crr.fit caused by extracting column when input data set is a tibble (#1)QHScrnomo::prostate.dat) instead of using the data() functionrms is now the only package that QHScrnomo “Depends” on (i.e., it will be loaded when this package is loaded)cmprsk and Hmisc have been moved to the “Imports” field and are accessed internally with the pkg::func format. Therefore, users should not expect these packages to load with QHScrnomo (though they are required to be installed).sas.cmprsk to print the base failure probability (1 - exp(-cumsum(f$bfitj)) when the time argument is used instead of the survival probability (exp(-cumsum(f$bfitj))pred.crr function from the package. This function was not previously exported or used, and was highly duplicative of predict.cmprsk. Nevertheless, it is no longer in the package.addOffset4ModelFrame, nomo2.crr, pred2.crr, pred3.crr, predictDesign)failcode in pred.ci to failcode=1 to match cmprsk::crr and QHScrnomo::crr.fittime in tenf.crr and predict.crr to time=NULL; also set default arguments for g, cuts, xlab, ylab arguments in groupcitrace argument to tenf.crr to optionally trace the process in the console. It still does it by default, but previously it always traced it with no option to turn it off.groupci, the ci argument allows the user to control whether we work on the scale of survival or failure (default) probabilities. When the argument was set to FALSE, this would apply a 1-value operation to both the within-group cumulative incidence estimate (to convert to survival) and the group-level mean (of x). However, x is supposed to be an arbitrary continuous variable that we can assess calibration for, not necessarily a probability. Therefore, the change made in this version is to only apply the 1-value transformation to the within-group cumulative incidence and not the group level mean for x.
x, simply pass 1-x into the function call.a and b arguments (for the intercept and slope, respectively), as well as ab, xlim, and ylim arguments to adjust the graph accordingly.predict.cmprsk, sas.cmprsk, pred.ci, tenf.crr, groupci, nomogram.crrtestthatoldUnclass utility (internal) function. It’s definition was function(x) unclass(x), so we just use unclass(x) instead.groupci, the user is now able to supply xlab = "" as an argument. Also removed the usage of single in the function definition in favor of double as the former is only to be used in the context of .C/.Fortran (per documentation), which is not the case here.nomogram.crr, changed some arguments:
NULL default for failtime to make it more clear that this is a required argumentnomogram.crr and nomogram.mk6. Moved short utility functions to be housed in R/nomogram.R directly (nomo2.crr, is.category, getOldDesign, Design.levels, value.chk, axisf)
R/ for Getlim, predictDesign (contains addOffset4ModelFrame), VarcovAdding historical change-tracking here that was included in the previous version’s NEWS file (2.2.0) (in reverse order), but in a Markdown-friendly format: