Releases: graemeleehickey/joineRML
v0.4.5
v0.4.4
New features
- Added
broom
compatability.
Bug patches
- Fixed issue that required subject IDs to be first column in dataset.
Housekeeping
- Added @ellessenne as package author.
- Updates to DESCRIPTION.
- Documentation updates.
v0.4.3
Housekeeping
- Graeme Hickey taken over the package as creator and maintainer.
- Updates to DESCRIPTION
- Updates to Makevars and Makevars.win
- Updates to appveyor.yml and .travis.yml settings
- Updates to .gitignore
v0.4.1
New features
-
Added smoothed predicted survival curves to the
plot.dynSuv()
. Smoothing is based on the contrainsed B-splines method. -
dynSurv()
now includes an argument to specify a horizon time from the last known observation time. -
simData()
now includes an argument to choose multivariate t-distributed random effects with varying degrees of freedom, thus allowing for sensitivity analyses of heavier tail distributions.
Housekeeping
-
Minor corrections to documentation.
-
Minor bug fixes to plotting functions.
-
Added MRC to DESCRIPTION as funder.
v0.4.0
New features
-
The MCEM algorithm can be implemented with vanilla Monte Carlo and quasi-Monte Carlo (using either the scrambled Sobol sequence or the Halton sequence). This is implemented through the
type
argument passed to the list ofcontrol
parameters inmjoint()
. -
bootSE()
now has option to use parallel computing via theforeach
package.
Bug patches
-
Fixed some small errors in the
epileptic.qol
dataset. -
Fixed situation where a tibble might be given as the dataset (#55 @ellessenne).
-
Catches errors in bootstrap due to "bad" data and automatically restarts the bootstrap (#57 @ellessenne)
Housekeeping
-
Added hex sticker badge.
-
Moved the make files and raw data for
qol
andrenal
datasets into the~/data-raw/
directory. -
Added @ellessenne as package contributor for testing and bug corrections (PRs #55 and #57).
Canada Workshop 2017
New features
-
Added new functions
dynSurv()
anddynLong()
, which generates survival probabilities and xpected longitudinal predictions, respectively, for a new subject conditional on their last measurement time and longitudial history. Prediction can be implemented using either a first order approximation or a Monte Carlo simulation approach. -
Added an associated
print()
method fordynSurv
anddynLong
objects. -
Added an associated
plot()
method fordynSurv
anddynLong
objects. -
Added a function
baseHaz()
for extracting the centered and uncetered estimates of the baseline hazard function. -
print()
andsummary()
now report the total computation time in addition to just the EM algorithm time. This was deemed useful after some examples showed that the time to get initial values was more expensive than the time for the MCEM algorithm to converge.
Bug patches
-
Fixed a bug that prevented models being fitted with no covariates in the survival sub-model, i.e.
Surv() ~ 1
. -
Correction to the vignette description of
mjoint()
arguments. -
Removed
enumintem
package for Sweave vignette to satisfy CRAN checks on macOS (release).
Housekeeping
-
Updated
Makevars
andMarkvars.win
to allow for OpenMP, which can be used by RcppArmadillo. -
Minor tidy-up of in-code comments.
-
Minor updates and corrections to documentation.
-
Added unit tests for new features.
v0.2.2
- This update is an attempt to overcome a FAIL status on the CRAN checks for macOS.
Housekeeping
-
Changed the technical vignette to Rnw (with engine = Sweave) from ltx (with engine = R.rsp) in attempt to remove some CMD check warnings.
-
Shortened the vignette to make it compile quicker (removed execution of bootstrapping).
-
Lots of tweaks of minor formatting tweaks in the documentation.
v0.2.1
Bug patches
-
Fixed a bug that prevented factors with >2 levels being included in the time-to-event submodel.
-
Fixed package registration, which strangely broke on R 3.4.0 for OSX platform.
Housekeeping
-
joineRML
version 0.2.1 will depend on R version >=3.3.0 to remedy issue withsigma.mjoint()
S3 issue. -
Added a new badge to the README.
v0.2.0
New features
-
Add
residual()
andfitted()
functions formjoint
objects. -
Added a plot function --
plot.ranef.mjoint()
-- forranef.mjoint
objects. -
bootSE()
now uses control parameters from fitted model and allows for individual parameter overwrite. -
Added a check that any initial covariance matrix given is positive-definite.
-
Added a check that dimensions of any
inits
given match the calculated dimensions from the model formulae. -
Added a check that if multiple repeated longitudinal outcoems were given, that each subject contributes at least one measurement per outcome.
-
Changed the API so that
postRE
andapprox.se
arguments are now replaced by a singlepfs
argument, which stands for post fit statistics. IfTRUE
, then both the approximate SEs and the BLUPs (and SEs) are calculated and returned. This change is to facilitate other post fit statistics, e.g. residuals. -
sampleData()
now allows for sampling without replacement. -
plot()
andplotConvergence()
now have the option to discard burn-in phase iterations from the MCEM algorithm. -
plot()
andplotConvergence()
now plot the log-likelihood trace. -
vcov()
now calculates the variance-covariance matrix rather than insidemjoint()
and then extracting it. It also utilises the QR-decomposition inverse function and the Moore-Penrose matrix inverse, as in some cases the matrix was nearly singular. -
hessian()
(and thereforevcov()
) now calculate the contribution for the random effect variance terms rather than the random effect precision (1 divided by the variance) terms. The correct contribution to the score for off-diagonal terms is now also impleted. -
The left-hand side of the
formLongFixed
now handles transformations.
Bug patches
-
vcov()
now returns the variance-covariance matrix as intended. Previously it was only returning the profile empirical information matrix. -
Patched a major bug in
gammaUpdate()
where ties in failure times were not being properly handled. The code forgammaUpdate_approx()
always worked fine, as it was based only on the score vector. This bug manifested whenbootSE()
was called due to the resampling with replacement yielding datasets with many more ties than in the original dataset used to fit the model. To fix it, the information matrix required scaling at each failure time by the number of failures in the data. The formula for the information matrix in the Technical Details vignette has also been updated. -
Patched a minor bug with prevented univariate random-intercept models for being fitted.
-
Patched a minor bug in plotting convergence traces.
-
Patched a minor bug with bootstrapping univariate joint models without passing the MLEs as the initial values to the
mjoint()
call.
Housekeeping
-
Renamed
approxSE()
function tohessian()
. -
Renamed
control
argumentearlyPhase
toburnin
. -
Default settings for
control
parameters updated based on practical experience. -
Package now
Depends
onsurvival
andnlme
rather thanImports
to allowrequire()
statements to be removed from code. -
Prevented
roxygen
from exporting all functions. -
Fixed Imports following CRAN Checks of v0.1.1.
-
Minor documentation edits and corrections.
-
Minor code tidy-up with slight speed-ups and stabilisations where found.
-
LICENSE upgraded to GPL-3 to be compatible with
joineR
v1.1.0. -
Removed internal function
fast_nearPD()
from package code as was unused. -
Removed internal function
EexpArma()
from package code as was unused. -
Added unit tests.
-
Registered native C++ routines and disabled symbol search to satisfy CRAN CMD checks.
v0.1.1
Patches v0.1.0 to allow it to build on R versions <3.3.0