From b09154bcc402073e8a12ee10a2917018727fddd1 Mon Sep 17 00:00:00 2001 From: shaesen2 Date: Sun, 17 Apr 2022 04:33:18 -0400 Subject: [PATCH 01/15] Updated NEWS with changelog Quick fixes for readme to remove contributor stats and cover stats (can be accessed through the badge) --- DESCRIPTION | 59 +++++++++++++++++++++++++++++++++++++++++++---------- NEWS.md | 12 +++++++++++ README.md | 42 +------------------------------------- 3 files changed, 61 insertions(+), 52 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 69c173be..6994faff 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,17 +3,54 @@ 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 Description: To enable fit-for-purpose, reusable clinical and medical diff --git a/NEWS.md b/NEWS.md index af90b8ec..3ad18882 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,17 @@ +# visR 0.3.0 + + +### Utility functions +* AlignPlots has been renamed to align_plots + +### 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() + # visR 0.2.0 + # visR 0.1.1.9004 * 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. diff --git a/README.md b/README.md index dabd1d5c..4a5dcc57 100644 --- a/README.md +++ b/README.md @@ -103,44 +103,4 @@ 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. - - - - -## Code coverage - -Last time readme built. - -``` 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% -``` +usethis::use_tidy_thanks() \ No newline at end of file From c6f4eb51b65c1b42266b5bf86171d58b59412b31 Mon Sep 17 00:00:00 2001 From: shaesen2 Date: Sun, 17 Apr 2022 04:44:53 -0400 Subject: [PATCH 02/15] fixed typo --- DESCRIPTION | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6994faff..781a9c2f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,7 +28,8 @@ Authors@R: c( role = "aut", email = "pawel.kawski@contractors.roche.com"), person(given = "Steven", - family = "Haesendonckx", role = "aut" + family = "Haesendonckx", + role = "aut", email = "shaesen2@its.jnj.com"), person(given = "James", family = "Black", From 717915b28a8c7db33d0049545856e76d5a492905 Mon Sep 17 00:00:00 2001 From: shaesen2 Date: Sun, 17 Apr 2022 04:50:37 -0400 Subject: [PATCH 03/15] fixed typo --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 781a9c2f..0f2db766 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -14,7 +14,7 @@ Authors@R: c( person(given = "Charlotta", family = "Fruechtenicht", role = "aut", - email = "charlotta.fruechtenicht@roche.com",), + email = "charlotta.fruechtenicht@roche.com"), person(given = "Marc", family = "Vandemeulebroecke", role = "aut", @@ -46,7 +46,7 @@ Authors@R: c( person(given = "Rebecca", family = "Albrecht", role = "aut", - email = "rebecca.albrecht.dietsch@gmail.com") + email = "rebecca.albrecht.dietsch@gmail.com"), person(given = "Daniel D.", family = "Sjoberg", role = "aut", From 5b535b0318c21cbb7cf67b85fcf8f198a9e29ff1 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Sun, 17 Apr 2022 08:55:41 +0000 Subject: [PATCH 04/15] Re-build README.Rmd --- README.md | 42 +++++++++++++++++++++++++++++++++++++++++- 1 file changed, 41 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 4a5dcc57..dabd1d5c 100644 --- a/README.md +++ b/README.md @@ -103,4 +103,44 @@ 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. -usethis::use_tidy_thanks() \ No newline at end of file + + + + +## Code coverage + +Last time readme built. + +``` 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% +``` From a5c7ee2a746f03651a7e2b9f763c70ce6d95e798 Mon Sep 17 00:00:00 2001 From: shaesen2 Date: Sun, 17 Apr 2022 06:54:33 -0400 Subject: [PATCH 05/15] update ReadMe and trigger readme flow from inside pushed branch --- .github/workflows/rebuild-readme.yaml | 4 ++- README.md | 42 +-------------------------- 2 files changed, 4 insertions(+), 42 deletions(-) diff --git a/.github/workflows/rebuild-readme.yaml b/.github/workflows/rebuild-readme.yaml index 82769813..6fd4e8c8 100644 --- a/.github/workflows/rebuild-readme.yaml +++ b/.