CRAN submission v0.2.0 (#75)

* Prep for CRAN submission * Removed script-replication * Add BugReports url and GeoTox return value * Some weird format issue with Authors@R * Updates from spell_check * Add CRAN-SUBMISSION to .Rbuildignore * New infographic
NIEHS · Nov 19, 2024 · be49abb · be49abb
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -9,8 +9,8 @@
 ^CODE_OF_CONDUCT.md$
 ^cran-comments\.md$
 ^\.github$
-^script-replication$
 ^data-raw$
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^CRAN-SUBMISSION$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,10 +1,13 @@
 Package: GeoTox
 Title: Spatiotemporal Mixture Risk Assessment
-Version: 0.1.4
+Version: 0.2.0
 Authors@R: c(
-    person("Skylar", "Marvel", , "[email protected]", role = c("aut", "ctb"), comment = c(ORCID = "0000-0002-2971-9743")),
-    person("David", "Reif", , "[email protected]", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-7815-6767")),
-    person("Kyle", "Messier", , "[email protected]", role = c("cre", "aut", "ctb"), comment = c(ORCID = "0000-0001-9508-9623")),
+    person("Skylar", "Marvel", , "[email protected]", role = c("aut"),
+           comment = c(ORCID = "0000-0002-2971-9743")),
+    person("David", "Reif", , "[email protected]", role = c("aut"),
+           comment = c(ORCID = "0000-0001-7815-6767")),
+    person("Kyle", "Messier", , "[email protected]", role = c("cre", "aut"),
+           comment = c(ORCID = "0000-0001-9508-9623")),
     person("Spatiotemporal Exposures and Toxicology Group", role = c("cph"))
   )
 Description: Connecting spatiotemporal exposure to individual and
@@ -47,3 +50,4 @@ Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
+BugReports: https://github.com/NIEHS/GeoTox/issues
diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,3 @@
-# GeoTox 0.1.4
-- Updated unit test coverage and function examples
+# GeoTox 0.2.0
 
-# GeoTox 0.0.1
-- Adding supporting documents to the `GeoTox` repository such as this news.md, issue templates, and contributor's guide
-- NC areal level analysis vignette is complete
-- Key developments on the object oriented approach: simulate and sensitivity wrappers
-- oo-s3.Rmd is updated to include object oriented improvements including more plotting options 
+* Initial CRAN submission.
diff --git a/R/GeoTox.R b/R/GeoTox.R
@@ -4,6 +4,7 @@
 #' An S3 object that can be used to help organize the data and results of a
 #' GeoTox analysis.
 #'
+#' @return a GeoTox S3 object
 #' @export
 #' 
 #' @examples

diff --git a/R/calc_independent_action.R b/R/calc_independent_action.R
@@ -5,7 +5,7 @@
 #' concentration-response curves.
 #'
 #' @param conc concentrations in regular space
-#' @param max maximal (asymtotic) responses
+#' @param max maximal (asymptotic) responses
 #' @param AC50 concentrations of half-maximal response
 #' @param Emax maximum mixture response
 #' @param n Hill coefficients (slopes)

diff --git a/R/get_fixed_age.R b/R/get_fixed_age.R
@@ -1,10 +1,10 @@
-#' Get C_ss Data for Fixed Age
+#' Get `C_ss` Data for Fixed Age
 #'
-#' @param simulated_css list of pre-generated C_ss data, for details see:
+#' @param simulated_css list of pre-generated `C_ss` data, for details see:
 #' \code{vignette("package_data", package = "GeoTox")}.
 #' @param age list of atomic vectors containing ages.
 #'
-#' @return list of matrices containing median C_ss values.
+#' @return list of matrices containing median `C_ss` values.
 #' @export
 #' 
 #' @examples

