## Version 1.3.13

- Changes to DESCRIPTION for CRAN and updated URLs for references.

## Version 1.3.12

- Resolves Issue #23 where passing matrices to `melt.data.table` cause a silent
failure for `coxsimtvc`.

- Updated internal function `IntervalConstrict` to dplyr 0.7.0 `group_by` syntax.
Function no longer returns a deprecation warning.

## Version 1.3.11

- Resolves Issue #23 with passing matrices to `data.table.melt`

## Version 1.3.10

- hmohiv data now stored internally to avoid breaking URL.

## Version 1.3.9

- Fixed a bug when including rug plots with `simGG.siminteract`. Thanks to
Ting Shuo Huang for reporting.

- Corrected a bug in `simGG.siminteract` and `simGG.simlinear` where the
`shape` parameter was incorrectly supplied to `geom_line`.

## Version 1.3.8

- No longer suggests rio package. Thanks to Jan Gorecki.

## Version 1.3.7

- Enable compatibility with dplyr version 0.4.4.

- Fixes bugs when finding hazard rates.

- Minor internal code readability improvements.

## Version 1.3.6

- Improve sim function messages so that `Xl` message
is only shown if `Xl` is incorrectly specified.

## Version 1.3.5

- Fixed issues with `ggfitStrata` and its documentation caused by changes to
the survival and gridExtra packages.

- Minor documentation change removing links to ggplot2 documentation
that no longer exists from version 2.0.0.

## Version 1.3.4

- Internally, `melt` is loaded from the data.table package rather than
reshape2 (which is no longer a dependency). This should provide speed
improvements.

## Version 1.3.3

- `coxsimInteract` can now handle interactions with categorical variables.

## Version 1.3.2

- Minor internal changes to `SurvExpand` that improves speed and stability.

## Version 1.3.1

- Add citation to JSS article.

    Gandrud, Christopher. 2015. simPH: An R Package for Illustrating Estimates
    from Cox Proportional Hazard Models Including for Interactive and Nonlinear
    Effects. Journal of Statistical Software. 65(3)1-20.

## Version 1.3

- !!!!NOTE!!!!: This version alters default behaviour and
functionality in a way that could break your code.

- `simGG` now includes rug plots.

    + Note that for `simGG.simtvc` rug plots are not produced. All x-axes
are "Time".

- `simGG` default type is now `ribbons`, rather than `points`.

- For `simGG` plots with a covariate represented on the x-axis,
the variable name is printed by default on the plot.

- `as.data.frame.coxsim` added to convert the output of a coxsim function to
a data frame

- `simGG.simspline` no longer supports scatter3d plots for Hazard Rates.

- Bug fixes in `simGG.simspline` with Hazard Rates.

- Minor internal code and documentation improvements.

## Version 1.2.6.1

Trivial README.md change to address CRAN Markdown processor issue.

## Version 1.2.6

- No longer depends on DataCombine.

- Minor documentation improvements.

## Version 1.2.5

- Minor documentation and internal code improvements.

## Version 1.2.4

- Bug fix for `coxsimSpline` where the `SimID` was not correctly identified.

Addressed minor bug in `SurvExpand` from data.table.

## Version 1.2.3

- Minor changes to `SurvExpand` to work with dplyr 0.3.

- Now requires dplyr 0.3.

- coxsim objects now also given the class `data.frame`.

- No longer depends on plyr.

## Version 1.2.2

- Added `PartialData` argument to `SurvExpand`. The argument allows the user to
determine whether or not to only keep the expanded data needed to find the Cox
partial likelihood.

- Made `MinMaxLines` a top level function that is useful for returning basic
summary statistics from coxsim constricted simulation intervals. Using the
argument `clean = TRUE` returns the simulations' medians, the minimum and
maximum of the constricted intervals (as set in the `coxsim` call) and the lower
and upper 50% of the constricted intervals.

- `MinMaxLines` also now relies on *dplyr* rather than *plyr*. This improves
performance.

## Version 1.2.1

- Minor documentation improvements.

## Version 1.2

- !!!! `smoother` argument for `simGG` is deprecated. Use `method` instead.
The functionality is exactly the same. !!!!

- `tvc` now accepts a vector of variable names.

- jss-example demo added.

- simPH-overview vignette added.

- `extremesDrop` argument added to `coxsim` functions. This drops simulated
quantity of interest values that are Inf/NA/NaN/>1000000. These can create
problems with plotting and finding the `spin`.

- Small utility `setXl` created that makes it easier to set `Xl` values.

- Automatic `bspline` cleaning features added for `coxsimSpline`.

- Minor documentation improvements.

- Internal code cleaning.

## Version 1.1.1

- `coxsimPoly` is able to simulate quantities of interest for only the polynomial
terms without the linear component. Feature request from Mattia Valente.

- Minor error message improvements.

## Version 1.1

- Added `SurvExpand` for converting a data frame of non-equal interval continuous
observations into equal interval continuous observations. This is very useful if
you intend to create time interactions. Thanks to Mintao Nie and an anonymous
reviewer for the suggestion.

- Roxyegen documentation improvements.

