ggsurvfit

https://github.com/pharmaverse/ggsurvfit

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
○
Committers with academic emails
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (19.0%) to scientific vocabulary

Last synced: 9 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: pharmaverse
License: other
Language: R
Default Branch: main
Homepage: http://www.danieldsjoberg.com/ggsurvfit/
Size: 33.4 MB

Statistics

Stars: 90
Watchers: 5
Forks: 23
Open Issues: 16
Releases: 7

Created almost 4 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog Contributing License Codemeta

README.Rmd

---
output: github_document
---



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

# ggsurvfit 


[![R-CMD-check](https://github.com/pharmaverse/ggsurvfit/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/pharmaverse/ggsurvfit/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/pharmaverse/ggsurvfit/graph/badge.svg)](https://app.codecov.io/gh/pharmaverse/ggsurvfit)
[![CRAN status](https://www.r-pkg.org/badges/version/ggsurvfit)](https://CRAN.R-project.org/package=ggsurvfit)
[![](https://cranlogs.r-pkg.org/badges/ggsurvfit)](https://cran.r-project.org/package=ggsurvfit)
[](https://pharmaverse.org)


## Introduction

The **ggsurvfit** package eases the creation of time-to-event (aka survival) summary figures with ggplot2.
The concise and modular code creates images that are ready for publication or sharing.
Competing risks cumulative incidence is also supported via `ggcuminc()`.

## Why ggsurvfit?

- **Use ggplot2 functions:** Each **ggsurvfit** add-on function (e.g. `add_confidence_interval()`, `add_risktable()`, etc.) is written as a proper ggplot2 ['geom'](https://ggplot2.tidyverse.org/reference/index.html), meaning the package functions can be woven with ggplot2 functions seamlessly. You don't need to learn how to style the plot within the ggsurvfit functions: rather, rely on the suite of ggplot2 functions you already know.

- **Publishable Legends:** Raw variable names do not appear in the figure legend, e.g. `"sex=Female"`.

- **Limitless Customization:** You can modify the x-axis scales or any other plot feature and the risk table will still align with the plot.

- **Simple Saving:** Save individual images easily with `ggplot2::ggsave()`.

## Installation

Install **ggsurvfit** from CRAN with:

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

You can install the development version from [GitHub](https://github.com/pharmaverse/ggsurvfit) with:

``` r
# install.packages("devtools")
devtools::install_github("pharmaverse/ggsurvfit")
```

## Examples

Review the [**figure gallery**](https://www.danieldsjoberg.com/ggsurvfit/articles/gallery.html) for many more examples. 

The code below constructs a basic {ggsurvfit} figure without customization.

```{r example, fig.height=5.5}
library(ggsurvfit)

p <- survfit2(Surv(time, status) ~ surg, data = df_colon) |>
  ggsurvfit(linewidth = 1) +
  add_confidence_interval() +
  add_risktable() +
  add_quantile(y_value = 0.6, color = "gray50", linewidth = 0.75) +
  scale_ggsurvfit()
```

Any figure created with {ggsurvfit} can be customized using {ggplot2} functions.

```{r}
p +
  # limit plot to show 8 years and less
  coord_cartesian(xlim = c(0, 8)) +
  # update figure labels/titles
  labs(
    y = "Percentage Survival",
    title = "Recurrence by Time From Surgery to Randomization",
  )
```

## `survfit2()` vs `survfit()`

Both functions have identical inputs, so why do we need `survfit2()`?
The `survfit2()` tracks the environment from which the function was called, resulting in the following benefits.

- We can reliably remove the raw variable names from the figure legend, e.g. `SEX=Female`.
- P-values can be calculated with `survfit_p()` and added to figures.
- The items above are often *possible* using `survfit()`. However, by utilizing the calling [environment](https://adv-r.hadley.nz/environments.html) we are assured the correct elements are found, rather than crossing our fingers that the search path contains the needed elements.

## CDISC ADaM ADTTE

The package also includes gems for those using the [CDISC ADaM ADTTE v1.0](https://www.cdisc.org/standards/foundational/adam/adam-basic-data-structure-bds-time-event-tte-analyses-v1-0) data model.