diff --git a/R/get_fixed_css.R b/R/get_fixed_css.R
@@ -1,15 +1,15 @@
-#' Get Fixed C_ss Data
+#' Get Fixed `C_ss` Data
 #' 
 #' @description
-#' Get C_ss values for use in [sensitivity_analysis] and [compute_sensitivity].
+#' Get `C_ss` values for use in [sensitivity_analysis] and [compute_sensitivity].
 #'
-#' @param simulated_css list of pre-generated C_ss data, for details see:
+#' @param simulated_css list of pre-generated `C_ss` data, for details see:
 #' \code{vignette("package_data", package = "GeoTox")}.
 #' @param age list of atomic vectors containing ages.
 #' @param obesity list of atomic vectors containing obesity status.
-#' @param C_ss list of matrices containing C_ss values.
+#' @param C_ss list of matrices containing `C_ss` values.
 #'
-#' @return list of matrices or atomic vectors containing C_ss values.
+#' @return list of matrices or atomic vectors containing `C_ss` values.
 #' @export
 #' 
 #' @examples

diff --git a/R/get_fixed_obesity.R b/R/get_fixed_obesity.R
@@ -1,10 +1,10 @@
-#' Get C_ss Data for Fixed Obesity Status
+#' Get `C_ss` Data for Fixed Obesity Status
 #'
-#' @param simulated_css list of pre-generated C_ss data, for details see:
+#' @param simulated_css list of pre-generated `C_ss` data, for details see:
 #' \code{vignette("package_data", package = "GeoTox")}.
 #' @param obesity list of atomic vectors containing obesity status.
 #'
-#' @return list of matrices containing median C_ss values.
+#' @return list of matrices containing median `C_ss` values.
 #' @export
 #' 
 #' @examples

diff --git a/R/get_fixed_other.R b/R/get_fixed_other.R
@@ -1,8 +1,8 @@
-#' Get median C_ss Values
+#' Get median `C_ss` Values
 #'
-#' @param C_ss list of matrices containing C_ss data
+#' @param C_ss list of matrices containing `C_ss` data
 #'
-#' @return list of atomic vectors containing median C_ss values.
+#' @return list of atomic vectors containing median `C_ss` values.
 #' @export
 #' 
 #' @examples

diff --git a/R/get_fixed_params.R b/R/get_fixed_params.R
@@ -1,10 +1,10 @@
-#' Get C_ss Data for Fixed C_ss Generation Parameters
+#' Get `C_ss` Data for Fixed `C_ss` Generation Parameters
 #'
-#' @param simulated_css list of pre-generated C_ss data, for details see:
+#' @param simulated_css list of pre-generated `C_ss` data, for details see:
 #' \code{vignette("package_data", package = "GeoTox")}.
 #' @param age list of atomic vectors containing ages.
 #'
-#' @return list of matrices containing C_ss values.
+#' @return list of matrices containing `C_ss` values.
 #' @export
 #' 
 #' @examples

diff --git a/R/hill_conc.R b/R/hill_conc.R
@@ -4,7 +4,7 @@
 #' Calculate the concentration in regular space for a given response value.
 #'
 #' @param resp response value
-#' @param max maximal (asymtotic) response
+#' @param max maximal (asymptotic) response
 #' @param AC50 concentration of half-maximal response
 #' @param n Hill coefficient (slope)
 #'

diff --git a/R/hill_val.R b/R/hill_val.R
@@ -4,7 +4,7 @@
 #' Calculate the response for a given concentration in regular space.
 #'
 #' @param conc concentration in regular space
-#' @param max maximal (asymtotic) response
+#' @param max maximal (asymptotic) response
 #' @param AC50 concentration of half-maximal response
 #' @param n Hill coefficient (slope)
 #'

diff --git a/R/sample_Css.R b/R/sample_Css.R
@@ -1,11 +1,11 @@
-#' Sample from pre-generated C_ss data
+#' Sample from pre-generated `C_ss` data
 #'
-#' @param simulated_css list of pre-generated C_ss data, for details see:
+#' @param simulated_css list of pre-generated `C_ss` data, for details see:
 #' \code{vignette("package_data", package = "GeoTox")}.
 #' @param age list or atomic vector of ages.
 #' @param obesity list or atomic vector of obesity status.
 #'
-#' @return list of matrices containing C_ss values. Columns are sorted to have
+#' @return list of matrices containing `C_ss` values. Columns are sorted to have
 #' consistent order across functions.
 #' 
 #' @examples

diff --git a/README.Rmd b/README.Rmd
@@ -32,16 +32,13 @@ The GeoTox framework was first described in
 
