diff --git a/.Rbuildignore b/.Rbuildignore index a38903b..771419c 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -6,3 +6,5 @@ ^dev$ ^CRAN-RELEASE$ ^data-raw$ +^CRAN-SUBMISSION$ +^man/figures diff --git a/.gitignore b/.gitignore index edf4413..5e32c18 100644 --- a/.gitignore +++ b/.gitignore @@ -42,3 +42,6 @@ rsconnect/ # R installed data *.rds + +# CRAN +CRAN-SUBMISSION diff --git a/LICENSE.md b/LICENSE.md index 523138c..7a2b892 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -169,16 +169,6 @@ accepting any such warranty or additional liability. _END OF TERMS AND CONDITIONS_ -### APPENDIX: How to apply the Apache License to your work - -To apply the Apache License to your work, attach the following boilerplate -notice, with the fields enclosed by brackets `[]` replaced with your own -identifying information. (Don't include the brackets!) The text should be -enclosed in the appropriate comment syntax for the file format. We also -recommend that a file or class name and description of purpose be included on -the same “printed page” as the copyright notice for easier identification within -third-party archives. - Copyright 2020 Ian D. Buller; NCI Licensed under the Apache License, Version 2.0 (the "License"); diff --git a/README.md b/README.md index 28e8668..db26638 100644 --- a/README.md +++ b/README.md @@ -2,16 +2,16 @@ gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation - -[![CRAN -version](https://www.r-pkg.org/badges/version-ago/gateR)](https://cran.r-project.org/package=gateR) -[![CRAN RStudio mirror -downloads](https://cranlogs.r-pkg.org/badges/grand-total/gateR?color=blue)](https://r-pkg.org/pkg/gateR) -![license](https://img.shields.io/badge/license-apache-yellow) +[![CRAN status](http://www.r-pkg.org/badges/version/gateR)](https://cran.r-project.org/package=gateR) +[![CRAN version](https://www.r-pkg.org/badges/version-ago/gateR)](https://cran.r-project.org/package=gateR) +[![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/grand-total/gateR?color=blue)](https://r-pkg.org/pkg/gateR) +[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) +![GitHub last commit](https://img.shields.io/github/last-commit/Waller-SUSAN/gateR) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5347893.svg)](https://doi.org/10.5281/zenodo.5347893) - +**Date repository last updated**: August 08, 2022 +

Overview @@ -32,7 +32,7 @@ For a two-group comparison of two conditions we estimate two relative risk surfa 2. Condition 1B v. Condition 1A 2. Estimate relative risk surface for the ratio: -![equation](https://latex.codecogs.com/gif.latex?%5Cfrac%7B%28%5Cfrac%7BCondtion2B%7D%7BCondition2A%7D%29%7D%7B%28%5Cfrac%7BCondition1B%7D%7BCondition1A%7D%29%7D) +\frac{ \big(\frac{Condition2B}{Condition2A}\big)}{\big(\frac{Condition1B}{Condition1A}\big)} Within areas where the relative risk exceeds an asymptotic normal assumption, the `gateR` package has functionality to examine the features of these cells. Basic visualization is also supported. @@ -119,15 +119,16 @@ Authors

-* **Ian D. Buller** - *Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland* - [GitHub](https://github.com/idblr) +* **Ian D. Buller** - *Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland* - [GitHub](https://github.com/idblr) - [ORCID](https://orcid.org/0000-0001-9477-8582) See also the list of [contributors](https://github.com/Waller-SUSAN/gateR/graphs/contributors) who participated in this project. Main contributors include: -* **Elena Hsieh** - *Immunology & Microbiology and Pediatrics, University of Colorado Anschutz School of Medicine* - [GitHub](https://github.com/elenahsieh1407) -* **Debashis Ghosh** - *Biostatistics & Informatics, Colorado School of Public Health, Aurora, Colorado* - [GitHub](https://github.com/ghoshd) -* **Lance A. Waller** - *Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia* - [GitHub](https://github.com/lance-waller) +* **Elena Hsieh** - *Immunology & Microbiology and Pediatrics, University of Colorado Anschutz School of Medicine* - [GitHub](https://github.com/elenahsieh1407) - [ORCID](https://orcid.org/0000-0003-3969-6597) +* **Debashis Ghosh** - *Biostatistics & Informatics, Colorado School of Public Health, Aurora, Colorado* - [GitHub](https://github.com/ghoshd) - [ORCID](https://orcid.org/0000-0001-5672-7645) +* **Lance A. Waller** - *Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia* - [GitHub](https://github.com/lance-waller) - [ORCID](https://orcid.org/0000-0001-5002-8886) ## Usage + ``` r set.seed(1234) # for reproducibility @@ -218,9 +219,7 @@ graphics::legend("topright", ``` ![](man/figures/gate1.png) - ![](man/figures/gate2.png) - ![](man/figures/postgate.png) ```r @@ -248,3 +247,17 @@ test_rrs <- gateR::rrs(dat = obs_dat[ , -7:-6]) ## For "arcsinh_CD8" and "arcsinh_CD3" test_lotrrs <- gateR::lotrrs(dat = obs_dat[ , -5:-4]) ``` + +### Funding + +This package was developed while the author was a doctoral student at in the [Environmental Health Sciences doctoral program](https://www.sph.emory.edu/departments/eh/degree-programs/phd/index.html) at [Emory University](https://www.emory.edu) and a postdoctoral fellow supported by the [Cancer Prevention Fellowship Program](https://cpfp.cancer.gov/) at the [National Cancer Institute](https://www.cancer.gov/). + +### Acknowledgments + +When citing this package for publication, please follow: + + citation("gateR") + +### Questions? Feedback? + +For questions about the package please contact the maintainer [Dr. Ian D. Buller](mailto:ian.buller@nih.gov) or [submit a new issue](https://github.com/Waller-SUSAN/gateR/issues).