version 1.2.4

cran · Dec 15, 2019 · 6b59ffb · 6b59ffb
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: multistateutils
 Type: Package
 Title: Utility Functions for Parametric Multi-State Models
-Version: 1.2.3
-Date: 2019-11-07
+Version: 1.2.4
+Date: 2019-12-14
 Author: Stuart Lacy
 Maintainer: Stuart Lacy <stuart.lacy@gmail.com>
 Description: Provides functions for working with multi-state modelling, 
@@ -16,9 +16,9 @@ Suggests: covr, knitr, flexsurv, mstate, microbenchmark, rmarkdown,
 URL: https://github.com/stulacy/multistateutils
 BugReports: https://github.com/stulacy/multistateutils/issues
 LinkingTo: Rcpp
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 VignetteBuilder: knitr
 NeedsCompilation: yes
-Packaged: 2019-11-07 21:17:12 UTC; stuart
+Packaged: 2019-12-14 23:54:48 UTC; stuart
 Repository: CRAN
-Date/Publication: 2019-11-07 22:50:02 UTC
+Date/Publication: 2019-12-15 16:50:07 UTC
diff --git a/MD5 b/MD5
@@ -1,6 +1,6 @@
-6cfa156e03e842a8b84f0783a1cf4da7 *DESCRIPTION
+f449813f542c09ae6f64763442798baf *DESCRIPTION
 a1ae93d2c87fcc5f98452956facfdedf *NAMESPACE
-79233a95319564d327ca10c567659416 *NEWS.md
+86d48d123cc8e734ded681a9c6955877 *NEWS.md
 0a91d61ac2ba351a6ca6a640bea450a8 *R/RcppExports.R
 b1dbcdf5b70b84232533a3cfe8cf0ec2 *R/cohort.R
 5795f711de63e297c77b4b61e5d1fcc7 *R/length_of_stay.R
@@ -9,26 +9,26 @@ ac7e40966b058f5596304f9b7e3516ca *R/multistateutils.R
 1f182e54f53c05a90a759b5e3c3e599a *R/run_simulation.R
 aa5c6bd41802ac1354513df6612de673 *R/statepathways.R
 438b1342adbd6fc74092e2dd0b8d0499 *R/transition_probabilities.R
-ef88f74fe85ac74eec6bd37ddb2116b2 *R/utils.R
+8427576549844a2b20589a5796e0603a *R/utils.R
 725ec67436f98afd433693db94193e00 *README.md
 d41d8cd98f00b204e9800998ecf8427e *TODO
 d76ab1ddde1f2984861068978adfbd99 *build/vignette.rds
-26f953065122cd33ff110e10fdecf17b *inst/doc/Examples.R
+2d6989b9de5b6a47e8ccbd78ef0dc82f *inst/doc/Examples.R
 c28411b84a26af651d53480d3a39082b *inst/doc/Examples.Rmd
-68f84f52a3e8470de3de8aa6b3ff691f *inst/doc/Examples.html
-6b3f2cc5910bce7dfe286c5e106ddebb *man/cohort_simulation.Rd
-7db3576cf60e4e65a16117f021608430 *man/length_of_stay.Rd
-8b4c29799f2a385cafd351c601e8b0b3 *man/msprep2.Rd
-9e0ca400531a052050b92d9af7090f71 *man/multistateutils.Rd
-a5727825046d69ecd638dfc32e12ec8b *man/plot_predicted_pathway.Rd
-27b90cf9061911ba15390514271257d4 *man/predict_transitions.Rd
+364108fd54aede174001437672564fd6 *inst/doc/Examples.html
+d1073645dfc1b9e8b19f8aa858aa8b22 *man/cohort_simulation.Rd
+a96a8585f0eb3c3ae6364e8b9da360ed *man/length_of_stay.Rd
+38a8902a4adf37d4b97f4426a8851d22 *man/msprep2.Rd
+a083f778fcbe856f1ce351a2e7c079a3 *man/multistateutils.Rd
+c3ac7b71f9f5f1578e7fb9328585db92 *man/plot_predicted_pathway.Rd
+190a5c890116d5ea6ccbbcfc3008d04b *man/predict_transitions.Rd
 f330bfb0bf13be4aea36ac587f1d7868 *src/Makevars
 dafd74bc0ab6201ca5841bf709777eb4 *src/RcppExports.cpp
 7f3211520255214525d5f3b6031fe81d *src/des.cpp
 4f41451269f1eb10e8cf4589745c3b14 *src/event.cpp
 d9fe25cf905c2e202d85e1aeb727cfa1 *src/event.h
 437adecc034a16fe7ab7735343e89a27 *src/simulation.cpp
-7ef2202601e0bb2fb4dd0a02a1523a83 *src/simulation.h
+d80f9877a1a48538d8734223363b9845 *src/simulation.h
 493d4d4ec65764b7e5f02d5ea8e6e124 *src/state.cpp
 3b941394ca173084866651d88b048c39 *src/state.h
 d3989e9b9945dffc0cca614a00812188 *src/transitions.cpp
@@ -38,7 +38,7 @@ d3989e9b9945dffc0cca614a00812188 *src/transitions.cpp
 d6381e6929a139f71170c5202ad5cfdf *tests/testthat/test_lengthofstay.R
 deb2f87b0b3b6fc268f091f9720ec019 *tests/testthat/test_msprep2.R
 e080ddbcb09e99211ed92e745b4e110b *tests/testthat/test_transitionprobs.R
-c2bd43e35bae9820cfb0df47dbc5b8ff *tests/testthat/test_utils.R
+ea34a638211d96839c82dabcd21af542 *tests/testthat/test_utils.R
 c28411b84a26af651d53480d3a39082b *vignettes/Examples.Rmd
 dced1ef2ff01ec54d457df7ede8e6cda *vignettes/state_pathway.png
 73731be9e5634faf2854c0a8d1f3eb94 *vignettes/treatmentpathways.png
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# multistateutils 1.2.4
+
+Bug fixes. Tests for object class now use `inherits` and clock is now `double` to allow for greater range of values.
+
 # multistateutils 1.2.3
 
