2281 lines
105 KiB
Plaintext
2281 lines
105 KiB
Plaintext
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\name{NEWS}
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\title{NEWS file for the survival package}
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\section{Changes in version 3.7-0}{
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\itemize{
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\item Add n.id element to the coxph object, for a call that uses the
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id argument
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\item Remove as.integer.Surv and as.numeric.Surv; essentially treat Surv as
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a matrix for this purpose. The as.numeric.Surv method never worked anyway, as
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it should have been as.double.Surv
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\item Run all tests and submit to CRAN
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}}
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\section{Changes in version 3.6-5}{
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\itemize{
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\item Update nearly all uses of partially matched arguments, e.g.,
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fit$coef to fit$coefficients. (MichaelChirico)
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\item Fix error in concordance for a coxph model with (time1, time2)
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data and timewt='S'. Add new test to tests/concordance3.R. Error
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pointed out by Shaunson26.
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\item Begin movement of many vignettes to the survivalVignettes
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package. See the "other vignettes" vignette stub for more
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information.
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\item Fix error in predict.coxph pointed out by Julianna
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Harwood. Add text to the help file to clarify prediction at per-subject
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vs a global time. Add new test file predsurv.R
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\item Add a data.frame option to summary.survfit and summary.survfitms;
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it causes the result to be in data frame form.
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}}
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\section{Changes in version 3.6-4}{
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\itemize{
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\item Oversight in final CRAN submission, change version number and
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resubmit
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}}
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\section{Changes in version 3.6-3}{
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\itemize{
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\item Fix small bug in residuals.survfit wrt labeling rows of the
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output. Update helpfile to describe the dimnames.
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\item Submit to CRAN
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}}
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\section{Changes in version 3.6-2}{
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\itemize{
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\item Change survfitaj.c to avert a spurious compiler warning which
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made the CRAN input unhappy
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}}
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\section{Changes in version 3.6-1}{
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\itemize{
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\item Major update to survfit routines. Infinitesimal jackknife (IJ)
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residuals are now primarily computed using the residuals() function
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post fit, de-emphasizing return of an influence component from the
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fit, with significant work to make the residuals function
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computationally efficient. New tests for many edge cases.
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\item Addition of a "methods" vignette to more fully document
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formulas and code, begining a move away from noweb documentation.
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\item Add test case for the 'extended KM', one where subjects change
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arms in mid-stream. (I'm not a fan, but some advocate it.) This
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uncovered some inconsistencies in the n.risk and n.censor values;
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the survival estimates themselves were correct. For a subject with data
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of (1, 5+), (5, 7), say, there is no "censor" at time 5; the prior code
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sometimes emited an unneeded output line for such rows.
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\item Add n.id to the survfit object= number of unique id values
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used in creating a curve; available when the survfit call contains
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an id argument. This is used as "n" in the default printout.
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Useful when a subject spans multiple rows.
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\item Add a new option to survfit. If \code{entry=TRUE} the output
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will contain \code{n.enter} = the number of entries at this time;
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new rows are added for each unique entry time. The default option
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of FALSE creates rows only at event/censor times; the historical behavior.
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\item Fix a bug in survfit.coxph. If the start.time option resulted
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in 0 subjects for a curve it didn't catch it properly.
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\item Update the US and Minnesota rate tables, adding years up to
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2020.
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\item Updates to the Aalen-Johansen, i.e., survfit when 'status' is
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a factor variable. 1. If case weights varied between rows in the
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same cluster, the infinitesimal jackknife could be wrong and hence
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the variance incorrect. 2. n.censor is now reported per state 3. new
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elements of n.transtions and count.
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}}
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\section{Changes in version 3.5-7}{
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\itemize{
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\item Improve the algorithm for score residuals from O(ndp) to
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O((n+d)p), where n= number of observations, d= number of events, p =
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number of covariates. For large data sets this can have a substantial
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impact. (Score residuals are used for robust variance.)
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\item Add short vignette on how we compute mulitstate Cox model
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curves.
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\item 13Aug23, check dependent CRAN packages (860) and submit
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to CRAN
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}}
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\section{Changes in version 3.5-6}{
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\itemize{
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\item Fix error in a (time1, time2) coxph model with both strata and
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tt() terms; pointed out by Pierre Joly. Add a new test case for
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this to the tests directory.
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\item Small update to coxph prompted by a user query: for a model
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with an offset, the mean offset is no longer subtracted from the
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linear.predictor component. This make it agree with predict.coxph.
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\item Add the brier function, along with tests and a new vignette.
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Update rttright and strengthen the tests.
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\item Update coxph.detail; the roder argument now applies to the x,
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y, and riskmat components.
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}}
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\section{Changes in version 3.5-5}{
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\itemize{
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\item Add the hoel data set, cancer in irradiated male mice, found
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in Kalbfleisch and Prentice. It is useful for illustrating
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competing risks.
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\item Update some S3 methods in NAMESPACE, and rename the
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internal terms.inner function to innerterms. Both were generating
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warnings with the latest CRAN check suite.
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\item Submit to CRAN
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}}
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\section{Changes in version 3.5-4}{
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\itemize{
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\item Update the help file for the finegray command. It was
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incorrect with respect to time-dependent covariates.
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\item Add model= as an option to survfit, and add a
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model.frame.survfit method. These are needed to call the
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survfit/pseudo pair inside another function.
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\item Small bug in survfit: if start.time was present, the 'type' element
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could be missing from the output object.
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\item Enhance the concordance command: one can now put multiple
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predictions on the right hand side of the equation; this will give
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the set of concordances and their variance-covariance matrix.
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\item Add a couple of overlooked S3 methods to the NAMESPACE
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}}
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\section{Changes in version 3.5-3}{
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\itemize{
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\item Fix final compiler warnings that affect CRAN
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\item Restore backwards compatability for ratetable() calls in a
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formula. The feature is used by the relsurv package.
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\item Add information on trust regions to the fail directory.
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}}
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\section{Changes in version 3.5-2}{
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\itemize{
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\item New release for CRAN; chase down some challenging (for me)
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C-code memory issues
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\item Clean up test case for drop.special
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}}
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\section{Changes in version 3.5-1}{
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\itemize{
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\item Minor edits to survreg (fit$coef to fit$coefficients) and
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summary.coxph (a model with only an offset)
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\item Fix error in fastkm.c (new routine, edge case, no one had
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found it yet.)
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\item Fix a few niggles in .c code, found by the new compiler chain
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\item Remove backwards compatability for ratetable() calls in a
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formula; this was changed in the main code many years ago.
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}}
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\section{Changes in version 3.5-0}{
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\itemize{
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\item Final check and updates for CRAN submission
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}}
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\section{Changes in version 3.4-2}{
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\itemize{
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\item For a multi-state coxph model, the default is now
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ties='breslow'. When there is a tied transition of the same type, A:B
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and A:B say, the Efron approx is justified and was correctly computed.
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However, ties of different types such as an A:B and A:C (competing risks)
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transition at the same time or A:B and C:D are effectively ignored
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by the code; and this would be very hard to change. Using Breslow
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rather than a partial Efron was felt to be more defensible.
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\item Add the survcondense function.
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\item Improve tmerge handling of a wide data set and add a test case
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for it. Add a caution to the vignette wrt using wide data sets.
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\item Improve the speed of concordance (request of Frank H). Update
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the vignette and add more tests.
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\item Fix bug in cox.zph: if there was any NA coefficient in the
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coxph fit, the residuals used for the plot would also be NA.
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\item Run all tests and submit to CRAN (2023-01-06)
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}}
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\section{Changes in version 3.4-1}{
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\itemize{
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\item Add newdata argument to basehaz, along with more documentation
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\item survfit.coxph would fail for the combination of newdata and a
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model with only an offset term, fixed
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\item Add a check to pseudo. The algorithm was not designed for a
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survfit curve from interval censored data, but still produced a
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result (assuredly an incorrect one). Interval censored curves now
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have type='interval' to help support this.
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\item Predict.coxph with reference='zero' and missing newdata
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incorrectly assumed it could simply return fit$residuals. Pointed
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out by David Collett.
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\item Change the prototype in a few .c routines, per a request from
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CRAN. (chinv.c for instance was using the old K&R style declaration,
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which shows how long ago it was written.)
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\item Check and submit to CRAN
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}}
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\section{Changes in version 3.4-0}{
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\itemize{
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\item Replace .[terms call in predict.coxph with drop.term();
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due to an error in [.term discovered by Jorge Menezes. Add
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dropterm.R to the test suite.
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\item Fix all errors in R CMD check, and submit to CRAN
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}}
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\section{Changes in version 3.3-2}{
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\itemize{
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\item Error in concordance(fit, newdata) if newdata had missing
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values: the derived x and y could be different lengths.
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\item Add test cases for the (rather difficult) case of predicted
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survival for multi-state coxph model that has shared hazards
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\item nsk(..., Boundary.knots=FALSE) was not being handled properly.
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\item Fix error in terms.inner; it failed for a function with no
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arguments. Pointed out by Daniel Sjberg and Duncan Murdoch.
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\item Remove Sint from C code.
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\item anova.coxph sometimes used P(>Chi) and somtimes Pr(>Chi) as a
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printout label, depending on the argument; the base packages all use
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"Pr". Changed this to be consistent.
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}}
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\section{Changes in version 3.3-1}{
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\itemize{
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\item Update the saved tests/Examples/survival-Ex.Rout.save file so
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as to remove timings, at the behest of CRAN. (Footnote 21 in the
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packages manual talks about this.)
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}}
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\section{Changes in version 3.3-0}{
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\itemize{
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\item Change any calls to Calloc or Free in the C code to R_Calloc
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and R_Free, at the request of R core.
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\item Fix an oversight in aareg: when coxph and survreg were
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converted from using +cluster() in a formula to cluster as an
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argument, that same change needed to be made in aareg. Pointed out
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by zdgager.
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\item The std of the cumulative hazard is now present, for select
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cases of a coxph model curve. More work remains to be done to
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return the std for all cases.
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\item Add a paragraph to the help page for survfit.Rd, pointing out
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that robust variance is now the default for interval censored data,
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and why.
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\item Add the median.survfit method
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\item Improve the examples in pseudo.Rd
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\item Fix error in survreg.distributions$gaussian$deviance. The
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deviance of an interval censored observation was NA due to a sign
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that was backwards, leading to log of a negative value. (Simple
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typo.)
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\item Error in predict.coxph: it would fail for a model that had two
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strata terms. Reported by Hanna Frick.
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\item Fix github issue 130. If newdata contained the strata
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information, and there was only one curve requested, survfit.coxph
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would return too many curves.
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}}
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\section{Changes in version 3.2-15}{
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\itemize{
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\item Fix an inconsistency with the start.time argument. One of
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the survfit paths would include an event at start.time (curve starts
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with an immediate drop) others did not. All paths now do so. This
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makes start.time=0 behave the same as ordinary survfit, without the
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argument, when there is a death at time 0.
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}}
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\section{Changes in version 3.2-14}{
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\itemize{
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\item Update the royston function to report the scaled Cox-Snell
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R-squared as the Nagelkerke estimate, and clarify the documentation.
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\item Update for coxph with ties=exact, for the case of an infinite
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coefficient where the information matrix becomes singular. Code for
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this case had been developed for coxfit6.c (Breslow/Efron) but not
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replicated in coxexact.c
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}}
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\section{Changes in version 3.2-13}{
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\itemize{
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\item Clarify some sentences in tmerge help file.
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\item Fix a memory access error in concordance3.c, found by CRAN.
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\item Add the drop.special function (internal) to work around offset
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problems in [.terms.
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}}
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\section{Changes in version 3.2-12}{
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\itemize{
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\item Avoid a downstream error from infinte coefficients in
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coxph. In special case it would fail by passing an NA to C code.
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\item The df column from cox.zph could be incorrect for a coxme
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model.
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\item cox.zph would crash for a coxme model whose random effect
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contained a factor (odd issue with model.frame).
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\item yates error for a coxph model with a strata * covariate
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interaction
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\item Clarify documentation for the royston command.
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\item Add error for survexp applied to a multistate model.
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\item Make the labeling of restricted mean consistent in print and
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summary, for single state and multistate survfit.
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\item With just the right data the coxexact.c routine would do a
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very inefficient calculation: so slow it appeared to be an infinite
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loop.
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\item Bug in pspline.R: I had neglected to include 'degree' in the
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retained arguments for makepredictcall.
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\item Fix scale factor error in cholesky3.c, which could cause it to
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incorrectly mark a column as singular. Found via a survreg example
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from Nathan Adams, where y had large values.
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\item 2021-08-12: update CRAN
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}}
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\section{Changes in version 3.2-11}{
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\itemize{
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\item Missing labels for the "pairwise" option in yates(), fixed.
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\item Bug in plot.survfit -- could not use conf.int=T and xmax in
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the same call. Pointed out by Dirk Larson.
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\item Failure of survfit, when applied to a multi-state coxph model with
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strata(). Repaired and added this as a test case.
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\item Change seq(along= to seq(along.with=, to match the complete
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argument name.
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\item In pyears(...,data.frame=TRUE), if the levels of a tcut are
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numeric return a numeric rather than a factor. (Version 2.4 feature
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that had been inadvertently removed.)
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\item Fix mistake in survfit.coxphms(..., stype=1): had pmin when I
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meant pmax. (Resulting curves were not even close.) Add a test
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case.
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\item update anova.survreg to have class("anova", "data.table").
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Error pointed out by Daniel Sjoberg.
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}}
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\section{Changes in version 3.2-10}{
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\itemize{
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\item CRAN valgrind checks discovered an uninitialized vector in
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one of the C routines. Now fixed. Updated version is now on CRAN.
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}}
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\section{Changes in version 3.2-9}{
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\itemize{
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\item More careful tests of the rttright function.
