8 +49,10 @@ gsdesign.survival(ifrac, haz.ratio, r = 1, sig.level = 0.05,
 }
 \value{
   a list with ifrac, sig.level, power, alternative, delta.eb, delta.fb and:
-  \item{efbdry}{the critical value to use at the different looks.}
-  \item{futbdry}{the critical value to use at the different looks.}
+  \item{efbdry}{the critical value to use at the different looks. For
+  two-sided alternative the absolute test statistic should exceed this.}
+  \item{futbdry}{the critical value to use at the different looks. For
+  two-sided alternative the absolute test statistic should be below this.}
   \item{sample.size}{the sample size per arm for binomial/normal data.}
   \item{num.events}{the total number of failures which should be
     converted to number of subjects using censoring proportion.}  
@@ -59,11 +61,24 @@ gsdesign.survival(ifrac, haz.ratio, r = 1, sig.level = 0.05,
   The futility boundary is not returned when delta.fb is not specified
   i.e. stopping for futility is not requested.  The futility boundary is
   non-binding.  That is the significance level is not adjusted to account
-  for early stopping for utility.  This makes the test a bit conservative
+  for early stopping for futility.  This makes the test a bit conservative 
   in that the true size is less than the nominal level.
 
+  If the alternative is two-sided by default the futility boundary will
+  also be two-sided i.e. continuation region is wedge shaped. However,
+  if the goal is to show the superiority of the experimental treatment
+  then futility boundary should be one sided. This can be achieved by
+  deriving the boundaries for one-sided alternative and significance
+  level set at half of the value used for two sided alternative. See the
+  examples section for a representative design for which the trial
+  cannot be stopped at the first look for futility.
+
   The Casagrande-Pike-Smith type continuity correction is obtained using
-  the formula n*{1 + sqrt{1+4/{abs(pC-pE)*n}}}^2 where n is the
-  uncorrected sample size.
+  the formula \deqn{n*[1 + \sqrt{1+4/(|pC-pE|*n)}]^2} where n is
+  the uncorrected sample size.
+}
+\examples{
+  gsdesign.normal(1:4/4, 0.25, sig.level=0.05, alt="t", delta.fb=0.5)
+  gsdesign.normal(1:4/4, 0.25, sig.level=0.025, alt="o", delta.fb=0.5)
 }
 \keyword{design}