   - Added class `msdata` to the output from `msprep2` so that it is compatible with other `mstate` functions, such as `events`. 

diff --git a/R/utils.R b/R/utils.R
@@ -9,15 +9,15 @@
 #     being a list itself, containing 2 items. The first item is the (zero-based) indices in
 #     attrs of the model coefficients, and the second contains the coefficients themselves.
 obtain_model_coef <- function(mod, attrs, M=1) {
-    if (class(mod) == 'oldage') {
+    if (inherits(mod, 'oldage')) {
         list(name='oldage',
              coefs=list(list(which(colnames(attrs) == mod$col)-1,
                         mod$scale),
                    list(0,
                         mod$limit
                         )))
 
-    } else if (class(mod) == 'flexsurvreg') {
+    } else if (inherits(mod, 'flexsurvreg')) {
         dist <- mod$dlist$name
         dist <- gsub("\\.[a-zA-Z]+", "", dist)
         attr_names <- colnames(attrs)
@@ -132,7 +132,7 @@ get_state_entries <- function(x) {
 }
 
 get_sink_states <- function(tmat) {
-    if (class(tmat) != 'matrix')
+    if (!inherits(tmat, 'matrix'))
         stop("Error: must provide a square transition matrix.")
     if (ncol(tmat) != nrow(tmat))
         stop("Error: must provide a square transition matrix.")
@@ -224,7 +224,7 @@ obtain_individual_starting_states <- function(trans_mat, ninds, nreps) {
 
 # Obtains covariates that are used by these models
 get_covariates <- function(models) {
-    if (!"list" %in% class(models))
+    if (!inherits(models, "list"))
         stop("Error: must provide a list of flexsurvreg objects.")
 
     if (!all(sapply(models, class) %in% c('flexsurvreg', 'oldage')))