If columns `"PARAM"` or `"PARAMCD"` are present in the data frame passed to `survfit2()`, their values will be used to construct default labels in the `ggsurvfit()` figure. 

The event indicator in ADTTE data sets is named `"CNSR"` and is coded in the opposite way the survival package expects outcomes---`1 = 'censored'` and `0 = 'event'`.
This difference creates an opportunity for errors to be introduced in an analysis.
The **ggsurvfit** package exports a function called `Surv_CNSR()` to resolve this concern.
The function creates a survival object (e.g. `survival::Surv()`) that uses CDISC ADaM ADTTE coding conventions as the default values.
The function can be used in **ggsurvfit** as well as any other package that uses `survival::Surv()`.

```{r}
survfit(Surv_CNSR() ~ 1, adtte)
```

## Related Packages

```{r, related-pkgs, echo = FALSE}
gt_related_pkgs <-
  dplyr::tribble(
    ~pkg,                 ~cran,   ~survfit,   ~survfit_risktable,   ~cmprsk,   ~cmprsk_risktable, ~ggplot2,    ~gh_owner,               ~gh_repo, ~gh_branch,
    "ggsurvfit",            "X",        "X",                  "X",       "X",                 "X",      "X",  "pharmaverse",            "ggsurvfit",     "main",
    "survminer",            "X",        "X",                  "X",       "X",                  "",       "", "kassambara",            "survminer",   "master",
    "KMunicate",            "X",        "X",                  "X",        "",                  "",       "", "ellessenne",    "KMunicate-package",   "master",
    "GGally",               "X",        "X",                   "",        "",                  "",       "",      "ggobi",               "ggally",   "master",
    "ggfortify",            "X",        "X",                   "",        "",                  "",       "",    "sinhrks",            "ggfortify",   "master",
    "iwillsurvive",          "",        "X",                  "X",        "",                  "",       "", "ndphillips",         "iwillsurvive",   "master"
  ) |> 
  dplyr::mutate(
    covr_badge = 
      sprintf(
        "![](%s)", 
        glue::glue("https://codecov.io/gh/{gh_owner}/{gh_repo}/branch/{gh_branch}/graph/badge.svg")
      )
  ) |> 
  dplyr::select(-dplyr::starts_with("gh_")) |> 
  gt::gt() |> 
  gt::cols_label(
    pkg = gt::md("**Package**"),
    cran = gt::md("**CRAN**"),
    survfit = gt::md("**Estimates**"),
    survfit_risktable = gt::md("**Risktable**"),
    cmprsk = gt::md("**Estimates**"),
    cmprsk_risktable = gt::md("**Risktable**"),
    ggplot2 = gt::md("**{ggplot2}  \nIntegration**"),
    covr_badge = gt::md("**Code Coverage**")
  ) |> 
  gt::tab_spanner(c(survfit, survfit_risktable), label = gt::md("**Kaplan-Meier**")) |> 
  gt::tab_spanner(c(cmprsk, cmprsk_risktable), label = gt::md("**Competing Risks**")) |> 
  gt::fmt_markdown(c(pkg, covr_badge)) |> 
  gt::tab_footnote(
    footnote = "Use any {ggplot2} function to modify plot area (including scales) and the risktable will align with  the plot.",
    locations = gt::cells_column_labels(ggplot2)
  ) |> 
  gt::text_transform(
    locations = 
      gt::cells_body(columns = c(cran, survfit, survfit_risktable, cmprsk, cmprsk_risktable, ggplot2)),
    fn = function(x) {
      ifelse(x == "X", emoji::emoji("check_mark"), x)
    }
  ) |> 
  gt::cols_align(align = "center", columns = c(cran, survfit, survfit_risktable, cmprsk, cmprsk_risktable, ggplot2)) |> 
  gt::tab_options(table.font.size = 13, data_row.padding = gt::px(1), 
                  summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1), 
                  footnotes.padding = gt::px(1), source_notes.padding = gt::px(1), 
                  row_group.padding = gt::px(1))
```

```{r related-pkgs-save, include = FALSE}
gt::gtsave(gt_related_pkgs, filename = here::here("man", "figures" , "README-gt-related-pkgs.png"))
```

```{r echo=FALSE}
knitr::include_graphics(path = here::here("man", "figures" , "README-gt-related-pkgs.png"))
```