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\item Fix bug in tmerge that was introduced in 3.2-8. A new
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|
|
consistency check was too aggressive and would flag a legal dataset.
|
||
|
|
\item Fix tmerge bug reported by E Lundt: if two or more additions
|
||
|
|
were before the start of a subject's timeline, tdc would pick the
|
||
|
|
first rather than the last.
|
||
|
|
sou \item Add the last test case for residuals.survfit (auc for tstart,
|
||
|
|
tstop data), and yes, it uncovered an error.
|
||
|
|
\item Error in survit.coxph for a multistate fit with strata, an array
|
||
|
|
dimension was wrong (but contents correct). It led to downstream
|
||
|
|
problems with print and plot. Pointed out by Matthew Hall.
|
||
|
|
\item Add ability for a multistate coxph model to have shared
|
||
|
|
(proportional) baselines for transitions.
|
||
|
|
\item The coxph routine no longer recenters 0/1 predictors (fit$mean
|
||
|
|
will be 0), per the default value of the new \code{nocenter}
|
||
|
|
argument. Application of survfit to a coxph model without specifying
|
||
|
|
newdata remains a bad idea, but this change makes it a little
|
||
|
|
less bad since for factors the curve will refer to the reference
|
||
|
|
level. The results of predict(fit) are now more defensible for a
|
||
|
|
factor variable.
|
||
|
|
\item Add an explicit error message for survreg() with a frailty
|
||
|
|
term. This usage was never supported -- it is integrating out the
|
||
|
|
appropriate density for a coxph model, which is the wrong one for
|
||
|
|
survreg -- but because the code would run we've found that people
|
||
|
|
assumed it must be right, despite a statement to the contrary in the
|
||
|
|
survival vignette. Long overdue fix.
|
||
|
|
}}
|
||
|
|
\section{Changes in version 3.2-8}{
|
||
|
|
\itemize{
|
||
|
|
\item In tmerge, if data2 contains identifiers not found in data1
|
||
|
|
these rows are now counted in the "missid" column of the tcount
|
||
|
|
attribute, rather than treated as an error.
|
||
|
|
\item In a survfit() call with the start.time option, if one curve
|
||
|
|
had no subjects past the start time the dim of the result was wrong,
|
||
|
|
leading to multiple downstream failures.
|
||
|
|
\item Add a scale argument to quantile.survfit.
|
||
|
|
\item Revert a change to plot.survfit, which was the use of clip() to
|
||
|
|
keep lines away from the right margin. This had some unforseen downstream
|
||
|
|
consequences, e.g., later addition of a legend.
|
||
|
|
\item Minor fix to survcheck: if the events table had only 1 row the
|
||
|
|
matrix property was lost. Pointed out by Oleguer Plana-Ripoll.
|
||
|
|
\item Error in plot.survfit: the noplot argument had been overlooked
|
||
|
|
for the confidence intervals, and the wrong interval could be matched to
|
||
|
|
each curve.
|
||
|
|
\item The neardate routine implicitly assumed that data set 2 was in
|
||
|
|
sorted order, if it is not an error message ensues from the internal
|
||
|
|
call to findInterval. Now repaired and a new test added. Pointed
|
||
|
|
out by Bruce Macwilliams.
|
||
|
|
\item Add an error message to survfit recognizing that it can not
|
||
|
|
yet deal with multistate coxph models that have shared baseline
|
||
|
|
hazards.
|
||
|
|
\item Add the pseudo function for psuedo-values. The vignette is in
|
||
|
|
vignette2 since it uses svyglm (survey) to get proper standard
|
||
|
|
errors (see the 'other' vignette).
|
||
|
|
Add supporting routine residuals.survfit (which does the real work.)
|
||
|
|
\item Add the nsk function.
|
||
|
|
\item Add the aggregate.survfit method
|
||
|
|
\item Formally depricate survConcordance, replaced with the more capable
|
||
|
|
concordance method which has formula, lm, glm, and coxph methods.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.2-7}{
|
||
|
|
\itemize{
|
||
|
|
\item Fix one URL, revealed by the CRAN submission.
|
||
|
|
\item Column labels had been lost on the riskmat argument of
|
||
|
|
coxph.detail, which broke the linERR package. Found in reverse
|
||
|
|
dependency checks for CRAN.
|
||
|
|
}}
|
||
|
|
\section{Changes in version 3.2-5}{
|
||
|
|
\itemize{
|
||
|
|
\item Fix error in summary.coxph.penal; it was incorrectly copying
|
||
|
|
se(concordance) to the new object.
|
||
|
|
\item Minor error in survfit.coxphms; it would fail if the model had
|
||
|
|
an NA coefficient.
|
||
|
|
\item Relax a check in concordance, to allow comparing two models
|
||
|
|
with the same subjects but different response vector.
|
||
|
|
\item If multiple strata() terms were first in a coxph model, the labels
|
||
|
|
of the assign component would be incorrect, which affected labeling of
|
||
|
|
cox.zph results (numeric values were correct, however).
|
||
|
|
\item The riskmat option of the coxph.detail command now returns the
|
||
|
|
matrix in data order rather than time-sorted order.
|
||
|
|
\item The summary.survfit function had overlooked the std.chaz
|
||
|
|
component when subsetting based on the times argument.
|
||
|
|
\item The documentation for print.survfit stated that rmean="common"
|
||
|
|
would use the largest time across curves, the code had the median.
|
||
|
|
Make code agree with the documentation. Pointed out by Qingxia Chen.
|
||
|
|
\item Add the rttright function (redistribute to the right) and the
|
||
|
|
R^2 measure of Royston and Sauerbrei.
|
||
|
|
\item Add residuals.survfit, which will be important for
|
||
|
|
pseudo-values. Still incomplete.
|
||
|
|
\item Better hardening of coxph against a particular kind of skewed
|
||
|
|
variable, based on a test case from Michael Young. This had led to the
|
||
|
|
"This should never happen, please contact the author" message.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.2-4}{
|
||
|
|
\itemize{
|
||
|
|
\item Add na.omit to the output of survcheck.
|
||
|
|
\item Undo an ifelse typo (added in 3.2-3) in survexpm that caused it to
|
||
|
|
return NULL for an upper triangular rate matrix, breaking survfit
|
||
|
|
for a multi-state coxph model. (Upper triangular has the simplest
|
||
|
|
algorithm, and all the tests in the suite were for the more complex
|
||
|
|
cases of course -- aargh.)
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.2-3}{
|
||
|
|
\itemize{
|
||
|
|
\item Fix error in survfit.coxphms: an internal routine was being
|
||
|
|
called with arguments in the wrong order.
|
||
|
|
\item Add support routines for the derivative of a matrix
|
||
|
|
exponential, needed for survival curve variance (post Cox model).
|
||
|
|
\item Add explicit error message to summary.survfit, when the times
|
||
|
|
argument asks only for times beyond the end of a curve and extend=FALSE.
|
||
|
|
\item Clipping could be too tight in plot.survfit.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.2-2}{
|
||
|
|
\itemize{
|
||
|
|
\item Add support for "timeline" style survival data. I
|
||
|
|
hope this will be a step forward in usability for multi-state
|
||
|
|
models, since data sets can be built with standard data manipulation tools.
|
||
|
|
\item Fix error in survfit.coxphms, the weight vector could be the
|
||
|
|
wrong length when the start.time option was used.
|
||
|
|
\item Formulas in a multistate coxph model can now have "-x1" to
|
||
|
|
delete variable x1, in secondary formulas. (Update.formula is now used
|
||
|
|
behind the scenes).
|
||
|
|
\item Multistate coxph models now handle strata in full generality
|
||
|
|
-- a stratum can apply to all transitions or just to some. One
|
||
|
|
consequence is that the cmap element of the returned fit has been broken into
|
||
|
|
two portions: stratum_map contains strata information and cmap the
|
||
|
|
coefficient information.
|
||
|
|
\item Revert (partially) a change to tmerge. Using tdc() to update a
|
||
|
|
variable that already exists in the baseline data was a problem, so
|
||
|
|
tdc had been changed to replace rather than update. Now allow updates to
|
||
|
|
variables created by a prior tdc.
|
||
|
|
\item Fix error in survfit, 0/1 status variable: the start.time
|
||
|
|
option worked correctly only if the data set was sorted by time,
|
||
|
|
which unfortunately was true of the test data in tests/survtest.R.
|
||
|
|
Fix code and strengthen the test.
|
||
|
|
\item Multiple updates to multi-state coxph models + follow-on
|
||
|
|
curves. A current clinical project is providing a stress test.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.1-12}{
|
||
|
|
\itemize{
|
||
|
|
\item Change the default for a robust variance: if there is a
|
||
|
|
cluster argument, non-integer case weight, or an id statement and
|
||
|
|
at least one id has more than one event.
|
||
|
|
\item cox.zph would fail if the coxph fit had NA coefficients
|
||
|
|
(something that used to work). Add a test case to futureproof
|
||
|
|
this. Caught by Ville Ponkilainen.
|
||
|
|
\item Minor: pyears + data.frame option would not preserve the order
|
||
|
|
of factor levels from a tcut operator.
|
||
|
|
\item Edge case from Andrea Jaensch: a coxph model with strata +
|
||
|
|
psline terms, plus a (time1, time2) data set containing observations
|
||
|
|
that do not overlap any events, in just the right spot, could cause an
|
||
|
|
infinite loop in agmart3.c.
|
||
|
|
\item Add subset and na.action arguments to survcheck.
|
||
|
|
\item Minor updates to plot.survfit and survcheck.
|
||
|
|
\item Add cluster= option to replace +cluster() in a formula.
|
||
|
|
Remove all mention of the latter from documentation and
|
||
|
|
examples. Make the cluster, id, and robust options consistent across
|
||
|
|
all the functions.
|
||
|
|
\item Fix bug in plot.survfit with xaxs='S'. At some point one line
|
||
|
|
of code got lost.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.1-11}{
|
||
|
|
\itemize{
|
||
|
|
\item Add 'n' vector to survcheck, update tests.
|
||
|
|
\item Improve multistate coxph printout
|
||
|
|
\item Fix a memory reference error in multicheck.c
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.1-10}{
|
||
|
|
\itemize{
|
||
|
|
\item Fix error in concordance(fit, newdata= xxx): it used the old
|
||
|
|
data at one point. Pointed out by Matjin van't Hooft.
|
||
|
|
\item Minor update to tmerge -- print a warning when a user attempts
|
||
|
|
to update a variable using tdc, namely that this results in complete
|
||
|
|
replacement of said variable, with no retention of prior values.
|
||
|
|
\item Minor fixes to plot.survfit, when both xlim and xaxs='S' are
|
||
|
|
specified. Error and suggested fixes from Heinz Tuechler.
|
||
|
|
\item Two failures in makepredictcall.pspline, found by 2 different
|
||
|
|
users, both cases of options that should have been carried forward.
|
||
|
|
A subsequent termplot() call failed if pspline had 'nterm' or
|
||
|
|
'combine'.
|
||
|
|
\item Fix memory leak (forgotten PROTECT) in zph[12].c; caught by B Ripley
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.1-9}{
|
||
|
|
\itemize{
|
||
|
|
\item The plot.cox.zph function would fail for a stratified model,
|
||
|
|
if some covariate was a constant in one of the strata. The cox.zph
|
||
|
|
routine correctly labeled those points as uninformative via NA, the
|
||
|
|
plot routine needed to actually ignore them.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.1-8}{
|
||
|
|
\itemize{
|
||
|
|
\item For a multistate model with no covariates, the start.time
|
||
|
|
value (if present) was inadvertently omitted from the result. This
|
||
|
|
affects the default plot.
|
||
|
|
\item Per user request, the tmerge function can now use Dates as the
|
||
|
|
time variable for the merge.
|
||
|
|
\item Fix an invalid read (one element past the end of a vector)
|
||
|
|
that could occur in tmerge.c; reported by Brian Ripley.
|
||
|
|
\item A multi-state coxph model with strata would fail when parsing
|
||
|
|
the formula, pointed out by Martin van't Hooft.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.1-7}{
|
||
|
|
\itemize{
|
||
|
|
\item For a coxph model with covariate*strata interactions the
|
||
|
|
information matrix will be block diagonal, and the cox.zph function
|
||
|
|
would generate a 0/0 when scaling it for plots. This led to a
|
||
|
|
BLAS error on some architectures (reported by B. Ripley within 24
|
||
|
|
hours of 3.1-6 being published on CRAN). Tests were unaffected,
|
||
|
|
subsequent plots fail due to an infinite axis.
|
||
|
|
Repair, and add more checks to the test suite.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Change in version 3.1-6}{
|
||
|
|
\itemize{
|
||
|
|
\item Repair issues in coxph.getdata and lines.survfit that were
|
||
|
|
found with reverse dependency checks
|
||
|
|
\item Submit to CRAN
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.1-5}{
|
||
|
|
\itemize{
|
||
|
|
\item Update coxph.getdata and coxph.detail to work with coxphms
|
||
|
|
objects. A deficiency in the first affected cox.zph results for
|
||
|
|
multi-state coxph fits.
|
||
|
|
\item Add a formal test suite for the cox.zph routine.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.1-4}{
|
||
|
|
\itemize{
|
||
|
|
\item Move some vignettes to the vignette2 directory, found on the
|
||
|
|
github website. Add an index to those files.
|
||
|
|
\item Add the timefix option to coxph results, and ensure that
|
||
|
|
downstream survfit calls correctly retain it.
|
||
|
|
\item Expand the main survival vignette.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.1-3}{
|
||
|
|
\itemize{
|
||
|
|
\item The results of anova.coxph were incorrect for the case of a
|
||
|
|
single model with ties="breslow" and tied event times: the breslow
|
||
|
|
option was not being passed forward to the secondary fits.
|
||
|
|
\item Add more sanity checks to anova.coxph, e.g., all models must
|
||
|
|
have used the same ties option.
|
||
|
|
\item Update tmerge to allow more variable types as the argument to
|
||
|
|
tdc. A user pointed out that Dates were not preserved; now fixed.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.1-2}{
|
||
|
|
\itemize{
|
||
|
|
\item The cox.zph command now refuses models with tt() terms, before
|
||
|
|
it had an incorrect computation.
|
||
|
|
\item Fix 2 errors in plot, for survfit of a coxph model. (I had not
|
||
|
|
scanned the pdf pages from the vignettes, which is the only way to
|
||
|
|
verify plots.)
|
||
|
|
\item Fix labeling error for combination of pyears, tcut variable,
|
||
|
|
data.frame option. (The numerical values were correct).
