CRAN comments (#53)

Fixes final CRAN comments

Signed-off-by: niessl <64351230+niessl@users.noreply.github.com>
Co-authored-by: Alexandra Niessl <alexandra.niessl@uni-ulm.de>
Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>

Author: 3 people

DESCRIPTION

@@ -1,8 +1,7 @@
 Type: Package
 Package: simIDM
-Title: Simulating Clinical Trials with Endpoints Progression-Free Survival
-    and Overall Survival using an Illness-Death Model
-Version: 0.0.4.9000
+Title: Simulating Oncology Trials using an Illness-Death Model
+Version: 0.0.5
 Authors@R: c(
     person("Alexandra", "Erdmann", , "alexandra.erdmann@uni-ulm.de", role = c("aut", "cre")),
     person("Kaspar", "Rufibach", , "kaspar.rufibach@roche.com", role = "aut"),

NEWS.md

@@ -1,12 +1,12 @@
-# simIDM 0.0.4.9000
+# simIDM 0.0.5
 
-* First CRAN version of the package.
-* The package simulates illness-death models with constant, Weibull or piecewise constant transition hazards.
+- First CRAN version of the package.
+- The package simulates illness-death models with constant, Weibull or piecewise constant transition hazards.
 
 ### New Features
 
-* Exponentially, Weibull and piecewise exponentially distributed survival times.
-* Random censoring and event-driven censoring after a pre-specified number of PFS or OS events.
-* Arbitrary number of treatment arms and flexible randomization ratio.
-* Staggered study entry.
-* Derivation of PFS and OS survival functions from transition hazards.
+- Exponentially, Weibull and piecewise exponentially distributed survival times.
+- Random censoring and event-driven censoring after a pre-specified number of PFS or OS events.
+- Arbitrary number of treatment arms and flexible randomization ratio.
+- Staggered study entry.
+- Derivation of PFS and OS survival functions from transition hazards.

R/eventTracking.R

@@ -45,7 +45,7 @@ getTimePoint <- function(data, eventNum, typeEvent, byArm = FALSE) {
     dataTemp <- data[data$trt == trt, ]
     sortedTimes <- sort(dataTemp$time[dataTemp$event == 1])
     if (eventNum > length(sortedTimes)) {
-      cat("Less events occur till EOS than specified \n")
+      warning("Less events occur till EOS than specified \n")
     }
     timePoint <- sortedTimes[eventNum]
   })

R/getWaitTimeSum.R

@@ -42,10 +42,10 @@ getWaitTimeSum <- function(U, haz1, haz2, p1, p2, entry) {
       stime[i] <- res$root
       i <- i + 1
       if (res$root == 0) {
-        cat("Error uniroot: accuracy (tol=10^-16) is not enough.")
+        warning("uniroot: accuracy (tol=10^-16) is not enough.")
       }
     } else {
-      cat("Error uniroot: Values at interval endpoints (interval=c(0,10000)) are not of opposite signs. \n")
+      warning("uniroot: Values at interval endpoints (interval=c(0,10000)) are not of opposite signs. \n")
     }
   }
   stime