Owner

Name: pharmaverse
Login: pharmaverse
Kind: organization
Location: Switzerland

Repositories: 25
Profile: https://github.com/pharmaverse

CodeMeta (codemeta.json)

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "identifier": "ggsurvfit",
  "description": "Ease the creation of time-to-event (i.e. survival) endpoint figures. The modular functions create figures ready for publication. Each of the functions that add to or modify the figure are written as proper 'ggplot2' geoms or stat methods, allowing the functions from this package to be combined with any function or customization from 'ggplot2' and other 'ggplot2' extension packages.",
  "name": "ggsurvfit: Easy and Flexible Time-to-Event Figures",
  "relatedLink": [
    "http://www.danieldsjoberg.com/ggsurvfit/",
    "https://CRAN.R-project.org/package=ggsurvfit"
  ],
  "codeRepository": "https://github.com/ddsjoberg/ggsurvfit",
  "issueTracker": "https://github.com/ddsjoberg/ggsurvfit/issues",
  "license": "https://spdx.org/licenses/MIT",
  "version": "0.1.0.9001",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "url": "https://r-project.org"
  },
  "runtimePlatform": "R version 4.2.1 (2022-06-23 ucrt)",
  "provider": {
    "@id": "https://cran.r-project.org",
    "@type": "Organization",
    "name": "Comprehensive R Archive Network (CRAN)",
    "url": "https://cran.r-project.org"
  },
  "author": [
    {
      "@type": "Person",
      "givenName": "Daniel D.",
      "familyName": "Sjoberg",
      "email": "danield.sjoberg@gmail.com",
      "@id": "https://orcid.org/0000-0003-0862-2018"
    },
    {
      "@type": "Person",
      "givenName": "Mark",
      "familyName": "Baillie",
      "email": "bailliem@gmail.com"
    }
  ],
  "copyrightHolder": [
    {
      "@type": "Person",
      "givenName": "Daniel D.",
      "familyName": "Sjoberg",
      "email": "danield.sjoberg@gmail.com",
      "@id": "https://orcid.org/0000-0003-0862-2018"
    }
  ],
  "maintainer": [
    {
      "@type": "Person",
      "givenName": "Daniel D.",
      "familyName": "Sjoberg",
      "email": "danield.sjoberg@gmail.com",
      "@id": "https://orcid.org/0000-0003-0862-2018"
    }
  ],
  "softwareSuggestions": [
    {
      "@type": "SoftwareApplication",
      "identifier": "covr",
      "name": "covr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=covr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "knitr",
      "name": "knitr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=knitr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rmarkdown",
      "name": "rmarkdown",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "scales",
      "name": "scales",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=scales"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "spelling",
      "name": "spelling",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=spelling"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "testthat",
      "name": "testthat",
      "version": ">= 3.0.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=testthat"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "tidycmprsk",
      "name": "tidycmprsk",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tidycmprsk"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "vdiffr",
      "name": "vdiffr",
      "version": ">= 1.0.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=vdiffr"
    }
  ],
  "softwareRequirements": {
    "1": {
      "@type": "SoftwareApplication",
      "identifier": "R",
      "name": "R",
      "version": ">= 3.5"
    },
    "2": {
      "@type": "SoftwareApplication",
      "identifier": "broom",
      "name": "broom",
      "version": ">= 1.0.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=broom"
    },
    "3": {
      "@type": "SoftwareApplication",
      "identifier": "cli",
      "name": "cli",
      "version": ">= 3.0.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=cli"
    },
    "4": {
      "@type": "SoftwareApplication",
      "identifier": "dplyr",
      "name": "dplyr",
      "version": ">= 1.0.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=dplyr"
    },
    "5": {
      "@type": "SoftwareApplication",
      "identifier": "glue",
      "name": "glue",
      "version": ">= 1.6.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=glue"
    },
    "6": {
      "@type": "SoftwareApplication",
      "identifier": "ggplot2",
      "name": "ggplot2",
      "version": ">= 3.3.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=ggplot2"
    },
    "7": {
      "@type": "SoftwareApplication",
      "identifier": "gtable",
      "name": "gtable",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=gtable"
    },
    "8": {
      "@type": "SoftwareApplication",
      "identifier": "patchwork",
      "name": "patchwork",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=patchwork"
    },
    "9": {
      "@type": "SoftwareApplication",
      "identifier": "rlang",
      "name": "rlang",
      "version": ">= 1.0.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rlang"
    },
    "10": {
      "@type": "SoftwareApplication",
      "identifier": "survival",
      "name": "survival",
      "version": ">= 3.4-0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=survival"
    },
    "11": {
      "@type": "SoftwareApplication",
      "identifier": "tidyr",
      "name": "tidyr",
      "version": ">= 1.0.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tidyr"
    },
    "SystemRequirements": null
  },
  "fileSize": "2577.806KB",
  "releaseNotes": "https://github.com/ddsjoberg/ggsurvfit/blob/master/NEWS.md",
  "readme": "https://github.com/ddsjoberg/ggsurvfit/blob/main/README.md",
  "contIntegration": [
    "https://github.com/ddsjoberg/ggsurvfit/actions/workflows/R-CMD-check.yaml",
    "https://app.codecov.io/gh/ddsjoberg/ggsurvfit?branch=main"
  ],
  "developmentStatus": "https://lifecycle.r-lib.org/articles/stages.html#experimental"
}

