Changes in version: JM_1.4-7

  * Changed the definition of JM:::rmvt() to work under the shifted method (noted by Graeme Hickey).
  * Resolved issue with non-ordered id numbers in the longitudinal submodel.

==============================

Changes in version: JM_1.4-6

  * Updated aucJM() method.
   
==============================

Changes in version: JM_1.4-5


  * Fixed a bug in fixef.jointModel().
   
==============================

Changes in version: JM_1.4-4


  * Fixed a bug in phGH.fit().
   
==============================

Changes in version: JM_1.4-3


  * Small updates.
   
==============================

Changes in version: JM_1.4-2


  * Small updates.
   
==============================

Changes in version: JM_1.3-0


  * Several minor improvements.
   
==============================

Changes in version: JM_1.2-0


  * the new generic function aucJM() calculates time-dependent AUCs for joint models.

  * an updated version of function dynCJM() calculates a dynamic discrimination index 
    (weighted average of time-dependent AUCs) for joint models.

  * the new generic function prederrJM() calculates prediction errors for joint models.

  * survfitJM() is now a generic function with a method for 'jointModel' objects.

  * new versions of functions ins() and ibs() with updated 'weight.fun' argument, and makepredictcall() methods.
   

==============================

Changes in version: JM_1.1-0

  * a small bug has been corrected in the plot() method for 'jointModel' objects, when
    method = "piecewise-PH-aGH" or method "piecewise-PH-GH" was used.
   

==============================

Changes in version: JM_1.0-1

  * use of globalVariables() in source code.

  * a small bug has been corrected in the plot() method for 'jointModel' objects, when
    a random intercepts linear mixed model was used
   

==============================

Changes in version: JM_1.0-0

  * This is the version of the package related to the book: Rizopoulos, D. (2012). Joint 
    Models for Longitudinal and Time-to-Event Data: with Applications in R. 
    Boca Raton: Chapman & Hall/CRC.

  * functions dns(), dbs(), ins() and ibs() calculate numerically derivative and integrals for functions
    ns() and bs(), respectively.

  * a coef() method has been added for objects of class 'summary.jointModel'.
   

==============================

Changes in version: JM_0.9-2

  * prediction.jointModel() can also compute now prediction intervals.

  * rocJM() has a new logical argument 'directionSmaller' denoting whether smaller
    values for the longitudinal outcome are associated with higher risk for an event.
  
  * fitted.jointModel() has the new option 'Slope' for the 'type' argument that returns
    the fitted values corresponding to the slope term when 
    parameterization %in% c('slope', 'both') in jointModel().
  

==============================

Changes in version: JM_0.9-1

  * minor bug fixes.
  

==============================

Changes in version: JM_0.9-0

  * jointModel() can now also handle exogenous time-dependent covariates when 
    method = "spline-PH-aGH".

  * jointModel() can now also handle competing risks settings when method = "spline-PH-aGH".

  * new function crLong() expands a data frame in the long format in the competing 
    risks setting.

  * predict() method now calculates marginal and subject-specific predictions for the 
    longitudinal outcome.
  

==============================

Changes in version: JM_0.8-4

  * method ranef() has now the extra argument 'type' the specifies whether to compute
    the mean (default) or the mode of the posterior distribution of the random effects.

  * the anova() method now also produces marginal Wald tests when a single joint model
    is provided.

  * plot.survfitJM() produces a more informative plot when argument 'include.y' is set to
    TRUE.

  * a bug has been corrected in residuals.jointModel() that it did not work when 'MI = TRUE',
    and 'parameterization = "slope"' in jointModel().
  

==============================

Changes in version: JM_0.8-3

  * the default method is now the Weibull model under the relative risk parameterization
    using the pseudo-adaptive Gauss-Hermite rule.

  * the plot() method has a new logical argument called 'return', which 
    if set to TRUE the values use to create the plot are returned.

  * a typo in the code creating the scaling for the pseudo-adaptive 
    Gauss-Hermite points has been corrected. This was primarily affecting 
    the standard errors in the longitudinal submodel. The point estimates may 
    also slightly change in some datasets.  
  

==============================

Changes in version: JM_0.8-2

  * a bug was corrected in the internal function ModelMats().
  

==============================

Changes in version: JM_0.8-1

  * the new function xtable.jointModel() in conjunction with the xtable 
    package can be used to produce a LaTeX table with the results of joint 
    modeling analysis.
  