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.1-1}{
|
||
|
|
\itemize{
|
||
|
|
\item Fix error in [.cox.zph, when applied to a stratified model
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.1-0}{
|
||
|
|
\itemize{
|
||
|
|
\item Respond to some CRAN queries and resubmit.
|
||
|
|
\item Better documentation of the survfit0 routine
|
||
|
|
\item Add the sas.Rnw vignette to inst/doc: it takes too long to
|
||
|
|
run for inclusion in the vignettes directory
|
||
|
|
\item Fix two edge case errors pointed out on github: coxph on a
|
||
|
|
data set with 0 events, and models with only a frailty term
|
||
|
|
\item Update residuals.coxph to deal with larger matrices, i.e.,
|
||
|
|
change two .C calls to .Call
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.0-11}{
|
||
|
|
\itemize{
|
||
|
|
\item Multiple small updates, after running tests for all
|
||
|
|
reverse dependencies
|
||
|
|
\item Send to CRAN
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 3.0-10}{
|
||
|
|
\itemize{
|
||
|
|
\item Make sure all calls to data.frame explicitly select a value
|
||
|
|
for the stringsAsFactors option.
|
||
|
|
\item Updates to cox.zph for the singledf option
|
||
|
|
\item Add formal test of the cox.zph statistics
|
||
|
|
\item Add the sas vignette to the vignettes2 directory (it takes too
|
||
|
|
long to run).
|
||
|
|
}}
|
||
|
|
\section{Changes in version 3.0}{
|
||
|
|
\itemize{
|
||
|
|
\item Major revision of the survfit routines, see the survival vignette.
|
||
|
|
\item Allow multi-state coxph models.
|
||
|
|
\item Rename remaining .S files as .R
|
||
|
|
\item vcov of a survreg object now contains dimnames (important for the
|
||
|
|
stats::confint function)
|
||
|
|
\item Subscripting survfit object removes the na.action. This is a
|
||
|
|
loss in the sense that the printout no longer tells us that
|
||
|
|
observations were removed, but the information about which and how
|
||
|
|
many rows were removed was incorrect after the selection.
|
||
|
|
\item The survexp function, applied to a coxph model with strata,
|
||
|
|
would sometimes produce extraneous y=0 values at the start of a
|
||
|
|
curve.
|
||
|
|
\item Multiple small bug fixes.
|
||
|
|
}}
|
||
|
|
\section{Changes in version 2.44-1}{
|
||
|
|
\itemize{
|
||
|
|
\item Fix error in survreg when the init argument was used.
|
||
|
|
\item B. Ripley found/fixed an incorrect size in survfitkm.c, that
|
||
|
|
could lead to memory overwrite and a hard crash.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.44-0}{
|
||
|
|
\itemize{
|
||
|
|
\item Add several data sets from the reliability literature, which
|
||
|
|
had been used in the tests directory, to the package's
|
||
|
|
data and add a help page of 'reliability'.
|
||
|
|
\item Fix error in residuals.survreg, type="matrix", pointed out by
|
||
|
|
Achim Zelies. Another check has been added to the tests.
|
||
|
|
\item The survfit routine now returns the cumulative hazard along
|
||
|
|
with its standard error, and allows for robust variance.
|
||
|
|
\item For (start, stop) data, the survfit result only includes
|
||
|
|
unique stop times.
|
||
|
|
\item Update plot.survfit to plot the cumulative hazard when
|
||
|
|
fun='cumhaz', rather than plotting log(surv).
|
||
|
|
\item The Nagelkerke R^2 has been removed from summary.coxph.
|
||
|
|
The shortcomings of this measure are well known, concordance is a
|
||
|
|
better measure.
|
||
|
|
\item A cluster() term is not allowed in the finegray function; now
|
||
|
|
give an explicit error message to that effect.
|
||
|
|
|
||
|
|
\item Track down a failure that occured with some infinite
|
||
|
|
coefficient data sets. When iterations run out, the routine now
|
||
|
|
returns the last successful iterate rather than the last attempt, e.g.,
|
||
|
|
if the loglik maximizes at infinity the routine now returns the
|
||
|
|
last step at which the partial likelihood, first and second
|
||
|
|
derivatives were all finite. This stops some downstream
|
||
|
|
"non-finite" messages.
|
||
|
|
|
||
|
|
\item Add concordancefit function to help pages and exports, so
|
||
|
|
other packages can more easily invoke it.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.43-4}{
|
||
|
|
\itemize{
|
||
|
|
\item Added a hex sticker. It is found in man/figures.
|
||
|
|
\item Small grammar changes in a help page.
|
||
|
|
\item Fix bug pointed out by A Ruten-Budde. The coxph routine was
|
||
|
|
not passing the timefix option forward to a subseqent concordance
|
||
|
|
call.
|
||
|
|
\item Fine tune the checks for an infinite coefficient. A data set
|
||
|
|
from rehbergT managed to have overflows in the first and second
|
||
|
|
derivative at the same iteration, leading to an update of inf * 0.
|
||
|
|
\item Formally add some small reliability data sets to the package, with a
|
||
|
|
help page of 'reliability'. They had been used in the tests.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
\section{Changes in version 2.43-2}{
|
||
|
|
\itemize{
|
||
|
|
\item In concordance, allow y to be an orderable factor (either
|
||
|
|
is.ordered=TRUE or it has only 2 levels), instead of giving an error
|
||
|
|
message. Repair some missing references in the vignette.
|
||
|
|
|
||
|
|
\item Fix an error check in survSplit, when the response has missing
|
||
|
|
values. The routine would fail with an error message when there was
|
||
|
|
no error. (Pointed out by Daniel Wollschläger.)
|
||
|
|
|
||
|
|
\item Fix serious error in the finegray function when called with
|
||
|
|
(start, stop) data, e.g., with time-dependent covariates: the
|
||
|
|
censoring distribution G was incorrect which leads to incorrect weights,
|
||
|
|
including NA. Pointed out by Deqiang Zheng along with an example.
|
||
|
|
(The use of time-dependent covariates in a FG model has serious -- I
|
||
|
|
think fatal -- statistical issues, however. The FG approach adds
|
||
|
|
extra 'imputed' follow-up to each subject; but what is the future
|
||
|
|
value of a time-dependent covariate over this new interval?)
|
||
|
|
|
||
|
|
\item Update the finegray function to allow case weights. If the
|
||
|
|
original data has sampling weights, for instance, this propogates
|
||
|
|
them properly to the created fgwt variable.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.43-1}{
|
||
|
|
\itemize{
|
||
|
|
\item Minor change to the concordance method to better accomodate
|
||
|
|
another package; add one more test case as well.
|
||
|
|
\item Change coxph to use concordance() rather than survConcordance.
|
||
|
|
Be aware that this changes the default variance estimate (to a
|
||
|
|
better estimator however).
|
||
|
|
\item Add a test to verify that tmerge works with Date objects as
|
||
|
|
the time scale
|
||
|
|
\item Add timefix=TRUE option to survdiff
|
||
|
|
\item Add code for an edge case to coxph: a data set with no events.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.43.0}{
|
||
|
|
\itemize{
|
||
|
|
\item Finish test suite and vignette for concordance.
|
||
|
|
\item Run the tests for all packages that depend on survival.
|
||
|
|
Submit to CRAN
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.42-7}{
|
||
|
|
\itemize{
|
||
|
|
\item Add arguments to survfit: survfit.matrix did not have
|
||
|
|
start.time, and survfitCI did not have p0. Now both of them have
|
||
|
|
both.
|
||
|
|
|
||
|
|
\item Fix two small errors triggered by the new checks for the use
|
||
|
|
of && or || with arguments whose length is >1. Pointed out by
|
||
|
|
Martin Maechler.
|
||
|
|
|
||
|
|
\item Add the concordance function, an upgrade of the older
|
||
|
|
survConcordance function. The latter will be depricated. (The draft
|
||
|
|
vignette still needs some polish.)
|
||
|
|
|
||
|
|
\item Change survreg so that a returned "y" in the object is the
|
||
|
|
original response, not the transformed y used for computation. This
|
||
|
|
was prompted by the concordance.survreg method, but is also more
|
||
|
|
consistent. It forced a change in residuals.survreg and uncovered
|
||
|
|
a long standing bug for any fit that had specified y=FALSE.
|
||
|
|
|
||
|
|
\item Fix bug pointed out by C McCort: tmerge with "tdc(time, x)"
|
||
|
|
would fail if x is of mode character. Add this case to the test suite.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.42-6}{
|
||
|
|
\itemize{
|
||
|
|
\item Remove the cbind.Surv and rbind.Surv methods.
|
||
|
|
The problem is when one is called with mixed arguments, e.g.
|
||
|
|
cbind(Surv(1:4), data.frame(x=6:9, z=c('a', 'b', 'a', 'a'))
|
||
|
|
In the above cbind.Surv is never called, but the \emph{presence}
|
||
|
|
of a cbind.Surv method messes up the default behavior, see the
|
||
|
|
Dispatch section of help('cbind').
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.42-5}{
|
||
|
|
\itemize{
|
||
|
|
\item Add a plot.Surv method per the suggestion of Goran Brostram.
|
||
|
|
Improve the cbind.Surv and rbind.Surv methods to handle mixed
|
||
|
|
argument lists (when there are some Surv arguments and some not).
|
||
|
|
|
||
|
|
\item Add a Survmethods.Rd page documenting the added methods.
|
||
|
|
|
||
|
|
\item Add "F" and "S" to the list of fun= arguments to plot.survfit,
|
||
|
|
they are aliases for "event" and "identity", respectively.
|
||
|
|
}}
|
||
|
|
\section{Changes in version 2.42-4}{
|
||
|
|
\itemize{
|
||
|
|
\item Undo a bug that was introduced in tmerge in 2.42-3; an essential
|
||
|
|
line got commented out with the result that if sequential tmerge calls
|
||
|
|
modify the same variable only the final change was retained. Add a
|
||
|
|
check to the test suite to prevent this in the future.
|
||
|
|
|
||
|
|
\item Improve multi-state survfit when the input data has extra
|
||
|
|
censored rows, e.g., a subject with transitions to state 1 at time 2
|
||
|
|
and state 2 at time 8 but data of (0,2,1), (2,5,0), (5,8,2); the
|
||
|
|
survSplit routine often generates such rows.
|
||
|
|
Formerly the transitions table in the output would be incorrect for
|
||
|
|
this case, and the life table would get an extra "censoring" line at
|
||
|
|
time 5. The estimated P(state) and its se was correct.
|
||
|
|
|
||
|
|
\item Fix an edge case in tmerge, when using cumevent and the input
|
||
|
|
data has a 'censored' row. Add a test for this, and for another edge
|
||
|
|
case of repeated updates at the same time point.
|
||
|
|
|
||
|
|
\item repair xtfrm.Surv: it had returned a partial ordering for
|
||
|
|
survival objects (like order()), it instead needs to be the analog
|
||
|
|
of order(order(x)), a vector of integers with the same sort order as
|
||
|
|
x. Add test cases and a manual page.
|
||
|
|
|
||
|
|
\item Add more Surv methods: head, tail, rep, rbind, c, rev, t,
|
||
|
|
mean, median, plot, points, lines, levels.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.42-3}{
|
||
|
|
\itemize{
|
||
|
|
\item Remove the coxph warning "X matrix deemed to be singular".
|
||
|
|
The coefficients are NA, just as before, we simply say less.
|
||
|
|
|
||
|
|
\item Fix minor bug in coxph: a covariate that was a constant would
|
||
|
|
have its coefficent reported as 0 rather than NA, if (and only if)
|
||
|
|
it was the only variable in the model, e.g.,
|
||
|
|
coxph(Surv(1:10) ~ rep(4,10)).
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.42-1}{
|
||
|
|
\itemize{
|
||
|
|
\item Add xtfrm method for Surv objects.
|
||
|
|
\item Fix error in logLik.coxph.null (incorrect class)
|
||
|
|
\item Fix error in pyears, would fail for a model with no
|
||
|
|
predictors and dataframe=TRUE.
|
||
|
|
\item tmerge would fail if an id was missing, give a message
|
||
|
|
instead
|
||
|
|
\item Stronger date checks in survexp, i.e., that the column
|
||
|
|
of a data frame is a date if and only if the matching ratetable
|
||
|
|
dimension is a date.
|
||
|
|
\item Restore the order of the elements of coxph objects; as some
|
||
|
|
other packages depend on both the names and the order. It had been
|
||
|
|
modified when the residual argument was added to coxph.fit.
|
||
|
|
\item Add a more rigorous check for overflow in the coxph iteration:
|
||
|
|
M Tsagris supplied an edge case example where the information matrix
|
||
|
|
fails one iteration before anything else.
|
||
|
|
}}
|
||
|
|
|
||
|
|
|
||
|
|
\section{Changes in version 2.42-0}{
|
||
|
|
\itemize{
|
||
|
|
\item Fix a bug in the agfit4.c routine, based on data sets from Ivo
|
||
|
|
Sousa Ferreira and Marloes Derks. This was introduced in 2.39-1 and
|
||
|
|
leads to incorrect solutions for selected data sets. Such data sets
|
||
|
|
are a rare edge case, however. In detail:
|
||
|
|
In a start stop data set with strata assume two adjacent event times
|
||
|
|
in one stratum of d1 and d2, say, and a set of k censored intervals
|
||
|
|
(a,b) also in that stratum such that a>=d1 and b<d2. (Such intervals are
|
||
|
|
never at risk for an event and could be elminated from the data set
|
||
|
|
without loss.) If k >= the number of intervals that overlap both d1
|
||
|
|
and d2, and in the prior stratum the smallest time was an event,
|
||
|
|
some variables that track who is in the risk set got out of sync,
|
||
|
|
and contributions to the loglik, first and second derivative at d1
|
||
|
|
would be incorrect. I expect such data sets are extremely rare.
|
||
|
|
However, the survSplit routine and mstate packages can generate data
|
||
|
|
sets with a LOT of the unneeded intervals. (The data set in
|
||
|
|
question came from mstate.)
|
||
|
|
|
||
|
|
\item Use format.pval() and printCoefmat in more of the print
|
||
|
|
functions. This aligns the format with that of base R.
|
||
|
|
|
||
|
|
\item Update the vcov function to accept the new complete= argument.
|
||
|
|
\item Update statefig to accept vectors of colors.
|
||
|
|
|
||
|
|
\item The [.survfit routine would complain on the use of fit[1]
|
||
|
|
when fit contained a single curve. This is now legal.
|
||
|
|
\item Change NAMED() to MAYBE_REFERENCED() at the suggestion of R
|
||
|
|
core
|
||
|
|
|
||
|
|
\item Add the yates() routine for population prediction,
|
||
|
|
and accompanying vignette.
|
||
|
|
\item Update the survival rate tables (survexp.mn, survexp.us,
|
||
|
|
survexp.usr), to add data for more calendar years.
|
||
|
|
|
||
|
|
\item Bow to user pressure: marks now appear on survival curves for
|
||
|
|
censoring times that are tied with an event time, plotted at the
|
||
|
|
midpoint of the vertical step. Also, replace the outdated
|
||
|
|
\code{mark} option with \code{pch}.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
\section{Changes in version 2.41-5}{
|
||
|
|
\itemize{
|
||
|
|
\item Update the survexp.us and survexp.usr rate tables. They now
|
||
|
|
contain years 1940 to 2012. They however lost the breakdown of the
|
||
|
|
first year of life into smaller intervals as the recent US census data
|
||
|
|
lacks that information. Update the code for ratetables: a cutpoint
|
||
|
|
attribute vector can now be of class Date, and names(dimnames) can
|
||
|
|
supplant the dimid attribute. (Only creators of rate tables are impacted
|
||
|
|
by these last two.)
|
||
|
|
|
||
|
|
\item Change all instances of "1-pchisq(...)" to instead use the
|
||
|
|
lower.tail=FALSE argument.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.41-4}{
|
||
|
|
\itemize{
|
||
|
|
\item The coxph routine did not check for infinite predictors (these
|
||
|
|
are not screened out by na.action), and these could cause the
|
||
|
|
iteration to fail. Added a check and stop() statement. The example
|
||
|
|
was provided by Glenn Tisdale.
|
||
|
|
|
||
|
|
\item When conf.times was used in plot.survfit, the bars were not
|
||
|
|
perfectly centered on the target values
|
||
|
|
|
||
|
|
\item Add the residual and concordance argument to coxph.fit and
|
||
|
|
agreg.fit, at the request of S Venkat. These speed up the function
|
||
|
|
when a calling routine only needs the partial likelihood.
|
||
|
|
|
||
|
|
\item Fix error in survfit: if timefix=FALSE was specified we forgot
|
||
|
|
to set a key variable and the routine fails. Pointed out by Sarah
|
||
|
|
Streett. 8Apr2017.
|
||
|
|
|
||
|
|
\item Change the scale argument of summary.coxph so that it affects
|
||
|
|
the coefficient and se(coef), not just the confidence interval.
|
||
|
|
|
||
|
|
\item Fix an error in survfitCI when using the start.time argument, and
|
||
|
|
add a test case for it.
|
||
|
|
|
||
|
|
\item Add tail.Surv method per a request from Michael Lawrence.
|
||
|
|
Also add duplicated, anyDuplicated, and unique methods.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.41-3}{
|
||
|
|
\itemize{
|
||
|
|
\item A check for infinite loglik was incorrect in agfit4.c, and could
|
||
|
|
fail to detect the need for step halving. It required a very
|
||
|
|
unusual data set to trigger this.