 ## Installation
 
-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:
+The development version can be installed from GitHub.
 
 ```{r, eval=FALSE}
 #install.packages("pak")
@@ -50,7 +47,7 @@ pak::pak("NIEHS/GeoTox")
 
 ## Overview
 
-Figure 1 below shows the steps in the source-to-outcome-continuum or GeoTox modelling framework that is capable in the `GeoTox` package. <span style="color: blue;">blue text</span> nodes represent an object and <span style="color: green;">green text</span>, rounded nodes represent a methodology or function required to go from one to the next. The `GeoTox` package uses R S3 object-oriented programming to create the **GeoTox** object. The **GeoTox** object is a list that contains all of the information required to run the analysis including tracking exposure, assays, dose-response, and geospatial referencing. 
+Figure 1 below shows the steps in the source-to-outcome-continuum or GeoTox modeling framework that is capable in the `GeoTox` package. <span style="color: blue;">blue text</span> nodes represent an object and <span style="color: green;">green text</span>, rounded nodes represent a methodology or function required to go from one to the next. The `GeoTox` package uses R S3 object-oriented programming to create the **GeoTox** object. The **GeoTox** object is a list that contains all of the information required to run the analysis including tracking exposure, assays, dose-response, and geospatial referencing. 
 
 <p align="center">
   <img src="man/figures/GeoTox.png" alt="GeoTox">

diff --git a/README.md b/README.md
@@ -31,18 +31,13 @@ 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.
-
-<!--
 ``` r
 install.packages("GeoTox")
 ```
--->
 
 ## Development Version
 
-The development version can be installed from
-[GitHub](https://github.com/NIEHS/GeoTox) with:
+The development version can be installed from GitHub.
 
 ``` r
 #install.packages("pak")
@@ -52,7 +47,7 @@ pak::pak("NIEHS/GeoTox")
 ## Overview
 
 Figure 1 below shows the steps in the source-to-outcome-continuum or
-GeoTox modelling framework that is capable in the `GeoTox` package.
+GeoTox modeling framework that is capable in the `GeoTox` package.
 <span style="color: blue;">blue text</span> nodes represent an object
 and <span style="color: green;">green text</span>, rounded nodes
 represent a methodology or function required to go from one to the next.
@@ -63,8 +58,8 @@ exposure, assays, dose-response, and geospatial referencing.
 
 <p align="center">
 
-<img src="man/figures/GeoTox-Workflow.png" alt="GeoTox-Workflow"> <br>
-<em>Figure 1: Overview of the steps in the GeoTox framework</em>
+<img src="man/figures/GeoTox.png" alt="GeoTox"> <br> <em>Figure 1:
+Overview of the steps in the GeoTox framework</em>
 </p>
 
 ## Getting Started

diff --git a/man/GeoTox-package.Rd b/man/GeoTox-package.Rd
diff --git a/man/GeoTox.Rd b/man/GeoTox.Rd
diff --git a/man/calc_independent_action.Rd b/man/calc_independent_action.Rd
diff --git a/man/get_fixed_age.Rd b/man/get_fixed_age.Rd
diff --git a/man/get_fixed_css.Rd b/man/get_fixed_css.Rd
diff --git a/man/get_fixed_obesity.Rd b/man/get_fixed_obesity.Rd
diff --git a/man/get_fixed_other.Rd b/man/get_fixed_other.Rd