2.4-4: (Sep 21, 2016)
* rpch: Bug fixed (spotted by Brigitte Mueller).
* plot.phreg: parameters 'changeLog' and '...'
enhanced. Documentation updated.
* plot.coxreg: Bug concerning 'printLegend' fixed.
* weibreg: Note added in documentation: "Use phreg
instead". weibreg will soon be deprecated.
2.4-3: (May 5, 2015)
* coxreg: Changed the default for 'hazards' to TRUE.
* getHaz: Modified to handle missing strats and score.
* print.risksets: Added '...' to argument list.
* coxreg: Fitting a NULL model didn't produce enough information
like log likelihood ('loglik'), for comparison of models. Fixed.
* glmmboot: 'frail' set to Inf or -Inf for appropriate clusters.
* plot.hazdata: Updated to acknowledge the argument 'hazards' that was
included in 'coxreg' in version 2.4-2.
* plot.coxreg: Updated to acknowledge the argument 'hazards' that was
included in 'coxreg' in version 2.4-2. Errors in the manual page
corrected.
* risksets: Risk set sampling did not always work (memory leak in
C code); fixed.
* risksets: New value in the Value list: sample_fraction.
* plot.aftreg: Now registered as an S3 method.
* print.aftreg: Scale and shape parameters are only printed on the
log scale.
2.4-2: (Dec 15, 2014)
* src: 'abs' corrected to 'fabs' in two places in C code.
* coxreg: Argument 'hazards' added, with default = FALSE.
* plot.Surv: Argument 'printLegend' added.
* coxreg: Changed labels in case of ordered factors.
* Foreign calls: 'DUP = FALSE' removed everywhere.
* print.pch: Bug preventing printing(!) fixed.
* plot.pch: Bug preventing plotting(!) fixed.
2.4-1: (Feb 14, 2014)
* phreg: Fails often for the lognormal and loglogistic models with
badly fitting data. A warning is included in the documentation,
and better error handling in case of a failure. Example under
'check.dist' changed accordingly.
2.4-0: (Feb 10, 2014)
* coxreg: Call to survival::[agreg,coxph].fit in "standard" cases
reintroduced; Thanks to Terry Therneau, who exports these
functions from survival_2.37-6. So this version of 'eha' requires
survival (>= 2.37-6). Argument 'center' reintroduced, with slightly
different meaning.
* plot.coxreg: argument 'newdata' not used.
* phreg: Stratified analysis in the piecewise constant hazards
model introduced. Argument 'center' reintroduced, with slightly
different meaning.
* plot.phreg: Argument 'newdata' not used.
2.3-5: (Jan 17, 2014)
* plot.coxreg: Added the argument lty, for line type, and the
logical parameter 'printLegend' (default: TRUE). Setting it to FALSE
skips the legend in the figure.
2.3-4: (Dec 5, 2013)
* plot.coxreg: added the argument col, for color line(s).
* plot.hazdata: Ditto.
2.3-3: (Oct 10, 2013)
* coxreg: Restoring equity.
* glmmML: Removed spurious printing in 'glmmml.c'.
2.3-2: (Oct 10, 2013)
* aftreg: Updated start values for the Gompertz distribution,
matching the (now mandatory) 'canonical' parametrisation.
2.3-1: (Oct 03, 2013)
* coxreg: Downgraded due to limitations in using
non-exported function (agreg) from 'survival'. This will be taken
care of ASAP. Meanwhile, live with slightly slower 'coxreg' and
choking on huge data sets.
* Coxreg: Removed for the same reason as the downgrade of coxreg.
2.3-0: (Oct 03, 2013)
* phreg: The lognormal and loglogistic distributions have
an intercept added to the linear predictor; in effect extending
these distributions to three-parameter families.
A bug (found by Claire Williams) affecting the covariance matrix
of the parameter estimates has been eliminated.
* aftreg: The same bug as for phreg eliminated. The available
parametrizations are changed to 'lifeAcc' and 'lifeExp'. For the
Gompertz distribution, the 'canonical' representation is used
regardless.