|
||
|
|
|
||
|
|
\item The survfit routine would fail for interval censored data, on
|
||
|
|
a group that had only a single step in the curve. (Needed to add
|
||
|
|
drop=FALSE to a matrix subscript.)
|
||
|
|
|
||
|
|
\item Minor change to Surv to ensure that its check for difftime
|
||
|
|
objects will not trigger a "length >1 inside an if ()" warning.
|
||
|
|
|
||
|
|
\item The summary.survfit function had n.censor wrong when there
|
||
|
|
were multiple curves and censor=TRUE (spurious NA values). Added more
|
||
|
|
lines to the test suite.
|
||
|
|
|
||
|
|
\item Pointed out by Mikko Korpela: the dynamic symbols check added
|
||
|
|
in 2.41-0 requires R version 2.16 or later. Add an ifdef to init.c
|
||
|
|
that checks the version of R, mimicking a similar line in the MASS library.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.41-2}{
|
||
|
|
\itemize{
|
||
|
|
\item Fix two memory leaks and an uninitialized array, found by B Ripley.
|
||
|
|
|
||
|
|
\item With Surv(a,b, type='interval2') and a or b infinite, the
|
||
|
|
infinite values were incorrectly retained rather then being
|
||
|
|
transformed into left or right censoring. The downstream survfit
|
||
|
|
and/or survreg results could then sometimes be in error.
|
||
|
|
|
||
|
|
\item Update cch to correctly deal with nearly tied times, in line
|
||
|
|
with the many changes in version 2.40.
|
||
|
|
|
||
|
|
\item Update the README.md file, for github users who didn't read
|
||
|
|
noweb/Readme and then get R CMD build errors.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
\section{Changes in version 2.41-0}{
|
||
|
|
\itemize{
|
||
|
|
\item Per request if the R-core, add R_useDynamicSymbols(dll,FALSE)
|
||
|
|
to the initialization. This prevents .Call from accessing the
|
||
|
|
library when its first argument is a character string. The reason
|
||
|
|
is to stop accidental linking to the routines.
|
||
|
|
\item Fix a bug in tmerge, if data2 was not sorted by time within id
|
||
|
|
then a tdc(time, x) call's outcomte was incorrect. Add the ability
|
||
|
|
to use a factor as the second variable in a tdc call, and add the
|
||
|
|
tdcstart option.
|
||
|
|
\item Expose the aeqSurv routine, which is used rectify tied
|
||
|
|
time issues.
|
||
|
|
\item The survfit routines now save the start.time option (if used) in
|
||
|
|
the output object. This is then used as a default starting point for
|
||
|
|
the x-axis in any plots.
|
||
|
|
\item Allow survfit.matrix to use different p0 values for different
|
||
|
|
curves.
|
||
|
|
\item Add type="survival" to predict.coxph
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.40-2}{
|
||
|
|
\itemize{
|
||
|
|
\item Fix an error in the finegray routine: with strata() the
|
||
|
|
resulting data sets could have incorrect status values. Pointed out
|
||
|
|
by Mark Donoghoe. Added a strata test to tests/finegray.R.
|
||
|
|
|
||
|
|
\item Remove many "is.R" and "oldClass" calls (vestiges of Splus).
|
||
|
|
\item The summary.pyears routine now prints pandoc style tables.
|
||
|
|
\item Fix multiple spelling errors in the Rd files; contributed by
|
||
|
|
Luca Braglia.
|
||
|
|
\item For a multi-state curve, the cumhaz component accidentally had
|
||
|
|
the final state removed. All values were correct, simply an
|
||
|
|
overzealous trimming of the final result.
|
||
|
|
|
||
|
|
\item Add a short vignette describing the issue with round off error
|
||
|
|
and tied survival times.
|
||
|
|
|
||
|
|
\item Errors in survSplit: a factor status was not propogated, and a
|
||
|
|
missing time gave a spurious error message.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.40-1}{
|
||
|
|
\itemize{
|
||
|
|
\item For multi-state survival with a big data set and the
|
||
|
|
influence=TRUE option, the resulting object could be so long that it
|
||
|
|
overflowed an integer counter in the C code. Add a check in the R
|
||
|
|
code and a caution in the help file.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
\section{Changes in version 2.40-0}{
|
||
|
|
\itemize{
|
||
|
|
\item Code changes to avoid the new warnings for multiplication of a
|
||
|
|
vector * (1 by 1 matrix).
|
||
|
|
|
||
|
|
\item Add a more thorough test case for multi-state survival:
|
||
|
|
not all subjects start in the same state, delayed entry, and
|
||
|
|
case weights that change within a subject. This uncovered some
|
||
|
|
errors. More carefully document the influence option.
|
||
|
|
|
||
|
|
\item Consistently deal with "almost tied" survival times in the survfit and
|
||
|
|
coxph routines. Uses the same rule and tolerance as the all.equal
|
||
|
|
function to declare two time value equal. The issue arises due to
|
||
|
|
round off errors, e.g., from cacluations using days/365.25.
|
||
|
|
|
||
|
|
\item Add the statefig function and a multi-state vignette.
|
||
|
|
|
||
|
|
\item The rsurvreg function was not exported. NAMESPACE fix.
|
||
|
|
|
||
|
|
\item Fix some labeling errors in the graphs for the adjusted
|
||
|
|
survival curves vignette (consequences of the xscale change in
|
||
|
|
2.38-5).
|
||
|
|
|
||
|
|
\item Update multi-state survival so that the robust (default)
|
||
|
|
variance for a weighted data set treats these as sampling weights
|
||
|
|
rather than case weights. This makes it consistent with the
|
||
|
|
behavior of coxph. (Multiplication of all the weights by a constant
|
||
|
|
now leaves the variance unchanged.) (9/2016)
|
||
|
|
|
||
|
|
\item Surv(time, status) would fail when status was a factor with
|
||
|
|
only two levels. This was due to an assumption that no user would
|
||
|
|
ever want this, i.e., ever do it on purpose, and so it must be a mistake
|
||
|
|
which should be caught. This was a bad assumption.
|
||
|
|
|
||
|
|
\item Add the start.time argument to survfit.coxph. 10Sep2017
|
||
|
|
}}
|
||
|
|
\section{Changes in version 2.39-5}{
|
||
|
|
\itemize{
|
||
|
|
\item The summary.survfit routine assumed that the times argument
|
||
|
|
was sorted, contrary to the documentation. Pointed out by Torsten
|
||
|
|
Hothorn.
|
||
|
|
\item The tmerge function would fail if the time variable was a Date
|
||
|
|
object. It was due to the fact that as.Date(as.numeric(x))
|
||
|
|
fails when x is a date. (A design flaw in Date, IMHO). There were
|
||
|
|
also flaws when both the first and second data set were not sorted
|
||
|
|
by id; added a more complete test case for this.
|
||
|
|
|
||
|
|
\item An earlier change in dim.survfit had felled the survfit.matrix
|
||
|
|
function: it incorrectly assumed strata when there were none.
|
||
|
|
Unfortunately this didn't generate an error but rather multiple
|
||
|
|
copies of a single curve (and an incomprehensible explanation of
|
||
|
|
this single curve in the vignette). Pointed out by E Lundt.
|
||
|
|
|
||
|
|
\item print.summary.survfitms would complain if only a single time
|
||
|
|
was returned. A case where drop=FALSE was needed.
|
||
|
|
|
||
|
|
\item Add a test for survSplit to ensure that it works with both the
|
||
|
|
formula based and old interface. Add documention on
|
||
|
|
how variable names are chosen to the help file.
|
||
|
|
|
||
|
|
\item Error in subscripting survival curves: if fit was a survfit
|
||
|
|
curve from left-truncated data, fit[k] had an incorrect n.enter
|
||
|
|
component. (An old error, which shows how rarely that component is
|
||
|
|
used.) Pointed out by Beth Atkinson.
|
||
|
|
|
||
|
|
\item Remove n.enter from the default printout of summary.survfit,
|
||
|
|
to make the printout more compact.
|
||
|
|
It remains in the summary object but was very rarely used.
|
||
|
|
\item Update the points.survfit function to handle multiple colors
|
||
|
|
and/or plotting characters. If a survfit object has multiple curves
|
||
|
|
we cycle through these in the same manner as matpoints would.
|
||
|
|
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.39-4}{
|
||
|
|
\itemize{
|
||
|
|
\item Create a stronger test suite for summary.survfit, and use
|
||
|
|
it to actually fix the error that 2.39-3 claimed to fix. This
|
||
|
|
uncovered a long-standing inaccuracy with n.risk for in-between
|
||
|
|
time points.
|
||
|
|
\item Add a section on monotone splines to the splines vignette.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.39-3}{
|
||
|
|
\itemize{
|
||
|
|
\item For multi-state curves, the returned n.event component lost
|
||
|
|
its dimensions if any of the curves had only one observation.
|
||
|
|
|
||
|
|
\item Fix error in summary.survreg. For multiple curves and
|
||
|
|
requested time points at or before the first time point in the data,
|
||
|
|
the values from curve 1 was used for all. Pointed out by T Eigentler.
|
||
|
|
|
||
|
|
\item Fix an unitialized variable in C code, pointed out by Brian Ripley.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.39-2}{
|
||
|
|
\itemize{
|
||
|
|
\item Small updates based on feedback from CRAN
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.39-1}{
|
||
|
|
\itemize{
|
||
|
|
\item Label the output dimnames from pyears with the variable names
|
||
|
|
from the model. This makes it easier to read.
|
||
|
|
|
||
|
|
\item Replace any refrences to model.frame with "stats::model.frame"
|
||
|
|
(all 38 of them). The model.frame function uses non-standard
|
||
|
|
evaluation rules, and holding its hand like this is the only way to
|
||
|
|
ensure that we don't call a user function of the same name.
|
||
|
|
|
||
|
|
\item The Surv function would almost always label the columns of the
|
||
|
|
resulting matrix, and the glmnet function depended on this. It now
|
||
|
|
always labels them per a request from Trevor Hastie.
|
||
|
|
|
||
|
|
\item Add the finegray function and expand the competing risks
|
||
|
|
vignette to document it.
|
||
|
|
|
||
|
|
\item Add a check to the quantile.survfit function for multi-state
|
||
|
|
models; quantiles are not well defined for this case.
|
||
|
|
|
||
|
|
\item Changes to the iteration path and convergence tests for coxph
|
||
|
|
models with (start, stop] data, driven by two user examples that
|
||
|
|
failed. The data sets had serious statistical issues of
|
||
|
|
collinearity and/or outliers such that the final fits are not
|
||
|
|
practically useful, but now the routine finishes gracefully instead
|
||
|
|
of dying. The upshot is much more care about the order in which
|
||
|
|
additions and subtractions of large numbers are done so as to avoid
|
||
|
|
cancellation error.
|
||
|
|
|
||
|
|
\item Fix an error to summary.survfit with the times argument: for
|
||
|
|
intermediate time points it would sometimes choose the wrong value
|
||
|
|
for the number at risk. (Number at risk is a left continuous
|
||
|
|
function.)
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.38-5}{
|
||
|
|
\itemize{
|
||
|
|
\item Add more graphical arguments to plot.cox.zph in response to a user
|
||
|
|
request.
|
||
|
|
|
||
|
|
\item Remove some of last vestiges of Splus support from the header
|
||
|
|
files for the C code, per a request from R core to remove mention of S.h.
|
||
|
|
|
||
|
|
\item Multiple updates and corrections to the tmerge function,
|
||
|
|
including improvements to the vignette. (As a result of using it in
|
||
|
|
a class where the TA tried out all manner of combinations.)
|
||
|
|
|
||
|
|
\item Update survSplit: it now handles all types of status variables
|
||
|
|
(0/1, TRUE/FALSE, factors), the id and episode arguments are useful
|
||
|
|
for start/stop data, the data retains its original sort order (new
|
||
|
|
observations are inserted rather than put at the end), and the
|
||
|
|
function is illustrated in a vignette.
|
||
|
|
|
||
|
|
\item Add the conf.times argument to plot.survfit. This
|
||
|
|
allows for confidence bars at specified times, which are useful
|
||
|
|
when the plot is crowded.
|
||
|
|
|
||
|
|
\item Survfit changes that are NOT backward compatable!
|
||
|
|
\itemize{
|
||
|
|
\item Change the default for mark.time to FALSE
|
||
|
|
\item Change the behavior of xscale so that it matches that of
|
||
|
|
yscale, i.e., it changes only the label and not the underlying
|
||
|
|
scale. Follow on annotations such as legend or locator are in the
|
||
|
|
orignal scale of the data.
|
||
|
|
\item For a matrix of curves, e.g. competing risks, print and
|
||
|
|
plot them in column major order rather than row major, so as
|
||
|
|
to match the usual R behavior.
|
||
|
|
}
|
||
|
|
|
||
|
|
\item Fix an error in the help page for the cohort
|
||
|
|
argument of survexp, pointed out by Karl Ove Hufthammer.
|
||
|
|
|
||
|
|
\item The anova and logLik functions would fail when given a
|
||
|
|
null model (right hand side of 1 or only an offset). Pointed
|
||
|
|
out by Karl Ove Hufthammer.
|
||
|
|
|
||
|
|
\item The recently added code to generate an error when the same
|
||
|
|
variable appears on both sides of a formula in coxph (a good idea)
|
||
|
|
caused a failure if there was offset statement that contains a '-'
|
||
|
|
sign. Pointed out by Abra Jeffers.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.38-3}{
|
||
|
|
\itemize{
|
||
|
|
\item Add more imports to the NAMESPACE file per a request from CRAN
|
||
|
|
|
||
|
|
\item Add a length method for Surv objects. Requested by Max Kuhn.
|
||
|
|
(2015/6/17).
|
||
|
|
|
||
|
|
\item Fix an error in neardate. When both input data sets were
|
||
|
|
unsorted the last match could be wrong.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.38-2}{
|
||
|
|
\itemize{
|
||
|
|
\item Change print.coxph to use the printCoefmat routine, which l
|
||
|
|
leads to nicer p-values. Other print routines will follow unless
|
||
|
|
there is an outcry. (But I forced signif.stars=FALSE: my tolerance of
|
||
|
|
bad practice has limits.)
|
||
|
|
|
||
|
|
\item Make those parts of the competing risks vignette which depend
|
||
|
|
on the cmprsk library conditional. Otherwise the build fails for
|
||
|
|
those without the pacakge.
|
||
|
|
|
||
|
|
\item The coxph function could fail converge for a set of very collinear
|
||
|
|
predictors when using (start, stop) data; revealed in a test case
|
||
|
|
sent by G Borstrom. This was due to deficiency in a check for
|
||
|
|
near infinite coefficients, which had already been updated for some
|
||
|
|
but not all cases. (2015/6/3)
|
||
|
|
|
||
|
|
\item Update anova.coxph to use the model.frame.coxph function; the
|
||
|
|
current code had scoping errors if embedded in a function. Add an
|
||
|
|
anova.coxph.penal function to correctly handle models with pspline
|
||
|
|
terms.
|
||
|
|
|
||
|
|
\item Fix an error in the tmerge function. Using the options
|
||
|
|
argument would generate a spurious error.
|
||
|
|
\item Pyears could fail on very long formulas due to a deparse() issue.