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 diff --git a/README.md b/README.md index dabd1d5c..4a5dcc57 100644 --- a/README.md +++ b/README.md @@ -103,44 +103,4 @@ 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. - - - - -## Code coverage - -Last time readme built. - -``` 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% -``` +usethis::use_tidy_thanks() \ No newline at end of file From 33be3fea92abb8e052d30d7393e69fd258590511 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Sun, 17 Apr 2022 11:03:08 +0000 Subject: [PATCH 06/15] Re-build README.Rmd --- README.md | 44 ++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 42 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 4a5dcc57..1a81e31a 100644 --- a/README.md +++ b/README.md @@ -43,7 +43,7 @@ current focus on developing a stable API. | [![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 | -| | `riskmetric` score | +| | `riskmetric` score | @@ -103,4 +103,44 @@ 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. -usethis::use_tidy_thanks() \ No newline at end of file + + + + +## Code coverage + +Last time readme built. + +``` 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% +``` From 4903932bcf5b694a4e107891f79671e70129a1e8 Mon Sep 17 00:00:00 2001 From: shaesen2 Date: Mon, 18 Apr 2022 04:51:34 -0400 Subject: [PATCH 07/15] Implemented review and adjusted readme.RMD --- NEWS.md | 16 +++++--- README.Rmd | 110 +++++------------------------------------------------ 2 files changed, 20 insertions(+), 106 deletions(-) diff --git a/NEWS.md b/NEWS.md index 3ad18882..3982922c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,16 +1,20 @@ # visR 0.3.0 -### Utility functions -* AlignPlots has been renamed to align_plots +# 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() +* 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 +* Initial CRAN release. # visR 0.1.1.9004 @@ -19,4 +23,4 @@ # 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. \ No newline at end of file diff --git a/README.Rmd b/README.Rmd index 79fd8282..950e1f8b 100644 --- a/README.Rmd +++ b/README.Rmd @@ -15,6 +15,8 @@ knitr::opts_chunk$set( library(visR) library(riskmetric) +library(usethis) +library(glue) riskmetric_score <- "visR" %>% riskmetric::pkg_ref() %>% @@ -104,110 +106,18 @@ 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('link')) -# ), -# author = case_when( -# !is.na(name) ~ paste0(name,"(",author,")"), -# TRUE ~ author -# ), -# author = paste0(' ', 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 -) +contr <- usethis::use_tidy_thanks("https://github.com/openpharma/visR") +paste((paste0("[@",contr,"](https://github.com/", contr, ")")), collapse = ", ") ``` From 9743c9516aa2131ed7d5520661490d6f565f24d9 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Mon, 18 Apr 2022 08:54:55 +0000 Subject: [PATCH 08/15] Re-build README.Rmd --- README.md | 62 ++++++++++++++++++------------------------------------- 1 file changed, 20 insertions(+), 42 deletions(-) diff --git a/README.md b/README.md index 1a81e31a..c03cdd97 100644 --- a/README.md +++ b/README.md @@ -43,7 +43,7 @@ current focus on developing a stable API. | [![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 | -| | `riskmetric` score | +| | `riskmetric` score | @@ -97,50 +97,28 @@ adtte %>% -## Contribution +## Cite visR -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. - - - - +``` text +citation("visR") +``` -## Code coverage +## Contributing -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 -) -#> 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% +contr <- usethis::use_tidy_thanks("https://github.com/openpharma/visR") +#> ✔ Resolving timestamp for ref 'v0.2.0-beta' +#> ✔ Looking for contributors from 2021-06-11 to now +#> ℹ Running gh query +#> +#> ℹ Running gh query, got 100 records of about 200 +#> +#> ✔ Found 9 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), and [@timtreis](https://github.com/timtreis). +paste((paste0("[@",contr,"](https://github.com/", contr, ")")), collapse = ", ") +#> [1] "[䂺illiem](https://github.com/bailliem), [䃝sjoberg](https://github.com/ddsjoberg), [Ўpijim](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)" ``` From 12697f63ecdae764fc4ec1f39dab7a2a870369cb Mon Sep 17 00:00:00 2001 From: shaesen2 Date: Mon, 18 Apr 2022 05:06:24 -0400 Subject: [PATCH 09/15] fixed readme --- README.Rmd | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/README.Rmd b/README.Rmd index 950e1f8b..3883da79 100644 --- a/README.Rmd +++ b/README.Rmd @@ -16,7 +16,6 @@ knitr::opts_chunk$set( library(visR) library(riskmetric) library(usethis) -library(glue) riskmetric_score <- "visR" %>% riskmetric::pkg_ref() %>% @@ -109,7 +108,7 @@ adtte %>% ## Cite visR ```{text, comment="", eval = FALSE} -citation("visR") +> citation("visR") ``` ## Contributing @@ -117,7 +116,7 @@ citation("visR") 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} +```{r