* hlnorm, Hlnorm, hllogis, Hllogis: New parameter, 'prop',
added. It simply multiplies the previous definitions by its value.
* age.window, cal.window: speed up and handling of empty intervals
* perstat: speed up.
2.2-6: (June 23, 2013)
* plot.phreg, plot.coxreg: legend added for stratified fits.
* Coxreg: New function designed to handle huge data sets. coxreg
chokes on 'integer overflow', and memory overflow, when the
collection of risk sets is created and saved. Coxreg is
essentially a wrapper for 'coxph' in the 'survival' package, but
with methods for nice(r) printing.
* coxreg: Error in the calculation of 'total time at risk' fixed
(gave negative values when no left truncation!).
2.2-5: (May 13, 2013)
* Gompertz, ltx: Too long lines in the documentation fixed.
2.2-4: (May 13, 2013)
* phreg: The gompertz 'scale' parameter is now a real scale
parameter through a reparametrization of the baseline gomperz
distribution. It follows now the 'canonical' parametrization.
There is also a new argument, 'param', which can take the values
"canonical" (default) and "rate". Better start values
for the Gompertz regressions.
* check.dist : Has failed due to different scaling in coxreg and
phreg since 2.2-2. Now fixed.
2.2-3: (April 17, 2013)
* risksets: Added an argument, 'members', a logical with default
value 'TRUE'. If TRUE, the members of all risk sets are returned.
With huge data sets, this may be too much, and not wanted. In such
cases, set 'members = FALSE'.
* coxreg: Memory leaks fixed in getHaz.f, sizes.c and risk.c.
2.2-2: (March 23, 2013)
* phreg: argument 'center' deprecated; centering of covariates is
done internally, but uncentered results reported. If you want
centered results, center covariates yourself!
2.2-1: (November 6, 2013)
* weibreg, phreg, aftreg: Error messages refreshed.
2.2-0: (October 30, 2012)
* ltx is made generic, with methods for coxreg, phreg, and aftreg
2.1-3: (September 6, 2012)
* Gompertz distribution: new parameter 'param'; values 'default'
(default, nothing changes), and 'canonical', which gives meaning
'PH' and 'AFT' to the shape and scale parameters, respectively.
* aftreg: New input argument: 'param', with three values, 'default'
(which is the default;), 'survreg', and 'canonical'. The value
'default' uses the standard parametrization, while 'survreg' uses
the same parametrization as the survreg function in the survival
package. 'canonical' is especially useful in the Gompertz
distribution for separating PH and AFT parameters.
2.1-2 (August 30, 2012)
* glmmboot, glmmbootFit: Reduced the numbers of iterations in the
examples.
2.1-1 (August 29, 2012)
* aftreg: There was a bug when using 'dist="gompertz"' and
the 'id' argument with more than one record per id. This is now
hopefully solved.
2.1-0 (June 25, 2012)
* glmmML: Added the gamma distribution to the possible priors in
the case of the Poisson model.
2.0-7 (January 3, 2012)
* C code cleaned (avoiding some Warnings at CRAN).
* check.dist: New argument, col, added. Default is now
black-and-white plotting.
2.0-6 (December 9, 2011)
* plot.Surv: Can now handle missing values in strata variable (by
deleting corresponding cases!)
2.0-5 (October 13, 2011)
* ltx: New function for printing coxreg fits in latex format.
* plot.Surv: New arguments, col and lty, added. The default is now
black-and-white plotting.
* data: Two new data sets, "logrye" and "scania".
2.0-4 (August 27, 2011)
* oldmort: Data set updated.
* aftreg.fit: Errors in documentation corrected.
2.0-3 (August 12, 2011)
* SurvSplit: Bug fixed. It works now.
* glmmboot: Bug in calculation of 'frail' fixed.
* plot.phreg: Bug in argument 'ylim' fixed. Bug with stratified
fits fixed.
* aftreg, phreg: summary method added (just printing).
2.0-2 (August 8, 2011)
* coxreg: 'x = TRUE' now really returns the design matrix.
2.0-1 (August 7, 2011)
* sw_fun: C function (internal) now declared and defined.
