Updated NEWS with changelog

.github/workflows/rebuild-readme.yaml

@@ -9,7 +9,9 @@ jobs:
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+              ref: ${{ github.ref }}
       - uses: r-lib/actions/setup-r@v1
       - uses: r-lib/actions/setup-pandoc@v1
       - name: Install rmarkdown, remotes, and the local package

DESCRIPTION

@@ -3,17 +3,55 @@ Package: visR
 Title: Clinical Graphs and Tables Adhering to Graphical Principles
 Version: 0.2.0
 Authors@R: c(
-    person("Diego", "Saldana", , "diego.saldana@roche.com", role = "aut"),
-    person("Charlotta", "Fruechtenicht", , "charlotta.fruechtenicht@roche.com", role = "aut"),
-    person("Mark", "Baillie", , "bailliem@gmail.com", role = c("aut", "cre")),
-    person("Marc", "Vandemeulebroecke", , "marc.vandemeulebroecke@novartis.com", role = "aut"),
-    person("Thanos", "Siadimas", , "thanos.siadimas@roche.com", role = "aut"),
-    person("Pawel", "Kawski", , "pawel.kawski@contractors.roche.com>", role = "aut"),
-    person("Steven", "Haesendonckx", , "shaesen2@its.jnj.com", role = "aut"),
-    person("James", "Black", , "james.black.jb2@roche.com", role = "aut"),
-    person("Pelagia", "Alexandra Papadopoulou", , "PPapadop@its.jnj.com", role = "aut"),
-    person("Tim", "Treis", , "tim.treis@outlook.de", role = "aut"),
-    person("Rebecca", "Albrecht", , "rebecca.albrecht.dietsch@gmail.com", role = "aut")
+    person(given = "Mark",
+           family = "Baillie", 
+           role = c("aut", "cre"),
+           email = "bailliem@gmail.com"),
+    person(given = "Diego",
+           family = "Saldana",
+           role = "aut",
+           email = "diego.saldana@roche.com"),
+    person(given = "Charlotta",
+           family = "Fruechtenicht",
+           role = "aut",
+           email = "charlotta.fruechtenicht@roche.com"),
+    person(given = "Marc",
+           family = "Vandemeulebroecke",
+           role = "aut",
+           email = "marc.vandemeulebroecke@novartis.com"),
+    person(given = "Thanos",
+           family = "Siadimas",
+           role = "aut",
+           email = "thanos.siadimas@roche.com"),
+    person(given = "Pawel",
+           family = "Kawski", 
+           role = "aut",
+           email = "pawel.kawski@contractors.roche.com"),
+    person(given = "Steven",
+           family = "Haesendonckx",
+           role = "aut",
+           email = "shaesen2@its.jnj.com"),
+    person(given = "James",
+           family = "Black",
+           role = "aut",
+           email = "james.black.jb2@roche.com"),
+    person(given = "Pelagia",
+           family = "Alexandra Papadopoulou",
+           role = "aut",
+           email = "PPapadop@its.jnj.com"),
+    person(given = "Tim",
+           family = "Treis",
+           role = "aut",
+           email = "tim.treis@outlook.de"),
+    person(given = "Rebecca",
+           family = "Albrecht",
+           role = "aut", 
+           email = "rebecca.albrecht.dietsch@gmail.com"),
+    person(given = "Daniel D.",
+           family = "Sjoberg",
+           role = "aut",
+           email = "danield.sjoberg@gmail.com",
+           comment = c(ORCID = "0000-0003-0862-2018"))
   )
 Maintainer: Mark Baillie <bailliem@gmail.com>
 Description: To enable fit-for-purpose, reusable clinical and medical

NEWS.md

@@ -1,10 +1,21 @@
+# visR (development version)
+
+### New functions
+* Highlight specific strata in survival plots using `add_highlight()`.
+* Indicate quantiles in survival plots using `add_quantiles()`.
+* Estimation and Plotting of cumulative competing risks via `estimate_cuminc()` and `visr()`. (#293)
+
+### Utility functions
+* AlignPlots has been renamed to `align_plots()`.
+
+
 # visR 0.2.0
 
-# visR 0.1.1.9004
+* Initial CRAN release. 
 
