Updated README

* Added badges, ORCIDs, funding, acknowledgements, and questions sections to README
* ignore CRAN-SUBMISSIONS and figures in R build
* Remove superfluous langauge in LICENSE

.Rbuildignore

@@ -6,3 +6,5 @@
 ^dev$
 ^CRAN-RELEASE$
 ^data-raw$
+^CRAN-SUBMISSION$
+^man/figures

.gitignore

@@ -42,3 +42,6 @@ rsconnect/
 
 # R installed data
 *.rds
+
+# CRAN
+CRAN-SUBMISSION

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");

README.md

@@ -2,16 +2,16 @@ gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation <img src
 ===================================================
 
 <!-- badges: start -->
-
-[![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)
-
 <!-- badges: end -->
 
+**Date repository last updated**: August 08, 2022
+
 <h2 id="overview">
 
 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)
+<img src="http://www.sciweavers.org/tex2img.php?eq=%5Cfrac%7B%20%5Cbig%28%5Cfrac%7BCondition2B%7D%7BCondition2A%7D%5Cbig%29%7D%7B%5Cbig%28%5Cfrac%7BCondition1B%7D%7BCondition1A%7D%5Cbig%29%7D&bc=White&fc=Black&im=jpg&fs=12&ff=arev&edit=0" align="center" border="0" alt="\frac{ \big(\frac{Condition2B}{Condition2A}\big)}{\big(\frac{Condition1B}{Condition1A}\big)}" width="100" height="58" />
 
 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
 
 </h2>
 
-* **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:[email protected]) or [submit a new issue](https://github.com/Waller-SUSAN/gateR/issues).