2.0 (August 6, 2011)
* glmmML: Merged into eha. This adds binary and count data
regression for clustered data to eha. glmmML is still a standalone
package on CRAN, for how long remains to be seen.
* Pch: New class of distributions; Piecewise constant hazards (Pch).
* phreg: piecewise constant baseline hazard function introduced.
* phreg: 'center' reinstalled as a logical, default = TRUE, so
nothing changes if 'center' is left untouched.
* age.window: If the selected window is empty, an error was
previously thrown. Now NULL is returned, with a warning.
* cal.window: Now returns NULL, with a warning, if the selected
window is empty.
1.4 (June 26, 2011)
* aftreg: Gompertz distribution added (back again). Better start values.
* phreg: Better start values for Gompertz distribution.
1.3-7 (June 20, 2011)
* eha: Depends (R >= 2.13.0)
* phreg, aftreg, weibreg: Errors in documentation corrected.
* ChangeLog: Errors in 1.3-6 corrected.
1.3-6 (June 18, 2011)
* coxph, phreg, aftreg: Bug fix: Logical covariates now OK.
(converted to factor).
* phreg: Removed "coxph" from "class".
* aftreg: Ditto.
* weibreg: Ditto.
* oldmort: New data set.
* coxreg: added return values 'df' and 'n'.
* coxreg, phreg, aftreg: Added extractAIC and nobs methods.
1.3-5 (May 20, 2011)
* infants: New data set containing matched data on infant and
maternal mortality.
1.3-4 (May 10, 2011)
* toBinary: Now includes also risksets without survivors (if any).
* fert: Row names changed to row numbers.
* swe07: New data set.
* Spelling errors (some!) corrected in documentation.
1.3-3 (May 4, 2011)
* male.mortality: Old name (male.mortality) of data frame mort
reinstalled.
Now known under two names. Overlapping spells no longer exist.
* fert: Documentation corrected.
* toDate: Now works as intended.
1.3-2 (March 1, 2011)
* dllogis: Bug fixed.
* hllogis: Bux fixed.
1.3-1 (January 15, 2011)
* phreg: Fixed error and (some) numerical instability in the
estimation of the Gompertz proportionla hazards model (seems to be
very sensitive to good start values!).
* plot.phreg: Fixed 'ylim' for cumulative hazards plot.
* male.mortality: Data set renamed to
* mort: The new name. (Just for convenience!)
1.3-0 (January 4, 2011)
* coxreg: Major revision, calls 'coxph' in 'survival' (thanks to
Terry Therneau!) for ordinary requests. Reason: speed. The argument
'center' is deprecated, centering of covariates is now routinely
made. Affects the estimation of the baseline hazard, which is done
at the means of the columns of the original design matrix.
* phreg: Argument 'center' is deprecated. Centering is routinely
performed, so the baseline hazard is estimated at the means of the
columns of the original design matrix.
* aftreg: Corrected error in documentation and made the argument
'center' deprecated.
* aftreg: Estimation of intercept ("scale") is now comparable with
corresponding estimate of Intercept in 'survreg'. 'shape' in
aftreg is still '1 / scale' in survreg. Regression coefficients still
have different signs but the same absolute values.
* join.spells: a few bugs fixed, now allows for factor covariates.
* male.mortality: data set "joined".
* fert: is a new data set. Contains data on 19th century marital
fertility from a parish in northern Sweden.
1.2-18 (February 28, 2010)
* aftreg.fit: Check of data consistency in case of more than one
record per individual added.
* aftreg.fit: Fixed memory allocation bug in C code. This bug was
not fatal (too much memory was allocated), but caused a severe
performance problem, especially on Windows.
1.2-17 (February 23, 2010)
* aftreg: 'dist = "gompertz"' should now work (realizing that it
is a special case of 'dist = "EV").
* phreg: Fixed bugs for the cases with fixed shape (includes 'dist
= "gompertz"'.
* aftreg: 'offset' works now.
* phreg: Ditto.
* check.dist: Bug fixed for 'dist = "gompertz"' (again!)
* plot.phreg: Ditto.