warning=FALSE, echo=FALSE, message=FALSE} contr <- usethis::use_tidy_thanks("https://github.com/openpharma/visR") -paste((paste0("[@",contr,"](https://github.com/", contr, ")")), collapse = ", ") ``` +`r paste((paste0("[@",contr,"](https://github.com/", contr, ")")), collapse = ", ")` From 6b257edf3d3fcb673f5038de4fdb82924ed27b32 Mon Sep 17 00:00:00 2001 From: shaesen2 Date: Mon, 18 Apr 2022 05:07:01 -0400 Subject: [PATCH 10/15] fixed readme --- README.md | 73 ++++++++++++++++++------------------------------------- 1 file changed, 23 insertions(+), 50 deletions(-) diff --git a/README.md b/README.md index 1a81e31a..30c30b3d 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,5 @@ - # visR @@ -18,9 +17,9 @@ By using a common package for visualising data analysis results in the clinical development process, we want to have a **positive influence** on - - **choice of visualisation** by making it easy explore different +- **choice of visualisation** by making it easy explore different visualisation and to use impactful visualisations fit-for-purpose - - effective visual communication by making it easy to **implement best +- effective visual communication by making it easy to **implement best practices** We are not judging on what visualisation you chose for your research @@ -37,13 +36,13 @@ current focus on developing a stable API. | 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 | -| | `riskmetric` score | +| | `riskmetric` score | @@ -95,52 +94,26 @@ adtte %>% ) ``` - - -## 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. - - + - +## 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: + +[&\#x0040bailliem](https://github.com/bailliem), +[&\#x0040ddsjoberg](https://github.com/ddsjoberg), +[&\#x0040epijim](https://github.com/epijim), +[&\#x0040gdario](https://github.com/gdario), +[&\#x0040lcomm](https://github.com/lcomm), +[&\#x0040prabhushanmup](https://github.com/prabhushanmup), +[&\#x0040rebecca-albrecht](https://github.com/rebecca-albrecht), +[&\#x0040SHAESEN2](https://github.com/SHAESEN2), +[&\#x0040timtreis](https://github.com/timtreis) From 7c357382b67350795f91c3c3a1c1ddc9e3ff5d7b Mon Sep 17 00:00:00 2001 From: shaesen2 Date: Mon, 18 Apr 2022 05:14:50 -0400 Subject: [PATCH 11/15] dunno --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 30c30b3d..0ddbf421 100644 --- a/README.md +++ b/README.md @@ -116,4 +116,4 @@ agree to abide by its terms. Thank you to all contributors: [&\#x0040prabhushanmup](https://github.com/prabhushanmup), [&\#x0040rebecca-albrecht](https://github.com/rebecca-albrecht), [&\#x0040SHAESEN2](https://github.com/SHAESEN2), -[&\#x0040timtreis](https://github.com/timtreis) +[&\#x0040timtreis](https://github.com/timtreis) \ No newline at end of file From 7424f8bbc5f37843140ddf6e93b04306d9d1af84 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Mon, 18 Apr 2022 09:17:47 +0000 Subject: [PATCH 12/15] Re-build README.Rmd --- README.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 0ddbf421..9ac636b0 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ + # visR @@ -17,9 +18,9 @@ By using a common package for visualising data analysis results in the clinical development process, we want to have a **positive influence** on -- **choice of visualisation** by making it easy explore different + - **choice of visualisation** by making it easy explore different visualisation and to use impactful visualisations fit-for-purpose -- effective visual communication by making it easy to **implement best + - effective visual communication by making it easy to **implement best practices** We are not judging on what visualisation you chose for your research @@ -36,7 +37,7 @@ current focus on developing a stable API. | 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 | @@ -94,7 +95,7 @@ adtte %>% ) ``` - + ## Cite visR @@ -116,4 +117,4 @@ agree to abide by its terms. Thank you to all contributors: [&\#x0040prabhushanmup](https://github.com/prabhushanmup), [&\#x0040rebecca-albrecht](https://github.com/rebecca-albrecht), [&\#x0040SHAESEN2](https://github.com/SHAESEN2), -[&\#x0040timtreis](https://github.com/timtreis) \ No newline at end of file +[&\#x0040timtreis](https://github.com/timtreis) From 4a5656bbcfba0d5585ad128244b48f704deecfb7 Mon Sep 17 00:00:00 2001 From: shaesen2 Date: Mon, 18 Apr 2022 05:38:18 -0400 Subject: [PATCH 13/15] Updated contributors --- README.Rmd | 2 +- README.md | 29 +++++++++++++++-------------- 2 files changed, 16 insertions(+), 15 