Merge branch 'main' into 74_pwcsurvos_smooth

NAMESPACE

@@ -22,7 +22,6 @@ export(ExpQuantOS)
 export(ExpSurvOS)
 export(ExpSurvPFS)
 export(PCWInversionMethod)
-export(PFSOSInteg)
 export(PWCsurvOS)
 export(PWCsurvPFS)
 export(WeibOSInteg)
@@ -62,7 +61,6 @@ export(integrateVector)
 export(logRankTest)
 export(log_p11)
 export(negLogLik)
-export(p11Integ)
 export(passedLogRank)
 export(piecewise_exponential)
 export(prepareData)

R/corPFSOS.R

@@ -1,3 +1,5 @@
+# survPFS ----
+
 #' PFS Survival Function for Different Transition Models
 #'
 #' @param transition (`TransitionParameters`)\cr
@@ -53,6 +55,8 @@ survPFS.PWCTransition <- function(transition, t) {
   )
 }
 
+# survOS ----
+
 #' OS Survival Function for Different Transition Models
 #'
 #' @param transition (`TransitionParameters`)\cr
@@ -113,6 +117,8 @@ survOS.PWCTransition <- function(transition, t) {
   )
 }
 
+# expval ----
+
 #' Helper Function for Computing E(PFS^2)
 #'
 #' @param x (`numeric`)\cr variable of integration.
@@ -145,28 +151,26 @@ expvalOSInteg <- function(x, transition) {
   x * survOS(transition = transition, t = x)
 }
 
+# p11 ----
+
 #' Helper Function for `log_p11()`
 #'
 #' @param x (`numeric`)\cr variable of integration.
 #' @param transition (`TransitionParameters`)\cr
 #'   see [exponential_transition()], [weibull_transition()] or [piecewise_exponential()] for details.
 #'
 #' @return Hazard rate at the specified time for the transition from progression to death.
-#' @export
-#'
-#' @examples
-#' transition <- exponential_transition(h01 = 1.2, h02 = 1.5, h12 = 1.6)
-#' p11Integ(2, transition)
+#' @keywords internal
 p11Integ <- function(x, transition) {
   haz(transition = transition, t = x, trans = 3)
 }
 
-#' Probability of Remaining in Progression Between Two Time Points for Different Transition Models.
+#' Probability of Remaining in Progression Between Two Time Points for Different Transition Models
 #'
 #' @param transition (`TransitionParameters`)\cr
 #'   see [exponential_transition()], [weibull_transition()] or [piecewise_exponential()] for details.
-#' @param s (`numeric`)\cr lower time point.
-#' @param t (`numeric`)\cr higher time point.
+#' @param s (`numeric`)\cr lower time points.
+#' @param t (`numeric`)\cr higher time points.
 #' @return This returns the natural logarithm of the probability of remaining in progression (state 1)
 #' between two time points, conditional on being in state 1 at the lower time point.
 #'
@@ -176,6 +180,11 @@ p11Integ <- function(x, transition) {
 #' transition <- exponential_transition(h01 = 1.2, h02 = 1.5, h12 = 1.6)
 #' log_p11(transition, 1, 3)
 log_p11 <- function(transition, s, t) {
+  assert_numeric(s, finite = TRUE, any.missing = FALSE, lower = 0)
+  assert_numeric(t, finite = TRUE, any.missing = FALSE, lower = 0)
+  assert_true(identical(length(s), length(t)))
+  assert_true(all(t > s))
+
   intval <- mapply(function(s, t) {
     stats::integrate(p11Integ,
       lower = s,
@@ -186,19 +195,19 @@ log_p11 <- function(transition, s, t) {
   -intval
 }
 
+# PFSOS ----
+
 #' Helper Function for `survPFSOS()`
 #'
 #' @param u (`numeric`)\cr variable of integration.
 #' @param t (`numeric`)\cr time at which the value of the PFS*OS survival function is to be computed.
 #' @param transition (`TransitionParameters`)\cr
 #'   see [exponential_transition()], [weibull_transition()] or [piecewise_exponential()] for details.
 #'
-#' @return Numeric result of the integrand used to calculate the PFS*OS survival function.
-#' @export
+#' @note Not all vectors `u` and `t` work here due to assertions in [log_p11()].
 #'
-#' @examples
-#' transition <- exponential_transition(h01 = 1.2, h02 = 1.5, h12 = 1.6)
-#' PFSOSInteg(1, 2, transition)
+#' @return Numeric result of the integrand used to calculate the PFS*OS survival function.
+#' @keywords internal
 PFSOSInteg <- function(u, t, transition) {
   exp(log_p11(transition, u, t / u) + log(survPFS(transition, u)) + log(haz(transition, u, 1)))
 }
@@ -222,6 +231,8 @@ survPFSOS <- function(t, transition) {
   })
 }
 
+# correlation ----
+
 #' Correlation of PFS and OS event times for Different Transition Models
 #'
 #' @param transition (`TransitionParameters`)\cr

R/estimateParams.R

@@ -11,7 +11,10 @@
 #' - id (`integer`): patient id.
 #' - from (`integer`): start event state.
 #' - to (`integer`): end event state.
-#' - trans (`integer`): transition (1, 2 or 3) identifier.
+#' - trans (`integer`): transition (1, 2 or 3) identifier
+#'   - `1`: Transition from state 0 (stable) to 1 (progression).
+#'   - `2`: Transition from state 0 (stable) to 2 (death).
+#'   - `3`: Transition from state 1 (progression) to 2 (death).
 #' - entry (`numeric`): time at which the patient begins to be at risk for the transition.
 #' - exit (`numeric`): time at which the patient ends to be at risk for the transition.
 #' - status (`logical`): event indicator for the transition.
@@ -92,6 +95,12 @@ negLogLik <- function(transition, data) {
 #' @param t (`numeric`)\cr time at which hazard is to be computed.
 #' @param trans (`integer`)\cr index specifying the transition type.
 #'
+#' @details
+#' The transition types are:
+#' - `1`: Transition from state 0 (stable) to 1 (progression).
+#' - `2`: Transition from state 0 (stable) to 2 (death).
+#' - `3`: Transition from state 1 (progression) to 2 (death).
+#'
 #' @return The hazard rate for the specified transition and time.
 #' @export
 #'

_pkgdown.yaml

@@ -110,8 +110,6 @@ reference:
       - expvalPFSInteg
       - expvalOSInteg
       - log_p11
-      - p11Integ
-      - PFSOSInteg
       - survPFS
       - survPFSOS
       - survOS