GitHub Events

Total

Create event: 11
Issues event: 21
Watch event: 15
Delete event: 5
Member event: 1
Issue comment event: 51
Push event: 48
Pull request review event: 40
Pull request review comment event: 38
Pull request event: 26
Fork event: 1

Last Year

Create event: 11
Issues event: 21
Watch event: 15
Delete event: 5
Member event: 1
Issue comment event: 51
Push event: 48
Pull request review event: 40
Pull request review comment event: 38
Pull request event: 26
Fork event: 1

Committers

Last synced: about 1 year ago

All Time

Total Commits: 300
Total Committers: 8
Avg Commits per committer: 37.5
Development Distribution Score (DDS): 0.05

Past Year

Commits: 2
Committers: 2
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.5

Top Committers

Name	Email	Commits
Daniel Sjoberg	d**g@g**m	285
Mark Baillie	b**m@g**m	8
Dan Chaltiel	d**l@g**m	2
Teun van den Brand	4****d	1
Matt Secrest	m**t@g**m	1
Kirina Sirohi	8****7	1
Avishai M Tsur	5****r	1
Alan Haynes	a****s	1

Packages

Total packages: 1
Total downloads:
- cran 4,306 last-month
Total docker downloads: 131

Total dependent packages: 2
Total dependent repositories: 1
Total versions: 7
Total maintainers: 1

cran.r-project.org: ggsurvfit

Flexible Time-to-Event Figures

Homepage: https://github.com/pharmaverse/ggsurvfit
Documentation: http://cran.r-project.org/web/packages/ggsurvfit/ggsurvfit.pdf
License: MIT + file LICENSE
Latest release: 1.1.0
published about 2 years ago

Versions: 7
Dependent Packages: 2
Dependent Repositories: 1
Downloads: 4,306 Last month
Docker Downloads: 131

Rankings

Downloads: 5.7%

Forks count: 6.3%

Stargazers count: 7.2%

Average: 13.1%

Docker downloads count: 17.3%

Dependent packages count: 18.1%

Dependent repos count: 23.8%

Maintainers (1)

danield.sjoberg@gmail.com

Last synced: 9 months ago

Dependencies

DESCRIPTION cran

R >= 3.5 depends
broom >= 1.0.0 imports
cli >= 3.0.0 imports
dplyr >= 1.0.0 imports
ggplot2 >= 3.3.0 imports
gtable * imports
patchwork * imports
rlang >= 1.0.0 imports
survival >= 3.4 imports
tidyr >= 1.0.0 imports
covr * suggests
glue * suggests
knitr * suggests
rmarkdown * suggests
scales * suggests
spelling * suggests
testthat >= 3.0.0 suggests
tidycmprsk * suggests
vdiffr >= 1.0.0 suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v2 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action 4.1.4 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pr-commands.yaml actions

actions/checkout v2 composite
r-lib/actions/pr-fetch v2 composite
r-lib/actions/pr-push v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science