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casebase 0.9.0
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@sahirbhatnagar sahirbhatnagar released this 06 Jul 14:58
· 68 commits to master since this release
v0.9.0
2a695bd

This is a Major new release

Breaking changes

  • The output of absoluteRisk() now always contains the time variable in the first column, regardless of the length of time. This will break earlier code that depended on the previous behaviour.
  • Population time plots now use ggplot2::geom_ribbon() instead of ggplot2::geom_segment().
  • Population time functions now allow for more flexible plots with user defined arguments including sequentially adding base, case, and competing event series. These are now passed as a list to the *.params arguments. Several arguments are now deprecated.
  • Removed popTimeExposure class and the corresponding plot method. popTime() now returns an exposure attribute which contains the name of the exposure variable in the dataset. The plot method for objects of class popTime will use this exposure attribute to create exposure stratified population time plots.

New features

  • Major refactoring of absoluteRisk(). Trapezoidal rule to perform numerical integration for absolute risk estimation, providing significant speed up.
  • Users now have further control on the output of absoluteRisk() using the arguments type and addZero.
  • New plotting method for time-dependent hazard functions and hazard ratios. These include confidence intervals. See plot.singleEventCB(). The hazard function plot requires the visreg package to be installed.
  • New plotting method for cumulative incidence and survival curves. See plot.absRiskCB().
  • When time is unspecified, absoluteRisk() now computes the cumulative incidence at ntimes equidistant points between 0 and the max failure time.
  • absoluteRisk() can now compute the cumulative incidence for a "typical" covariate profile with newdata = "typical". "Typical" corresponds to the median for continuous variables and the mode for factors (each variable is summarised independently).
  • Added eprchd, brcancer, support and simdat datasets to the package.
  • Implemented riskRegression::predictRisk() method for singleEventCB objects.

Minor improvements and fixes

  • No longer importing the entire namespace of data.table and ggplot2.
  • Moved from make the docs to pkgdown for package website.
  • A warning is given when family="gbm" and nonlinear functions of time or interactions are specified.
  • Add singleEventCB class to object returned by fitSmoothHazard()
  • Add absRiskCB class to object returned by absoluteRisk()
  • Use glmnet::prepareX to convert factors into indicator variables
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