|
||
|
|
|
||
|
|
\item Add the number of observations used and deleted due to missing
|
||
|
|
to summary.pyears.
|
||
|
|
|
||
|
|
\item Allow the combination of a null coxph model (~1 on the right)
|
||
|
|
and the exact calculation for tied times. No one had ever asked for
|
||
|
|
this before. (2015/3/25)
|
||
|
|
|
||
|
|
\item Shorten the default printout for survfit. The records, n.max
|
||
|
|
and n.start columns are often the same: if so suppress duplicates.
|
||
|
|
|
||
|
|
\item Move the anova.coxphlist function from the survival package to
|
||
|
|
coxme. (2015/3/3)
|
||
|
|
|
||
|
|
\item Change the logLik method for coxph models so that the nobs
|
||
|
|
component is the number of events rather than the number of rows in
|
||
|
|
the data. This is superior for follow on methods such as AIC.
|
||
|
|
|
||
|
|
\item Add a test to the coxexact.c routine for too large a data set;
|
||
|
|
too many tied times could lead to integer overflow. "Fixing" the error
|
||
|
|
is not sensible: the computation for such a data set would take decades.
|
||
|
|
Add some more explanation to the help pages as well.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.38-1}{
|
||
|
|
\itemize{
|
||
|
|
\item Fix an error discovered by CRAN, which triggered a core dump
|
||
|
|
for them on a particular manual page (but never for me). The linear
|
||
|
|
predictors from a frailty model contained NA values (incorrect),
|
||
|
|
leading to failure in survConcordance.fit. (2015/2/16).
|
||
|
|
|
||
|
|
\item An error was found in the mgus data set (a progression after
|
||
|
|
death). Now corrected, and added a little more follow-up time for
|
||
|
|
some subjects.
|
||
|
|
|
||
|
|
\item Add error check for infitinte weights or offsets. This in respose
|
||
|
|
to a bug report where someone did this on purpose, trying to mimic
|
||
|
|
cure fractions, and then found that survfit.coxph failed.
|
||
|
|
|
||
|
|
\item Robust variance is not supported for a coxph model with the
|
||
|
|
"exact" approximation. (Rarely requested and a lot of work to add.)
|
||
|
|
Add an error message to clogit(), so users get a more useful notice of
|
||
|
|
the issue rather than a late error from residuals.coxph.
|
||
|
|
|
||
|
|
\item Update the rats data set: it now includes both female and male
|
||
|
|
litters so as to match the documentation.
|
||
|
|
|
||
|
|
\item The term frailty(x) would fail if x were a factor, and not all
|
||
|
|
levels were present. Pointed out by Theodor Balan.
|
||
|
|
|
||
|
|
\item Fix error of "abs" instead of "fabs" in the agfit4.c code;
|
||
|
|
pointed out to me by CRAN.
|
||
|
|
|
||
|
|
\item Replace all instances of the obsolete prmatrix function.
|
||
|
|
|
||
|
|
\item Modify pyears to allow cbind(time, count) as the response,
|
||
|
|
giving a cumulative sum of counts, when the counts per observation
|
||
|
|
may be other than 0/1.
|
||
|
|
|
||
|
|
\item The lines.survfit function was incorrect for data sets that
|
||
|
|
used the start.time option and xscale (it neglected to rescale the
|
||
|
|
start time.)
|
||
|
|
|
||
|
|
\item An increasingly common error is for user to put the time
|
||
|
|
variable on both sides of a coxph equation in the mistaken belief
|
||
|
|
that this is a way to create time-dependent coefficients. Generate
|
||
|
|
a warning message for this case.
|
||
|
|
|
||
|
|
\item Update the basehaz function to a simple alias for "survfit".
|
||
|
|
Prior versions called surfit but then only returned part of the
|
||
|
|
object. Update 2/2015: reverted the change. It turns out that 6
|
||
|
|
different packages that depend on survival also depended on the
|
||
|
|
old behavior.
|
||
|
|
|
||
|
|
\item Make the default value for the shortlabel argument of strata()
|
||
|
|
more nuanced. If the argument is a single factor, assume that we
|
||
|
|
don't need to prepend the variable name to its levels.
|
||
|
|
|
||
|
|
\item Return the weights vector, if present, as part of the survreg
|
||
|
|
object.
|
||
|
|
|
||
|
|
\item For interval censored points and the symmetric distributions
|
||
|
|
(Gaussian and logistic) response type residuals were incorrect.
|
||
|
|
Silly error: needed (x-mean)/scale not x/scale - mean.
|
||
|
|
|
||
|
|
\item Martingale residuals could be incorrect for the case of model with
|
||
|
|
(start, stop] data and a pspline term. Refactor the code so that
|
||
|
|
all of the possible code paths call the same C routine to do the residuals.
|
||
|
|
Add a new test for this case, and further tests to verify that
|
||
|
|
predict(type='expected') and residuals agree.
|
||
|
|
|
||
|
|
\item Fix bug pointed out by D Dunker: if a model had both tt() and
|
||
|
|
cluster() terms it would fail with a length error.
|
||
|
|
|
||
|
|
\item Fix a rare bug in plot.survfit: if a multistate curve rose and
|
||
|
|
then later fell to exactly the same value, the line would be
|
||
|
|
incorrect.
|
||
|
|
|
||
|
|
\item Add calls to the R_CheckUserInterrupt to several routines, so
|
||
|
|
that long calculations can be interrupted by the user.
|
||
|
|
|
||
|
|
\item The anova.coxph function would fail if the original call had a
|
||
|
|
subset argument. Pointed out by R Fisher. 11May2014
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.37-7}{
|
||
|
|
\itemize{
|
||
|
|
\item Remove a dependency on the survey package from the adjusted
|
||
|
|
survival curves vignette, at the request of CRAN. (The base +
|
||
|
|
required bundle needs to be capable of a stand-alone build.)
|
||
|
|
|
||
|
|
\item Fix error in calcuation of the y-axis range for survival curve
|
||
|
|
plots whenever the "fun" argument could produce infinite values,
|
||
|
|
e.g., complimentary log-log plots transform 1 to -Inf. Pointed out
|
||
|
|
by Eva Boj del Val. (Add finite=TRUE to range() call).
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.37-6}{
|
||
|
|
\itemize{
|
||
|
|
\item The plot for competing risk curves could have a spurious
|
||
|
|
segment. (Found within 3 hours of submitting 2.37-5 to CRAN.)
|
||
|
|
|
||
|
|
\item The lines method for survexp objects was defaulting to a
|
||
|
|
step function, restore the documented default of a connected
|
||
|
|
line.
|
||
|
|
\item Add a levels method for tcut objects. 14Jan2014
|
||
|
|
}
|
||
|
|
}
|
||
|
|
\section{Changes in version 2.37-5}{
|
||
|
|
\itemize{
|
||
|
|
\item Add vignette on adjusted survival curves.
|
||
|
|
\item Add vignette concerning "type 3" tests.
|
||
|
|
|
||
|
|
\item Make the tt() function invisible outside of a coxph formula.
|
||
|
|
There was a complaint about conflicts with another package, and
|
||
|
|
there is not really a good reason to have it be a global name.
|
||
|
|
An R-devel discussion just over 1 year ago showed how to accomplish this.
|
||
|
|
|
||
|
|
\item The modeling routines are set in two parts, e.g., coxph sets
|
||
|
|
up the model and coxph.fit does the work. Export more of the ".fit"
|
||
|
|
routines to make it easier for other packages to build on top of
|
||
|
|
this one.
|
||
|
|
|
||
|
|
\item Updates to the model.matrix and model.frame logic for
|
||
|
|
coxph. A note from F Harrell showed that I was not correctly
|
||
|
|
dealing with the "assign" attribute when there are strata * factor
|
||
|
|
interactions. This led to cleanup in other cases that I had missed
|
||
|
|
but which never had proven fatal. Also added support for tt() terms
|
||
|
|
to the stand alone model.matrix and model.frame functions.
|
||
|
|
(Residuals for tt models are still not available, but this was a
|
||
|
|
necessary first step to that end.) 26Dec13
|
||
|
|
|
||
|
|
\item The Surv function now remembers attributes of the input
|
||
|
|
variables that were passed to it; they are saved as
|
||
|
|
"inputAttributes". This allows the rms package, for instance, to
|
||
|
|
retain labels and units through the call.
|
||
|
|
|
||
|
|
\item Update summary.coxph.penal to produce an object, which in turn
|
||
|
|
has a print method, i.e., make it a "standard" summary function.
|
||
|
|
|
||
|
|
\item Add a logLik method for coxph and survfit objects.
|
||
|
|
|
||
|
|
\item Allow for Inf as the end of the time interval, for interval
|
||
|
|
censored data in the Surv function.
|
||
|
|
|
||
|
|
\item The predict.coxph function would fail if it had both a newdata
|
||
|
|
and a collapse argument. Pointed out by Julian Bothe. 25Sep13
|
||
|
|
|
||
|
|
\item Survexp can now produce expecteds based on a stratified Cox
|
||
|
|
model. Add the 'individual.s' and 'individual.h' options to return
|
||
|
|
indivudual survival and cumulative hazard estimates, respectively.
|
||
|
|
The result of survfit now (sometimes) includes the cumulative
|
||
|
|
hazard. This will be expanded. 29Jul13
|
||
|
|
|
||
|
|
2 \item Change code in the coxpenal.fit routine: the use of a vector of
|
||
|
|
symbols as arguments to my .C calls was confusing to a new CRAN
|
||
|
|
consistency check. Both the old and new are legal R; but the old
|
||
|
|
was admittedly an unusual construction and it was simpler to change it.
|
||
|
|
|
||
|
|
\item Fix a bug in survfit.coxph pointed out by Chris Andrews, whose
|
||
|
|
root cause was incorrect curve labels when the id option is used. 27Jun13
|
||
|
|
|
||
|
|
\item Add rsurvreg routine.
|
||
|
|
|
||
|
|
\item Change survfit.coxph routine so that it detects whether
|
||
|
|
newdata contains or does not contain strata variables, and acts
|
||
|
|
accordingly. If newdata does containe strata then the output will
|
||
|
|
contain only those data-value and strata combinations specified by the
|
||
|
|
user. Retain strata levels in the coxph routine for use
|
||
|
|
in the survfit routine, to correctly reconstruct strata levels.
|
||
|
|
Warn about curves with interactions. 18Ju13
|
||
|
|
|
||
|
|
\item Add a dim method for survival curves.
|
||
|
|
|
||
|
|
\item For competing risks curves that use the istate option, the
|
||
|
|
plotted curves now start with the correct (initial) prevalence of
|
||
|
|
each state. 22May13
|
||
|
|
|
||
|
|
\item The survreg function failed with the "robust=T"
|
||
|
|
option. Pointed out by Jon Peck. Test case added. 6May13
|
||
|
|
|
||
|
|
\item Kazuki Yoshida pointed out that rep() had no method for Surv
|
||
|
|
objects. This caused the survSplit routine to fail if the data
|
||
|
|
frame contained a Surv object. 3May13
|
||
|
|
|
||
|
|
\item Per a request from Milan Bouchet-Valet fix an issue in survfit
|
||
|
|
that arose when the OutDec option is set to ',': it did not
|
||
|
|
correctly convert times back from character to numeric.
|
||
|
|
|
||
|
|
\item The plot.survfit function now obeys "cex" for the size of the
|
||
|
|
marks used for censored observations.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.37-4}{
|
||
|
|
\itemize{
|
||
|
|
\item Subscripting error in predict.coxph for type=expected, se=T,
|
||
|
|
strata in the model, newdata, and multiple strata in the new data
|
||
|
|
set. Pointed out by Chris Andrews. The test program has been
|
||
|
|
tweaked to include multiple strata in newdata.
|
||
|
|
}}
|
||
|
|
|
||
|
|
|
||
|
|
\section{Changes in version 2.37-3}{
|
||
|
|
\itemize{
|
||
|
|
\item Minor flaw in [.survfit. If "fit" had multiple curves, and
|
||
|
|
fit$surv was a matrix, and one of those curves had only a single observation
|
||
|
|
time, fit[i,] would collapse columns when "i" selected that curve,
|
||
|
|
though it shouldn't.
|
||
|
|
|
||
|
|
\item Changed all of the .C and .Call statements to make use of
|
||
|
|
"registered native routines", per R-core request. Add file src/init.c
|
||
|
|
|
||
|
|
\item Error in plot.survfit pointed out by K Hoggart -- the "+"
|
||
|
|
signs for censored observations were printing one survival time to
|
||
|
|
the left of the proper spot. Eik Vettorazi found another error if
|
||
|
|
mark.time is a vector of numerics. These are the results of merging
|
||
|
|
the code for plot, lines and points due to some discrepancies between
|
||
|
|
them, plus not having any graphical checks in the test suite.
|
||
|
|
|
||
|
|
\item Repair an error in using double subscripts for the survfitms
|
||
|
|
objects.
|
||
|
|
|
||
|
|
\item Add the US population data set, with yearly totals by age and sex
|
||
|
|
for 2000 onward. It is named uspop2, since there is already a "uspop"
|
||
|
|
data set containing decennial totals from 1790 to 1970.
|
||
|
|
|
||
|
|
\item Not all combinations of strata Y/N and CI Y/N worked in the
|
||
|
|
quantile.survfit function, pointed out by Daniel Wallschlaeger
|
||
|
|
(missing a function argument in one if-else combination).
|
||
|
|
Added a new test routine that verifies all paths.
|
||
|
|
|
||
|
|
\item The first example in predict.survreg help file needed to have
|
||
|
|
\code{I(age^2)} instead of \code{age^2} in the model: R ignores the
|
||
|
|
second form. (I'm almost sure this worked at one time, perhaps in Splus).
|
||
|
|
It also needed different plot symbols to actually match the
|
||
|
|
referenced figure. Pointed out by Evan Newell.
|
||
|
|
|
||
|
|
\item Fix a long-standing problem with cch pointed out by Ornulf Borgan
|
||
|
|
leading to incorrect standard errors. A check in the underlying
|
||
|
|
coxph routines to deal with out of bounds exponents, added in
|
||
|
|
version 2.36-6, interacted badly with the -100 offset used in cch.
|
||
|
|
It only affected models using (start, stop) survival times.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.37-2}{
|
||
|
|
\itemize{
|
||
|
|
\item Two bugs were turned up by running tests for all the
|
||
|
|
packages that depend on survival (158 of them).
|
||
|
|
}}
|
||
|
|
\section{Changes in version 2.37-1}{
|
||
|
|
\itemize{
|
||
|
|
\item Add a new multi-state type to the Surv object. Update the
|
||
|
|
survfit routine to work with it. The major change is addition
|
||
|
|
of a proper variance for this case.
|
||
|
|
More functionality is planned.
|
||
|
|
|
||
|
|
\item Remove the fr_colon.R test program. It tests an ability that
|
||
|
|
has been superseded by coxme, on a numerically touchy data set, and
|
||
|
|
it was slow besides. For several other tests that produce warning
|
||
|
|
messages and are supposed to produce said messages, add extra
|
||
|
|
comments to that effect so testers will know it is expected.