 * Changed API for survival outputs. Experimenting with a pipe like interface to start to layer components of reports for example uncertainty intervals, annotations, risk tables, model summaries, etc. 
 
 
 # visR 0.1.0
 
-* Added a `NEWS.md` file to track changes to the package.
+* Added a `NEWS.md` file to track changes to the package.

README.Rmd

@@ -15,6 +15,7 @@ knitr::opts_chunk$set(
 
 library(visR)
 library(riskmetric)
+library(usethis)
 
 riskmetric_score <- "visR" %>%
   riskmetric::pkg_ref() %>%
@@ -50,14 +51,12 @@ The package is still experimental and under active development with a current fo
 
 <!-- badges: start -->
 
-| Badge | Description
-|----------------------|-------------------|
-| [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)    | Development stage |
-| [![Codecov test coverage](https://codecov.io/gh/openpharma/visR/branch/develop/graph/badge.svg)](https://codecov.io/gh/openpharma/visR?branch=main) | Unit testing coverage - on `main` |
-| [![R-CMD-check](https://github.com/openpharma/visR/workflows/R-CMD-check/badge.svg)](https://github.com/openpharma/visR/actions) | `main` branch |
-| [![pkgdown](https://github.com/openpharma/visR/actions/workflows/makedocs.yml/badge.svg)](https://github.com/openpharma/visR/actions/workflows/makedocs.yml) | Documentation building to [Github pages](https://openpharma.github.io/visR/) |
-| [![CRAN status](https://www.r-pkg.org/badges/version/visR)](https://CRAN.R-project.org/package=visR)| Latest CRAN release |
-| <a href=https://github.com/pharmaR/riskmetric><img src=https://img.shields.io/badge/riskmetric-`r riskmetric_score`-green></img></a>| `riskmetric` score |
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Codecov test coverage](https://codecov.io/gh/openpharma/visR/branch/develop/graph/badge.svg)](https://codecov.io/gh/openpharma/visR?branch=main)
+[![R-CMD-check](https://github.com/openpharma/visR/workflows/R-CMD-check/badge.svg)](https://github.com/openpharma/visR/actions)
+[![pkgdown](https://github.com/openpharma/visR/actions/workflows/makedocs.yml/badge.svg)](https://github.com/openpharma/visR/actions/workflows/makedocs.yml)
+[![CRAN status](https://www.r-pkg.org/badges/version/visR)](https://CRAN.R-project.org/package=visR)
+<a href=https://github.com/pharmaR/riskmetric><img src=https://img.shields.io/badge/riskmetric-`r riskmetric_score`-green></img></a>
 <!-- badges: end -->
 
