NEWS.md
In survrec: Survival Analysis for Recurrent Event Data

survrec 2.0.0

The dot-separated function names of survrec 1.x were renamed to snake_case: psh_fit(), wc_fit(), mlefrailty_fit(), surv_search() and q_search(). The old names (psh.fit(), wc.fit(), mlefrailty.fit(), surv.search(), q.search()) still work but emit a deprecation warning and will be removed in a future release. S3 methods (plot.survfitr(), ...) and the argument names shared with the survival ecosystem (conf.int, boot.F, ...) are unchanged.
The computational core has been rewritten from Fortran 77 to modern C++ (via Rcpp). The public R API (Survr(), survfitr(), psh_fit(), wc_fit(), mlefrailty_fit(), survdiffr(), q_search(), surv_search() and the S3 methods) is unchanged.
New maintainer: Dolors Pelegri-Siso.
The bootstrap (survdiffr()) now uses R's random number generator, so results are reproducible with set.seed(). The previous implementation used the non-standard GNU rand() generator, which R could not seed. The seed argument now defaults to NULL (use the current RNG state) and is honoured when supplied; in 1.2-5 it was silently ignored.
The semiparametric (gamma frailty) bootstrap of survdiffr() (boot.F = "semiparametric") is now available; it existed in the Fortran code but was disabled in the R layer.
mlefrailty_fit() now returns the posterior frailty estimates ($frailties), previously computed internally and discarded.
The proprietary IMSL routine ZXGSP (golden-section search) and the copied Netlib Brent/D1MACH code have been replaced by a clean implementation of Brent's minimization algorithm.
All fixed-size internal buffers (800 elements) have been removed; data size is now unlimited.

summary() on a fit without strata no longer fails with "$ operator is invalid for atomic vectors".
wc_fit() no longer reads an undefined loop variable when counting events of subjects whose only gap time is censored (undefined behaviour in the Fortran wc2 routine).
The EM algorithm of mlefrailty_fit() now honours the requested convergence tolerance tol. In 1.2-5 the inner alpha search overwrote it with 1e-4 after the first iteration and computed part of the convergence criterion in single precision, so estimates may differ slightly (they are now more accurate).
The 7-seed retry loop of mlefrailty_fit() is now really executed when the EM does not converge (a status-flag bug made it dead code).
survdiffr() no longer fails when boot.G or seed are supplied together with a grouping formula (they leaked into the model frame).
q_search() returns NA with a warning (instead of failing) when the survival estimates are unavailable.
wc_fit() now reports m as the number of recurrences per subject, consistently with psh_fit(); it previously counted the censored record as well.
Several plot, summary and q_search internals accessed $surv relying on partial matching; they now use the actual component name.

New ggplot2 graphics sharing the visual style of the companion package gcmrec: autoplot() methods for survival fits (with fun = "surv"/"event"/"cumhaz" and pointwise log-log confidence bands), plotEstimators() to overlay the three estimators on the same data, autoplot() for mcf and grouped survdiffr results, and the exported theme_survrec(). The base-graphics plot()/lines() methods are kept for backwards compatibility.
New mcf(): Nelson-Aalen type estimate of the mean cumulative function (expected number of events by calendar time), optionally by group.
New quantile() and as.data.frame() methods for survfitr objects.
Grouped survdiffr() results now have class survdiffr with a summary() method that reports percentile bootstrap intervals per group and pairwise differences of quantiles with bootstrap p-values (the per-group elements keep class boot, so boot::boot.ci() keeps working).
Fits no longer depend on the ordering of the input rows: subjects are regrouped by order of first appearance. In 1.2-5 the estimators silently misaligned subjects and gap times when the ids did not appear in sorted, contiguous blocks.
Survr() now checks that every subject has exactly one censored time (the old check could be fooled by compensating subjects).
The bootstrap re-estimation of survdiffr() runs in parallel with OpenMP when available. The number of threads is controlled with the new survrecThreads() function (default: let OpenMP decide, honouring OMP_NUM_THREADS). Resampling stays serial on R's RNG, so results are identical for any number of threads.
plot.survfitr() no longer draws meaningless confidence bands when the fit provides no standard errors or conf.int = FALSE is given.

Registered native routines via Rcpp; DESCRIPTION uses Authors@R; documentation migrated from hand-written latin1 .Rd files to roxygen2 (UTF-8), with the NAMESPACE generated by roxygen2.
R sources reorganized into one file per exported function; interpreted code vectorized (colSums(), rowsum(), findInterval() replace explicit loops and outer()/apply() constructions).
Regression test suite (testthat) validating the C++ port against reference values generated with the original Fortran implementation (see tools/build-reference-fits.R).