version 1.2.3

cran · Nov 7, 2019 · 49b88e7 · 49b88e7
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,16 +1,16 @@
 Package: multistateutils
 Type: Package
 Title: Utility Functions for Parametric Multi-State Models
-Version: 1.2.2
-Date: 2019-02-03
+Version: 1.2.3
+Date: 2019-11-07
 Author: Stuart Lacy
 Maintainer: Stuart Lacy <stuart.lacy@gmail.com>
 Description: Provides functions for working with multi-state modelling, 
     such as efficient simulation routines for estimating transition probabilities and length of stay.
     It is designed as an extension to multi-state modelling capabilities provided with the 'flexsurv' 
     package (see Jackson (2016) <doi:10.18637/jss.v070.i08>).
 License: GPL (>= 3)
-Imports: data.table, dplyr, magrittr, networkD3, tidyr, webshot
+Imports: data.table, dplyr, magrittr, networkD3, tidyr
 Suggests: covr, knitr, flexsurv, mstate, microbenchmark, rmarkdown,
         testthat
 URL: https://github.com/stulacy/multistateutils
@@ -19,6 +19,6 @@ LinkingTo: Rcpp
 RoxygenNote: 6.1.1
 VignetteBuilder: knitr
 NeedsCompilation: yes
-Packaged: 2019-02-03 22:34:45 UTC; stuart
+Packaged: 2019-11-07 21:17:12 UTC; stuart
 Repository: CRAN
-Date/Publication: 2019-02-04 08:30:11 UTC
+Date/Publication: 2019-11-07 22:50:02 UTC
diff --git a/MD5 b/MD5
@@ -1,34 +1,34 @@
-e6f30b513bb0a362d91fbdd6a7f1c4e6 *DESCRIPTION
+6cfa156e03e842a8b84f0783a1cf4da7 *DESCRIPTION
 a1ae93d2c87fcc5f98452956facfdedf *NAMESPACE
-ad0555e1573e283fb9a54d398bac1870 *NEWS.md
+79233a95319564d327ca10c567659416 *NEWS.md
 0a91d61ac2ba351a6ca6a640bea450a8 *R/RcppExports.R
 b1dbcdf5b70b84232533a3cfe8cf0ec2 *R/cohort.R
 5795f711de63e297c77b4b61e5d1fcc7 *R/length_of_stay.R
-3a50addd2e64e90239e5d1e6eebfec87 *R/msprep2.R
+a18d5847d5ed8bd5a65dbf2651b2ca79 *R/msprep2.R
 ac7e40966b058f5596304f9b7e3516ca *R/multistateutils.R
 1f182e54f53c05a90a759b5e3c3e599a *R/run_simulation.R
 aa5c6bd41802ac1354513df6612de673 *R/statepathways.R
 438b1342adbd6fc74092e2dd0b8d0499 *R/transition_probabilities.R
 ef88f74fe85ac74eec6bd37ddb2116b2 *R/utils.R
 725ec67436f98afd433693db94193e00 *README.md
 d41d8cd98f00b204e9800998ecf8427e *TODO
-2f05c1bf3d22113ebb6c9fcf010bb011 *build/vignette.rds
+d76ab1ddde1f2984861068978adfbd99 *build/vignette.rds
 26f953065122cd33ff110e10fdecf17b *inst/doc/Examples.R
 c28411b84a26af651d53480d3a39082b *inst/doc/Examples.Rmd
-8a615a4fd2ebfa52236d77aa5c18fc18 *inst/doc/Examples.html
+68f84f52a3e8470de3de8aa6b3ff691f *inst/doc/Examples.html
 6b3f2cc5910bce7dfe286c5e106ddebb *man/cohort_simulation.Rd
 7db3576cf60e4e65a16117f021608430 *man/length_of_stay.Rd
-1ff74eeb09e7d3d6d1713dd83e3af696 *man/msprep2.Rd
+8b4c29799f2a385cafd351c601e8b0b3 *man/msprep2.Rd
 9e0ca400531a052050b92d9af7090f71 *man/multistateutils.Rd
 a5727825046d69ecd638dfc32e12ec8b *man/plot_predicted_pathway.Rd
 27b90cf9061911ba15390514271257d4 *man/predict_transitions.Rd
-e3d3cb360fbfdb3c6974e14eb5f09870 *src/Makevars
+f330bfb0bf13be4aea36ac587f1d7868 *src/Makevars
 dafd74bc0ab6201ca5841bf709777eb4 *src/RcppExports.cpp
 7f3211520255214525d5f3b6031fe81d *src/des.cpp
 4f41451269f1eb10e8cf4589745c3b14 *src/event.cpp
 d9fe25cf905c2e202d85e1aeb727cfa1 *src/event.h
 437adecc034a16fe7ab7735343e89a27 *src/simulation.cpp
-b06773afbb4393b539af4ccff2a68535 *src/simulation.h
+7ef2202601e0bb2fb4dd0a02a1523a83 *src/simulation.h
 493d4d4ec65764b7e5f02d5ea8e6e124 *src/state.cpp
 3b941394ca173084866651d88b048c39 *src/state.h
 d3989e9b9945dffc0cca614a00812188 *src/transitions.cpp

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# multistateutils 1.2.3
+
+  - Added class `msdata` to the output from `msprep2` so that it is compatible with other `mstate` functions, such as `events`. 
+
 # multistateutils 1.2.2
 
   - Fix for changes in data.table 1.12.1

diff --git a/R/msprep2.R b/R/msprep2.R
@@ -28,6 +28,8 @@
 #' @param idcol The column that indexes these patients, must be present in
 #'   \code{entry} and \code{censors}, \code{start_times}, \code{start_states},
 #'   and \code{covars} if supplied.
+#' @return An object of class \code{msdata}, representing the transition data
+#'   in long format.
 #' @examples
 #'  library(multistateutils)
 #'  library(mstate)
@@ -241,6 +243,9 @@ msprep2 <- function(entry, tmat, censors=NULL,
     to_int <- c('id', 'from', 'to', 'trans', 'status')
     entry4[to_int] <- lapply(entry4[to_int], as.integer)
 
-    entry4 %>%
+    out <- entry4 %>%
         dplyr::arrange(id, Tstart, trans)
+    attr(out, "trans") <- tmat
+    class(out) <- c('msdata', class(out))
+    out
 }
diff --git a/build/vignette.rds b/build/vignette.rds
diff --git a/inst/doc/Examples.html b/inst/doc/Examples.html
diff --git a/man/msprep2.Rd b/man/msprep2.Rd
diff --git a/src/Makevars b/src/Makevars
@@ -1 +1,3 @@
-CXX_STD = CXX11
+CXX=clang++
+CC=clang
+CXX_STD=CXX11
diff --git a/src/simulation.h b/src/simulation.h
@@ -22,7 +22,7 @@ class Simulation {
         double get_sim_entry_time(int);
         double get_previous_state_entry_time(int);
         void run();
-        unsigned int clock;
+        unsigned long clock;
         State* get_state(int);
         double get_next_event_time();
         Rcpp::NumericVector get_patient_attrs(int);