Prep for CRAN submission (#74)

* Added @nord to internal functions * Added 'cph' and references to DESCRIPTION * Updated install for CRAN release * Updated document for previous DESCRIPTION change * Export hill_conc and hill_val * Hide CRAN install until accepted
NIEHS · Nov 7, 2024 · 8e7aa49 · 8e7aa49
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -4,9 +4,14 @@ Version: 0.1.4
 Authors@R: c(
     person("Skylar", "Marvel", , "skylar.marvel@nih.gov", role = c("aut", "ctb"), comment = c(ORCID = "0000-0002-2971-9743")),
     person("David", "Reif", , "david.reif@nih.gov", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-7815-6767")),
-    person("Kyle", "Messier", , "kyle.messier@nih.gov", role = c("cre", "aut", "ctb"), comment = c(ORCID = "0000-0001-9508-9623"))
+    person("Kyle", "Messier", , "kyle.messier@nih.gov", role = c("cre", "aut", "ctb"), comment = c(ORCID = "0000-0001-9508-9623")),
+    person("Spatiotemporal Exposures and Toxicology Group", role = c("cph"))
   )
-Description: Connecting spatiotemporal exposure to individual and population-level risk via source-to-outcome continuum modeling.
+Description: Connecting spatiotemporal exposure to individual and
+    population-level risk via source-to-outcome continuum modeling. The package,
+    methods, and case-studies are described in Messier, Reif, and Marvel (2024)
+    <doi:10.1101/2024.09.23.24314096> and Eccles et al. (2023)
+    <doi:10.1016/j.scitotenv.2022.158905>.
 License: MIT + file LICENSE
 URL: https://niehs.github.io/GeoTox/, https://github.com/NIEHS/GeoTox
 Depends: 

diff --git a/NAMESPACE b/NAMESPACE
@@ -15,6 +15,8 @@ export(get_fixed_css)
 export(get_fixed_obesity)
 export(get_fixed_other)
 export(get_fixed_params)
+export(hill_conc)
+export(hill_val)
 export(plot_exposure)
 export(plot_hill)
 export(plot_resp)

diff --git a/R/check_lengths.R b/R/check_lengths.R
@@ -4,6 +4,7 @@
 #' @param y list of arrays
 #' 
 #' @keywords internal
+#' @noRd
 #'
 #' @return boolean, TRUE for error
 .check_lengths <- function(x, y) {

diff --git a/R/check_names.R b/R/check_names.R
@@ -4,6 +4,7 @@
 #' @param names names to look for
 #'
 #' @keywords internal
+#' @noRd
 #'
 #' @return boolean, TRUE for error
 .check_names <- function(x, names) {

diff --git a/R/check_types.R b/R/check_types.R
@@ -5,6 +5,7 @@
 #' @param msg error message
 #'
 #' @keywords internal
+#' @noRd
 #'
 #' @return list version of input
 .check_types <- function(x, types, msg = "Incorrect type") {

diff --git a/R/hill_conc.R b/R/hill_conc.R
@@ -8,9 +8,8 @@
 #' @param AC50 concentration of half-maximal response
 #' @param n Hill coefficient (slope)
 #'
-#' @keywords internal
-#'
 #' @return concentration in regular space
+#' @export
 #' 
 #' @details
 #' This is a regular space version of
@@ -20,6 +19,10 @@
 #' \deqn{conc = AC50 * (\frac{max}{resp} - 1)^{-1 / n}}
 #' 
 #' @seealso \code{\link{hill_val}}
+#' 
+#' @examples
+#' hill_conc(c(0.2, 0.5, 0.75), 1, 0.01, 1)
+#' hill_conc(c(0.2, 0.5, 0.9), 1, c(0.1, 0.01, 0.001), 2)
 hill_conc <- function(resp, max, AC50, n) {
 
   if (any(AC50 < 0)) {

diff --git a/R/hill_val.R b/R/hill_val.R
@@ -8,9 +8,8 @@
 #' @param AC50 concentration of half-maximal response
 #' @param n Hill coefficient (slope)
 #'
-#' @keywords internal
-#'
 #' @return response value
+#' @export
 #' 
 #' @details
 #' This is a regular space version of
@@ -20,6 +19,10 @@
 #' \deqn{resp = \frac{max}{1 + (\frac{AC50}{conc})^{n}}}
 #' 
 #' @seealso \code{\link{hill_conc}}
+#' 
+#' @examples
+#' hill_val(c(0.0025, 0.01, 0.03), 1, 0.01, 1)
+#' hill_val(c(0.05, 0.01, 0.003), 1, c(0.1, 0.01, 0.001), 2)
 hill_val <- function(conc, max, AC50, n) {
 
   if (any(conc < 0) || any(AC50 < 0)) {

diff --git a/R/obj_ECx.R b/R/obj_ECx.R
@@ -12,6 +12,7 @@
 #' @param AC50 concentrations of half-maximal response
 #'
 #' @keywords internal
+#' @noRd
 #'
 #' @return objective value
 obj_ECx <- function(conc_mix, resp, conc, max, AC50) {

diff --git a/R/obj_GCA.R b/R/obj_GCA.R
@@ -10,6 +10,7 @@
 #' @param AC50 concentrations of half-maximal response
 #'
 #' @keywords internal
+#' @noRd
 #'
 #' @return objective value
 obj_GCA <- function(ln_resp, conc, max, AC50) {

diff --git a/R/obj_hill.R b/R/obj_hill.R
@@ -5,6 +5,7 @@
 #' @param resp response
 #'
 #' @keywords internal
+#' @noRd
 #'
 #' @return value of the objective function
 obj_hill <- function(par, log10_conc, resp) {

diff --git a/README.Rmd b/README.Rmd
@@ -22,22 +22,30 @@ knitr::opts_chunk$set(
 [![pkgdown](https://github.com/NIEHS/GeoTox/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/NIEHS/GeoTox/actions/workflows/pkgdown.yaml)
 [![cov](https://NIEHS.github.io/GeoTox/badges/coverage.svg)](https://github.com/NIEHS/GeoTox/actions)
 [![CRAN status](https://www.r-pkg.org/badges/version/GeoTox)](https://CRAN.R-project.org/package=GeoTox)
-<!-- badges: end -->
 