|
||
|
|
|
||
|
|
\item The code has had several "if.R" clauses to accomodate Splus vs
|
||
|
|
R differences, which are mostly class vs oldClass. These are now being
|
||
|
|
removed as I encounter them; since our institution no longer uses
|
||
|
|
Splus I can no longer test the clauses' validity.
|
||
|
|
|
||
|
|
\item The fast subsets routine coxexact.fit incorrectly returned the
|
||
|
|
linear predictor vector in the (internal) sorted order rather than
|
||
|
|
data set order. Pointed out by Tatsuki Koyama, affecting the result
|
||
|
|
of a clogit call. 6Nov2012
|
||
|
|
|
||
|
|
\item Jason Law pointed out that the sample data set "rats" is from
|
||
|
|
the paper by Mantel et.al, but the documentation was for a data
|
||
|
|
set from Gail, Santner and Brown. Added the Gail data as rats2 and
|
||
|
|
fixed the documentation for rats.
|
||
|
|
|
||
|
|
\item For predict.coxph with type="terms", use "sample" as the
|
||
|
|
default value for the reference option. For all others the default
|
||
|
|
remains "strata", the current value. Type terms are nearly always passed
|
||
|
|
forward for further manipulation and per strata centering can mess
|
||
|
|
things up: termplot() for instance will no longer show a smooth
|
||
|
|
function if the results are recentered within strata.
|
||
|
|
|
||
|
|
\item Fix bug in summary.aareg, which was unhappy (without cause) if
|
||
|
|
the maxtime option was used for a fit that did not include the
|
||
|
|
dfbeta option. Pointed out by Asa Johannesen.
|
||
|
|
|
||
|
|
\item The coxph fitting functions would report an error for a null model
|
||
|
|
(no X variables) if init was specified as numeric(0) rather than NULL.
|
||
|
|
|
||
|
|
\item Update the description and citation files to use the new
|
||
|
|
"person" function described in the R Journal. Also add the
|
||
|
|
ByteCompile directive per suggestion of R core.
|
||
|
|
|
||
|
|
\item Allow an ordinary vector as the left hand side of survConcordance.
|
||
|
|
|
||
|
|
\item Update anova.coxphlist to reject models with a robust variance.
|
||
|
|
|
||
|
|
\item The survfit function had an undocumented backwards-compatability
|
||
|
|
that allows the newdata argument to be a vector with no names. An
|
||
|
|
example from Damon Krstajic showed that this does not work when the
|
||
|
|
original model has a matrix in the formula. Removed the feature.
|
||
|
|
(This is for survfit.coxph.) Also clarified the code and its
|
||
|
|
documentation about what is found where -- environments, formulas,
|
||
|
|
and the arguments of eval, which fixes a problem pointed out by xxx
|
||
|
|
where the result of a Surv call is used in the coxph formula.
|
||
|
|
|
||
|
|
\item Fix an issue in summary.survfit pointed out by Frank Harrell. The
|
||
|
|
strata variable for the output always had its labels in sorted order,
|
||
|
|
even when a factor creating the survival curves was otherwise. (This was
|
||
|
|
due to a call to factor() in the code.) The print routine would then
|
||
|
|
list curves in sorted order, which might well be contrary to the user's
|
||
|
|
wishes. The curves were numerically correct.
|
||
|
|
|
||
|
|
\item Add the anova.coxmelist function to the namespace so that it is
|
||
|
|
visible. If someone has a list of models the first of which was
|
||
|
|
a coxph fit and the list includes coxme fits, then anova.coxph will
|
||
|
|
be the function called by R, and it will call anova.coxmelist.
|
||
|
|
|
||
|
|
\item Fix a bug pointed out by Yi Zhang and Mickael Hartweg.
|
||
|
|
If a coxph model used an offset, then a predicted survival curve
|
||
|
|
that used newdata (and the offset variable of course) would be
|
||
|
|
wrong, e.g. survival values > 1.
|
||
|
|
A simple misplaced parenthesis was the cause.
|
||
|
|
A recent paper by Langholz shows how to get absolute survival from
|
||
|
|
case-control data using an offset, which seems to have suddenly made this
|
||
|
|
feature popular.
|
||
|
|
|
||
|
|
\item Per further interaction with Yi Zhang, a few items were
|
||
|
|
missing from the S3methods in the NAMESPACE file: as.matrix.Surv,
|
||
|
|
model.matrix.coxph, model.matrix.survreg, model.frame.survreg.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.36-14}{
|
||
|
|
\itemize{
|
||
|
|
\item A supposedly cosmetic change to coxph in the last release
|
||
|
|
caused formulas with a "." on the right hand side to fail. Fix this
|
||
|
|
and add a case with "." to the test suite.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
\section{Changes in version 2.36-13}{
|
||
|
|
\itemize{
|
||
|
|
\item Add the anova.coxmelist function. This is in the survival
|
||
|
|
package rather than in coxme since "anova(fit1, fit2)" is valid when
|
||
|
|
fit1 is a coxph and fit2 a coxme object, a case which will cause this
|
||
|
|
function to be called by way of anova.coxph.
|
||
|
|
|
||
|
|
\item More work on "predvars" handling for the pspline function,
|
||
|
|
when used in predict calls. Add a new test of this to the suite,
|
||
|
|
and the makepredictcall method to the namespace.
|
||
|
|
Fixes a bug pointed out by C Crowson.
|
||
|
|
|
||
|
|
\item Deprecate the "robust" option of coxph. When there are
|
||
|
|
multiple observations per subject it is almost surely the wrong
|
||
|
|
thing to do, while adding a "cluster(id)" term does the correct
|
||
|
|
thing. When there is only one obs per subject both methods work
|
||
|
|
correctly.
|
||
|
|
|
||
|
|
\item Add documentation of the output structure to the aareg help
|
||
|
|
file.
|
||
|
|
|
||
|
|
\item Change ratetableDate so that it still allows use of chron
|
||
|
|
objects, but doesn't need the chron library. This eliminates a
|
||
|
|
warning messge from the package checks, but is also a reasonable
|
||
|
|
support strategy for a moribund package. (Some of the local users keep
|
||
|
|
datasets for a long long time.)
|
||
|
|
|
||
|
|
\item Fix a bug in summary.survfit for a multiple-strata survival
|
||
|
|
object. If one of the curves had no data after application of the
|
||
|
|
times argument, an output label was the wrong length.
|
||
|
|
|
||
|
|
\item Fix a bug pointed out by Charles Berry: predict for a Cox
|
||
|
|
model which has strata, and the strata is a factor with not all its
|
||
|
|
levels represented in the data. I had a mistake in the subscripting
|
||
|
|
logic: number of groups is not equal to max(as.integer(strata)).
|
||
|
|
|
||
|
|
\item Changes to avoid overflow in the exponent made in 2.36-6
|
||
|
|
caused failure for one special usage: in case-cohort designs a dummy
|
||
|
|
offset of -100 could be added to some observations. This was being
|
||
|
|
rounded away. The solution is to 1: have coxsafe not truncate small
|
||
|
|
exponents and 2: do not recenter user provided offset values.
|
||
|
|
|
||
|
|
\item Fix bug in survfit.coxph. Due to an indexing error I would
|
||
|
|
sometimes create a huge scratch vector midway through the
|
||
|
|
calculations (size = max value of "id"); the final result was always
|
||
|
|
correct however. Data set provided by Cindy Crowson which had a
|
||
|
|
user id in the billions.
|
||
|
|
|
||
|
|
\item Fix bug pointed out by Nicholas Horton: predictions of
|
||
|
|
type expected, with newdata, from a Cox model without a strata
|
||
|
|
statement would fail with "x not found". A misplaced parenthesis
|
||
|
|
from an earlier update caused it to not recreate the X matrix even
|
||
|
|
though it was needed later. Also add some further information to
|
||
|
|
the predict manual page to clarify an issue with frailty terms.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.36-12}{
|
||
|
|
\itemize{
|
||
|
|
\item Fix a bug in the new fast subsets code. The test suite had no
|
||
|
|
examples of strata + lots of tied times, so of course that's the
|
||
|
|
case where I had an indexing error. Add a test case using the
|
||
|
|
clogit function, which exercises this.
|
||
|
|
|
||
|
|
\item Further memory tuning for survexp.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.36-11}{
|
||
|
|
\itemize{
|
||
|
|
\item Make survexp more efficient. The X matrix was being modified
|
||
|
|
in several places, leading to multiple copies of the data. When the
|
||
|
|
data set was large this would lead to a memory shortage.
|
||
|
|
|
||
|
|
\item Cause anova.coxph to call anova.coxme when a list of models
|
||
|
|
has both coxph and coxme objects.
|
||
|
|
|
||
|
|
\item Add the quantile.survfit function. This allows a user to
|
||
|
|
extract arbitrary quantiles from a fitted curve (and std err).
|
||
|
|
|
||
|
|
\item Fix an error in predict.coxph. When the model had a strata
|
||
|
|
and the newdata and reference="sample" arguments were used, it
|
||
|
|
would (incorrectly) ask for a strata variable in the new data set.
|
||
|
|
|
||
|
|
\item Incorporate the fast subsets algorithm of Gail et al, when
|
||
|
|
using coxph with the "exact" option. The speed increase is profound
|
||
|
|
though at the cost of some memory. Reflect this in the
|
||
|
|
documentation for the clogit routine.
|
||
|
|
Note that the fast computation is not yet implemented for
|
||
|
|
(start,stop) coxph models.
|
||
|
|
|
||
|
|
\item Change the C routine used by coxph.fit from .C to .Call
|
||
|
|
semantics to improve memory efficiency, in particular fewer copies
|
||
|
|
of the X matrix.
|
||
|
|
|
||
|
|
\item Add scaling to the above routine. This was prompted by a user
|
||
|
|
who had some variables with a 0-1 range and others that were
|
||
|
|
0 - 10^7, resulting in 0 digits of accuracy in the variance matrix.
|
||
|
|
(Economics data).
|
||
|
|
|
||
|
|
\item Comment out some code sections that are specific to Splus.
|
||
|
|
This reduced the number of "function not found" warnings from R CMD check.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.36-10}{
|
||
|
|
\itemize{
|
||
|
|
\item 30 Sept 2011: The na.action argument was being ignored in
|
||
|
|
predict.coxph; pointed out by Cindy Crowson.
|
||
|
|
|
||
|
|
\item The log-likelihood for survreg was incorrect when there are
|
||
|
|
case weights in the model. The error is a fixed constant for any
|
||
|
|
given data set, so had no impact on tests or inferences. The error
|
||
|
|
and correction were pointed out by Robert Kusher.
|
||
|
|
|
||
|
|
\item A variable name was incorrect in survpenal.fit. This was in a
|
||
|
|
program path that had never been traversed until Carina Salt used
|
||
|
|
survreg with a psline(..., method='aic') call, leading to a
|
||
|
|
"variable not found" message.
|
||
|
|
|
||
|
|
\item Punctuation error in psline made it impossible for a user to
|
||
|
|
specify the boundary.knots argument. Pointed out by Brandon
|
||
|
|
Stewart.
|
||
|
|
|
||
|
|
\item Add an "id" variable to the output of survobrien.
|
||
|
|
|
||
|
|
\item The survfitCI routine would fail for a curve with only one
|
||
|
|
jump point (a matrix collapsed into a vector).
|
||
|
|
|
||
|
|
\item Fix an error in survfit.coxph when the coxph model has both a
|
||
|
|
strata by covariate interaction and a cluster statement. The
|
||
|
|
cluster term was not dropped from the Terms object as it should have
|
||
|
|
been, led to a spurious "variable not found" error. Pointed out
|
||
|
|
by Eva Bouguen.
|
||
|
|
|
||
|
|
\item If a coxph model with penalized terms (frailty, pspline) also
|
||
|
|
had a redundant covariate, the linear predictor would be returned as
|
||
|
|
NA. Pointed out by Pavel Krivitsky.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.36-9}{
|
||
|
|
\itemize{
|
||
|
|
\item Due to a mistake in my script that submits to CRAN, the fix in
|
||
|
|
2.36-8 below was actually not propogated to the CRAN submission.
|
||
|
|
|
||
|
|
\item Fix an error in the Cauchy example found in the survreg.distributions
|
||
|
|
help page, pointed out by James Price.
|
||
|
|
|
||
|
|
\item Update the coxph.getdata routine to use the model.frame.coxph
|
||
|
|
and model.matrix.coxph methods.
|
||
|
|
|
||
|
|
\item Add the concordance statistic to the printout for penalized models.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.36-8}{
|
||
|
|
\itemize{
|
||
|
|
\item Unitialized variable in calcuation of the variance of the
|
||
|
|
concordance. Found on platform cross-checking by Brian Ripley.
|
||
|
|
\item Changed testci to use a fixed file of results from cmprsk
|
||
|
|
rather than invoking that package on-the-fly. Suggested by the CRAN
|
||
|
|
maintainers.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
\section{Changes in version 2.36-7}{
|
||
|
|
\itemize{
|
||
|
|
\item Due to changes in R 2.13 default printout, the results of many of
|
||
|
|
the test programs change in trivial way (one more or fewer digits).
|
||
|
|
Update the necessary test/___.Rout.save files. Per the core team's
|
||
|
|
suggestion the dependency for the package is marked as >=2.13.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.36-6}{
|
||
|
|
\itemize{
|
||
|
|
\item An example from A Drummond caused iteration failure in
|
||
|
|
coxph: x=c(1,1,1,0,1, rep(0,35)), time=1:40, status=1. The first
|
||
|
|
iteration overshoots the solution and lands on an almost perfectly
|
||
|
|
linear part of the loglik surface, which made the second iteration
|
||
|
|
go to a huge number and exp() overflows. A sanity check routine
|
||
|
|
coxsafe is now invoked on all values of the linear predictor.
|
||
|
|
|
||
|
|
\item 1 April: Fix minor bug in survfit. For left censored data
|
||
|
|
where all the left censored are on the very left, it would give a
|
||
|
|
spurious warning message when trying to create a 0 row matrix that
|
||
|
|
it didn't need or use. Pointed out by Steve Su.
|
||
|
|
|
||
|
|
\item 31 March 2011: One of the plots in the r_sas test was wrong
|
||
|
|
(it's been a long time since I visually checked these). The error
|
||
|
|
was in predict.survreg; it had not taken into account a change in
|
||
|
|
R2.7.1: the intercept attribute is reset to 1 whenever one
|
||
|
|
subscripts a terms object, leading to incorrect results for a model
|
||
|
|
with "-1" in the formula and a strata(): the intercept returned
|
||
|
|
when removing the strata. I used this opportunity to move most of
|
||
|
|
the logic into model.frame.survreg and model.matrix.survreg
|
||
|
|
functions. Small change to the model.frame.coxph and
|
||
|
|
model.matrix.coxph functions due to a better understanding of
|
||
|
|
xlevels processing.
|
||
|
|
|
||
|
|
\item Round off error issue in survfit: it used both unique(time)
|
||
|
|
and table(time), and the resulting number of unique values is not
|
||
|
|
guarranteed to be the same for times that differ by a tiny amount.
|
||
|
|
Now times are coverted to a factor first. Peter Savicky from the R
|
||
|
|
core team provided a nice discussion of the issue and helped me
|
||
|
|
clarify how best to deal with it. The prior fix of first rounding
|
||
|
|
to 15 digits was good enough for almost every data set -- except the
|
||
|
|
one found by a local user just last week.
