About to send it to CRAN. Now the vignette is rendered correctly.

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: msmtools
 Type: Package
 Title: Building Augmented Data to Run Multi-State Models with 'msm' Package
-Version: 2.0.0
-Date: 2021-04-07
+Version: 2.0.1
+Date: 2021-04-10
 Authors@R: person("Francesco", "Grossetti",
     email = "[email protected]",
     role = c("aut", "cre"), comment = c(ORCID = "0000-0002-5130-7745"))

NEWS.md

@@ -1,4 +1,14 @@
-# msmtools 2.0.0 (development version)
+# msmtools 2.0.1
+***
+
+This is a maintenance update. There are no major updates worth of notice besides few tweaks in 
+the vignette which was not rendered appropriately.
+
+### Minor changes
+
+* Fixed few issues in the vignette where plots were not rendered nicely.
+
+# msmtools 2.0.0
 ***
 
 **msmtools** sees several updates which come with potential breaking changes due to the dropping

README.md

@@ -1,7 +1,7 @@
 # Building augmented data for multi-state models: the `msmtools` package
 
 [![lifecycle](https://lifecycle.r-lib.org/articles/figures/lifecycle-maturing.svg)](https://lifecycle.r-lib.org/articles/stages.html)
-[![release](https://img.shields.io/badge/dev.%20version-2.0.0-blue)](https://github.com/contefranz/msmtools)
+[![release](https://img.shields.io/badge/dev.%20version-2.0.1-blue)](https://github.com/contefranz/msmtools)
 [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/msmtools)](https://cran.r-project.org/package=msmtools)
 
 ***

cran-comments.md

@@ -1,22 +1,45 @@
+# msmtools 2.0.1
+
+### Release summary
+
+This is a maintenance update. There are no major updates worth of notice besides few tweaks in 
+the vignette which was not rendered appropriately.
+
+### Package development
+
+* macOS 10.15.7 with R 4.0.4
+
+### R CMD build
+
+* local MacOS 10.15.7
+* win build created with `devtools::check_win_release()`
+* multiplatform builds created with `devtools::check_rhub()`
+
+### R CMD check results
+
+* Everything looks amazing so far.
+
+***
+
 # msmtools 2.0.0
 
-## Release summary
+### Release summary
 
 This marks a major redesign in how the package manages plots. It now uses **ggplot2**.
 Also, most of the cumbersome arguments related to devices and plot layering have been improved and
 substantially removed. The above changes are enough to declare that **msmtools** has now
 reached full maturity and thus justify the jump to version 2.0.0.
 
-## Package development
+### Package development
 
 * macOS 10.15.7 with R 4.0.4
 
-## R CMD build
+### R CMD build
 
 * local MacOS
 * win build through devtools::build_win()
 
-## R CMD check results
+### R CMD check results
 
 * There were no ERRORs nor WARNINGs nor NOTEs. 
 
@@ -27,26 +50,24 @@ Though the file is correct.
 README. The former is included in the bibliography and the latter is due to
 a Github link.
 
-
 ***
 
-
 # msmtools 1.3
 
-## Release summary
+### Release summary
 
 This is version 1.3 of **msmtools**
 
-## Package development
+### Package development
 
 * macOS 10.12.5 with R 3.4.0
 
-## R CMD build
+### R CMD build
 
 * local macOS
 * win build through devtools::build_win()
 
-## R CMD check results
+### R CMD check results
 
 * There were no ERRORs nor WARNINGs nor NOTEs. 
 
@@ -61,20 +82,20 @@ a Github link.
 ***
 # msmtools 1.2
 
-## Release summary
+### Release summary
 
 This is version 1.2 of **msmtools**
 
-## Package development
+### Package development
 
 * OS X 10.11.5 with R 3.3.0
 
-## R CMD build
+### R CMD build
 
 * local OS X
 * win build through devtools::build_win()
 
-## R CMD check results
+### R CMD check results
 
 There were no ERRORs or WARNINGs. 
 