  * the new function simulateJM() and the simulate() method for objects of 
    class 'jointModel' can be used to simulate data from a joint model.


==============================

Changes in version: JM_0.8-0

  * the new argument 'interFact' added in jointModel() allows the specification 
    of interaction terms between the longitudinal outcome and baseline covariates.

  * for all joint models fitted in JM there is now the option to use a pseudo 
    adaptive Gauss-Hermite rule. This is much faster than the default option and 
    produces results of equal or better quality.

  * a predict() method has been added. Currently this only calculates fitted 
    average longitudinal evolutions based on the information provided in the 
    'newdata' argument.

  * a new algorithm for calculating the starting values has been implemented. In most 
    of the cases these will be closer to the MLEs than in the previous version.

  * some small changes have been made in the default Gauss-Hermite quadrature rule. 
    This will result in minor changes in parameter estimates, standard errors and 
    log-likelihood value compared to the previous version.

  * a bug has been corrected in the code used to specify the design matrix for the 
    random effects in the longitudinal outcome, that did not allow this matrix not 
    to be a subset of the design matrix of the fixed effects.


==============================

Changes in version: JM_0.7-0

  * the new function rocJM() has been added that calculates time-dependent ROC curves 
    and the corresponding AUCs for joint models.

  * methods "weibull-AFT-GH", "weibull-PH-GH", "piecewise-PH-GH", and "spline-PH-GH" 
    support now the true slope parameterization. This is invoked be specifying the 
    'parameterization' and 'derivForm' arguments accordingly.


==============================

Changes in version: JM_0.6-2

  * a small bug was corrected in summary.jointModel().


==============================

Changes in version: JM_0.6-1

  * jointModel() has now the extra argument 'scaleWB' that allows to fix the scale 
    parameter for the Weibull baseline hazard to a specific value.


==============================

Changes in version: JM_0.6-0

  * method = "spline-PH-GH" allows now to include stratification factors for which 
    different spline coefficients are estimated. By default the knots positions are 
    the same across strata -- this can be changed by either directly specifying the 
    knots or by setting the control argument 'equal.strata.knots' to FALSE.

  * the new function wald.strata() can be used to test for equality of the spline 
    coefficients among strata.

  * a confint() method has been introduced for 'jointModel' objects.

  * jointModel() has now the extra argument 'lag' that allows for lagged effects in 
    the time-dependent covariate represented by the linear mixed model.

  * a bug was corrected in joint models with piecewise constant baseline risk function. 
    In particular, the 'xi' parameters were reported as double their actual value.


==============================

Changes in version: JM_0.5-0

  * function dynC() has been added that calculates a dynamic concordance index for 
    joint models.

  * method = "ch-GH" has been replaced by method = "spline-PH-GH" that fits a relative 
    risk model with a B-spline-approximated baseline risk function.

  * method = "ph-GH" that fits a relative risk with an unspecified baseline risk 
    function has been renamed to method = "Cox-PH-GH".


==============================

Changes in version: JM_0.4-0

  * function survfitJM() has been added that calculates predictions of subject-specific 
    probabilities of survival given a history of longitudinal responses.

  * the multiple-imputation residuals now work also for joint models with piecewise 
    constant baseline risk functions.

  * faster optimization algorithms have implemented for 'method = "weibull-PH-GH"' and 
    'method = "piecewise-PH-GH".


==============================

Changes in version: JM_0.3-0

  * the Weibull model is now available under both the relative risk and accelerated 
    failure time parameterizations.

  * a number of enhancements have been implemented in the functions that compute the 
    MI-based residuals.

  * new more robust algorithms have been written for the numerical approximation 
    of integrals; this will lead to some discrepancies in the results, especially in 
    the survival part, compared to the previous versions of the package.


==============================

Changes in version: JM_0.2-1

  * changes in e-mail addresses in .Rd files.


==============================

Changes in version: JM_0.2-0

  * the jointModel method for the residuals generic has further options: (i) MI residuals 
    for fixed and random visit times for the longitudinal process, and (ii) martingale, 
    Cox-Snell, and AFT residuals for the survival process.

  * Function weibull.frailty() is introduced (along with supporting methods) for fitting 
    multivariate survival data using the Weibull model with Gamma multiplicative frailties 
    under maximum likelihood.

  * several typos have been corrected in .Rd files.


==============================

Changes in version: JM_0.1-1

  * corrected some typos in .Rd files.