1.2-16 (February 19, 2010)
* aftreg: 'dist = "gompertz"' is unreliable, so changed the
example and added a note with a warning. Is also an item on the
ToDo list now.
1.2-15 (February 18, 2010)
* aftreg: argument 'id' now works as intended, i.e., is looked for
in 'data' (or 'parent.frame()')
* print: functions return invisibly 'x'.
* coxreg: argument 'weights' now works as intended, i.e., is looked for
in 'data' (or 'parent.frame()')
1.2-14 (October 29, 2009)
* check.dist: Bad 'ylim' fixed.
* aftreg: Gompertz distribution had a bug; now fixed.
1.2-13 (October 26, 2009)
* plot.coxreg: Bug fixed in call to plot.hazdata (wrong order of args).
1.2-12 (October 15, 2009)
* aftreg: Works now for time-varying covariates. Not polished.
1.2-7 (August 13, 2009)
* coxreg: Time-dependent offset introduced.
1.2-6 (August 11, 2009)
* coxreg.fit: Time-dependent weights work now.
1.2-5 (August 2, 2009)
* coxreg: Added (time-varying) weighted Cox regression. Returns
error code 1 if failure, with a warning.
* check.dist: Can now handle stratified models.
1.2-4 (Jan 12, 2009)
* Bugs in qEV, rEV, all Gompertz functions, plus documentation of
EV and Gompertz fixed. Note that these bugs did not affect aftreg
or phreg! However,
* check.dist had to be revised due to the above bugs.
1.2-2 (Aug 25, 2008)
* Bug in coxreg, method = "ml" fixed.
* Bug in coxreg, calculation of hazard, fixed.
* Several errors in the documentation fixed.
1.2-0 (Jul 18, 2008)
* Added functionality: Accelerated failure time models with
several distributions, parametric proportional hazards models
with the same distributions. All models allow for left truncated
and right censored data, as well as for stratification.
Plot methods for the new models.
1.0-1 (Jan 5, 2008)
* Added 'risktime' to toBinary output.
0.99 (June 9, 2007) This is the last release before version 1.0!
* Added full profiling to the "ml" and "mppl" methods in
coxreg.
* mlreg is now deprecated. Use coxreg with method = ml or = mppl
0.98
0.97
0.96-7 (Dec 29, 2006)
* Corrected a bug in the documentation of 'weibreg'.
0.96-6 (Dec 28, 2006)
* Corrected a bug in weibreg concerning 'center = FALSE'.
0.96-5 (Oct 24, 2006)
* added a 'terms' object to the output of coxreg and mlreg.
0.96-1 (May 15, 2006)
* plot.Surv improved. Suggestions by Dimitri Szerman. (Thanks!)
0.96-0 (April 14, 2006)
* Weibull regression updated; It is now possible to fit a Weibull
model to left-truncated and right-censored data without
covariates. A small error in the documentation of 'weibreg'
corrected.
0.94-3 (Aug 22, 2005)
* 'check.surv': If the 'id' was a factor with unused labels,
the result was unpredictable. Corrected.
0.94-2 (Jun 27, 2005)
* Errors in the documentation of 'weibreg' corrected.
0.93-0 (Sep 20, 2004)
* NAMESPACE introduced for R-2.0.0.
0.92-4 (May 5, 2004)
* coxreg: 'Error' changed to 'warning' for a singular hessian, in
which case the new return value is NULL.
0.92-3 (March 19, 2004)
* table.events: New parameter: 'strict = TRUE'.
* make.communal: In case of 'communal=FALSE', spells are no longer
truncated. Instead a value of NA is given if birthdate is out of
range. Previous behavior was unpredictable when birthdate was out
of range.
0.92 (November 12, 2003)
* mlreg: Geometric distribution (i.e., constant baseline discrete
hazard) added. Not for frailty models, yet (on the TODO list).
* mlreg: New argument, 'n.points', added to 'control'. Controls
the number of points used in the Gauss-Hermite quadrature.
* mlreg: Stricter control of numerical problems, especially in the
frailty fit.
* clean: Replaced by check.spells and join.spells.
* Return values changed to conform with R-1.8.0 (and later).