@@ -86,20 +107,20 @@ This is due to the presence of a GitHub link which points at the file NEWS.md.
 ***
 # msmtools 1.1
 
-## Release summary
+### Release summary
 
 This is version 1.1 of **msmtools**
 
-## Package development
+### Package development
 
 * OS X 10.11.4 with R 3.2.4
 
-## R CMD build
+### R CMD build
 
 * local OS X
 * win build through devtools::build_win()
 
-## R CMD check results
+### R CMD check results
 
 There were no ERRORs or WARNINGs. 
 

vignettes/msmtools.Rmd

@@ -320,7 +320,7 @@ msm_model = msm( status_num ~ augmented_int,
 To run a comparison between the estimated and the empirical survival curves, we run the following
 simple code:
 
-```{r survplot_1, fig.align = 'center', fig.width = 5, fig.height = 4}
+```{r survplot_1, fig.align = 'center', fig.width=7, fig.height=6, fig.fullwidth = TRUE}
 gof1 = survplot( x = msm_model, km = TRUE )
 ```
 
@@ -337,7 +337,7 @@ If `to` is missing, `survplot()` checks what is the higher value in the
 corresponding `msm` object and grabs it. Let's now plot the survival comparison for the transition 
 (OUT - DEAD):
 
-```{r survplot_2, fig.align = 'center', fig.width = 5, fig.height = 4}
+```{r survplot_2, fig.align = 'center', fig.width=7, fig.height=6, fig.fullwidth = TRUE}
 gof2 = survplot( x = msm_model, km = TRUE, from = 2 )
 ```
 
@@ -353,7 +353,7 @@ explicitly pass a custom time sequence. This can be achieved by passing to the a
 Consider our dataset and suppose we want to compute an estimated survival only for 
 specific points in time. The following code addresses this request.
 
-```{r custom_time_seq, fig.align = 'center', fig.width = 5, fig.height = 4}
+```{r custom_time_seq, fig.align = 'center', fig.width=7, fig.height=6, fig.fullwidth = TRUE}
 time_seq = seq( 300, 800, by = 30 )
 custom_time = survplot( x = msm_model, times = time_seq )
 ```
@@ -369,7 +369,7 @@ Kaplan-Meier curve is returned. The code below shows how this works.
 <!-- `data.table`. Passing only `km = TRUE` won't return any data, even if they must  -->
 <!-- be computed anyway to plot results. -->
 
-```{r returnKM, collapse = TRUE, fig.align = 'center', fig.width = 5, fig.height = 4}
+```{r returnKM, collapse = TRUE, fig.align = 'center', fig.width=7, fig.height=6, fig.fullwidth = TRUE}
 km_out = survplot( x = msm_model, km = TRUE, out = "km")
 ```
 
@@ -405,7 +405,7 @@ used to compute the estimated survival as well. This can be achieve by setting
 as many rows as the elements in `times`. If `times` is missing, then `survplot()` 
 uses `grid` to know how many time points are requested. An example is shown in the next snippet.
 
-```{r returnP, collapse = TRUE}
+```{r returnP, collapse = TRUE, fig.align='center', fig.width=7, fig.height=6, fig.fullwidth = TRUE}
 fitted = survplot( x = msm_model, grid = 10, out = "fitted" )
 ```
 
@@ -430,7 +430,7 @@ Of course, you can request `survplot()` to return both the datasets by specifyin
 In this case, a named list with three elements is returned. The mechanism to access the elements is
 the same described above. The snippet below reports an example.
 
-```{r return_all, collapse = TRUE, fig.align = 'center', fig.width = 5, fig.height = 4}
+```{r return_all, collapse = TRUE, fig.align = 'center', fig.width=7, fig.height=6, fig.fullwidth = TRUE}
 # just running survplot()
 out_all = survplot( x = msm_model, km = TRUE, out = "all")
 ```
@@ -446,7 +446,7 @@ prevalences using `prevalence.msm()` function. This produces a named list which
 will be used inside `prevplot()`. For instance, running the following code 
 builds a plot of prevalences for each state of the model.
 
-```{r prev, collapse = TRUE, fig.align = 'center', fig.width = 7, fig.height = 3}
+```{r prev, collapse = TRUE, fig.align = 'center', fig.width=7, fig.height=6, fig.fullwidth = TRUE}
 # defining the times at which compute the prevalences
 t_min = min( hosp_augmented$augmented_int )
 t_max = max( hosp_augmented$augmented_int )
@@ -468,10 +468,10 @@ It is also possible to plot the following statistic:
 $$
 M = \frac{(O_{is} - E_{is})^2} {E_{is}}
 $$
-which gives an idea of the deviance from the Markov model. This is computed 
+This gives an idea of the deviance from the Markov model and is computed 
 according to Titman and Sharples (2008). The following code addresses this request.
 
-```{r plot_M, collapse = TRUE, fig.align = 'center', fig.width = 7, fig.height = 3, warning = F}
+```{r plot_M, collapse = TRUE, fig.align = 'center', fig.width=7, fig.height=9, fig.fullwidth = TRUE, warning = F}
 gof = prevplot( x = msm_model, prev.obj = prev, exacttimes = TRUE, M = TRUE, ci = TRUE )
 ```