deletions(-) diff --git a/README.Rmd b/README.Rmd index 3883da79..ce6db45e 100644 --- a/README.Rmd +++ b/README.Rmd @@ -119,4 +119,4 @@ Thank you to all contributors: ```{r warning=FALSE, echo=FALSE, message=FALSE} contr <- usethis::use_tidy_thanks("https://github.com/openpharma/visR") ``` -`r paste((paste0("[@",contr,"](https://github.com/", contr, ")")), collapse = ", ")` +`r unique(c(paste((paste0("[@",contr,"](https://github.com/", contr, ")")), collapse = ", "), "[@cschaerfe ](https://github.com/cschaerfe)", "[@AlexandraP-21 ](https://github.com/AlexandraP-21)"))` \ No newline at end of file diff --git a/README.md b/README.md index 9ac636b0..fe0a5d03 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,5 @@ - # visR @@ -18,9 +17,9 @@ By using a common package for visualising data analysis results in the clinical development process, we want to have a **positive influence** on - - **choice of visualisation** by making it easy explore different +- **choice of visualisation** by making it easy explore different visualisation and to use impactful visualisations fit-for-purpose - - effective visual communication by making it easy to **implement best +- effective visual communication by making it easy to **implement best practices** We are not judging on what visualisation you chose for your research @@ -37,7 +36,7 @@ current focus on developing a stable API. | 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 | @@ -95,7 +94,7 @@ adtte %>% ) ``` - + ## Cite visR @@ -109,12 +108,14 @@ 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: -[&\#x0040bailliem](https://github.com/bailliem), -[&\#x0040ddsjoberg](https://github.com/ddsjoberg), -[&\#x0040epijim](https://github.com/epijim), -[&\#x0040gdario](https://github.com/gdario), -[&\#x0040lcomm](https://github.com/lcomm), -[&\#x0040prabhushanmup](https://github.com/prabhushanmup), -[&\#x0040rebecca-albrecht](https://github.com/rebecca-albrecht), -[&\#x0040SHAESEN2](https://github.com/SHAESEN2), -[&\#x0040timtreis](https://github.com/timtreis) +[@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) From 777ce25ed618752c9949f1fe5af1e98266a65ab7 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Mon, 18 Apr 2022 09:41:21 +0000 Subject: [PATCH 14/15] Re-build README.Rmd --- README.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index fe0a5d03..e37512cc 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ + # visR @@ -17,9 +18,9 @@ By using a common package for visualising data analysis results in the clinical development process, we want to have a **positive influence** on -- **choice of visualisation** by making it easy explore different + - **choice of visualisation** by making it easy explore different visualisation and to use impactful visualisations fit-for-purpose -- effective visual communication by making it easy to **implement best + - effective visual communication by making it easy to **implement best practices** We are not judging on what visualisation you chose for your research @@ -36,7 +37,7 @@ current focus on developing a stable API. | 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 | @@ -94,7 +95,7 @@ adtte %>% ) ``` - + ## Cite visR From fc93fb95cadb4a048e06ba6ded1057ff1186758c Mon Sep 17 00:00:00 2001 From: shaesen2 Date: Tue, 19 Apr 2022 00:18:48 -0400 Subject: [PATCH 15/15] Adressed review comments - Badges side-by-side - Updated NEWS --- NEWS.md | 5 ----- README.Rmd | 14 ++++++-------- README.md | 18 +++++++++--------- 3 files changed, 15 insertions(+), 22 deletions(-) diff --git a/NEWS.md b/NEWS.md index 3982922c..79d319e6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,3 @@ -# visR 0.3.0 - - # visR (development version) ### New functions @@ -16,8 +13,6 @@ * Initial CRAN release. -# visR 0.1.1.9004 - * 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. diff --git a/README.Rmd b/README.Rmd index ce6db45e..9f9fbdb2 100644 --- a/README.Rmd +++ b/README.Rmd @@ -51,14 +51,12 @@ The package is still experimental and under active development with a current fo -| 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 | -| | `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) + diff --git a/README.md b/README.md index fe0a5d03..ef8636a9 100644 --- a/README.md +++ b/README.md @@ -35,15 +35,15 @@ current focus on developing a stable API. -| 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 | -| | `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) + ## Installation