1.0.0 release to accompany JSS paper publication

chjackson · May 11, 2016 · 8f66d0b · 8f66d0b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: flexsurv
 Type: Package
 Title: Flexible Parametric Survival and Multi-State Models
-Version: 0.7.1
-Date: 2016-03-24
+Version: 1.0.0
+Date: 2016-05-10
 Author: Christopher Jackson <[email protected]>
 Maintainer: Christopher Jackson <[email protected]>
 Description: Flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions.   Any user-defined parametric distribution can be fitted, given at least an R function defining the probability density or hazard.  There are also tools for fitting and predicting from fully parametric multi-state models.

diff --git a/TODO b/TODO
@@ -22,6 +22,8 @@ Generic (restricted) mean of distributions, integration if necessary.
    See surv2sampleComp package
 Restricted SD in same way?
 
+Time dependent covs in summary.flexsurvreg
+
 Tidy up summary functions, including bootstrap, covariate handling.
 
 D can be non pos-def in QP (github #9). Worked around for now, but why does this happen?

diff --git a/inst/NEWS b/inst/NEWS
@@ -1,5 +1,12 @@
 -*- text -*-
 
+Version 1.0.0 (2016-05-10)
+-------------
+
+* Version number bumped to 1.0.0 to accompany the publication of the
+  vignette in Journal of Statistical Software.
+
+
 Version 0.7.1 (2016-03-24)
 -------------
 

diff --git a/man/flexsurv-package.Rd b/man/flexsurv-package.Rd
@@ -99,6 +99,10 @@
   Christopher Jackson \email{chris.jackson@mrc-bsu.cam.ac.uk}
 }
 \references{
+  Jackson, C. (2016). flexsurv: A Platform for Parametric
+  Survival Modeling in R. Journal of Statistical Software, 70(8),
+  1-33. doi:10.18637/jss.v070.i08
+
   Royston, P. and Parmar, M. (2002).  Flexible parametric
   proportional-hazards and proportional-odds models for censored survival
   data, with application to prognostic modelling and estimation of

diff --git a/man/flexsurvreg.Rd b/man/flexsurvreg.Rd
@@ -251,17 +251,21 @@ flexsurvreg(formula, anc=NULL, data, weights, bhazard, subset,
   \code{\link{model.frame.flexsurvreg}} or \code{\link{model.matrix.flexsurvreg}}.}
 }
 \references{
-  Jackson, C. H. and Sharples, L. D. and Thompson, S. G. (2010)
-  Survival models in health economic evaluations: balancing fit and
-  parsimony to improve prediction. International Journal of Biostatistics
-  6(1):Article 34.
+  Jackson, C. (2016). flexsurv: A Platform for Parametric
+  Survival Modeling in R. Journal of Statistical Software, 70(8),
+  1-33. doi:10.18637/jss.v070.i08
 
   Cox, C. (2008) The generalized \eqn{F} distribution: An umbrella for
   parametric survival analysis.  Statistics in Medicine 27:4301-4312.
 
   Cox, C., Chu, H., Schneider, M. F. and Muñoz, A. (2007)
   Parametric survival analysis and taxonomy of hazard functions for the
   generalized gamma distribution.  Statistics in Medicine 26:4252-4374
+
+  Jackson, C. H. and Sharples, L. D. and Thompson, S. G. (2010)
+  Survival models in health economic evaluations: balancing fit and
+  parsimony to improve prediction. International Journal of Biostatistics
+  6(1):Article 34.
 }
 \author{
   Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>

diff --git a/man/flexsurvspline.Rd b/man/flexsurvspline.Rd
@@ -208,6 +208,10 @@ and \eqn{(x - a)_+ = max(0, x - a)}.
   proportional-hazards and proportional-odds models for censored survival
   data, with application to prognostic modelling and estimation of
   treatment effects. Statistics in Medicine 21(1):2175-2197.
+
+  Jackson, C. (2016). flexsurv: A Platform for Parametric
+  Survival Modeling in R. Journal of Statistical Software, 70(8),
+  1-33. doi:10.18637/jss.v070.i08
 }
 \author{
   Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>

diff --git a/man/summary.flexsurvreg.Rd b/man/summary.flexsurvreg.Rd
@@ -133,6 +133,10 @@ It should return a vector of the
   distribution of the maximum likelihood estimates (see, e.g. Mandel
   (2013)).  
 }
+\details{
+  Time-dependent covariates are not currently supported.  The covariate
+  values are assumed to be constant through time for each fitted curve.
+}
 \seealso{
   \code{\link{flexsurvreg}}, \code{\link{flexsurvspline}}.
 }

diff --git a/vignettes/flexsurv.Rnw b/vignettes/flexsurv.Rnw
@@ -51,7 +51,10 @@ render_sweave()
   from fully-parametric multi-state models, and connects with the
   \pkg{mstate} package \citep{mstate:jss}.  This article explains the
   methods and design principles of the package, giving several worked
-  examples of its use. }
+  examples of its use. 
+
+\emph{[Note: A version of this vignette is published as \citet{flexsurv} in Journal of Statistical Software. There have been no substantial changes since.]}
+}
 
 \Keywords{survival, multi-state models, multistate models}
 
@@ -1189,7 +1192,7 @@ function $q_{rs}(t)$.
 \label{sec:multistate:data}
 
 \citet{andersen:keiding} and \citet{putter:mstate} explain how to implement multi-state models by
-manipulating the data into the a suitable form for survival modelling
+manipulating the data into a suitable form for survival modelling
 software --- an overview is given here.  For each permitted $r
 \rightarrow s$ transition in the multi-state model, there is a
 corresponding ``survival'' (time-to-event) model, with hazard rates
@@ -1604,7 +1607,7 @@ new class of models would ideally come with
   (\S\ref{sec:custom}).
 \end{itemize}
 
-The examples in this paper were run using version 0.6 of \pkg{flexsurv}, available from \url{http://CRAN.R-project.org/package=flexsurv}.  Development versions are available on \url{https://github.com/chjackson/flexsurv-dev}, and contributions are welcome.
+\pkg{flexsurv} is available from \url{http://CRAN.R-project.org/package=flexsurv}.  Development versions are available on \url{https://github.com/chjackson/flexsurv-dev}, and contributions are welcome.
 
 
 \section*{Acknowledgements}

diff --git a/vignettes/flexsurv.bib b/vignettes/flexsurv.bib
@@ -1,3 +1,14 @@
+@article{flexsurv,
+  title        = "{flexsurv}: A Platform for Parametric Survival Modeling in {R}",
+  author       = "Jackson, C.",
+  journal      = "Journal of Statistical Software",
+  year         = "2016",
+  volume       = "70",
+  number       = "8",
+  pages        = "1--33",
+  doi          = "10.18637/jss.v070.i08",
+}
+                  
 @Manual{R,
   title = {\proglang{R}: A Language and Environment for Statistical Computing},
   author = {{\proglang{R} Core Team}},