README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd as part of the CICD process. -->
<!-- Please edit README.Rmd - but you do not need to build it! -->

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

library(visR)

#library(riskmetric)
riskmetric_score <- "visR" %>%
  riskmetric::pkg_ref() %>%
  dplyr::as_tibble() %>%
  riskmetric::pkg_assess() %>%
  riskmetric::pkg_score() %>%
  dplyr::pull("pkg_score") %>%
  round(2)


```

# visR <img src='man/figures/logo.png' align="right" height="131.5" />

The goal of visR is to enable fit-for-purpose, reusable clinical and medical research focused visualizations and tables with sensible defaults and based on sound [graphical principles](https://graphicsprinciples.github.io/).

[Package documentation](https://openpharma.github.io/visR/)

## Motivation

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 visualisation and to use impactful visualisations fit-for-purpose
* effective visual communication by making it easy to **implement best practices** 

We are not judging on what visualisation you chose for your research question, but want to facilitate and support good practice.

You can read more about the philosophy and architecture in the [repo wiki](https://github.com/openpharma/visR/wiki).

## Lifecycle and status

The package is still experimental and under active development with a 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/actions/workflows/check-standard.yaml/badge.svg?branch=main)](https://github.com/openpharma/visR/actions/workflows/check-standard.yaml) | `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 |
<!-- badges: end -->


## Installation

The easiest way to get `visR` is to install from CRAN:

``` r
install.packages("visR")
```


Install the *development* version from [GitHub](https://github.com/) with:

``` r
# defaults to develop branch
devtools::install_github("openpharma/visR") 
```

Install the *latest stable* version from [GitHub](https://github.com/) with:

``` r
devtools::install_github("openpharma/visR", ref = "main")
```

## Example

This is a basic example to demonstrate how the API can be used to add layers to a visualization. In this example a time to event analysis. The example calculates stratified Kaplan-Meier by treatment and then plots. Additional functions can be used to add uncertainty intervals, censoring information and a risk table. 

```{r example, warning=FALSE, message = FALSE}
library(visR)
library(ggplot2)

theme_set(theme_minimal())

adtte %>%
  estimate_KM(strata = "TRTP", conf.int = 0.90) %>%
  visr(legend_position = "right", x_unit = "Days") %>%
  add_CI(style = "ribbon") %>%
  add_CNSR(shape = 3, size = 1) %>%
  add_risktable(
    statlist = c("n.risk", "n.event", "n.censor"),
    label = c("At risk", "Event", "Censor")
  )
```


## 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")
```


```{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.

```{r}
covr::package_coverage(
  type = "none", 
  code = "tools::testInstalledPackage(pkg = 'visR', types = c('tests'))", 
  quiet = FALSE
)
```