Merge pull request #92 from AstraZeneca/version_0_7_updates

Version 0 7 updates

Author: Monika-H

DESCRIPTION

@@ -1,13 +1,16 @@
 Package: maraca
-Version: 0.6
+Version: 0.7
 Type: Package
 Title: The Maraca Plot: Visualization of Hierarchical Composite Endpoints in Clinical Trials
 License: Apache License (>= 2)
 Authors@R: c(
-    person("Martin Karpefors", "", email = "[email protected]", role = "aut"),
-    person("Samvel B. Gasparyan", "", email = "[email protected]", role = "aut"),
-    person("Monika Huhn", "", email = "[email protected]", role = c("aut", "cre")),
-    person("Stefano Borini", "", email = "[email protected]", role = c("ctb")))
+    person("Martin Karpefors", "", email = "[email protected]", role = "aut",
+	   comment = c(ORCID = "0000-0003-3136-9882")),
+    person("Samvel B. Gasparyan", "", email = "[email protected]", role = "aut",
+	   comment = c(ORCID = "0000-0002-4797-2208")),
+    person("Stefano Borini", "", email = "[email protected]", role = c("ctb")),
+    person("Monika Huhn", "", email = "[email protected]", role = c("aut", "cre"),
+	   comment = c(ORCID = "0009-0000-7865-6008")))
 Description: Library that supports visual interpretation of hierarchical composite
     endpoints (HCEs). HCEs are complex constructs used as primary endpoints in
     clinical trials, combining outcomes of different types into ordinal endpoints,
@@ -20,12 +23,14 @@ Encoding: UTF-8
 LazyData: true
 Depends:
     R (>= 3.5),
-    hce (>= 0.5)
+    hce (>= 0.5),
+    ggplot2 (>= 3.3)
 Imports:
     dplyr (>= 1.0),
     tidyr (>= 1.2),
-    ggplot2 (>= 3.3),
-    checkmate (>= 2.1)
+    checkmate (>= 2.1),
+    patchwork(>= 1.0.0),
+    lifecycle
 RoxygenNote: 7.2.3
 Suggests:
     knitr (>= 1.39),

NAMESPACE

@@ -3,11 +3,16 @@
 S3method(component_plot,default)
 S3method(component_plot,hce)
 S3method(component_plot,maraca)
+S3method(cumulative_plot,default)
+S3method(cumulative_plot,hce)
+S3method(cumulative_plot,maraca)
 S3method(plot,hce)
 S3method(plot,maraca)
 S3method(print,maraca)
 export(component_plot)
+export(cumulative_plot)
 export(maraca)
 export(plot_maraca)
 export(validate_maraca_plot)
+import(ggplot2)
 import(hce)

NEWS.md

@@ -1,3 +1,33 @@
+# maraca 0.7
+
+## New features
+
+- The maraca package has been re-factored to allow flexibility in the type of
+  outcomes that can be visualized. The user can now also include binary endpoints
+  in their hierarchical endpoint. Details are given in the new vignette
+  "Maraca Plots - Alternative Endpoints".
+- Additionally to the `component_plot()`, there has been a new plot added called
+  `cumulative_plot()`. As opposed to the previous plot showing the individual
+  components of the win odds computation, this plot is displaying 
+  the endpoints cumulated instead (adding one component of hierarchical endpoint
+  at a time). Details can be found in the vignette "Maraca Plots - Plotting win odds".
+
+## Parameter change
+- As part of the re-factoring to allow for other endpoint types, the parameter
+  `tte_outcomes` has been changed to `step_outcomes` and the parameter
+  `continuous_outcome` to `last_outcome`.
+
+## Dependency change
+
+- The `ggplot2` is now automatically attached when loading `maraca`.
+- `maraca` has a new dependency - the `patchwork` package.
+
+## Bug fixes
+
+- The `trans` parameter in the plotting functions was not working as
+  intended. It now enables x-axis transformation for the continuous
+  endpoint part of the plot.
+
 # maraca 0.6
 
 ## New features
@@ -15,7 +45,7 @@
 
 - `maraca` now has increased the version dependency for the package `hce`
   to >= 0.5.
-- The `hce` is now automatically attached when loading `maraca`.
+- The `hce` package is now automatically attached when loading `maraca`.
 
 # maraca 0.5.1
 

R/aaa.R

@@ -4,6 +4,8 @@ utils::globalVariables("n")
 utils::globalVariables("n.event")
 utils::globalVariables("x")
 utils::globalVariables("y")
+utils::globalVariables("xend")
+utils::globalVariables("yend")
 utils::globalVariables("strata")
 utils::globalVariables("surv")
 utils::globalVariables("proportion")
@@ -17,13 +19,17 @@ utils::globalVariables("violiny")
 utils::globalVariables("violinx")
 utils::globalVariables("adjusted.time")
 utils::globalVariables("tte_outcomes")
+utils::globalVariables("step_values")
+utils::globalVariables("type")
+utils::globalVariables("t_cdf")
 utils::globalVariables("continuous_outcome")
 utils::globalVariables("treatments")
 utils::globalVariables("fixed_followup_days")
 utils::globalVariables("average")
+utils::globalVariables("estimate")
 utils::globalVariables("value")
 utils::globalVariables("percentage")
-utils::globalVariables("name")
+utils::globalVariables("count")
 utils::globalVariables(".env")
 utils::globalVariables("separation")
 utils::globalVariables("gap")
@@ -47,3 +53,8 @@ utils::globalVariables("TOTAL")
 utils::globalVariables("WIN_A")
 utils::globalVariables("WIN_P")
 utils::globalVariables("TIE_A")
+utils::globalVariables("linetype")
+utils::globalVariables("method")
+utils::globalVariables("UCL")
+utils::globalVariables("LCL")
+utils::globalVariables("tot")

R/general.R

@@ -3,6 +3,7 @@
 #' @docType package
 #' @name maraca
 #' @import hce
+#' @import ggplot2
 #' @aliases maraca-package
 NULL