|
||
|
|
|
||
|
|
\item Round off error in print.survfit pointed out by Micheal Faye.
|
||
|
|
If a survival value was .5 in truth, but .5- eps due to round off
|
||
|
|
the printed median was wrong. But it was ok for .5+eps. Simple
|
||
|
|
if-then logic error.
|
||
|
|
|
||
|
|
\item Re-fix a bug in survfit. It uses both unique and table in
|
||
|
|
various places, which do not round the same; I had added a
|
||
|
|
pre-rounding step to the code. A data set from Fan Chun showed that
|
||
|
|
I didn't round quite enough. But the prior rounding did work for a
|
||
|
|
time of 2 vs (sqrt(2))^2: this bug is very hard to produce. I now
|
||
|
|
use as.numeric(as.character(factor(x))), which induces exactly the
|
||
|
|
same rounding as table, since it is the same compuation path.
|
||
|
|
|
||
|
|
\item Further changes to pspline. The new Boundary.knots argument
|
||
|
|
allows a user to set the boundary knots inside the range of data.
|
||
|
|
Code for extrapolation outside that range was needed,
|
||
|
|
essentially a copy of the code found in ns() for the same issue.
|
||
|
|
Also added a psplineinverse function, which may be useful with
|
||
|
|
certain tt() calls in coxph.
|
||
|
|
|
||
|
|
\item 10 Mar 2011: Add the capablilty for time-dependent
|
||
|
|
transformations to coxph, along with a small vignette describing use
|
||
|
|
of the feature. This code is still incompletely incorporated in
|
||
|
|
that the models work but other methods (residuals, predict, etc) are
|
||
|
|
not yet defined.
|
||
|
|
|
||
|
|
\item 8 Mar 2011: Expand the survConcordance function. The function
|
||
|
|
now correctly handles strata and time dependent covariates, and
|
||
|
|
computes a standard error for the estimate. All computation is based
|
||
|
|
on a balanced binary tree strucure, which leads to computation in
|
||
|
|
\eqn{O(n \log_2(n))}{O(n log(n))} time.
|
||
|
|
The \code{coxph} function now adds concordance to its output, and
|
||
|
|
\code{summary.coxph} displays the result.
|
||
|
|
|
||
|
|
\item 8 Mar 2011: Add the "reference" option to predict.coxph, a
|
||
|
|
feature and need pointed out by Stephen Bond.
|
||
|
|
|
||
|
|
\item 4 Mar 2011: Add a makepredictcall method for pspline(), which
|
||
|
|
in turn required addition of a Boundary.knots argument to the
|
||
|
|
function.
|
||
|
|
|
||
|
|
\item 25 Feb 2011: Bug in pyears pointed out by Norm Phillips. If a
|
||
|
|
subject started out with "off table" time, their age was not
|
||
|
|
incremented by that amount as they moved forward to the next "in
|
||
|
|
table" cell of the result. This could lead to using the wrong
|
||
|
|
expected rate from the rate table.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
\section{Changes in version 2.36-5}{
|
||
|
|
\itemize{
|
||
|
|
\item 20 Feb 2011: Update survConcordance to correctly handle case
|
||
|
|
weights, time dependent covariates, and strata.
|
||
|
|
|
||
|
|
\item 18 Feb 2011: Bug in predict.coxph found by a user (1 day after
|
||
|
|
36-4!). If the coxph call had a subset and predict used newdata,
|
||
|
|
the subset clause was "remembered" in the newdata construction,
|
||
|
|
which is not appropriate.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\section{Changes in version 2.36-4}{
|
||
|
|
\itemize{
|
||
|
|
\item 17 Feb 2011: Fix to predict.coxph. A small typo that only was
|
||
|
|
exercised if the coxph model had x=T. Discovered via induced error in
|
||
|
|
the rankhazard package. Added lines to the test suite to test for
|
||
|
|
this in the future.
|
||
|
|
|
||
|
|
\item Removed some files from test and src that are no longer needed.
|
||
|
|
|
||
|
|
\item Update the configure script per suggestion from Kurt H.
|
||
|
|
}}
|
||
|
|
\section{Changes in version 2.36-3}{
|
||
|
|
\itemize{
|
||
|
|
|
||
|
|
\item 13 Feb 2011: Add the rmap argument to pyears, as was done for
|
||
|
|
survexp, and update the manual pages and examples. Fix one last bug
|
||
|
|
in predict.coxph (na.action use). Passes all the
|
||
|
|
tests for inclusion on the next R release.
|
||
|
|
|
||
|
|
\item 8 Feb 2011: Change the name of the new survfit.coxph.fit routine to
|
||
|
|
survfitcoxph.fit; R was mistaking it for a survfit method. Fix
|
||
|
|
errors in predict.coxph when there is a newdata argument, including
|
||
|
|
adding yet another test program.
|
||
|
|
|
||
|
|
\item 1 Feb 2011: Fix bugs in coxph and survreg pointed out by Heinz
|
||
|
|
Tuechler and dtdenes@cogpsyphy.hu, independently, that were the same
|
||
|
|
wrong line in both programs. With interactions, a non-penalized
|
||
|
|
term could be marked as penalized due to a mismatched vector length,
|
||
|
|
leading to a spurious error message later in the code.
|
||
|
|
|
||
|
|
\item 1 Feb 2011: Update survfit.coxph to handle the case of a strata by
|
||
|
|
covariate interaction. All prior releases of the code did this
|
||
|
|
wrong, but it is a very rare case (found by Frank Harrell). Added a
|
||
|
|
new test routine coxsurv4. Also found a bug in [.survfit; for a
|
||
|
|
curve with both strata and multiple columns, as produced by
|
||
|
|
survfit.coxph, it could drop the n.censored item when subscripting.
|
||
|
|
A minor issue was fixed in coxph: when iter=0 the output coefficient
|
||
|
|
vector should be equal to the input even when the variance is
|
||
|
|
singular.
|
||
|
|
|
||
|
|
\item 30 Jan 2011: Move the noweb files to a top level directory, out of
|
||
|
|
inst/. They don't need to be copied to binary installs.
|
||
|
|
|
||
|
|
\item 22 Jan 2011: Convert the Changelog files to the new inst/NEWS.Rd
|
||
|
|
format.
|
||
|
|
|
||
|
|
\item 1 Jan 202011: The match.ratetable would fail when passed a data
|
||
|
|
frame with a character variable. This was pointed out by Heinz
|
||
|
|
Tuechler, who also did most of the legwork to find it. It was
|
||
|
|
triggered by the first few lines of tests/jasa.R (expect <- ....)
|
||
|
|
when options(stringsAsFactors=FALSE) is set.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
\section{Changes in version 2.36-2}{
|
||
|
|
\itemize{
|
||
|
|
\item 20 Dec 2010: Add more test cases for survfit.coxph,
|
||
|
|
which led to significant updates in the code.
|
||
|
|
|
||
|
|
\item 18 Nov 2010: Add nevent to the coxph output and printout in
|
||
|
|
response to a long standing user request.
|
||
|
|
|
||
|
|
\item 14 Dec 2010: Add an as.matrix method for Surv objects.
|
||
|
|
|
||
|
|
\item 11 Nov 2010: The prior changes broke 5 packages: the dependencies form a bigger
|
||
|
|
test suite than mine! 1. Survival curve for a coxph model with sparse
|
||
|
|
frailty fit; fixed and added a new test case. 2. survexp could fail if
|
||
|
|
called from within a function due to a scoping error. 3. "Tsiatis" was once
|
||
|
|
a valid type (alias for 'aalen') for survfit.coxph; now removed from the
|
||
|
|
documentation but the code needed to be backwards compatable. The other two
|
||
|
|
conflicts were fixed in the packages that call survival. There are still
|
||
|
|
issues with the rms package which I am working out with Frank H.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
\section{Changes in version 2.36-1}{
|
||
|
|
\itemize{
|
||
|
|
\item{27 Oct 2010: Finish corrections and test to the new code. It now passes
|
||
|
|
the checks. The predict.coxph routine now does strata and standard errors
|
||
|
|
correctly, factors propogate through to predictions, and numerous small
|
||
|
|
errors are addressed. Predicted survival curves for a Cox model has been
|
||
|
|
rewritten in noweb and expanded. Change the version number to 2.36-1.}
|
||
|
|
|
||
|
|
\item{17 Oct 2010: Per a request from Frank Harrell (interaction with his library),
|
||
|
|
survfit.coxph no longer reconstructs the model frame unless it really needs
|
||
|
|
it: in some cases the 'x' and 'y' matrices may be sufficient, and may be
|
||
|
|
saved in the result. Add an argument "mf" to model.matrix.coxph for more
|
||
|
|
efficient interaction when a parent routine has already recovered the model
|
||
|
|
frame.
|
||
|
|
In general, we are trying to make use of model.matrix.coxph in many of the
|
||
|
|
routines, so that the logic contained there (remove cluster() calls, pull
|
||
|
|
out strata, how to handle intercepts) need not be replicated in multiple
|
||
|
|
places.}
|
||
|
|
|
||
|
|
\item{12 Oct 2010: Fix a bug in the modified lower limits for survfit (Dory & Korn).
|
||
|
|
A logical vector was being inadvertently converted to numeric. Pointed out
|
||
|
|
by Andy Mugglin. A new case was added to the test suite. }
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
\section{Changes in version 2.35}{
|
||
|
|
\itemize{
|
||
|
|
\item{15 July 2010: Add a coxph method for the logLik function. This is used by
|
||
|
|
the AIC function and was requested by a user.}
|
||
|
|
|
||
|
|
\item{29 July 2010: Fix 2 bugs in pyears. The check for a US rate table was off
|
||
|
|
(minor effect on calculations), and there was a call to julian which assumed
|
||
|
|
that the origin argument could be a vector. }
|
||
|
|
|
||
|
|
\item{21 July 2010: Fix a problem pointed out by a user: calling survfit with almost
|
||
|
|
tied times, e.g., c(2, sqrt(2)^2), could lead to an inconsistent result. Some
|
||
|
|
parts of the code saw these as 2 unique values per the unique() function, some
|
||
|
|
as a single value using the results of table(). We now pre-round the input
|
||
|
|
times to one less decimal digit than the max from .Machine$double.digits.
|
||
|
|
Also added the noweb.R processing function from the coxme package, so that
|
||
|
|
the noweb code can be extracted "on the fly" during installation using
|
||
|
|
commands in the configure and cleanup scripts. }
|
||
|
|
|
||
|
|
\item{11 July 2010: A rewrite of the majority of the survfit.coxph code. The primary
|
||
|
|
benefits are 1: finally tracked down and eliminated the bug for standard errors
|
||
|
|
of case weights + Cox survival + Efron method; 2: the individual=TRUE and FALSE
|
||
|
|
options now use the same underlying code for curves, before there were some
|
||
|
|
options valid only for one or the other; 3: code was rewritten using noweb
|
||
|
|
with a considerable increase in documentation; 4: during the verification
|
||
|
|
process some errors were found in the test suite and corrected, e.g., a
|
||
|
|
typo in my book led to failure of an all.equal test in book4.R. Similar
|
||
|
|
to the rewrite for survfit several years ago, the new code has far less use
|
||
|
|
of .C to help transparency.}
|
||
|
|
|
||
|
|
\item{21 May 2010: Fix bug in summary.survfit. For a survival curve from a Cox model
|
||
|
|
with start,stop data, the 'times' argument would generate an error.}
|
||
|
|
|
||
|
|
\item{24 May 2010: Fix an annoyance in summary.survfit. When the survival data
|
||
|
|
had an event or censor at time 0 and summary is called with a times argument,
|
||
|
|
then my constructed call to approx() would have duplicate x values. The answer
|
||
|
|
was always right, but approx has begun to print a bothersome warning message.
|
||
|
|
A small change to the constructed argument vector avoids it.}
|
||
|
|
|
||
|
|
\item{7 April 2010: Minor bug pointed out by Fredrik Lundgren. In survfit if the
|
||
|
|
method was KM (default) and error = Tsiatis an error message results. Simple
|
||
|
|
fix: code went down the wrong branch.}
|
||
|
|
|
||
|
|
\item{24 Feb 2010: Serious bug pointed out by Kevin Buhr. In Surv(time1, time2,stat)
|
||
|
|
if there were i) missing values in time1 and/or time2, ii) illegal value
|
||
|
|
sets with time1 >=time2, and iii) all the instances of ii do not preceed all
|
||
|
|
the instances of i, then the wrong observation (not the illegal) will be
|
||
|
|
thrown out. Repaired, and a new test added.
|
||
|
|
Minor updates to 3 test files: survreg2, testci, ratetable.}
|
||
|
|
|
||
|
|
\item{8 Feb 2010: Bug pointed out by Heinz Tuechler -- if a subscript was dropped from
|
||
|
|
a rate table the 'type' attribute got dropped, e.g. survexp.usr[,1,,].}
|
||
|
|
|
||
|
|
\item{26 Jan 2010: At the request of Alex Bokov, added the xmax, xscale, and fun
|
||
|
|
arguments to points.survfit.}
|
||
|
|
|
||
|
|
\item{26 Jan 2010: Fix bug pointed out by Thomas Lumley -- with case weights <1 a Cox
|
||
|
|
model with (start, stop) input would inappropriately decide it needed to do
|
||
|
|
step halving to find a solution, eventually failing to converge. It was
|
||
|
|
treating a loglik >0 as an indication of failure, but such values arise for
|
||
|
|
small case weights. Let L(w) be the loglik for a data set where everyone is
|
||
|
|
given a weight of w, then L(w)= wL(1) - d log(w) where d=number of deaths in
|
||
|
|
the data. For small enough w positivity of L(w) is certain.}
|
||
|
|
|
||
|
|
\item{25 Jan 2010: Fix bug in summary.ratetable pointed out by Heinze Tuechler. Added
|
||
|
|
a call to the function to the test suite as well.}
|
||
|
|
|
||
|
|
\item{15 Dec 2009: Two users pointed out a bug that crept into survreg() with a
|
||
|
|
cluster statement, when a t(x)%*%x was replaced with crossprod. A trivial
|
||
|
|
fix, but in response I added another test that more formally checks the
|
||
|
|
dfbeta residuals and found a major oversight for the case of multiple
|
||
|
|
strata. }
|
||
|
|
|
||
|
|
\item{14 Dec 2009: 1.Fix bug in frailty.xxx, if there is a missing value in the levels
|
||
|
|
it gets counted by "length(unique(x))" (frailty is called before NA
|
||
|
|
removal.) 2.SurvfitCI had an incorrect CI with case weights, and 3. in
|
||
|
|
survreg a call to resid instead of residuals.survreg, before the class
|
||
|
|
was attached.}
|
||
|
|
|
||
|
|
\item{11 Nov 2009: The 'type' argument does not make sense for plot.survfit. (If
|
||
|
|
type='p', should one plot the tops of the step function, the bottoms, or
|
||
|
|
both?). Make it explicitly disallowed in response to an R-help query,
|
||
|
|
rather than the confusing error message that currently arose.}
|
||
|
|
|
||
|
|
\item{28 Oct 2009: The basehaz function would reorder the labels of the strata
|
||
|
|
factor. Not a bug really, but a "why do this?" Unintended consequence of
|
||
|
|
a character -> factor conversion.}
|
||
|
|
|
||
|
|
\item{1 Oct 2009: Fix a bug pointed out by Ben Domingue. There was one if-then-else
|
||
|
|
path into step-halving in the frailty.controldf routine that would refer to
|
||
|
|
a non-existent variable. A very rarely followed path, obviously, and with
|
||
|
|
the obvious fix. The mathematics of the update was fine.}
|
||
|
|
|
||
|
|
\item{30 Sep 2009: For coxph and model.matrix.coxph, re-attach the
|
||
|
|
attributues lost from the X matrix when the intercept is removed,
|
||
|
|
i.e., X <- X[,1]. In particular, some downstream libraries depend on
|
||
|
|
the assign attribute.