 
@@ -104,110 +103,18 @@ adtte %>%
   )
 ```
 
+## Cite visR
 
-## Contribution 
-
-Please note that the `visR` project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.
-
-```{r getcontributions, echo=FALSE, warning=FALSE, message = FALSE}
-library(dplyr)
-library(ggplot2)
-#library(GithubMetrics) #remotes::install_github("openpharma/GithubMetrics")
-library(gitsum) #remotes::install_github("lorenzwalthert/gitsum")
-
-local_repo <- parse_log_detailed()
-
-# commits <- gh_commits_get(
-#   full_names = "openpharma/visR",
-#   days_back = 365*10,
-#   .token = Sys.getenv("GH_API_TOKEN_README")
-#   ) %>%
-#   mutate(date = as.Date(datetime)) %>%
-#   filter(!author %in% c(".gitconfig missing email","actions-user"))
-# 
-# left_join(
-#   commits %>%
-#     group_by(author) %>%
-#     summarise(commits_all = n()),
-#   commits %>%
-#     filter(date > Sys.Date() - 28*6) %>%
-#     group_by(author) %>%
-#     summarise(commits_6months = n())
-#   ) %>%
-#   arrange(-commits_6months) %>%
-#   left_join(
-#     gh_user_get(unique(commits$author),
-#     .token = Sys.getenv("GH_API_TOKEN_README")
-#     ),
-#     by = c("author"="username")
-#   ) %>%
-#   mutate(
-#     blog = case_when(
-#       blog == "" ~ "",
-#       TRUE ~ as.character(paste0('<a href="', blog, '">link</a>'))
-#       ),
-#     author = case_when(
-#       !is.na(name) ~ paste0(name,"(",author,")"),
-#       TRUE ~ author
-#     ),
-#     author = paste0('<img src="', avatar, '" alt="" height="30"> ', author)
-#     ) %>%
-#   select(author,commits_all,commits_6months,company,location,blog) %>%
-#   knitr::kable()
-```
-
-```{r plotcontriuptake, echo=FALSE, warning=FALSE, message = FALSE}
-# plot
-local_repo %>%
-  arrange(
-    date
-  ) %>%
-  group_by(author_email) %>% 
-  slice(1) %>% ungroup %>%
-  ggplot(aes(x = date)) +
-  stat_bin(aes(y = cumsum(..count..)),geom = "step") +
-  theme_minimal() +
-  labs(
-    title = "Uptake in new contributors to visR",
-    subtitle = "Based email address attached to commits",
-    y = "Contributors",
-    x = "Date"
-  ) + theme(legend.position = "none")
+```{text, comment="", eval = FALSE}
+> citation("visR")
 ```
 
+## Contributing
 
-```{r plotcontributions, echo=FALSE, warning=FALSE, message = FALSE}
-
-# plot
-local_repo %>%
-  mutate(date = gsub("([0-9]{4}\\-[0-9]{2})\\-.*","\\1", date)) %>%
-  mutate(date = as.POSIXct(paste0(date, "-01 UTC"), tz = "UTC")) %>%
-  group_by(
-    Month = date,
-    author_name
-    ) %>%
-  summarise(
-    Commits = n()
-  ) %>%
-  ggplot() +
-  geom_col(
-    aes(x = Month, y = Commits, fill = author_name)
-  ) +
-  theme_minimal() +
-  labs(
-    title = "Commit activity in openpharma/visR",
-    subtitle = "Colour = author (names hidden)"
-  ) + theme(legend.position = "none")
-```
-
-## Code coverage 
-
-Last time readme built.
+Please note that the `visR` project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.
+Thank you to all contributors:
 