## Version 1.0

- Added `type` argument to `simGG.spline`. Allows the user to plot using
`points`, `ribbons`, or `lines`. NOTE: the `ribbons` standalone argument is
depricated.

- Added `SmoothSpline` argument to `simGG.simspline` to use smoothing splines on
the simulations. Creates a smoother graph.

- Uses `mvrnorm` from the `MASS` package instead of `rmultnorm` to draw the
simulations.

- Documentation and other internal improvements.

## Version 0.8.6

- Documentation improvements.

## Version 0.8.5

- Added the ability to choose whether or not to exponentiate marginal effects
for `coxsimInteract` with the `expMarg` argument.

## Version 0.8.4

- Minor bug fix for `simGG.siminteract`.

## Version 0.8.3

- License change and minor message changes.

## Version 0.8.2

- Added `legend` argument to allow the user to hide plot legends, when applicable.

- Minor aesthetic updates and documentation clarifications.

## Version 0.8.1

- Minor changes for CRAN check.

## Version 0.8

- Added the argument `ribbons` to the simGG method. This produces a plot with
shaded areas ('ribbons') for the minimum and maximum simulation values as well
as the central 50% of this area. It also plots a line for the median value of
this area. (Thanks to Jeff Chwieroth for the suggestion.)

- Internal improvements to minimise the size of simulation output objects and
improve performance if qi = "Hazard Rate".

- A number of bug fixes.

## Version 0.7.3

- Documentation improvements.

## Version 0.7.2

- Clean up for CRAN.

## Version 0.7.1

- Added an error message to `coxsimSpline` if white spaces are not entered
before and after equal (=) signs in the `bspline` argument.

## Version 0.7

- Added package vignette (partially completed).

- Expanded `coxsimPoly` so that it is capable of simulating other quantities of
interest. Also, bug fixes.

- `spin = TRUE` works for quantities of interest when Xj - Xl = 0, i.e. in
situations when all of the simulated quantities are 1 (or 0 for First
Differences).

- Documentation improvements.

- Bug fixes, including:
  - SPIn lower bound for different quantities of interest.
  - Fixed an error in the calculation of quantities of interest from Splines.

## Version 0.6

- Increased flexibility for setting confidence levels. Now they may be set at
any numeric value from 0 through 1.

- Choice of using confidence levels for the middle simulation values or the
shortest probability interval.

	- Many thanks to Ying Liu. Code from his SPIn function is fundamental for
    making this possible.

- `qi` now automatically determined by `simGG`.

- `means` argument added to `coxsimLinear` and coxsimInteract`. This allows the
user to choose if they would like Hazard Rates to be fitted using the variables
(other than the variables of interest) set to their means rather than 0. Note:
it does not currently support models that include polynomials created by `I`.

	- `means` will be added to the other simulation commands in future versions.

- Minor bug fixes and documentation updates.

## Version 0.05

**Major update** to the way simPH plots simulated objects. Instead of using
separate commands for plotting objects of different sim classes it now uses the
method `simGG`.

In practical terms this means that you can now just use the command `simGG`
rather than the old gg. . . commands.

## Version 0.04.62

Minor bug fix for `ci` argument.

## Version 0.04.6.1

Minor change: now line drawn.

## Version 0.04.6

Standardise how hazard rates are calculated.

## Version 0.04.5

Made updates so that the package is compatible with data.table package version
1.8.8.

## Version 0.04.4

Minor improvement to ggtvc legend

## Version 0.04.3

Minor bug fixes.

## Version 0.04.2

Updated the syntax for `simcoxtvc` and `ggtvc` for hazard ratios and stratified
hazard rates so that it matches the syntax for the other commands.

Other bug fixes.

## Version 0.04.1

Minor bug fix for `ggspline` when `qi == 'First Difference'`.

## Version 0.04

Added `coxsimSpline` and `ggspline` to simulate and plot quantities of interest
for penalised splines.

## Version 0.03.2

Minor bug fixes, documentation improvements for `coxsimInteract`.


## Version 0.03.1

Improved error messages in `coxsimInteract` and minor documentation changes.


## Version 0.03

Added `coxsimInteract` to simulate quantities of interest for linear
multiplicative interactions and `gginteract` for plotting these simulations.

Also made an important fix to how `coxsimLinear` calculates hazard rates and how
`gglinear` plots these simulations.

Other documentation fixes.


## Version 0.02.2

Minor change to how `coxsimtvc` runs so that it is no longer dependent on
**reshape**.


## Version 0.02.1

Updated documentation and added the ability to change the smoothing line colour
for first difference and relative hazard plots.

## Version 0.02

Added functions for simulating and plotting linear non-time-varying hazards.

- `coxsimLinear`: simulates linear non-time-varying hazards

- `gglinear`: plots linear non-time-varying-hazards

## Version 0.01

First version, largely ported from simtvc version 0.04
(<https://christophergandrud.github.com/simtvc/>), with the addition of the
ability to work with polynomials. This includes two functions

- `coxsimPoly` simulates polynomial relative hazards

- `ggpoly` graphs the simulated polynomial relative hazards