+<!-- badges: end -->
 
-`GeoTox` open-source R software package for characterizing the risk of perturbing molecular targets involved in adverse human health outcomes based on exposure to spatially-referenced stressor mixtures via the GeoTox framework - otherwise known as source-to-outcome-continuum modeling. The package, methods, and case-studies are described in [Messier, Reif, and Marvel, 2024, medRxiv-Preprint](https://www.medrxiv.org/content/10.1101/2024.09.23.24314096v1).
+`GeoTox` open-source R software package for characterizing the risk of perturbing molecular targets involved in adverse human health outcomes based on exposure to spatially-referenced stressor mixtures via the GeoTox framework - otherwise known as source-to-outcome-continuum modeling. The package, methods, and case-studies are described in [Messier, Reif, and Marvel, 2024, medRxiv-Preprint](https://www.medrxiv.org/content/10.1101/2024.09.23.24314096).
 
 The GeoTox framework was first described in
 [Eccles et al. A geospatial modeling approach to quantifying the risk of exposure to environmental chemical mixtures via a common molecular target. Sci Total Environ. 2023 Jan 10;855:158905.](https://pubmed.ncbi.nlm.nih.gov/36152849/)
 
 ## Installation
 
-The package will be on CRAN in the near future - please stay tuned. You can install the development version of GeoTox from
-[GitHub](https://github.com/NIEHS/GeoTox) with:
+The package will be on CRAN in the near future - please stay tuned.
+<!--
+```{r, eval=FALSE}
+install.packages("GeoTox")
+```
+-->
+
+## Development Version
+
+The development version can be installed from [GitHub](https://github.com/NIEHS/GeoTox) with:
 
 ```{r, eval=FALSE}
-install.packages("pak")
-pak::pkg_install("NIEHS/GeoTox")
+#install.packages("pak")
+pak::pak("NIEHS/GeoTox")
 ```
 
 ## Overview

diff --git a/README.md b/README.md
@@ -13,6 +13,7 @@ developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.re
 [![cov](https://NIEHS.github.io/GeoTox/badges/coverage.svg)](https://github.com/NIEHS/GeoTox/actions)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/GeoTox)](https://CRAN.R-project.org/package=GeoTox)
+
 <!-- badges: end -->
 
 `GeoTox` open-source R software package for characterizing the risk of
@@ -21,7 +22,7 @@ based on exposure to spatially-referenced stressor mixtures via the
 GeoTox framework - otherwise known as source-to-outcome-continuum
 modeling. The package, methods, and case-studies are described in
 [Messier, Reif, and Marvel, 2024,
-medRxiv-Preprint](https://www.medrxiv.org/content/10.1101/2024.09.23.24314096v1).
+medRxiv-Preprint](https://www.medrxiv.org/content/10.1101/2024.09.23.24314096).
 
 The GeoTox framework was first described in [Eccles et al. A geospatial
 modeling approach to quantifying the risk of exposure to environmental
@@ -30,13 +31,21 @@ Jan 10;855:158905.](https://pubmed.ncbi.nlm.nih.gov/36152849/)
 
 ## Installation
 
-The package will be on CRAN in the near future - please stay tuned. You
-can install the development version of GeoTox from
+The package will be on CRAN in the near future - please stay tuned. <!--
+
+``` r
+install.packages("GeoTox")
+```
+-->
+
+## Development Version
+
+The development version can be installed from
 [GitHub](https://github.com/NIEHS/GeoTox) with:
 
 ``` r
-install.packages("pak")
-pak::pkg_install("NIEHS/GeoTox")
+#install.packages("pak")
+pak::pak("NIEHS/GeoTox")
 ```
 
 ## Overview

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -44,6 +44,8 @@ reference:
   desc: Auxillary and helper functions
 - contents:
   - fit_hill
+  - hill_conc
+  - hill_val
   - starts_with("get_")
 - subtitle: Datasets
   desc: Package datasets

diff --git a/man/GeoTox-package.Rd b/man/GeoTox-package.Rd
diff --git a/man/dot-check_lengths.Rd b/man/dot-check_lengths.Rd
diff --git a/man/dot-check_names.Rd b/man/dot-check_names.Rd
diff --git a/man/dot-check_types.Rd b/man/dot-check_types.Rd
diff --git a/man/hill_conc.Rd b/man/hill_conc.Rd
diff --git a/man/hill_val.Rd b/man/hill_val.Rd
diff --git a/man/obj_ECx.Rd b/man/obj_ECx.Rd
diff --git a/man/obj_GCA.Rd b/man/obj_GCA.Rd
diff --git a/man/obj_hill.Rd b/man/obj_hill.Rd