-```{r}
-covr::package_coverage(
-  type = "none", 
-  code = "tools::testInstalledPackage(pkg = 'visR', types = c('tests'))", 
-  quiet = FALSE
-)
+```{r warning=FALSE, echo=FALSE, message=FALSE}
+contr <- usethis::use_tidy_thanks("https://github.com/openpharma/visR")
 ```
+`r unique(c(paste((paste0("[&#x0040;",contr,"](https://github.com/", contr, ")")), collapse = ", "), "[&#x0040;cschaerfe ](https://github.com/cschaerfe)", "[&#x0040;AlexandraP-21 ](https://github.com/AlexandraP-21)"))`

README.md

@@ -36,15 +36,15 @@ current focus on developing a stable API.
 
 <!-- badges: start -->
 
-| Badge                                                                                                                                                        | Description                                                                  |
-| ------------------------------------------------------------------------------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------- |
-| [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)  | Development stage                                                            |
-| [![Codecov test coverage](https://codecov.io/gh/openpharma/visR/branch/develop/graph/badge.svg)](https://codecov.io/gh/openpharma/visR?branch=main)          | Unit testing coverage - on `main`                                            |
-| [![R-CMD-check](https://github.com/openpharma/visR/workflows/R-CMD-check/badge.svg)](https://github.com/openpharma/visR/actions)                             | `main` branch                                                                |
-| [![pkgdown](https://github.com/openpharma/visR/actions/workflows/makedocs.yml/badge.svg)](https://github.com/openpharma/visR/actions/workflows/makedocs.yml) | Documentation building to [Github pages](https://openpharma.github.io/visR/) |
-| [![CRAN status](https://www.r-pkg.org/badges/version/visR)](https://CRAN.R-project.org/package=visR)                                                         | Latest CRAN release                                                          |
-| <a href=https://github.com/pharmaR/riskmetric><img src=https://img.shields.io/badge/riskmetric-0.46-green></img></a>                                         | `riskmetric` score                                                           |
-
+[![Lifecycle:
+experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Codecov test
+coverage](https://codecov.io/gh/openpharma/visR/branch/develop/graph/badge.svg)](https://codecov.io/gh/openpharma/visR?branch=main)
+[![R-CMD-check](https://github.com/openpharma/visR/workflows/R-CMD-check/badge.svg)](https://github.com/openpharma/visR/actions)
+[![pkgdown](https://github.com/openpharma/visR/actions/workflows/makedocs.yml/badge.svg)](https://github.com/openpharma/visR/actions/workflows/makedocs.yml)
+[![CRAN
+status](https://www.r-pkg.org/badges/version/visR)](https://CRAN.R-project.org/package=visR)
+<a href=https://github.com/pharmaR/riskmetric><img src=https://img.shields.io/badge/riskmetric-0.46-green></img></a>
 <!-- badges: end -->
 
 ## Installation
@@ -97,50 +97,26 @@ adtte %>%
 
 <img src="man/figures/README-example-1.png" width="100%" />
 
-## Contribution
-
-Please note that the `visR` project is released with a [Contributor Code
-of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you
-agree to abide by its terms.
-
-<img src="man/figures/README-plotcontriuptake-1.png" width="100%" />
-
-<img src="man/figures/README-plotcontributions-1.png" width="100%" />
+## Cite visR
 
-## Code coverage
+``` text
+> citation("visR")
+```
 
-Last time readme built.
+## Contributing
 
-``` r
-covr::package_coverage(
-  type = "none", 
-  code = "tools::testInstalledPackage(pkg = 'visR', types = c('tests'))", 
-  quiet = FALSE
-)
-#> visR Coverage: 99.88%
-#> R/visr.R: 99.12%
-#> R/add_annotation.R: 100.00%
-#> R/add_CI.R: 100.00%
-#> R/add_CNSR.R: 100.00%
-#> R/add_highlight.R: 100.00%
-#> R/add_quantiles.R: 100.00%
-#> R/add_risktable.R: 100.00%
-#> R/apply_attrition.R: 100.00%
-#> R/apply_theme.R: 100.00%
-#> R/estimate_cuminc.R: 100.00%
-#> R/estimate_KM.R: 100.00%
-#> R/get_attrition.R: 100.00%
-#> R/get_COX_HR.R: 100.00%
-#> R/get_pvalue.R: 100.00%
-#> R/get_quantile.R: 100.00%
-#> R/get_risktable.R: 100.00%
-#> R/get_summary.R: 100.00%
-#> R/get_tableone.R: 100.00%
-#> R/render.R: 100.00%
-#> R/tableone.R: 100.00%
-#> R/tidyme.R: 100.00%
-#> R/utils_general.R: 100.00%
-#> R/utils_pipe.R: 100.00%
-#> R/utils_table.R: 100.00%
-#> R/utils_visr.R: 100.00%
-```
+Please note that the `visR` project is released with a [Contributor Code
+of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you
+agree to abide by its terms. Thank you to all contributors:
+
+[@bailliem](https://github.com/bailliem),
+[@ddsjoberg](https://github.com/ddsjoberg),
+[@epijim](https://github.com/epijim),
+[@gdario](https://github.com/gdario),
+[@lcomm](https://github.com/lcomm),
+[@prabhushanmup](https://github.com/prabhushanmup),
+[@rebecca-albrecht](https://github.com/rebecca-albrecht),
+[@SHAESEN2](https://github.com/SHAESEN2),
+[@timtreis](https://github.com/timtreis),
+[@cschaerfe](https://github.com/cschaerfe),
+[@AlexandraP-21](https://github.com/AlexandraP-21)