Large initial commit for gateR package

One main function
gating()

Five internal functions
rrs()
lotrrs()
pval_correct()
lrr_plot()
pval_plot()

Full README.md with example using data from {flowWorkspaceData}

Full vignette using toy data

.Rbuildignore

@@ -1,2 +1,7 @@
+^LICENSE\.md$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^vignette\.Rmd$
+^build$
+^figures$
+^gator\.png$

.gitignore

@@ -16,21 +16,29 @@
 
 # RStudio files
 .Rproj.user/
+.Rproj
 
 # produced vignettes
-vignettes/*.html
+#vignettes/*.html
 vignettes/*.pdf
 
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
 
 # knitr and R markdown default cache directories
-/*_cache/
+*_cache/
 /cache/
+*_files/
 
 # Temporary files created by R markdown
 *.utf8.md
 *.knit.md
 
 # Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
 rsconnect/
+
+# Mac OSX
+.DS_Store
+
+# R installed data
+*.rds

DESCRIPTION

@@ -1,11 +1,66 @@
-Package: gateRR
+Package: gateR
 Type: Package
-Title: What the Package Does (Title Case)
-Version: 0.1.0
-Author: Who wrote it
-Maintainer: The package maintainer <[email protected]>
-Description: More about what it does (maybe more than one line)
-    Use four spaces when indenting paragraphs within the Description.
-License: What license is it under?
+Title: Gating strategy for mass cytometry using kernel density estimation
+Version: 0.1.0.9000
+Date: 2020-09-12
+Authors@R: 
+    c(person(given = "Ian D.",
+             family = "Buller",
+             role = c("aut", "cre", "cph"),
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0001-9477-8582")),
+      person(given = "Elena",
+             family = "Hsieh",
+             role = "ctb",
+             email = "[email protected]"),
+      person(given = "Debashis",
+             family = "Ghosh",
+             role = "ctb",
+             email = "[email protected]"),
+      person(given = "Lance A.",
+             family = "Waller",
+             role = "ctb",
+             email = "[email protected]"),
+      person(given = "NCI",
+             role = c("cph"))
+             )
+Maintainer: Ian D. Buller <[email protected]>
+Description: Estimates statistically significant flourescent marker combination values within
+        which one immunologically distinctive group (i.e., disease case) is more associated than
+        another group (i.e., healthy control), successively, using various combinations (i.e.,
+        "gates") of flourescent markers to examine features of cells that may be different between
+        groups. For a two group comparison, the {gateR} package uses the spatial relative risk
+        function that is estimated using the {sparr} package. Details about the {sparr} package
+        methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details
+        about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>.
+        More information about relative risk functions using kernel density estimation can be
+        found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
+License: Apache License (>= 2.0)
 Encoding: UTF-8
 LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.1
+Depends: R (>= 3.5.0)
+Imports: 
+    fields,
+    graphics,
+    grDevices,
+    maptools,
+    raster,
+    sp,
+    sparr,
+    spatstat.core,
+    stats,
+    tibble,
+    utils
+Suggests: 
+    flowWorkspaceData,
+    knitr,
+    ncdfFlow,
+    spelling,
+    testthat
+VignetteBuilder: knitr
+Language: en-US
+URL: https://github.com/Waller-SUSAN/gateR
+BugReports: https://github.com/Waller-SUSAN/gateR/issues
+Author: Ian D. Buller [aut, cre, cph]