|
||
|
|
For predict.coxph remove an earlier edit so that a single variable model
|
||
|
|
+ type='terms' returns a matrix, not a vector. This is expected by the
|
||
|
|
termplot() function. It led to a whole lot of changes in the test suite
|
||
|
|
results, though, due to more "matrix" printouts.}
|
||
|
|
|
||
|
|
\item{4 Sep 2009: Added a model.matrix.coxph and model.frame.coxph methods. The
|
||
|
|
model.matrix.default function ceased to work for coxph models sometime
|
||
|
|
between R 2.9 and 2.9.2 (best guess). This wasn't picked up in the test
|
||
|
|
suite but rather by failure of 3 packages that depend on survival. Also added
|
||
|
|
a test. Update CRAN since this broke other's packages.}
|
||
|
|
|
||
|
|
\item{20 Aug 2009: One more fix to predict.coxph. It needed to use
|
||
|
|
delete.response(Terms) rather than Terms, so as to not look for (unnecessarily)
|
||
|
|
the response variable when the newdata argment is used. Pointed out by Michael
|
||
|
|
Conklin.}
|
||
|
|
|
||
|
|
\item{17 Aug 2009: Small bug in survfit.coxph.null pointed out by Frank Harrell. The
|
||
|
|
'n' component would be missing if the input data included strata, i.e., the
|
||
|
|
initial model had used x=TRUE. He also pointed out the fix.}
|
||
|
|
|
||
|
|
\item{10 June 2009: Fix an error pointed out by Nick Reich, who was the first to use
|
||
|
|
interval censored data + user defined distribution in survreg, jointly. There
|
||
|
|
was no test case and creating one uncovered several errors (but only for this
|
||
|
|
combination). All the error cases led to catastrophic failure, highlighting
|
||
|
|
the extreme rarity of a user requesting this combination.}
|
||
|
|
|
||
|
|
\item{2 June 2009: Surv(time1, time2, status, type='interval') would fail for an NA
|
||
|
|
status code. Pointed out by Achim Zeilus.}
|
||
|
|
|
||
|
|
\item{22 May 2009: Allow single subscripts to rate tables, e.g. survexp[1:10: .
|
||
|
|
Returns a simple vector of values. The str() function does this to print out
|
||
|
|
a short summary. Problem pointed out by Heinz Tuechler.}
|
||
|
|
|
||
|
|
\item{21 May 2009: Create a test case for factor variables/newdata/predict for coxph
|
||
|
|
and survreg. This led to a set of minor fixes; the code is now in line with
|
||
|
|
the R standard for model functions. One consequence is that model.frame.coxph
|
||
|
|
and model.frame.survreg are no longer needed, so have been removed.}
|
||
|
|
|
||
|
|
\item{20 May 2009: The manual page for survfit was confusing, since it tries to
|
||
|
|
document both the standard KM (formula method) and the coxph method. I've
|
||
|
|
split them out so that now survfit documents only the basic method and points
|
||
|
|
a user the appropriate specialized page.}
|
||
|
|
|
||
|
|
\item{1 May 2009: The anova.coxph function was incorrect for models with a strata
|
||
|
|
term. Fixed this, and made chisquare tests the default.}
|
||
|
|
|
||
|
|
\item{22 April 2009: The coxph code had an override to iter and eps, making both of
|
||
|
|
them more strict for a penalized model. However, the overall default values
|
||
|
|
have changed over time, so that these lines actually decreased accuracy - the
|
||
|
|
opposite of their intent. Removed the lines. Also removed the iter.miss and
|
||
|
|
eps.miss components (on which this check depended) from coxph.control, which
|
||
|
|
makes that function match its documentation.}
|
||
|
|
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
\section{Changes in version 2.34 and earlier}{
|
||
|
|
\subsection{Merge of the TMT source code tree with the Lumley code tree}{
|
||
|
|
\itemize{
|
||
|
|
|
||
|
|
\item Issues/decisions in remerging the Mayo and R code:
|
||
|
|
For most of routines, it was easier to start with the Lumley code and add
|
||
|
|
the Therneau fixes. This is because Tom had expanded a lot of partial
|
||
|
|
matches, e.g., fit$coef in the TT code vs fit$coefficients. Routines with
|
||
|
|
substantial changes were, of course, a special case.
|
||
|
|
The most common change is an is.R() construct to choose class vs oldClass.
|
||
|
|
\item xtras.R: Move anova.coxph and anova.coxphlist to their own
|
||
|
|
source files.
|
||
|
|
The remainder of the code is R only.
|
||
|
|
|
||
|
|
\item survsum: removed from package
|
||
|
|
|
||
|
|
\item survreg.old: has been removed from the package
|
||
|
|
|
||
|
|
\item survfit.s:
|
||
|
|
Depreciate the "formula with no ~1" option
|
||
|
|
Mayo code for [ allows for reordering curves
|
||
|
|
Separate out the R "basehaz" function as a separate source file
|
||
|
|
|
||
|
|
\item survfit.km.s: The major change of did not get copied into R, so lots of
|
||
|
|
changes. R had "new.time" and Splus 'start.time' for the same argument. Allow
|
||
|
|
them both as synonyms.
|
||
|
|
The output structure also changed: adapt the new one. This is mostly some
|
||
|
|
name changes in the components, removing unneeded redundancies created by
|
||
|
|
a different programmer.
|
||
|
|
|
||
|
|
\item survfit.coxph.s: TMT code finally fixed the "Can't (yet) to case weights"
|
||
|
|
problem. There must have been 10 years been the intent and execution.
|
||
|
|
|
||
|
|
\item survexp.s: Add "bareterms" function from R, which replaces a prior use of
|
||
|
|
terms.inner (in Splus but not R).
|
||
|
|
|
||
|
|
\item survdiff.s: R code had the old (incorrect) expected <- sum(1-offset), since
|
||
|
|
corrected to sum(-log(offset)) .
|
||
|
|
|
||
|
|
\item{summary.coxph.s: This was a mess, since Tom and I had independently made the
|
||
|
|
addition of a print.summary.coxph function. Below, TMT means that it was the
|
||
|
|
choice in the Splus code, TL means that it was the choice in R
|
||
|
|
1. Put the coef=T argument in the print function, not summary (TMT)
|
||
|
|
2. Change the output's name from coef to coefficients (suggestion of
|
||
|
|
Peter Dalgaard). Also change one column name to Pr(>|z|) for R.
|
||
|
|
3. Remove last vestiges of a reference to the 'icc' component (TMT)
|
||
|
|
4. Do not include score, rscore, naive.var in the result (TL)
|
||
|
|
5. Do include loglik in the result (TMT)
|
||
|
|
6. Compute the test statistics (loglik, Wald, etc) in the summary
|
||
|
|
function rather than in the print.summary function (TL)
|
||
|
|
7. Remove the digits option from summary, it belongs in print.summary.
|
||
|
|
(neither)}
|
||
|
|
|
||
|
|
\item{strata.s: R code added a sep argument, this is ok
|
||
|
|
R changed the character string NA to as.character(NA). Not okay
|
||
|
|
1. won't work with Splus,
|
||
|
|
2. This is a label, designed for printing,
|
||
|
|
and so it should be a character string. }
|
||
|
|
|
||
|
|
\item{residuals.coxph.s: R had added type='partial'. (Which I'm not very partial to,
|
||
|
|
from their statistical properties. But they are legal, and I assume that
|
||
|
|
someone requested them).}
|
||
|
|
|
||
|
|
\item{print.survfit.s: Rewritten as a part of the general survival rewrite. Created
|
||
|
|
the function 'survmean' which does most of the work, and is shared by print and
|
||
|
|
summary, so that the values from 'print' are now available.
|
||
|
|
Fix the minmin function: min(NULL) gives NA in Splus, which is the right
|
||
|
|
answer for a non-estimable median, but Inf in R. Explicitly deal with this
|
||
|
|
case, and add a bunch of comments.
|
||
|
|
R had the print.rmean option, this has been expanded to a more general
|
||
|
|
rmean option that allows setting the cutoff point.
|
||
|
|
R added a print.n option with 3 choices, my code includes all 3 in the
|
||
|
|
output. }
|
||
|
|
|
||
|
|
\item{lines.survfit.s:
|
||
|
|
The S version has a new block of code for guessing "firstx" more
|
||
|
|
intellegently when it is missing. (Or, one hopes is is more intellegent!)}
|
||
|
|
|
||
|
|
\item{coxph.control.s:
|
||
|
|
The R code had tighter tolerances (eps= 1e-9) than Splus (1e-4) and
|
||
|
|
a higher iterationn count (20 vs 10).
|
||
|
|
Set eps to 1e-8 and iter to 15, mostly bending to the world. The tighter
|
||
|
|
iteration is defensible, but I still maintain that a Cox model that takes >10
|
||
|
|
iterations is not going to finish if you give it 100. The likelihood surface
|
||
|
|
is almost perfectly quadratic near the minimum. (Not true for survreg by the
|
||
|
|
way).}
|
||
|
|
|
||
|
|
\item{: In Surv, the Mayo code creates NA's out of invalid status values or
|
||
|
|
start,stop pairs, rather than a stop and error message. This is to
|
||
|
|
allow for example
|
||
|
|
coxph(Surv(time1,time2, status).... , subset=(goodlines))
|
||
|
|
succeed, when "goodlines" is the subset with correct values.}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
\subsection{Older changes}{
|
||
|
|
\itemize{
|
||
|
|
\item{25SepO7: How embarrassing -- someone pointed out that I had Dave
|
||
|
|
Harrington's name spelled wrong in the options to survfit.coxph!}
|
||
|
|
|
||
|
|
\item{9Jul07: In a model with offsets, survreg mistakenly omitted the offset
|
||
|
|
from the returned linear.predictor component.}
|
||
|
|
|
||
|
|
\item{10May07: Change summary.coxph so that it returns an object of class
|
||
|
|
summary.coxph, and add a print method for that object.}
|
||
|
|
|
||
|
|
\item{22Jun06: Update match.ratetable, so that more liberal matches are now
|
||
|
|
allowed. For instance, 'F', 'f', 'female', 'fem', 'FEMA', etc are
|
||
|
|
now all considered matches to the dimname "female" in survexp.us.}
|
||
|
|
|
||
|
|
\item{26Apr06: Fix bug in summary.survfit, pointed out by Bob Treder. With
|
||
|
|
the times option, the value of n.risk would be wrong for "in between"
|
||
|
|
times; e.g., the data had events and/or censoring at times 10,
|
||
|
|
20,... and we asked for printout at time 15. It should give n.risk at time
|
||
|
|
20, it was returning the value at time 10. Interestingly, the code had
|
||
|
|
a very careful treatment of this case, along with an example in the
|
||
|
|
comments, and the "the right answer is" part of the comment was wrong!
|
||
|
|
So the code correctly computed an incorrect answer. Added another
|
||
|
|
test case to the test suite, survtest2.}
|
||
|
|
|
||
|
|
\item{21Apr06: Fix problem in [.survfit, pointed out by Thomas Lumley. If
|
||
|
|
fit <- survfit(Surv(time, status) ~ ph.ecog, lung), then fit[2:1] did
|
||
|
|
not reorder the output correctly. I had never tested putting the
|
||
|
|
subscripts in non-increasing order.}
|
||
|
|
|
||
|
|
\item{7Feb06: Fix a problem in the coxph iteration (coxfit2.c, coxfit5, agfit3,
|
||
|
|
agfit5, agexact). It will likely never catch anyone again, even if I
|
||
|
|
didn't fix it. In a particular data set, beta overshot and step halving
|
||
|
|
was invoked. During step halving, a loglik happened to occur that was
|
||
|
|
within eps of the prior step's loglik --- and the routine decided, erroneously,
|
||
|
|
that it had converged! (A nice quadratic curve, a first guess b1 to the
|
||
|
|
left of the desired max of the curve. The next guess b2 overshot and ends
|
||
|
|
up with a lower loglik, on the right side of the max. Back up to the
|
||
|
|
midpoint of b1 and b2, and this guess, still to the right of the max (still
|
||
|
|
too large) has EXACTLY the same value of y as b1 did, but on the other side
|
||
|
|
of the max from b1. "Last two guesses give the same answer, I'm done" said
|
||
|
|
the routine).}
|
||
|
|
|
||
|
|
\item{27Sep05: Found and fixed a nasty bug in survfit. When method='fh2' and
|
||
|
|
there were multiple groups I had a subscripting bug, leading to vectors
|
||
|
|
that were supposed to be the same length, but weren't, passed into C.
|
||
|
|
The resulting curves were obviously wrong -- survival precipitously drops
|
||
|
|
to zero.}
|
||
|
|
|
||
|
|
\item{5May05: Add the drop=F arg to one subscripting selection in survfit.coxph.
|
||
|
|
temp <- (matrix(surv$y, ncol=3))[ntime,,drop=F]
|
||
|
|
If you selected only 1 time point (1 row) in the final output, the code
|
||
|
|
would fail. Pointed out by Cindy Crowson.}
|
||
|
|
|
||
|
|
\item{18Apr05: Bug in survfit.turnbull. The strata variable was not being
|
||
|
|
filled in (number of points per curve). So if multiple curves were
|
||
|
|
generated at once, i.e., with something on the right hand side of ~ in
|
||
|
|
the formula, all the downstream print/plot functions would not work
|
||
|
|
with the result.}
|
||
|
|
|
||
|
|
\item{8Feb05: Fix small typo in is.ratetable, introduced on 24Nov04: (Today
|
||
|
|
was the first time I added to the standard library, and thus ended
|
||
|
|
up using the non-verbose mode.)}
|
||
|
|
|
||
|
|
\item{8Feb05: Add the data.frame argument to pyears. This causes the output
|
||
|
|
to contain a dataframe rather than a set of arrays. It is useful for
|
||
|
|
further processing of the data using Poisson regression.}
|
||
|
|
|
||
|
|
\item{7Feb05: Modified print.ratetable to be more useful. It now tells
|
||
|
|
about the ratetable, rather than printing all of its values.}
|
||
|
|
|
||
|
|
\item{8Dec04: Fix a small bug in survfit.turnbull. If there are people left
|
||
|
|
censored before the first
|
||
|
|
time point of any other kind (interval, exact, or right censored),
|
||
|
|
the the plotted height of the curve from "rightmost left censoring time"
|
||
|
|
to "leftmost event time", that is the flat tail on the left, was at
|
||
|
|
the wrong height.
|
||
|
|
Added another test to testreg/reliability.s for this.}
|
||
|
|
|
||
|
|
\item{24Nov04: Change is.ratetable to give longer messages}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|